bluuebunny/crossref_metadata_2025_split huggingface dataset:
Macroscale fluorescence imaging against autofluorescence under ambient light
Authors: Zhang Ruikang , Chouket Raja , Plamont Marie-Aude , Kelemen Zsolt , Espagne Agathe , Tebo Alison G. , Gautier Arnaud , Gissot Lionel , Faure Jean-Denis , Jullien Ludovic , Croquette Vincent , Le Saux Thomas 
Published: November 2018

AbstractMacroscale fluorescence imaging is increasingly used to observe biological samples. However, it may suffer from spectral interferences that originate from ambient light or autofluorescence of the sample or its support. In this manuscript, we built a simple and inexpensive fluorescence macroscope, which has been used to evaluate the performance of Speed OPIOM (Out of Phase Imaging after Optical Modulation), which is a reference-free dynamic contrast protocol, to selectively image reversibly photoswitchable fluorophores as labels against detrimental autofluorescence and ambient light. By tuning the intensity and radial frequency of the modulated illumination to the Speed OPIOM resonance and adopting a phase-sensitive detection scheme that ensures noise rejection, we enhanced the sensitivity and the signal-to-noise ratio for fluorescence detection in blot assays by factors of 50 and 10, respectively, over direct fluorescence observation under constant illumination. Then, we overcame the strong autofluorescence of growth media that are currently used in microbiology and realized multiplexed fluorescence observation of colonies of spectrally similar fluorescent bacteria with a unique configuration of excitation and emission wavelengths. Finally, we easily discriminated fluorescent labels from the autofluorescent and reflective background in labeled leaves, even under the interference of incident light at intensities that are comparable to sunlight. The proposed approach is expected to find multiple applications, from biological assays to outdoor observations, in fluorescence macroimaging.
The role of autophagy in colitis-associated colorectal cancer
Authors: Wu Yuhui , Yao Junlin , Xie Jiansheng , Liu Zhen , Zhou Yubin , Pan Hongming , Han Weidong 
Published: November 2018

AbstractAutophagy is an evolutionarily conserved catabolic process that eliminates harmful components through lysosomal degradation. In addition to its role in maintaining cellular homeostasis, autophagy is critical to pathological processes, such as inflammation and cancer. Colitis-associated colorectal cancer (CAC) is a specific type of colorectal cancer that develops from long-standing colitis in inflammatory bowel disease (IBD) patients. Accumulating evidence indicates that autophagy of microenvironmental cells plays different but vital roles during tumorigenesis and CAC development. Herein, after summarizing the recent advances in understanding the role of autophagy in regulating the tumor microenvironment during different CAC stages, we draw the following conclusions: autophagy in intestinal epithelial cells inhibits colitis and CAC initiation but promotes CAC progression; autophagy in macrophages inhibits colitis, but its function on CAC is currently unclear; autophagy in neutrophils and cancer-associated fibroblasts (CAFs) promotes both colitis and CAC; autophagy in dendritic cells (DCs) and T cells represses both colitis and CAC; autophagy in natural killer cells (NKs) inhibits colitis, but promotes CAC; and autophagy in endothelial cells plays a controversial role in colitis and CAC. Understanding the role of autophagy in specific compartments of the tumor microenvironment during different stages of CAC may provide insight into malignant transformation, tumor progression, and combination therapy strategies for CAC.
Molecular mechanism of a covalent allosteric inhibitor of SUMO E1 activating enzyme
Authors: Lv Zongyang , Yuan Lingmin , Atkison James H. , Williams Katelyn M. , Vega Ramir , Sessions E. Hampton , Divlianska Daniela B. , Davies Christopher , Chen Yuan , Olsen Shaun K. 
Published: November 2018

