bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel ABA functional analogue B2 enhances drought tolerance in wheat
Authors: Zhou Yuyi , He Rui , Guo Yuling , Liu Keke , Huang Guanmin , Peng Chuanxi , Liu Yiguo , Zhang Mingcai , Li Zhaohu , Duan Liusheng 
Published: February 2019

AbstractDrought stress negatively affects wheat growth and yield. Application of drought agent is an effective way to improve crop drought tolerance, therefore increasing crop yield. Based on the structure of abscisic acid (ABA), Pyrabactin and coronatine (COR), we designed the target compound B2. To investigate the function of B2 in alleviating drought stress on wheat, the drought-resistant variety ND212 and drought-sensitive variety LX99 were used under hydroponic conditions. The results showed that B2 had a similar function with ABA, especially 0.01 μmol·L−1 B2. Under drought stress conditions, 0.01 μmol·L−1 B2 increased the water content of wheat, enhanced the osmotic adjustment ability of leaves, and reduced the toxicity of reactive oxygen species on cells. What’s more, 0.01 μmol·L−1 B2 improved the expression level of ABA-responsive genes TaSnRK2.4 and TaMYB3R1. It also improved the expression level of drought-responsive genes TaSRHP and TaERF3. Taken together, B2 enhanced drought tolerance in wheat by activating ABA signaling pathway.
Long fragments achieve lower base quality in Illumina paired-end sequencing
Authors: Tan Ge , Opitz Lennart , Schlapbach Ralph , Rehrauer Hubert 
Published: February 2019

AbstractIllumina’s technology provides high quality reads of DNA fragments with error rates below 1/1000 per base. Sequencing runs typically generate millions of reads in which the vast majority of the reads has an average error rate below 1/1000. However, some paired-end sequencing data show the presence of a subpopulation of reads where the second read (R2) has lower average qualities. We show that the fragment length is a major driver of increased error rates in the R2 reads. Fragments above 500 nt tend to yield lower base qualities and higher error rates than shorter fragments. We use publicly available Illumina data to demonstrate that the fragment length dependency of the R2 read qualities exists in various library protocols, in different labs and using different sequencer models. Our finding extends the understanding of the Illumina read quality and has implications on error models for Illumina reads. It also sheds a light on the importance of controlling the fragment size during library preparation.
Towards Improving Embryo Prioritization: Parallel Next Generation Sequencing of DNA and RNA from a Single Trophectoderm Biopsy
Authors: Fuchs Weizman Noga , Wyse Brandon A. , Antes Ran , Ibarrientos Zenon , Sangaralingam Mugundhine , Motamedi Gelareh , Kuznyetsov Valeriy , Madjunkova Svetlana , Librach Clifford L. 
Published: February 2019

AbstractImproved embryo prioritization is crucial in optimizing the results in assisted reproduction, especially in light of increasing utilization of elective single embryo transfers. Embryo prioritization is currently based on morphological criteria and in some cases incorporates preimplantation genetic testing for aneuploidy (PGT-A). Recent technological advances have enabled parallel genomic and transcriptomic assessment of a single cell. Adding transcriptomic analysis to PGT-A holds promise for better understanding early embryonic development and implantation, and for enhancing available embryo prioritization tools. Our aim was to develop a platform for parallel genomic and transcriptomic sequencing of a single trophectoderm (TE) biopsy, that could later be correlated with clinical outcomes. Twenty-five embryos donated for research were utilized; eight for initial development and optimization of our method, and seventeen to demonstrate clinical safety and reproducibility of this method. Our method achieved 100% concordance for ploidy status with that achieved by the classic PGT-A. All sequencing data exceeded quality control metrics. Transcriptomic sequencing data was sufficient for performing differential expression (DE) analysis. All biopsies expressed specific TE markers, further validating the accuracy of our method. Using PCA, samples clustered in euploid and aneuploid aggregates, highlighting the importance of controlling for ploidy in every transcriptomic assessment.
Non-Markovianity of qubit evolution under the action of spin environment
Authors: Chakraborty Sagnik , Mallick Arindam , Mandal Dipanjan , Goyal Sandeep K. , Ghosh Sibasish 
Published: February 2019

