bluuebunny/crossref_metadata_2025_split huggingface dataset:
Space‐Time Characterization and Risk Assessment of Nutrient Pollutant Concentrations in China's Near Seas
Authors: Jiang Qutu , He Junyu , Wu Jiaping , He Mingjun , Bartley Evan , Ye Guanqiong , Christakos George 
Published: June 2019

AbstractHuman activities interacting with coastal waters lead to large amounts of nutrient loading and severe water pollution in China's near Seas. In this context, a comprehensive quantitative characterization of the spatiotemporal variation of nutrient pollutant concentrations is a key component of any reliable seawater quality assessment and integrated coastal management plan. The present work combines the Bayesian maximum entropy method with stochastic site indicators to estimate monthly nitrate and phosphate concentrations in China's near seas during 2015, explore their spatiotemporal variation, and provide an explicit quantitative assessment of seawater quality in conditions of in situ uncertainty. This makes it the first study of space‐time nutrient pollutant characterization at a national‐scale in a coastal seawater environment. The results showed that nitrate and phosphate distributions exhibit the same spatial trends along China's near seas, whereas high nutrient pollution levels are found in the Yangtze River, Liaohe River, and Pearl River estuaries. Local differences of temporal trends exist between nitrate and phosphate distributions, which suggest that distinct remediation strategies are needed to properly satisfy the required seawater quality standards. The average nitrate and phosphate concentrations across space‐time were found to be equal to 0.271 and 0.015 mg/L, respectively. The nitrate and phosphate concentrations exceeding the fourth grade seawater quality standard during 2015 were about 11% and 2.6%, respectively. The study of both the seasonal changes in human activities along the coastal cities and the temporal marine hydrodynamics can offer a better understanding of the seawater quality and the biogeochemical process of nutrient transport and distribution.
Statistics of chromatin organization during cell differentiation revealed by heterogeneous cross-linked polymers
Authors: Shukron O. , Piras V. , Noordermeer D. , Holcman D. 
Published: June 2019

AbstractChromatin of mammalian nucleus folds into discrete contact enriched regions such as Topologically Associating Domains (TADs). Folding hierarchy and internal organization of TADs is highly dynamic throughout cellular differentiation, and are correlated with gene activation and silencing. To account for multiple interacting TADs, we developed a parsimonious randomly cross-linked (RCL) polymer model that maps high frequency Hi-C encounters within and between TADs into direct loci interactions using cross-links at a given base-pair resolution. We reconstruct three TADs of the mammalian X chromosome for three stages of differentiation. We compute the radius of gyration of TADs and the encounter probability between genomic segments. We found 1) a synchronous compaction and decompaction of TADs throughout differentiation and 2) high order organization into meta-TADs resulting from weak inter-TAD interactions. Finally, the present framework allows to infer transient properties of the chromatin from steady-state statistics embedded in the Hi-C/5C data.
In situ structure and assembly of the multidrug efflux pump AcrAB-TolC
Authors: Shi Xiaodong , Chen Muyuan , Yu Zhili , Bell James M. , Wang Hans , Forrester Isaac , Villarreal Heather , Jakana Joanita , Du Dijun , Luisi Ben F. , Ludtke Steven J. , Wang Zhao 
Published: June 2019

AbstractMultidrug efflux pumps actively expel a wide range of toxic substrates from the cell and play a major role in intrinsic and acquired drug resistance. In Gram-negative bacteria, these pumps form tripartite assemblies that span the cell envelope. However, the in situ structure and assembly mechanism of multidrug efflux pumps remain unknown. Here we report the in situ structure of the Escherichia coli AcrAB-TolC multidrug efflux pump obtained by electron cryo-tomography and subtomogram averaging. The fully assembled efflux pump is observed in a closed state under conditions of antibiotic challenge and in an open state in the presence of AcrB inhibitor. We also observe intermediate AcrAB complexes without TolC and discover that AcrA contacts the peptidoglycan layer of the periplasm. Our data point to a sequential assembly process in living bacteria, beginning with formation of the AcrAB subcomplex and suggest domains to target with efflux pump inhibitors.
Strongly coupled magnon–phonon dynamics in a single nanomagnet
Authors: Berk Cassidy , Jaris Mike , Yang Weigang , Dhuey Scott , Cabrini Stefano , Schmidt Holger 
Published: June 2019