AbstractE1 enzymes activate ubiquitin (Ub) and ubiquitin-like modifiers (Ubls) in the first step of Ub/Ubl conjugation cascades and represent potential targets for therapeutic intervention in cancer and other life-threatening diseases. Here, we report the crystal structure of the E1 enzyme for the Ubl SUMO in complex with a recently discovered and highly specific covalent allosteric inhibitor (COH000). The structure reveals that COH000 targets a cryptic pocket distinct from the active site that is completely buried in all previous SUMO E1 structures and that COH000 binding to SUMO E1 is accompanied by a network of structural changes that altogether lock the enzyme in a previously unobserved inactive conformation. These structural changes include disassembly of the active site and a 180° rotation of the catalytic cysteine-containing SCCH domain, relative to conformational snapshots of SUMO E1 poised to catalyze adenylation. Altogether, our study provides a molecular basis for the inhibitory mechanism of COH000 and its SUMO E1 specificity, and also establishes a framework for potential development of molecules targeting E1 enzymes for other Ubls at a cryptic allosteric site.
Functional biodiversity loss along natural CO2 gradients
Authors: Teixidó Nuria , Gambi Maria Cristina , Parravacini Valeriano , Kroeker Kristy , Micheli Fiorenza , Villéger Sebastien , Ballesteros Enric 
Published: November 2018

AbstractThe effects of environmental change on biodiversity are still poorly understood. In particular, the consequences of shifts in species composition for marine ecosystem function are largely unknown. Here we assess the loss of functional diversity, i.e. the range of species biological traits, in benthic marine communities exposed to ocean acidification (OA) by using natural CO2 vent systems. We found that functional richness is greatly reduced with acidification, and that functional loss is more pronounced than the corresponding decrease in taxonomic diversity. In acidified conditions, most organisms accounted for a few functional entities (i.e. unique combination of functional traits), resulting in low functional redundancy. These results suggest that functional richness is not buffered by functional redundancy under OA, even in highly diverse assemblages, such as rocky benthic communities.
Bioinspired and bristled microparticles for ultrasensitive pressure and strain sensors
Authors: Yin Bing , Liu Xiaomeng , Gao Hongyan , Fu Tianda , Yao Jun 
Published: November 2018

AbstractBiological sensory organelles are often structurally optimized for high sensitivity. Tactile hairs or bristles are ubiquitous mechanosensory organelles in insects. The bristle features a tapering spine that not only serves as a lever arm to promote signal transduction, but also a clever design to protect it from mechanical breaking. A hierarchical distribution over the body further improves the signal detection from all directions. We mimic these features by using synthetic zinc oxide microparticles, each having spherically-distributed, high-aspect-ratio, and high-density nanostructured spines resembling biological bristles. Sensors based on thin films assembled from these microparticles achieve static-pressure detection down to 0.015 Pa, sensitivity up to 121 kPa−1, and a strain gauge factor >104, showing supreme overall performance. Other properties including a robust cyclability >2000, fast response time ~7 ms, and low-temperature synthesis compatible to various integrations further indicate the potential of this sensor technology in applying to wearable technologies and human interfaces.
Predicting Dirac semimetals based on sodium ternary compounds
Authors: Peng Bo , Yue Changming , Zhang Hao , Fang Zhong , Weng Hongming 
Published: November 2018

AbstractPredicting new Dirac semimetals, as well as other topological materials, is challenging since the relationship between crystal structure, atoms and band topology is complex and elusive. Here, we demonstrate an approach to design Dirac semimetals via exploring chemical degree of freedom. Based on understanding of the well-known Dirac semimetal, Na3Bi, three compounds in one family, namely Na2MgSn, Na2MgPb, and Na2CdSn, are located. Furthermore, hybrid-functional calculations with improved accuracy for estimation of band inversion show that Na2MgPb and Na2CdSn have the band topology of Dirac semimetals. The nontrivial surface states with Fermi arcs on the (100) and (010) surfaces are shown to connect the projection of bulk Dirac nodes. Most importantly, the candidate compounds are dynamically stable and have been experimentally synthesized. The ideas in this work could stimulate further predictions of topological materials based on understanding of existing ones.
Inversion and computational maturation of drug response using human stem cell derived cardiomyocytes in microphysiological systems
Authors: Tveito Aslak , Jæger Karoline Horgmo , Huebsch Nathaniel , Charrez Bérénice , Edwards Andrew G. , Wall Samuel , Healy Kevin E. 
Published: November 2018