AbstractThe question, whether an open system dynamics is Markovian or non-Markovian can be answered by studying the direction of the information flow in the dynamics. In Markovian dynamics, information must always flow from the system to the environment. If the environment is interacting with only one of the subsystems of a bipartite system, the dynamics of the entanglement in the bipartite system can be used to identify the direction of information flow. Here we study the dynamics of a two-level system interacting with an environment, which is also a heat bath, and consists of a large number of two-level quantum systems. Our model can be seen as a close approximation to the ‘spin bath’ model at low temperatures. We analyze the Markovian nature of the dynamics, as we change the coupling between the system and the environment. We find the Kraus operators of the dynamics for certain classes of couplings. We show that any form of time-independent or time-polynomial coupling gives rise to non-Markovianity. Also, we witness non-Markovianity for certain parameter values of time-exponential coupling. Moreover, we study the transition from non-Markovian to Markovian dynamics as we change the value of coupling strength.
Leptin receptor deficiency induces early, transient and hyperglycaemia-independent blood-brain barrier dysfunction
Authors: Corem Noa , Anzi Shira , Gelb Sivan , Ben-Zvi Ayal 
Published: February 2019

AbstractDiabetes mellitus (DM) significantly increases susceptibility to central nervous system (CNS) pathologies, including stroke, vascular dementia, cognitive deficits and Alzheimer’s disease. Previous studies (mostly using the streptozotocin model) suggested that blood-brain barrier (BBB) disruption is involved in these conditions. Here, we examined the integrity of brain capillaries and BBB permeability in Leprdb/db obesity-related diabetic mice. Surprisingly, significant BBB leakage was observed only in young mice at the pre-hyperglycemic stage. Thorough examination of barrier permeability at later diabetic stages showed no evidence for significant BBB leakage during the hyperglycemic state. Electron microscopy imaging of mice with short-term hyperglycaemia supported normal BBB permeability but indicated other stress-related changes in capillary ultrastructure, such as mitochondrial degeneration. Based on our study with this mouse genetic model of obesity-related DM, we suggest that previously reported hyperglycaemia-induced BBB leakage is most likely not the underlying mechanism of DM-related CNS pathologies. Finally we propose that BBB hyper-permeability might be an early and transient phenomenon while stress-related endothelial pathologies do correlate with a short-term diabetic state.
Multi-parameters of Magnetic Resonance Imaging to Estimate Ischemia-Reperfusion Injury after Stroke in Hyperglycemic Rats
Authors: Huang Wei-yuan , Wu Gang , Guo Shan-xi , Geng Dao-ying , Li Jian-jun , Yang Kai 
Published: February 2019

AbstractThe aim of the study is to verify the effect of hyperglycemia on ischemia-reperfusion injury and to explore the feasibility of noninvasive observation of ischemic-reperfusion injury in hyperglycemic ischemic stroke by MRI technique. According to the duration of ischemia and blood glucose levels, 40 rats were divided into hyperglycemic ischemic 2-hr (H-I2h), hyperglycemic ischemic 6-hr (H-I6h), non- hyperglycemic ischemic 2-hr (NH-I2h), and non- hyperglycemic ischemic 6-hr (NH-I6h) groups. T2W imaging, DW imaging, T2 mapping, T2* mapping, DCE, and T1 mapping after enhancement sequences were acquired before reperfusion and approximately 3-hr after reperfusion. ADC, T1, T2, T2*, and Ktrans values of ischemic lesion were obtained in different groups. After reperfusion, the variation of ADC values showed no significant difference between groups with diabetes and groups without diabetes and between different recanalization time-points (2-hr vs 6-hr). After reperfusion, T2, T2*, and Ktrans values increased in different degrees in all four groups. Only the T1 value decreased in all groups. The change of all parameters in groups with hyperglycemia was more obvious than that in groups without hyperglycemia and was more obvious in groups with H-I6h versus those with H-I2h. This study confirms that hyperglycemia aggravates ischemia-reperfusion injury and may be an important risk factor for the prognosis of ischemic stroke. The Ktrans values should be noninvasive imaging indicators to monitor blood brain barrier permeability and ischemic-reperfusion injury in ischemic stroke.
Dynamic generation of multi-qubit entanglement in the ultrastrong-coupling regime
Authors: Liu Xin , Liao Qinghong , Fang Guangyu , Liu Shutian 
Published: February 2019

