bluuebunny/crossref_metadata_2025_split huggingface dataset:
Predicting stimulation-dependent enhancer-promoter interactions from ChIP-Seq time course data
Authors: Dzida Tomasz , Iqbal Mudassar , Charapitsa Iryna , Reid George , Stunnenberg Henk , Matarese Filomena , Grote Korbinian , Honkela Antti , Rattray Magnus 
Published: September 2017

We have developed a machine learning approach to predict stimulation-dependent enhancer-promoter interactions using evidence from changes in genomic protein occupancy over time. The occupancy of estrogen receptor alpha (ERα), RNA polymerase (Pol II) and histone marks H2AZ and H3K4me3 were measured over time using ChIP-Seq experiments in MCF7 cells stimulated with estrogen. A Bayesian classifier was developed which uses the correlation of temporal binding patterns at enhancers and promoters and genomic proximity as features to predict interactions. This method was trained using experimentally determined interactions from the same system and was shown to achieve much higher precision than predictions based on the genomic proximity of nearest ERα binding. We use the method to identify a genome-wide confident set of ERα target genes and their regulatory enhancers genome-wide. Validation with publicly available GRO-Seq data demonstrates that our predicted targets are much more likely to show early nascent transcription than predictions based on genomic ERα binding proximity alone.
Extraction of Multithread Channel Networks With a Reduced‐Complexity Flow Model
Authors: Limaye Ajay B. 
Published: September 2017

AbstractQuantitative measures of channel network geometry inform diverse applications in hydrology, sediment transport, ecology, hazard assessment, and stratigraphic prediction. These uses require a clear, objectively defined channel network. Automated techniques for extracting channels from topography are well developed for convergent channel networks and identify flow paths based on land‐surface gradients. These techniques—even when they allow multiple flow paths—do not consistently capture channel networks with frequent bifurcations (e.g., in rivers, deltas, and alluvial fans). This paper uses multithread rivers as a template to develop a new approach for channel extraction suitable for channel networks with divergences. Multithread channels are commonly mapped using observed inundation extent, and I generalize this approach using a depth‐resolving, reduced‐complexity flow model to map inundation patterns for fixed topography across an arbitrary range of discharge. A case study for the Platte River, Nebraska, reveals that (1) the number of bars exposed above the water surface, bar area, and the number of wetted channel threads (i.e., braiding index) peak at intermediate discharge; (2) the anisotropic scaling of bar dimensions occurs for a range of discharge; and (3) the maximum braiding index occurs at a corresponding reference discharge that provides an objective basis for comparing the planform geometry of multithread rivers. Mapping by flow depth overestimates braiding index by a factor of 2. The new approach extends channel network extraction from topography to the full spectrum of channel patterns, with the potential for comparing diverse channel patterns at scales from laboratory experiments to natural landscapes.
Common Warming Pattern Emerges Irrespective of Forcing Location
Authors: Kang Sarah M. , Park Kiwoong , Jin Fei‐Fei , Stuecker Malte F. 
Published: September 2017

AbstractThe Earth's climate is changing due to the existence of multiple radiative forcing agents. It is under question whether different forcing agents perturb the global climate in a distinct way. Previous studies have demonstrated the existence of similar climate response patterns in response to aerosol and greenhouse gas (GHG) forcings. In this study, the sensitivity of tropospheric temperature response patterns to surface heating distributions is assessed by forcing an atmospheric general circulation model coupled to an aquaplanet slab ocean with a wide range of possible forcing patterns. We show that a common climate pattern emerges in response to localized forcing at different locations. This pattern, characterized by enhanced warming in the tropical upper troposphere and the polar lower troposphere, resembles the historical trends from observations and models as well as the future projections. Atmospheric dynamics in combination with thermodynamic air‐sea coupling are primarily responsible for shaping this pattern. Identifying this common pattern strengthens our confidence in the projected response to GHG and aerosols in complex climate models.
Geochemical Evolution of Groundwater Flowing Through Arsenic Source Sediments in an Aquifer System of West Bengal, India
Authors: Desbarats A. J. , Pal T. , Mukherjee P. K. , Beckie R. D. 
Published: September 2017

AbstractThe source of geogenic arsenic (As) contaminating a shallow aquifer in West Bengal was traced to fine‐grained sediments deposited in an abandoned river channel. Along with As‐bearing phases, these sediments contain 0.46% codeposited organic carbon. The release of As and the geochemistry of groundwater within the channel‐fill deposits is investigated using a detailed mass balance model supported by aqueous, solid‐phase, and mineralogical data. The model describes the evolution of groundwater chemistry along a flow path extending from its recharge in an abandoned channel pond, through the channel fill, to the underlying aquifer. Variations in groundwater composition are explained in terms of mineral weathering of host sediments driven by organic carbon decay. Arsenic is released through the reductive dissolution of goethite and the weathering of chlorite. Concomitantly, some As is sequestered in precipitating vivianite. These competing processes reach equilibrium deeper in the channel‐fill sequence as groundwater As concentrations stabilize. The model yields estimates of mineral reaction (or precipitation) rates including rates of organic carbon oxidation (1.15 mmol C L−1 a−1) and net As release (
mmol L−1 a−1). Fine‐grained, slightly permeable, deposits such as channel fill containing reactive organic carbon and As‐bearing goethite and phyllosilicates are centers of intense chemical weathering conducive to As mobilization.
A Stochastic Water Balance Framework for Lowland Watersheds
Authors: Thompson Sally , MacVean Lissa , Sivapalan Murugesu 
Published: September 2017