AbstractWhile cardiomyocytes differentiated from human induced pluripotent stems cells (hiPSCs) hold great promise for drug screening, the electrophysiological properties of these cells can be variable and immature, producing results that are significantly different from their human adult counterparts. Here, we describe a computational framework to address this limitation, and show how in silico methods, applied to measurements on immature cardiomyocytes, can be used to both identify drug action and to predict its effect in mature cells. Our synthetic and experimental results indicate that optically obtained waveforms of voltage and calcium from microphysiological systems can be inverted into information on drug ion channel blockage, and then, through assuming functional invariance of proteins during maturation, this data can be used to predict drug induced changes in mature ventricular cells. Together, this pipeline of measurements and computational analysis could significantly improve the ability of hiPSC derived cardiomycocytes to predict dangerous drug side effects.
Sequence Analysis of the Fusion Protein Gene of Human Respiratory Syncytial Virus Circulating in China from 2003 to 2014
Authors: Song Jinhua , Wang Huiling , Ng Teresa I. , Cui Aili , Zhu Shuangli , Huang Yanzhi , Sun Liwei , Yang Zifeng , Yu Deshan , Yu Pengbo , Zhang Hong , Zhang Yan , Xu Wenbo 
Published: November 2018

AbstractThe human respiratory syncytial virus (HRSV) fusion (F) protein is important for HRSV infection, but few studies have examined the genetic diversity of the F gene from Chinese samples. In this study, a total of 330 HRSV F sequences collected from different regions of China between 2003 and 2014 were analyzed to understand their genetic characteristics. In addition, these sequences were compared with 1150 HRSV F sequences in Genbank from 18 other countries. In phylogenetic analysis, Chinese HRSV F sequences sorted into a number of clusters containing sequences from China as well as other countries. F sequences from different genotypes (as determined based on the G gene sequences) within a HRSV subgroup could be found in the same clusters in phylogenetic trees generated based on F gene sequences. Amino acid analysis showed that HRSV F sequences from China and other countries were highly conserved. Of interest, F protein sequences from all Chinese samples were completely conserved at the palivizumab binding site, thus predicting the susceptibility of these strains to this neutralizing antibody. In conclusion, HRSV F sequences from China between 2003 and 2014, similar to those from other countries, were highly conserved.
The mitochondrial genome of Endoconidiophora resinifera is intron rich
Authors: Zubaer Abdullah , Wai Alvan , Hausner Georg 
Published: November 2018

AbstractEndoconidiophora resinifera (=Ceratocystis resinifera) is a blue-stain fungus that occurs on conifers. The data showed that the Endoconidiophora resinifera mitochondrial genome is one of the largest mitochondrial genomes (>220 kb) so far reported among members of the Ascomycota. An exceptional large number of introns (81) were noted and differences among the four strains were restricted to minor variations in intron numbers and a few indels and single nucleotide polymorphisms. The major differences among the four strains examined are due to size polymorphisms generated by the absence or presence of mitochondrial introns. Also, these mitochondrial genomes encode the largest cytochrome oxidase subunit 1 gene (47.5 kb) reported so far among the fungi. The large size for this gene again can be attributed to the large number of intron insertions. This study reports the first mitochondrial genome for the genus Endoconidiophora, previously members of this genus were assigned to Ceratocystis. The latter genus has recently undergone extensive taxonomic revisions and the mitochondrial genome might provide loci that could be applied as molecular markers assisting in the identification of taxa within this group of economically important fungi. The large mitochondrial genome also may provide some insight on mechanisms that can lead to mitochondrial genome expansion.
Nitrous oxide and nitric oxide emissions from lowland rice cultivation with urea deep placement and alternate wetting and drying irrigation
Authors: Islam S. M. Mofijul , Gaihre Yam Kanta , Biswas Jatish Chandra , Singh Upendra , Ahmed Md. Nayeem , Sanabria Joaquin , Saleque M. A. 
Published: November 2018

