bluuebunny/crossref_metadata_2025_split huggingface dataset:
Particle Size Specific Magnetic Properties Across the Norwegian‐Greenland Seas: Insights Into the Influence of Sediment Source and Texture on Bulk Magnetic Records
Authors: Hatfield Robert G. , Wheeler Benjamin H. , Reilly Brendan T. , Stoner Joseph S. , Housen Bernard A. 
Published: January 2019

AbstractWe make fundamental observations of the particle size variability of magnetic properties from 71 core tops that span the southern Greenland and Norwegian Seas. These data provide the first detailed regional characterization of how bulk magnetic properties vary with sediment texture, sediment source, and sediment transport. Magnetic susceptibility (MS) and hysteresis parameters were measured on the bulk sediment and the five constituent sediment particle size fractions (clay, fine silt, medium silt, coarse silt, and sand). The median MS value of the medium silt size fraction is ~3–5 times higher than that of the sand and clay size fractions and results in a strong sensitivity of bulk MS to sediment texture. Hysteresis properties of the clay size fraction are relatively homogeneous and contrast that silt and sand size fractions which show regional differences across the study area. These coarser fractions are more transport limited and using medium silt hysteresis measurements and low temperature MS behavior we establish three endmembers that effectively explain the variability observed across the region. We model the response of bulk magnetic properties to changes in sediment texture and suggest that variations in sediment source are required to explain the bulk magnetic property variability observed in cores across the southern Greenland and Norwegian Seas. These findings imply that sediment source has a greater influence on driving bulk magnetic property variability across this region than has previously been assumed.
Do We Need to Parameterize Mesoscale Convective Organization to Mitigate the MJO‐Mean State Trade‐Off?
Authors: Ahn Min‐Seop , Kim Daehyun , Park Sungsu , Ham Yoo‐Geun 
Published: January 2019

AbstractModifications in cumulus parameterizations that improve Madden‐Julian oscillation (MJO) simulation tend to degrade the mean state—known as the MJO‐mean state trade‐off. The impacts of parameterizing mesoscale convective organization on the relationship between the MJO and the mean state simulation fidelity are examined. A series of experiments are made with a general circulation model that parameterizes the mesoscale convective organization and simulates well both the MJO and the mean state. In the control simulation, a prognostic nondimensional variable (Ω) represents the degree of convective organization. In order to examine the effect of the parameterized convective organization, fixed Ω values are imposed in a series of constrained experiments. The fixed‐Ω simulations show a negative relationship between the MJO and the mean state simulation fidelity. The control simulation is deviated from the negative relationship, suggesting the parameterized mesoscale convective organization helps general circulation models to mitigate the MJO‐mean state trade‐off.
The Trend and Seasonal Change of Sediment in the East China Sea Detected by GRACE
Authors: Chang Le , Tang He , Yi Shuang , Sun Wenke 
Published: January 2019

AbstractThe deposition of land sediments onto the broad continental shelf of the East China Sea (ECS) is controlled by complex, dynamic hydrological mechanisms. In this study, we apply the data from Gravity Recovery and Climate Experiment (GRACE) satellite to detect the gravity signal caused by changes in sedimentation. The GRACE‐observed gravity signal is separated into the individual contributions using multisource data. After correction of each known individual signal, the sediment‐caused gravity change signal is used to invert for the sediment mass change in the ECS using a space domain inverse method. The results indicate that the total GRACE‐inverted sediment deposition rate was 0.82 ± 0.3 Gt/year from 2005 to 2015, which is in agreement with in situ sediment observations. The seasonal sediment change is also calculated and discussed. It is caused by sediment transport between the ECS and the Yellow Sea.
Permanent Thermohaline Staircases in the Tyrrhenian Sea
Authors: Durante S. , Schroeder K. , Mazzei L. , Pierini S. , Borghini M. , Sparnocchia S. 
Published: January 2019