AbstractThe water balance dynamics in lowland watersheds are influenced not only by local hydroclimatic controls on energy and water availability, but also by imports of water from the upstream watershed. These imports result in a stochastic extent of inundation in lowland watersheds that is determined by the local flood regime, watershed topography, and the rate of loss processes such as drainage and evaporation. Thus, lowland watershed water balances depend on two stochastic processes—rainfall and local inundation dynamics. Lowlands are high productivity environments that are disproportionately associated with urbanization, high productivity agriculture, biodiversity, and flood risk. Consequently, they are being rapidly altered by human development—generally with clear economic and social motivation—but also with significant trade‐offs in ecosystem services provision, directly related to changes in the components and variability of the lowland water balance. We present a stochastic framework to assess the lowland water balance and its sensitivity to two common human interventions—replacement of native vegetation with alternative land uses, and construction of local flood protection levees. By providing analytical solutions for the mean and PDF of the water balance components, the proposed framework provides a mechanism to connect human interventions to hydrologic outcomes, and, in conjunction with ecosystem service production estimates, to evaluate trade‐offs associated with lowland watershed development.
Selective intrathecal enrichment of G1m1‐positive B cells in multiple sclerosis
Authors: Lossius Andreas , Tomescu‐Baciu Alina , Holmøy Trygve , Vedeler Christian A. , Røsjø Egil , Lorentzen Åslaug R. , Casetta Ilaria , Vartdal Frode 
Published: September 2017

AbstractImmunoglobulin gamma (IgG) heavy chain genes are associated with susceptibility to multiple sclerosis (MS) and IgG levels in the cerebrospinal fluid (CSF). However, how these variants are implicated in disease mechanisms remains unknown. Here, we show that proliferating plasmablasts expressing the G1m1 allotype of IgG1 are selectively enriched in CSF of G1m1/G1m3 heterozygous MS patients, whereas plasmablasts expressing either G1m1 or G1m3 are evenly distributed in blood. Moreover, there was a preferential intrathecal synthesis of oligoclonal IgG1 of the G1m1 allotype in heterozygous patients, whereas controls with Lyme neuroborreliosis displayed oligoclonal IgG1 of both allotypes. This points to a disease‐specific mechanism involved in B‐cell establishment within the central nervous system in MS.
Combinatorial Particle Patterning
Authors: von Bojnicic‐Kninski Clemens , Popov Roman , Dörsam Edgar , Loeffler Felix F. , Breitling Frank , Nesterov‐Mueller Alexander 
Published: September 2017

AbstractThe unique properties of solid particles make them a promising element of micro‐ and nanostructure technologies. Solid particles can be used as building blocks for micro and nanostructures, carriers of monomers, or catalysts. The possibility of patterning different kinds of particles on the same substrate opens the pathway for novel combinatorial designs and novel technologies. One of the examples of such technologies is the synthesis of peptide arrays with amino acid particles. This review examines the known methods of combinatorial particle patterning via static electrical and magnetic fields, laser radiation, patterning by synthesis, and particle patterning via chemically modified or microstructured surfaces.
Fabrication of Chitosan‐18β‐Glycyrrhetinic Acid Modified Titanium Implants with Nanorod Arrays for Suppression of Osteosarcoma Growth and Improvement of Osteoblasts Activity
Authors: Zhang Meng , Cheng Haoyan , Gong Zheni , Zhang Jiting , Liu Xi , Wang Bingbing , Ban Lina , Zeng Yan , Zhu Zhihong 
Published: September 2017

AbstractSurgery has been combined with chemotherapy to treat osteosarcoma. However, the recovery rate of osteosarcoma patients is still low. To prevent post‐operative recurrence of the osteosarcoma, developing an alternative biomaterial is essential. 18β‐Glycyrrhetinic acid (GA) has shown potential anticancer activity in various malignancies. Here it is proposed that GA can induce osteosarcoma cell apoptosis, and a polydopamine‐mediated titanium oxide nanorod (TiO2NR) surface is functionalized by covalently grafting the chitosan‐18β‐glycyrrhetinic acid conjugate (CS–GA). In vitro and in vivo biological tests indicate that the CS–GA modified surface shows significant antiproliferation and apoptosis in osteosarcoma cells (MG63). Additionally, this modified surface with nanoarray structure stimulation and chitosan supplementation significantly promotes osteoblast (MC3T3‐E1) adhesion and proliferation in vitro. This dual‐functional, Ti‐based implant with balanced antitumor and biocompatibility properties represents an effective strategy for the surgical treatment of osteosarcoma.
Syntheses and Energy Storage Applications of MxSy (M = Cu, Ag, Au) and Their Composites: Rechargeable Batteries and Supercapacitors
Authors: Lu Yao , Li Bing , Zheng Shasha , Xu Yuxia , Xue Huaiguo , Pang Huan 
Published: September 2017