AbstractWe propose a dynamic evolution protocol for generating multi-qubit GHZ states in the ultrastrong-coupling regime of circuit QED. By varying the time length of sequences, the protocol works for any coupling strength g/ωr ≥ 0.25. The time for generating the GHZ states in our protocol can be in the subnanoseconds. By taking into account realistic parameters of circuit QED, the degeneracy of fidelity due to decoherence can be as low as 0.02%.
Insulin secretory granules labelled with phogrin-fluorescent proteins show alterations in size, mobility and responsiveness to glucose stimulation in living β-cells
Authors: Ferri Gianmarco , Digiacomo Luca , Lavagnino Zeno , Occhipinti Margherita , Bugliani Marco , Cappello Valentina , Caracciolo Giulio , Marchetti Piero , Piston David W. , Cardarelli Francesco 
Published: February 2019

AbstractThe intracellular life of insulin secretory granules (ISGs) from biogenesis to secretion depends on their structural (e.g. size) and dynamic (e.g. diffusivity, mode of motion) properties. Thus, it would be useful to have rapid and robust measurements of such parameters in living β-cells. To provide such measurements, we have developed a fast spatiotemporal fluctuation spectroscopy. We calculate an imaging-derived Mean Squared Displacement (iMSD), which simultaneously provides the size, average diffusivity, and anomalous coefficient of ISGs, without the need to extract individual trajectories. Clustering of structural and dynamic quantities in a multidimensional parametric space defines the ISGs’ properties for different conditions. First, we create a reference using INS-1E cells expressing proinsulin fused to a fluorescent protein (FP) under basal culture conditions and validate our analysis by testing well-established stimuli, such as glucose intake, cytoskeleton disruption, or cholesterol overload. After, we investigate the effect of FP-tagged ISG protein markers on the structural and dynamic properties of the granule. While iMSD analysis produces similar results for most of the lumenal markers, the transmembrane marker phogrin-FP shows a clearly altered result. Phogrin overexpression induces a substantial granule enlargement and higher mobility, together with a partial de-polymerization of the actin cytoskeleton, and reduced cell responsiveness to glucose stimulation. Our data suggest a more careful interpretation of many previous ISG-based reports in living β-cells. The presented data pave the way to high-throughput cell-based screening of ISG structure and dynamics under various physiological and pathological conditions.
Investigating causality in the association between vitamin D status and self-reported tiredness
Authors: Havdahl Alexandra , Mitchell Ruth , Paternoster Lavinia , Davey Smith George 
Published: February 2019

AbstractSelf-reported tiredness or low energy, often referred to as fatigue, has been linked to low levels of circulating 25-hydroxyvitamin D (25OHD), a biomarker of vitamin D status. Although it is uncertain if the association is causal, fatigue is a common indication for testing, and correcting, low 25OHD-levels. We used two-sample Mendelian randomization to test for genetic evidence of a causal association between low 25OHD-levels and fatigue. Genetic-25OHD associations were estimated from the largest genome-wide association study of vitamin D to date, and genetic-fatigue associations were estimated in 327,478 individuals of European descent in UK Biobank, of whom 19,526 (5.96%) reported fatigue (tiredness or low energy nearly every day over the past two weeks). Using seven genome-wide significant 25OHD-reducing genetic variants, there was little evidence for a causal effect of 25OHD on fatigue [odds ratio for fatigue was 1.05 with 95% confidence interval (CI) of 0.87–1.27 per unit decrease in log-transformed 25OHD (1.02 with 95% CI of 0.99-1.06 per 1-SD decrease in log-transformed 25OHD)]. There was also little evidence of association between any individual 25OHD-reducing variant and fatigue. Our results suggest that a clinically relevant protective effect of 25OHD-levels on fatigue is unlikely. Therefore, vitamin D supplementation of the general population to raise 25OHD-levels is not likely to be useful in preventing fatigue.
TSA restores hair follicle-inductive capacity of skin-derived precursors
Authors: Guo Ling , Wang Xiaoxiao , Yuan Jifan , Zhu Meishu , Fu Xiaobing , Xu Ren-He , Wu Chuanyue , Wu Yaojiong 
Published: February 2019