AbstractThe longest historical time series (14 years, from 2003 to 2016) of temperature and salinity of thermohaline staircases with highly homogeneous and reliable data ever observed is here presented and studied. The thermohaline staircase system of the central Tyrrhenian Sea is due to double diffusion in salt finger regime, and our study reveals its conservative behavior, oscillating among slightly different shapes, passing through merging processes, with a systematic upward drift of the interfaces. Data also show enhanced salt finger processes after 2010, near the bottom, promoted by the ingression from the Western Mediterranean of a new denser water mass due to the Western Mediterranean Transition. Our results are relevant for studying the mixing in the intermediate and deep region and open the way for modeling and theoretical follow‐up studies aimed to reproduce and explain these observations.
Structural basis for species-selective targeting of Hsp90 in a pathogenic fungus
Authors: Whitesell Luke , Robbins Nicole , Huang David S. , McLellan Catherine A. , Shekhar-Guturja Tanvi , LeBlanc Emmanuelle V. , Nation Catherine S. , Hui Raymond , Hutchinson Ashley , Collins Cathy , Chatterjee Sharanya , Trilles Richard , Xie Jinglin L. , Krysan Damian J. , Lindquist Susan , Porco John A. , Tatu Utpal , Brown Lauren E. , Pizarro Juan , Cowen Leah E. 
Published: January 2019

AbstractNew strategies are needed to counter the escalating threat posed by drug-resistant fungi. The molecular chaperone Hsp90 affords a promising target because it supports survival, virulence and drug-resistance across diverse pathogens. Inhibitors of human Hsp90 under development as anticancer therapeutics, however, exert host toxicities that preclude their use as antifungals. Seeking a route to species-selectivity, we investigate the nucleotide-binding domain (NBD) of Hsp90 from the most common human fungal pathogen, Candida albicans. Here we report structures for this NBD alone, in complex with ADP or in complex with known Hsp90 inhibitors. Encouraged by the conformational flexibility revealed by these structures, we synthesize an inhibitor with >25-fold binding-selectivity for fungal Hsp90 NBD. Comparing co-crystals occupied by this probe vs. anticancer Hsp90 inhibitors revealed major, previously unreported conformational rearrangements. These insights and our probe’s species-selectivity in culture support the feasibility of targeting Hsp90 as a promising antifungal strategy.
Contribution of rare and common variants to intellectual disability in a sub-isolate of Northern Finland
Authors: Kurki Mitja I. , Saarentaus Elmo , Pietiläinen Olli , Gormley Padhraig , Lal Dennis , Kerminen Sini , Torniainen-Holm Minna , Hämäläinen Eija , Rahikkala Elisa , Keski-Filppula Riikka , Rauhala Merja , Korpi-Heikkilä Satu , Komulainen–Ebrahim Jonna , Helander Heli , Vieira Päivi , Männikkö Minna , Peltonen Markku , Havulinna Aki S. , Salomaa Veikko , Pirinen Matti , Suvisaari Jaana , Moilanen Jukka S. , Körkkö Jarmo , Kuismin Outi , Daly Mark J. , Palotie Aarno 
Published: January 2019

AbstractThe contribution of de novo variants in severe intellectual disability (ID) has been extensively studied whereas the genetics of mild ID has been less characterized. To elucidate the genetics of milder ID we studied 442 ID patients enriched for mild ID (>50%) from a population isolate of Finland. Using exome sequencing, we show that rare damaging variants in known ID genes are observed significantly more often in severe (27%) than in mild ID (13%) patients. We further observe a significant enrichment of functional variants in genes not yet associated with ID (OR: 2.1). We show that a common variant polygenic risk significantly contributes to ID. The heritability explained by polygenic risk score is the highest for educational attainment (EDU) in mild ID (2.2%) but lower for more severe ID (0.6%). Finally, we identify a Finland enriched homozygote variant in the CRADD ID associated gene.
Effects of Chemical Insecticide Imidacloprid on the Release of C6 Green Leaf Volatiles in Tea Plants (Camellia sinensis)
Authors: Zhou Qiying , Cheng Xi , Wang Shuangshuang , Liu Shengrui , Wei Chaoling 
Published: January 2019