AbstractPolaritons are widely investigated quasiparticles with fundamental and technological significance due to their unique properties. They have been studied most extensively in semiconductors when photons interact with various elementary excitations. However, other strongly coupled excitations demonstrate similar dynamics. Specifically, when magnon and phonon modes are coupled, a hybridized magnon–phonon quasiparticle can form. Here, we report on the direct observation of coupled magnon–phonon dynamics within a single thin nickel nanomagnet. We develop an analytic description to model the dynamics in two dimensions, enabling us to isolate the parameters influencing the frequency splitting. Furthermore, we demonstrate tuning of the magnon–phonon interaction into the strong coupling regime via the orientation of the applied magnetic field.
Orchestrated ensemble activities constitute a hippocampal memory engram
Authors: Ghandour Khaled , Ohkawa Noriaki , Fung Chi Chung Alan , Asai Hirotaka , Saitoh Yoshito , Takekawa Takashi , Okubo-Suzuki Reiko , Soya Shingo , Nishizono Hirofumi , Matsuo Mina , Osanai Makoto , Sato Masaaki , Ohkura Masamichi , Nakai Junichi , Hayashi Yasunori , Sakurai Takeshi , Kitamura Takashi , Fukai Tomoki , Inokuchi Kaoru 
Published: June 2019

AbstractThe brain stores and recalls memories through a set of neurons, termed engram cells. However, it is unclear how these cells are organized to constitute a corresponding memory trace. We established a unique imaging system that combines Ca2+ imaging and engram identification to extract the characteristics of engram activity by visualizing and discriminating between engram and non-engram cells. Here, we show that engram cells detected in the hippocampus display higher repetitive activity than non-engram cells during novel context learning. The total activity pattern of the engram cells during learning is stable across post-learning memory processing. Within a single engram population, we detected several sub-ensembles composed of neurons collectively activated during learning. Some sub-ensembles preferentially reappear during post-learning sleep, and these replayed sub-ensembles are more likely to be reactivated during retrieval. These results indicate that sub-ensembles represent distinct pieces of information, which are then orchestrated to constitute an entire memory.
A case report of vanishing bile duct syndrome after exposure to pexidartinib (PLX3397) and paclitaxel
Authors: Piawah Sorbarikor , Hyland Colby , Umetsu Sarah E. , Esserman Laura J. , Rugo Hope S. , Chien A. Jo 
Published: June 2019

AbstractPexidartinib (PLX3397) is a small molecule tyrosine kinase and colony-stimulating factor-1 inhibitor with FDA breakthrough therapy designation for tenosynovial giant-cell tumor, and currently under study in several other tumor types, including breast cancer, non-Hodgkin’s lymphoma, and glioblastoma. Here, we report a case of severe drug-induced liver injury requiring liver transplantation due to vanishing bile duct syndrome (VBDS) after exposure to pexidartinib in the I-SPY 2 Trial, a phase 2 multicenter randomized neoadjuvant chemotherapy trial in patients with Stage II–III breast cancer. We also review the current literature on this rare, idiosyncratic, and potentially life-threatening entity.
Inexpensive and flexible nanographene-based electrodes for ubiquitous electrocardiogram monitoring
Authors: Romero Francisco J. , Castillo Encarnacion , Rivadeneyra Almudena , Toral-Lopez Alejandro , Becherer Markus , Ruiz Francisco G. , Rodriguez Noel , Morales Diego P. 
Published: June 2019

AbstractFlexible electronics is one of the fundamental technologies for the development of electronic skin, implant wearables, or ubiquitous biosensing. In this context, graphene-derived materials have attracted great interest due to their unique properties to fulfill the demands of these applications. Here we report a simple one-step method for the fabrication of electrophysical electrodes based on the photothermal production of porous nanographene structures on the surface of flexible polyimide substrates. This approach constitutes an inexpensive alternative to the commercial medical electrodes, leading to a lower and much more stable skin–electrode contact resistance and providing comparable signal transduction. This technology has been framed inside the IoT paradigm through the development of a denoising and signal classification clustering algorithm suitable for its implementation in wearable devices. The experiments have shown promising achievements regarding noise reduction, increasing the crest factor ~3.7 dB, as well as for the over 90% heart rate-monitoring accuracy.
What we learned from creating one of the world’s most popular MOOCs
Authors: Oakley Barbara A. , Sejnowski Terrence J. 
Published: June 2019