AbstractUrea deep placement (UDP) and the alternate wetting and drying (AWD) irrigation method are two promising rice production technologies. However, studies on the impact of UDP under AWD irrigation on nitrous oxide (N2O) and nitric oxide (NO) emissions are limited. In this study, the effects of UDP with AWD irrigation on these emissions, nitrogen use efficiency (NUE), and rice yields are investigated, compared to conventional broadcast application. N2O and NO emissions from three fertilizer treatments – no nitrogen, UDP, and broadcast application of prilled urea (PU) – were measured. Measurements were taken using an automated gas sampling and analysis system continuously for two consecutive Boro (dry) rice seasons. N2O emission peaks were observed after broadcast application of PU but not after UDP. In contrast, large spikes in N2O emission were observed after UDP, compared to broadcast application, during dry periods. Despite differences in emission peaks, seasonal cumulative N2O emissions from UDP and broadcast treatments were similar. However, NO emissions were minimal and unaffected by UDP or AWD. UDP increased rice yields by 28% and N recovery efficiency by 167%, compared to broadcast urea. This study demonstrates that UDP with AWD irrigation can increase yields and NUE without increasing N2O and NO emissions.
A polysaccharide-peptide with mercury clearance activity from dried fruiting bodies of maitake mushroom Grifola frondosa
Authors: Zhang Weiwei , Jiang Xuezhen , Zhao Shuang , Zheng Xiaojie , Lan Jin , Wang Hexiang , Ng Tzi Bun 
Published: November 2018

AbstractMercury is considered to be “a global pollutant” and raises concern worldwide. Once mercury enters the body, it will be distributed all over the body but will accumulate in the brain, kidney and liver. To date, no substance originating from edible fungi capable of adsorbing mercury has been reported. We found that the mushroomGrifola frondosaexhibited mercury adsorption capacity. A polysaccharide-peptide (GFPP), displaying the unique N-terminal amino acid sequence of APPGMHQKQQ and 7 partial sequences with high reliability obtained by LC-MS/MS, was isolated by hot-water extraction of its fruiting bodies followed by ion exchange chromatography and gel filtration chromatography. Two rat models were employed to determine the dose and the duration of HgCl2treatment (given by acute administration or continuous treatment) to test ifG. frondosacould promote mercury elimination. For rats subjected to acute treatment with HgCl2, both GFPP andG. frondosafruiting bodies (GFFF) could accelerate the decline of blood mercury level, which fell precipitously by 50% on the second day. GFPP and GFFF also promoted elimination of the burden of mercury in the liver and kidneys. For rats receiving continuous HgCl2treatment,G. frondosaprevented the progressive increase of blood mercury level, and kept the blood mercury level within a relatively stable range.
PECAM/eGFP transgenic mice for monitoring of angiogenesis in health and disease
Authors: Winkler Florian , Herz Katia , Rieck Sarah , Kimura Kenichi , Hu Tianyuan , Röll Wilhelm , Hesse Michael , Fleischmann Bernd K. , Wenzel Daniela 
Published: November 2018

AbstractFor the monitoring of vascular growth as well as adaptive or therapeutic (re)vascularization endothelial-specific reporter mouse models are valuable tools. However, currently available mouse models have limitations, because not all endothelial cells express the reporter in all developmental stages. We have generated PECAM/eGFP embryonic stem (ES) cell and mouse lines where the reporter gene labels PECAM+ endothelial cells and vessels with high specificity. Native eGFP expression and PECAM staining were highly co-localized in vessels of various organs at embryonic stages E9.5, E15.5 and in adult mice. Expression was found in large and small arteries, capillaries and in veins but not in lymphatic vessels. Also in the bone marrow arteries and sinusoidal vessel were labeled, moreover, we could detect eGFP in some CD45+ hematopoietic cells. We also demonstrate that this labeling is very useful to monitor sprouting in an aortic ring assay as well as vascular remodeling in a murine injury model of myocardial infarction. Thus, PECAM/eGFP transgenic ES cells and mice greatly facilitate the monitoring and quantification of endothelial cells ex vivo and in vivo during development and injury.
Optimised LAMP allows single copy detection of 35Sp and NOSt in transgenic maize using Bioluminescent Assay in Real Time (BART)
Authors: Hardinge Patrick , Kiddle Guy , Tisi Laurence , Murray James A. H. 
Published: November 2018