AbstractThe genesis of the hair follicle relies on signals derived from mesenchymal cells in the dermis during skin morphogenesis and regeneration. Multipotent skin-derived precursors (SKPs), which exhibit long term proliferation potential when being cultured in spheroids, have been shown to induce hair genesis and hair follicle regeneration in mice, implying a therapeutic potential of SKPs in hair follicle regeneration and bioengineering. However, the hair-inductive property of SKPs declines progressively upon ex vivo culture expansion, suggesting that the expressions of the genes responsible for hair induction are epigenetically unstable. In this study, we found that TSA markedly alleviated culture expansion induced SKP senescence, increased the expression and activity of alkaline phosphatase (AP) in the cells and importantly restored the hair inductive capacity of SKPs. TSA increased the acetylation level of histone H3, including the K19/14 sites in the promoter regions of bone morphogenetic proteins (BMPs) genes, which were associated with elevated gene expression and BMP signaling activity, suggesting a potential attribution of BMP pathway in TSA induced recovery of the hair inductive capacity of SKPs.
Flat-band localization and self-collimation of light in photonic crystals
Authors: Myoung Nojoon , Park Hee Chul , Ramachandran Ajith , Lidorikis Elefterios , Ryu Jung-Wan 
Published: February 2019

AbstractWe investigate the optical properties of a photonic crystal (PC) composed of a quasi-one-dimensional flat-band lattice array through finite-difference time-domain simulations. The photonic bands contain flat bands (FBs) at specific frequencies, which correspond to compact localized states as a consequence of destructive interference. The FBs are shown to be nondispersive along the Г → X line, prohibiting optical transmission with incident light in x direction. On the other hand, the photonic band for the FB frequency is found to be dispersive along the Г → Y line, resulting in nonzero optical transmission. Such anisotropic optical response of the PC due to the FB localization of light in a single direction only results in a self-collimation of light propagation throughout the PC at the FB frequency.
Alteration of specific cytokine expression patterns in patients with breast cancer
Authors: Kawaguchi Kosuke , Sakurai Masashi , Yamamoto Yasuko , Suzuki Eiji , Tsuda Moe , Kataoka Tatsuki R. , Hirata Masahiro , Nishie Mariko , Nojiri Takashi , Kumazoe Motofumi , Saito Kuniaki , Toi Masakazu 
Published: February 2019

AbstractSystemic inflammation has been associated with aggressive tumor growth, invasion, and metastasis. Here we performed a comprehensive analysis of 26 kinds of inflammatory cytokine expression patterns among 185 patients with breast cancer and 54 healthy volunteers followed by chemometric analysis. We identified the specific cytokine expression patterns of breast cancer patients compared to healthy volunteers with (1) VEGF, IL-9, GM-CSF, IL-13, IL-4, and IFNγ, (2) IL-8, IL-10, IL-12, IL-5, IL-7, IL-1α, GCSF, IL-1β, and TNFα and (3) IL-2, Eotaxin, MIP1β, MIP1α, IL-17, and bFGF. Among the patients with breast cancer, we identified the specific cytokine signature of metastatic patients compared to non-metastatic patients. We also established a mathematical model for distinguishing patients with breast cancer from healthy volunteers and metastatic patients from non-metastatic patients. This cytokine network analysis could provide new insights into early intervention and effective therapeutic strategy for patients with breast cancer.
Nuclear import of Xenopus egg extract components into cultured cells for reprogramming purposes: a case study on goldfish fin cells
Authors: Chênais Nathalie , Lorca Thierry , Morin Nathalie , Guillet Brigitte , Rime Hélène , Le Bail Pierre-Yves , Labbé Catherine 
Published: February 2019

AbstractReprogramming of cultured cells using Xenopus egg extract involves controlling four major steps: plasma membrane permeabilization, egg factors import into the nucleus, membrane resealing, and cell proliferation. Using propidium iodide to assess plasma membrane permeability, we established that 90% of the cultured fin cells were permeabilized by digitonin without any cell losses. We showed that egg extract at metaphase II stage was essential to maintain nuclear import function in the permeabilized cells, as assessed with a fusion GFP protein carrying the nuclear import signal NLS. Moreover, the Xenopus-egg-specific Lamin B3 was detected in 87% of the cell nuclei, suggesting that other egg extract reprogramming factors of similar size could successfully enter the nucleus. Lamin B3 labelling was maintained in most cells recovered 24 h after membrane resealing with calcium, and cells successfully resumed cell cycle in culture. In contrast, permeabilized cells that were not treated with egg extract failed to proliferate in culture and died, implying that egg extract provided factor essential to the survival of those cells. To conclude, fish fin cells were successfully primed for treatment with reprogramming factors, and egg extract was shown to play a major role in their survival and recovery after permeabilization.
Unprecedented Microbial Conversion of Biliverdin into Bilirubin-10-sulfonate
Authors: Shiels Ryan G. , Vidimce Josif , Pearson Andrew G. , Matthews Ben , Wagner Karl-Heinz , Battle Andrew R. , Sakellaris Harry , Bulmer Andrew C. 
Published: February 2019