AbstractLearning How to Learn (LHTL) is currently one of the world’s most popular massive open online course (MOOC), with nearly 2.5 million registered learners in its first 4 years. Here, we “reverse engineer” the design of the course’s videos to show how creative application of well-known principles of multimedia learning in an MOOC context appear to have fueled the course’s popularity. Gaps in knowledge of multimedia learning are also noted. There have been some 50 years of experience researching effective classroom teaching, but less there have been only 5 years since MOOCs became widespread. The success of LHTL may provide further insight into the importance of the principles of multimedia learning, and how those principles might be practically implemented to improve MOOC making and the general design of instructional videos.
Combinatorial perturbation analysis reveals divergent regulations of mesenchymal genes during epithelial-to-mesenchymal transition
Authors: Watanabe Kazuhide , Panchy Nicholas , Noguchi Shuhei , Suzuki Harukazu , Hong Tian 
Published: June 2019

AbstractEpithelial-to-mesenchymal transition (EMT), a fundamental transdifferentiation process in development, produces diverse phenotypes in different physiological or pathological conditions. Many genes involved in EMT have been identified to date, but mechanisms contributing to the phenotypic diversity and those governing the coupling between the dynamics of epithelial (E) genes and that of the mesenchymal (M) genes are unclear. In this study, we employed combinatorial perturbations to mammary epithelial cells to induce a series of EMT phenotypes by manipulating two essential EMT-inducing elements, namely TGF-β and ZEB1. By measuring transcriptional changes in more than 700 E-genes and M-genes, we discovered that the M-genes exhibit a significant diversity in their dependency to these regulatory elements and identified three groups of M-genes that are controlled by different regulatory circuits. Notably, functional differences were detected among the M-gene clusters in motility regulation and in survival of breast cancer patients. We computationally predicted and experimentally confirmed that the reciprocity and reversibility of EMT are jointly regulated by ZEB1. Our integrative analysis reveals the key roles of ZEB1 in coordinating the dynamics of a large number of genes during EMT, and it provides new insights into the mechanisms for the diversity of EMT phenotypes.
High-coverage, long-read sequencing of Han Chinese trio reference samples
Authors: Wang Ying-Chih , Olson Nathan D. , Deikus Gintaras , Shah Hardik , Wenger Aaron M. , Trow Jonathan , Xiao Chunlin , Sherry Stephen , Salit Marc L. , Zook Justin M. , Smith Melissa , Sebra Robert 
Published: June 2019

AbstractSingle-molecule long-read sequencing datasets were generated for a son-father-mother trio of Han Chinese descent that is part of the Genome in a Bottle (GIAB) consortium portfolio. The dataset was generated using the Pacific Biosciences Sequel System. The son and each parent were sequenced to an average coverage of 60 and 30, respectively, with N50 subread lengths between 16 and 18 kb. Raw reads and reads aligned to both the GRCh37 and GRCh38 are available at the NCBI GIAB ftp site (ftp://ftp-trace.ncbi.nlm.nih.gov/giab/ftp/data/ChineseTrio/). The GRCh38 aligned read data are archived in NCBI SRA (SRX4739017, SRX4739121, and SRX4739122). This dataset is available for anyone to develop and evaluate long-read bioinformatics methods.
Assemblage structure of ichthyoplankton in the NE Atlantic in spring under contrasting hydrographic conditions
Authors: Rodriguez J. M. 
Published: June 2019

AbstractThe ichthyoplankton assemblage in the Atlantic region off the NW Iberian peninsula (AR) and in the southern Bay of Biscay (SBB) and the response of the larval fish species distribution to the relatively rapidly changing hydrographic conditions in spring 2010 were studied using two ichthyoplankton cruises. The SBB showed a more abundant and diverse ichthyoplankton assemblage than the AR, although the larval fish assemblage (LFA) was structured into on-shelf and off-shelf assemblages in both regions. Inter-sampling variability related to downwelling/upwelling regimes was observed in the cross-shelf assemblage distribution in the SBB but not in the AR. This suggests that LFA distributions in the area of this study are good indicators of downwelling and weak coastal upwelling regimes but not of relatively strong coastal upwelling or upwelling filaments. Although depth was identified by multivariate analyses as being the most important variable explaining larval fish species distributions, a shelf-breakfront in the SBB and the surface offshore (onshore) flows associated with coastal downwelling (upwelling) in the AR seems to have been key in defining and maintaining assemblage boundaries. Results of this study should also encourage marine research institutions to use routine ichthyoplankton sampling to monitor fish communities and their responses to global warming.
Identification of a binding protein for sesamin and characterization of its roles in plant growth
Authors: Tera Masayuki , Koyama Tomotsugu , Murata Jun , Furukawa Ayako , Mori Shoko , Azuma Toshiaki , Watanabe Takehiro , Hori Katsuhito , Okazawa Atsushi , Kabe Yasuaki , Suematsu Makoto , Satake Honoo , Ono Eiichiro , Horikawa Manabu 
Published: June 2019