AbstractChemical insecticides are widely used for pest control worldwide. However, the impact of insecticides on indirect plant defense is seldom reported. Here, using tea plants and the pesticide imidacloprid, effects of chemical insecticides on C6-green leaf volatiles (GLVs) anabolism and release were investigated first time. Compared with the non-treated control plants, the treatment of imidacloprid resulted in the lower release amount of key GLVs: (Z)-3-hexenal, n-hexenal, (Z)-3-hexene-1-ol and (Z)-3-Hexenyl acetate. The qPCR analysis revealed a slight higher transcript level of the CsLOX3 gene but a significantly lower transcript level of CsHPL gene. Our results suggest that imidacloprid treatment can have a negative effect on the emission of GLVs due to suppressing the critical GLVs synthesis-related gene, consequently affecting plant indirect defense.
Kinetic and thermodynamic effects of phosphorylation on p53 binding to MDM2
Authors: Yadahalli Shilpa , Neira José L. , Johnson Christopher M. , Tan Yaw Sing , Rowling Pamela J. E. , Chattopadhyay Anasuya , Verma Chandra S. , Itzhaki Laura S. 
Published: January 2019

Abstractp53 is frequently mutated in human cancers. Its levels are tightly regulated by the E3 ubiquitin ligase MDM2. The complex between MDM2 and p53 is largely formed by the interaction between the N-terminal domain of MDM2 and the N-terminal transactivation (TA) domain of p53 (residues 15–29). We investigated the kinetic and thermodynamic basis of the MDM2/p53 interaction by using wild-type and mutant variants of the TA domain. We focus on the effects of phosphorylation at positions Thr18 and Ser20 including their substitution with phosphomimetics. Conformational propensities of the isolated peptides were investigated using in silico methods and experimentally by circular dichroism and 1H-NMR in aqueous solution. Both experimental and computational analyses indicate that the p53 peptides are mainly disordered in aqueous solution, with evidence of nascent helix around the Ser20-Leu25 region. Both phosphorylation and the phosphomimetics at Thr18 result in a decrease in the binding affinity by ten- to twenty-fold when compared to the wild-type. Phosphorylation and phosphomimetics at Ser20 result in a smaller decrease in the affinity. Mutation of Lys24 and Leu25 also disrupts the interaction. Our results may be useful for further development of peptide-based drugs targeting the MDM2/p53 interaction.
The viscosity-radius relationship for concentrated polymer solutions
Authors: Dunstan Dave E. 
Published: January 2019

AbstractA key assumption of polymer physics is that the random chain polymers extend in flow. Recent experimental evidence has shown that polymer chains compress in Couette flow in a manner counter to expectation. Here, scaling arguments and experimental evidence from the literature are used to determine the relationship between the viscosity, η, and chain radius of gyration,RG. The viscosity-radius of gyration relationship is found to be$${\boldsymbol{\eta }}{\boldsymbol{ \sim }}{{\boldsymbol{R}}}_{{\boldsymbol{G}}}^{{\boldsymbol{m}}{\boldsymbol{(}}\dot{{\boldsymbol{\gamma }}}{\boldsymbol{)}}}$$η~RGm(γ˙)where m($$\dot{{\boldsymbol{\gamma }}}$$γ˙) is the power law exponent of the viscosity-temperature relationship that depends on the specific polymer-solvent system and the shear rate,$$\dot{{\boldsymbol{\gamma }}}$$γ˙. The viscosity is shown to be a power law function of the radius, and to decrease with decreasing radius under conditions where the chains are ideal random walks in concentrated solution. Furthermore, this relationship is consistent with both the widely observed viscosity-temperature and viscosity-shear rate behavior observed in polymer rheology. The assumption of extension is not consistent with these observations as it would require that the chains increase in size with increasing temperature. Shear thinning is thus a result of a decreasing radius with increasing shear rate as$${{\boldsymbol{R}}}_{{\boldsymbol{G}}} \sim {\dot{{\boldsymbol{\gamma }}}}^{-{\boldsymbol{n}}{\boldsymbol{/}}{\boldsymbol{m}}{\boldsymbol{(}}\dot{{\boldsymbol{\gamma }}}{\boldsymbol{)}}}$$RG~γ˙−n/m(γ˙)where n is the power law exponent. Furthermore, the thermal expansion coefficients determine the variation in the power law exponents that are measured for different polymer systems. Typical values of n enable the measured reduction in coils size behavior to be fitted. Furthermore, the notion that polymer chains extend to reduce the viscosity implies that an increasing chain size results in a reduced viscosity is addressed. This assumption would require that the viscosity increases with reducing coil radius which is simply unphysical.
Chemically defined conditions for long-term maintenance of pancreatic progenitors derived from human induced pluripotent stem cells
Authors: Konagaya Shuhei , Iwata Hiroo 
Published: January 2019