AbstractBiliverdin (BV) possesses antioxidant and anti-inflammatory properties, with previous reports identifying protection against oxidant and inflammatory injury in animal models. Recent reports indicate that intra-duodenal administration of BV results in the formation of an uncharacterised metabolite, which is potently absorbed into the blood and excreted into the bile. This compound may be responsible for protection against inflammatory responses. This study aimed to identify novel, enterally-derived BV metabolites and determine the source of their metabolic transformation. Rat duodena and bacterial cultures of Citrobacter youngae were treated with BV and subsequently analysed via high performance liquid chromatography/high resolution tandem mass spectrometry to identify and characterise metabolites of BV. A highly abundant metabolite was detected in duodenal wash and bacterial culture supernatants with a 663.215 m/z (3 ppm mass accuracy) and a composition of C33N4O9H36S, which conformed to the predicted structure of bilirubin-10-sulfonate (BRS) and possessed a λmax of 440 nm. Bilirubin-10-sulfonate was then synthesized for comparative LCMS/MS analysis and matched with that of the biologically formed BV metabolite. This report confirms the formation of a previously undocumented metabolite of BV in mammals, indicating that a new metabolic pathway likely exists for BV metabolism requiring enteric bacteria, Citrobacter youngae. These data may have important implications with regard to understanding and harnessing the therapeutic efficacy of oral BV administration.
High-throughput LPS profiling as a tool for revealing of bacteriophage infection strategies
Authors: Kulikov Eugene E. , Golomidova Alla K. , Prokhorov Nikolai S. , Ivanov Pavel A. , Letarov Andrey V. 
Published: February 2019

AbstractO-antigens of Gram-negative bacteria modulate the interactions of bacterial cells with diverse external factors, including the components of the immune system and bacteriophages. Some phages need to acquire specific adhesins to overcome the O-antigen layer. For other phages, O-antigen is required for phage infection. In this case, interaction of phage receptor binding proteins coupled with enzymatic degradation or modification of the O-antigen is followed by phage infection. Identification of the strategies used by newly isolated phages may be of importance in their consideration for various applications. Here we describe an approach based on screening for host LPS alterations caused by selection by bacteriophages. We describe an optimized LPS profiling procedure that is simple, rapid and suitable for mass screening of mutants. We demonstrate that the phage infection strategies identified using a set of engineeredE. coli4 s mutants with impaired or altered LPS synthesis are in good agreement with the results of simpler tests based on LPS profiling of phage-resistant spontaneous mutants.
Isopycnal mixing of interhemispheric intermediate waters by subthermocline eddies east of the Philippines
Authors: Nan Feng , Yu Fei , Ren Qiang , Wei Chuanjie , Liu Yansong , Sun Shuhui 
Published: February 2019

AbstractBoth sporadic observations and modelling studies suggest that subthermocline eddies (SEs) exist east of the Philippines, where interhemispheric waters meet. However, effects of SEs on water mass mixing have never been observed. Here, using data from mooring and buoy deployed in the frontal region of the interhemispheric water masses, we show for the first time that the SEs act as an “underwater mixer” of intermediate waters from north and south Pacific oceans. The SEs have typical swirl speeds of 0.1~0.4 m s−1 between 200 and 800 m depth with a dominant period of ~90 days. Variation in intermediate water salinity also had a period of ~90 days, lagging eddy speed by ~8 days. Horizontal eddy diffusivity representative of eddy mixing rate was quantified using a mixing-length framework. Horizontal eddy diffusivity had both surface and subthermocline maxima. The vertically varying eddy diffusivity can be used to improve parameterization of eddy stirring in the tropical Pacific by coarse-resolution ocean climate models. The effect of the SEs on mixing of intermediate water masses seems not resolved by available eddy-resolving ocean models typically used for this region.