AbstractLoop-mediated amplification (LAMP) has been widely used to amplify and hence detect nucleic acid target sequences from various pathogens, viruses and genetic modifications. Two distinct types of primer are required for LAMP; hairpin-forming LAMP and displacement. High specificity arises from this use of multiple primers, but without optimal conditions for LAMP, sensitivity can be poor. We confirm here the importance of LAMP primer design, concentrations and ratios for efficient LAMP amplification. We further show that displacement primers are non-essential to the LAMP reaction at certain concentrations providing accelerating loop primers are present. We investigate various methods to quantify DNA extracts from GM maize certified reference materials to calculate the target copy numbers of template presented to the LAMP reaction, and show that LAMP can amplify transgenic promoter/terminator sequences in DNA extracted from various maize GM events using primers designed to target the 35S promoter (35Sp) or NOS terminator (NOSt) sequences, detection with both bioluminescence in real-time (BART) and fluorescent methods. With prior denaturation and HPLC grade LAMP primers single copy detection was achieved, showing that optimised LAMP conditions can be combined with BART for single copy targets, with simple and cost efficient light detection electronics over fluorescent alternatives.
RELACS nuclei barcoding enables high-throughput ChIP-seq
Authors: Arrigoni Laura , Al-Hasani Hoor , Ramírez Fidel , Panzeri Ilaria , Ryan Devon Patrick , Santacruz Diana , Kress Nadia , Pospisilik John Andrew , Bönisch Ulrike , Manke Thomas 
Published: November 2018

AbstractChromatin immunoprecipitation followed by deep sequencing (ChIP-seq) is an invaluable tool for mapping chromatin-associated proteins. Current barcoding strategies aim to improve assay throughput and scalability but intense sample handling and lack of standardization over cell types, cell numbers and epitopes hinder wide-spread use in the field. Here, we present a barcoding method to enable high-throughput ChIP-seq using common molecular biology techniques. The method, called RELACS (restriction enzyme-based labeling of chromatin in situ) relies on standardized nuclei extraction from any source and employs chromatin cutting and barcoding within intact nuclei. Barcoded nuclei are pooled and processed within the same ChIP reaction, for maximal comparability and workload reduction. The innovative barcoding concept is particularly user-friendly and suitable for implementation to standardized large-scale clinical studies and scarce samples. Aiming to maximize universality and scalability, RELACS can generate ChIP-seq libraries for transcription factors and histone modifications from hundreds of samples within three days.
Gaia Data Release 2
Authors: Clementini G. , Ripepi V. , Molinaro R. , Garofalo A. , Muraveva T. , Rimoldini L. , Guy L. P. , Jevardat de Fombelle G. , Nienartowicz K. , Marchal O. , Audard M. , Holl B. , Leccia S. , Marconi M. , Musella I. , Mowlavi N. , Lecoeur-Taibi I. , Eyer L. , De Ridder J. , Regibo S. , Sarro L. M. , Szabados L. , Evans D. W. , Riello M. 
Published: November 2018

Context. The Gaia second Data Release (DR2) presents a first mapping of full-sky RR Lyrae stars and Cepheids observed by the spacecraft during the initial 22 months of science operations.
Aims. The Specific Objects Study (SOS) pipeline, developed to validate and fully characterise Cepheids and RR Lyrae stars (SOS Cep&RRL) observed by Gaia, has been presented in the documentation and papers accompanying the Gaia first Data Release. Here we describe how the SOS pipeline was modified to allow for processing the Gaia multi-band (G, GBP, and GRP) time-series photometry of all-sky candidate variables and produce specific results for confirmed RR Lyrae stars and Cepheids that are published in the DR2 catalogue.
Methods. The SOS Cep&RRL processing uses tools such as the period–amplitude and the period–luminosity relations in the G band. For the analysis of the Gaia DR2 candidates we also used tools based on the GBP and GRP photometry, such as the period–Wesenheit relation in (G, GRP).
Results. Multi-band time-series photometry and characterisation by the SOS Cep&RRL pipeline are published in Gaia DR2 for 150 359 such variables (9575 classified as Cepheids and 140 784 as RR Lyrae stars) distributed throughout the sky. The sample includes variables in 87 globular clusters and 14 dwarf galaxies (the Magellanic Clouds, 5 classical and 7 ultra-faint dwarfs). To the best of our knowledge, as of 25 April 2018, the variability of 50 570 of these sources (350 Cepheids and 50 220 RR Lyrae stars) has not been reported before in the literature, therefore they are likely new discoveries by Gaia. An estimate of the interstellar absorption is published for 54 272 fundamental-mode RR Lyrae stars from a relation based on the G-band amplitude and the pulsation period. Metallicities derived from the Fourier parameters of the light curves are also released for 64 932 RR Lyrae stars and 3738 fundamental-mode classical Cepheids with periods shorter than 6.3 days.