AbstractLarge numbers of hormone-releasing cells, approximately 109 endocrine cells, are required to treat type I diabetes patients by cell transplantation. The SOX9-positive pancreatic epithelium proliferates extensively during the early stages of pancreatic development. SOX9-positive pancreatic epithelium is thought to be an expandable cell source of β cells for transplantation therapy. In this study, we attempted to expand pancreatic progenitors (PPs: PDX1+/SOX9+) derived from four human iPSC lines in three-dimensional (3D) culture using a chemically defined medium and examined the potential of the derived PPs to differentiate into β-like cells. PPs from four human iPSC lines were maintained and effectively proliferated in a chemically defined medium containing epidermal growth factor and R-spondin-1, CHIR99021, fibroblast growth factor-7, and SB431542. PPs derived from one iPSC line can be expanded by more than 104-fold in chemically defined medium containing two of the fives, epidermal growth factor and R-spondin-1. The expanded PPs were also stable following cryopreservation. After freezing and thawing, the PPs proliferated without a decrease in the rate. PPs obtained after 50 days of culture successfully differentiated into insulin-positive β-like cells, glucagon-positive α-like cells, and somatostatin-positive δ-like cells. The differentiation efficiency of expanded PPs was similar to that of PPs without expansion culture.
Polygenic impact of common genetic risk loci for Alzheimer’s disease on cerebral blood flow in young individuals
Authors: Chandler Hannah L. , Wise Richard G. , Murphy Kevin , Tansey Katherine E. , Linden David E. J. , Lancaster Thomas M. 
Published: January 2019

AbstractGenome-wide association studies (GWAS) show that many common alleles confer risk for developing Alzheimer’s disease (AD). These risk loci may contribute to MRI alterations in young individuals, preceding the clinical manifestations of AD. Prior evidence identifies vascular dysregulation as the earliest marker of disease progression. However, it remains unclear whether cerebrovascular function (measured via grey-matter cerebral blood flow (gmCBF)) is altered in young individuals with increased AD genetic risk. We establish relationships between gmCBF with APOE and AD polygenic risk score in a young cohort (N = 75; aged: 19–32). Genetic risk was assessed via a) possessing at least one copy of the APOE ɛ4 allele and b) a polygenic risk score (AD-PRS) estimated from AD-GWAS. We observed a reduction in gmCBF in APOE ɛ4 carriers and a negative relationship between AD-PRS and gmCBF. We further found regional reductions in gmCBF in individuals with higher AD-PRS across the frontal cortex (PFWE < 0.05). Our findings suggest that a larger burden of AD common genetic risk alleles is associated with attenuated cerebrovascular function, during young adulthood. These results suggest that cerebral vasculature is a mechanism by which AD risk alleles confer susceptibility.
High Quality ATAC-Seq Data Recovered from Cryopreserved Breast Cell Lines and Tissue
Authors: Fujiwara Saori , Baek Songjoon , Varticovski Lyuba , Kim Sohyoung , Hager Gordon L. 
Published: January 2019

AbstractDNA accessibility to transcription regulators varies between cells and modulates gene expression patterns. Several “open” chromatin profiling methods that provide valuable insight into the activity of these regulatory regions have been developed. However, their application to clinical samples has been limited despite the discovery that the Analysis of Transposase-Accessible Chromatin followed by sequencing (ATAC-seq) method can be performed using fewer cells than other techniques. Obtaining fresh rather than stored samples and a lack of adequate optimization and quality controls are major barriers to ATAC’s clinical implementation. Here, we describe an optimized ATAC protocol in which we varied nuclear preparation conditions and transposase concentrations and applied rigorous quality control measures before testing fresh, flash frozen, and cryopreserved breast cells and tissue. We obtained high quality data from small cell number. Furthermore, the genomic distribution of sequencing reads, their enrichment at transcription start sites, and transcription factor footprint analyses were similar between cryopreserved and fresh samples. This updated method is applicable to clinical samples, including cells from fine needle aspiration and tissues obtained via core needle biopsy or surgery. Chromatin accessibility analysis using patient samples will greatly expand the range of translational research and personalized medicine by identification of clinically-relevant epigenetic features.
Huaier n-butanol extract suppresses proliferation and metastasis of gastric cancer via c-Myc-Bmi1 axis
Authors: Wang Yiping , Lv Hang , Xu Zhiyuan , Sun Jiancheng , Ni Yixiu , Chen Zhe , Cheng Xiangdong 
Published: January 2019