AbstractSesamin is a furofuran-type lignan that is found abundantly in seeds of Sesamum indicum (sesame) and has been widely accepted as a dietary supplement with positive effects on human health. The biological activity of sesamin in human cells and organs has been analysed extensively, although comparatively few studies show biological functions for sesamin in planta. Herein we screened sesamin-binding proteins (SBP) from sesame seedling extracts using sesamin-immobilized nano-beads. In subsequent peptide mass fingerprinting analyses, we identified a SBP, Steroleosin B, which is one of the membrane proteins found in oil bodies. In addition, pull-down assays and saturation transfer difference-nuclear magnetic resonance (STD-NMR) experiments demonstrated that sesamin binds directly to recombinant Steroleosin B in vitro. Finally, ectopic accumulations of sesamin and Steroleosin B in transgenic Arabidopsis thaliana plants induced severe growth defects including suppression of leaf expansion and root elongation. Collectively, these results indicate that sesamin influences tissue development in the presence of Steroleosin B.
Strengthen of magnetic anisotropy of Au/Co/Au nanostructure by surface plasmon resonance
Authors: Kikuchi Yusuke , Tanaka Takuo 
Published: June 2019

AbstractWe experimentally demonstrated the increase of in-plane magnetic anisotropy in Au/Co/Au nanostructures by localized surface plasmon resonance (LSPR). When an array of Au/Co/Au square patch nanostructures was illuminated with linearly polarized light whose wavelength was 750 nm, the localized surface plasmons were resonantly excited in the nanostructures. From the measurement results of polar magneto-optical Kerr effect curves, we observed the magnetic anisotropy field increase in the Au/Co/Au nanostructure due to the excited surface plasmons. The in-plane magnetic anisotropy energy density was increased about 24%.
miR-29c overexpression and COL4A1 downregulation in infertile human endometrium reduces endometrial epithelial cell adhesive capacity in vitro implying roles in receptivity
Authors: Griffiths Meaghan , Van Sinderen Michelle , Rainczuk Katarzyna , Dimitriadis Evdokia 
Published: June 2019

AbstractThe endometrium is a highly complex tissue that is vulnerable to subtle gene expression changes and is the first point of contact for an implanting blastocyst. Successful blastocyst implantation can only occur when the endometrium is receptive during a short window with each menstrual cycle. microRNAs are small, non-coding RNAs that negatively regulate their gene targets. miR-29c has previously been identified to be differentially regulated across the fertile menstrual cycle, however it has not been investigated in association with infertility. We hypothesised that miR-29c dysregulation in the infertile endometrium would negatively influence endometrial adhesion and blastocyst implantation outcomes during the mid-secretory, receptive phase. miR-29c expression was elevated in early and mid-secretory phase infertile endometrium and localised to the epithelial compartments of endometrial tissue. Overexpression of miR-29c in vitro impaired endometrial epithelial adhesion, and reduced collagen type IV alpha 1 (COL4A1) mRNA expression. COL4A1 was immunolocalised to the luminal and glandular epithelial basement membranes in early and mid-secretory phase fertile and infertile endometrium for the first time. Knockdown of COL4A1 impaired endometrial epithelial adhesion suggesting a role in endometrial receptivity and implantation. Our data suggests miR-29c overexpression with infertility may impair the adhesive capacity of the endometrium, potentially contributing to implantation failure and infertility.
Comparison of two accelerated 4D-flow sequences for aortic flow quantification
Authors: Ebel Sebastian , Dufke Josefin , Köhler Benjamin , Preim Bernhard , Rosemeier Susan , Jung Bernd , Dähnert Ingo , Lurz Philipp , Borger Michael , Grothoff Matthias , Gutberlet Matthias 
Published: June 2019