AbstractGastric cancer (GC) ranks as the third leading cause of cancer-related mortality worldwide, and approximately 42% of all cases diagnosed each year worldwide are diagnosed in China. A large number of clinical applications have revealed that Trametes robiniophila Μurr. (Huaier) exhibits an anti-tumour effect. However, loss of the bioactive components of Huaier during the extraction procedure with water is unavoidable, and the underlying mechanism of the anti-cancer effect of Huaier remains poorly understood. In this study, we investigated the anti-cancer effect of Huaier n-butanol extract, which contained 51.4% total flavonoids, on HGC27, MGC803, and AGS human GC cell lines in vitro. At a low concentration, Huaier n-butanol extract inhibited the growth of these GC cell types, induced cell cycle arrest and reduced cell metastasis. Moreover, Huaier n-butanol extract suppressed the c-Myc-Bmi1 signalling pathway, and overexpression of Bmi1 reversed the effects of Huaier n-butanol extract on GC cells. Thus, our findings indicate that Huaier n-butanol extract suppresses the proliferation and metastasis of GC cells via a c-Myc-Bmi1-mediated approach, providing a new perspective for our understanding of the anti-tumour effects of Huaier. These results suggest that Huaier n-butanol extract could be an attractive therapeutic adjuvant for the treatment of human GC.
Elucidation of an intrinsic parameter for evaluating the electrical quality of graphene flakes
Authors: Lee Ha-Jin , Kim Ji Sun , Lee Kwang Young , Park Kyung Ho , Bae Jong-Seong , Mubarak Mahfuza , Lee Haeseong 
Published: January 2019

AbstractA test method for evaluating the quality of graphene flakes, such as reduced graphene oxide (rGO) and graphene nanopowder (GNP), was developed in this study. The pelletizer was selected for a sampling tool, which enables us to formulate the flake sample as a measurable sample. Various parameters were measured from the pelletized sample in order to elucidate the best parameter for representing the quality of the graphene flakes in terms of their electrical properties. Based on the analysis of 4-probe measurement data on the pelletized sample, the best intrinsic parameter is volume resistivity (or volume conductivity) rather than resistivity (or conductivity). Additionally, the possible modification of a sample before and after the pressurization was investigated by electron microscopy and Raman spectroscopy. No significant modification was observed. The volume conductivity in the two types of the graphene was different from their individual conductivities by one order of magnitude. Based on the results of X-ray photoelectron spectroscopy and Raman spectroscopy measurements, the volume conductivity of the graphene flake samples was governed by the oxygen content in the sample. Our achievements will promote the effective use of powder-type graphene products for further applications.
The cotton WRKY transcription factor (GhWRKY33) reduces transgenic Arabidopsis resistance to drought stress
Authors: Wang Na-Na , Xu Shang-Wei , Sun Yun-Lue , Liu Dong , Zhou Li , Li Yang , Li Xue-Bao 
Published: January 2019

AbstractAs the important source of natural fibers in the textile industry, cotton fiber quality and yield are often restricted to drought conditions because most of cotton plants in the world grow in the regions with water shortage. WRKY transcription factors regulate multiple plant physiological processes, including drought stress response. However, little is known of how the WRKY genes respond to drought stress in cotton. Our previous study revealed GhWRKY33 is leaf-specific and induced by drought stress. In this study, our data showed GhWRKY33 protein localizes to the cell nucleus and is able to bind to “W-box” cis-acting elements of the target promoters. Under drought stress, GhWRKY33 overexpressing transgenic Arabidopsis was withered much more quickly than wild type due to faster water loss. Moreover, GhWRKY33 transgenic plants displayed more tolerance to abscisic acid (ABA), relative to wild type. Expression of some drought stress-related genes and ABA-responsive genes were changed in the GhWRKY33 transgenic Arabidopsis with drought or ABA treatment. Collectively, our findings indicate that GhWRKY33 may act as a negative regulator to mediate plant response to drought stress and to participate in the ABA signaling pathway.