AbstractTo compare two broadly used 4D-flow- with a 2D-flow-sequence in healthy volunteers, regarding absolute flow parameters, image quality (IQ), and eddy current correction (ECC). Forty volunteers (42 ± 11.8 years, 22 females) were examined with a 3T scanner. Thoracic aortic flow was assessed using a 3D-T2w-SPACE-STIR-sequence for morphology and two accelerated 4D-flow sequences for comparison, one with k-t undersampling and one with standard GRAPPA parallel-imaging. 2D-flow was used as reference standard. The custom-made software tool Bloodline enabled flow measurements for all analyses at the same location. Quantitative flow analyses were performed with and without ECC. One reader assessed pathline IQ (IQ-PATH) and occurrence of motion artefacts (IQ-ART) on a 3-point grading scale, the higher the better. k-t GRAPPA allowed a significant mean scan time reduction of 46% (17:56 ± 5:26 min vs. 10:40 ± 3:15 min) and provided significantly fewer motion artefacts than standard GRAPPA (IQ-ART 1.57 ± 0.55 vs. 0.84 ± 0.48; p < 0.001). Neither 4D-flow sequence significantly differed in flow volume nor peak velocity results with or without ECC. Nevertheless, the correlation between both 4D-flow sequences and 2D-flow was better with ECC; the k-t GRAPPA sequence performed best (R = 0.96 vs. 0.90). k-t GRAPPA 4D-flow was not inferior to a standard GRAPPA-sequence, showed fewer artefacts, comparable IQ and was almost two-fold faster.
Strong charge polarization effect enabled by surface oxidized titanium nitride for lithium-sulfur batteries
Authors: Gao Xiaochun , Zhou Dong , Chen Yi , Wu Wenjian , Su Dawei , Li Baohua , Wang Guoxiu 
Published: June 2019

AbstractThe commercialization of high-energy-density and low-cost lithium-sulfur batteries has been severely impeded by capacity fading and electrochemical polarization. Here we report a strategy to entrap polysulfides and boost the cathodic redox kinetics by embedding the surface oxidized quantum-dot-size TiN (TiN-O) within the highly ordered mesoporous carbon matrix. While the carbon scaffold offers sufficient electrical contact to the insulate sulfur, benefiting the full usage of sulfur and physical confinement of polysulfides. The surface oxygen renders TiN-O with a strong charge polarization effect for polysulfides via S-O-Ti bond as verified experimentally and theoretically. The suppressed shuttle effect and high lithium ion diffusion coefficient (7.9 × 10−8 cm2 s−1) lead to a high capacity of 1264 mA h g−1 at 0.2 C with a negligible capacity fading rate of 0.06% per cycle. Additionally, TiN-O based prototype soft-package cells also exhibit excellent cycling stability with flexibility, demonstrating their potential for practical applications.
A sustainable mesoporous palladium-alumina catalyst for efficient hydrogen release from N-heterocyclic liquid organic hydrogen carriers
Authors: Oh Jinho , Bathula Hari Babu , Park Ji Hoon , Suh Young-Woong 
Published: June 2019

AbstractLiquid organic hydrogen carriers (LOHC) are interesting hydrogen vectors which can exploit existing infrastructure. Specifically, N-heterocyclic compounds are attractive due to lower dehydrogenation enthalpy than homocyclic ones and demand a viable palladium catalyst to guarantee high dehydrogenation activity at low temperatures and stability in recycle runs. Here, we employ one-pot solvent deficient precipitation yielding a mesoporous palladium-alumina. The prepared catalyst system offers higher hydrogen release capability by 20% than conventional palladium/γ-Al2O3 in the dehydrogenation of four different N-heterocyclic compounds at or below 250 °C. Futhermore, it shows negligible activity loss up to five consecutive runs for perhydro 2-(n-methylbenzyl)pyridine and perhydro 2-methylindole. Such dehydrogenation performance is caused by the solvent deficient environment that restricts palladium mobility by contiguous alumina particles and produces well-dispersed palladium phase with a higher density of (111) plane. Therefore, the reported synthesis method may contribute to the production of innovative dehydrogenation catalysts for LOHC compounds.