AbstractThe development of novel materials to improve energy storage efficiencies is essential to satisfy ever‐increasing energy demands. MxSy (M = Cu, Ag, Au) and their composites offer opportunities and enormous prospects in energy storage due to their extraordinary electrochemical properties, which promote promising energy storage characteristics in terms of stability, energy and power density, lifetime, etc. Recent developments of MxSy (M = Cu, Ag, Au) and their composites with various morphologies have received considerable attention. Multidimensional morphologies of MxSy (M = Cu, Ag, Au) and their composites have enriched charge‐storage and electron‐transport abilities. This review provides a detailed account of the synthetic strategies based on sulfur sources (i.e., inorganic sulfur sources, organosulfur sources, and other sulfur sources), which dictate the morphologies of nanosized MxSy (M = Cu, Ag, Au) and their composites. Notably, nanostructured silver sulfide can be prepared from the bulk to nanoscale. Moreover, the electrochemical applications of these materials for lithium‐ion batteries, sodium‐ion batteries, lithium‐sulfur batteries, and supercapacitors are summarized. Finally, future perspectives on the development challenges and major opportunities for MxSy (M = Cu, Ag, Au) and their composites, which must be overcome to achieve further improvements in electrochemical performance are outlined.
Preservation of Cell Structure, Metabolism, and Biotransformation Activity of Liver‐On‐Chip Organ Models by Hypothermic Storage
Authors: Gröger Marko , Dinger Julia , Kiehntopf Michael , Peters Frank T. , Rauen Ursula , Mosig Alexander S. 
Published: September 2017

AbstractThe liver is a central organ in the metabolization of nutrition, endogenous and exogenous substances, and xenobiotic drugs. The emerging organ‐on‐chip technology has paved the way to model essential liver functions as well as certain aspects of liver disease in vitro in liver‐on‐chip models. However, a broader use of this technology in biomedical research is limited by a lack of protocols that enable the short‐term preservation of preassembled liver‐on‐chip models for stocking or delivery to researchers outside the bioengineering community. For the first time, this study tested the ability of hypothermic storage of liver‐on‐chip models to preserve cell viability, tissue morphology, metabolism and biotransformation activity. In a systematic study with different preservation solutions, liver‐on‐chip function can be preserved for up to 2 d using a derivative of the tissue preservation solution TiProtec, containing high chloride ion concentrations and the iron chelators LK614 and deferoxamine, supplemented with polyethylene glycol (PEG). Hypothermic storage in this solution represents a promising method to preserve liver‐on‐chip function for at least 2 d and allows an easier access to liver‐on‐chip technology and its versatile and flexible use in biomedical research.
Toward Environmentally Robust Organic Electronics: Approaches and Applications
Authors: Lee Eun Kwang , Lee Moo Yeol , Park Cheol Hee , Lee Hae Rang , Oh Joon Hak 
Published: September 2017

AbstractRecent interest in flexible electronics has led to a paradigm shift in consumer electronics, and the emergent development of stretchable and wearable electronics is opening a new spectrum of ubiquitous applications for electronics. Organic electronic materials, such as π‐conjugated small molecules and polymers, are highly suitable for use in low‐cost wearable electronic devices, and their charge‐carrier mobilities have now exceeded that of amorphous silicon. However, their commercialization is minimal, mainly because of weaknesses in terms of operational stability, long‐term stability under ambient conditions, and chemical stability related to fabrication processes. Recently, however, many attempts have been made to overcome such instabilities of organic electronic materials. Here, an overview is provided of the strategies developed for environmentally robust organic electronics to overcome the detrimental effects of various critical factors such as oxygen, water, chemicals, heat, and light. Additionally, molecular design approaches to π‐conjugated small molecules and polymers that are highly stable under ambient and harsh conditions are explored; such materials will circumvent the need for encapsulation and provide a greater degree of freedom using simple solution‐based device‐fabrication techniques. Applications that are made possible through these strategies are highlighted.
Synergetic Enhancement in Photosensitivity and Flexibility of Photodetectors Based on Hybrid Nanobelt Network
Authors: Shahid Muhammad , Wang Yuting , Yang Jun , Li Tianjun , Cheng Jing , Zhang Mengfei , Xing Yan , Wan Chunlei , Pan Wei 
Published: September 2017

AbstractHigh photosensitivity, transparency, flexibility, and facile assembly are the main important features of photodetectors, which extend their use for vast range of applications. In this study, a highly stable transparent flexible ultraviolet–visible (UV–vis) hybrid photodetectors, with enhanced photosensitivity and fast photoresponse speed (on/off switching) based on In2O3‐ZnO hybrid nanobelts, is reported. A highly enhanced photosensitivity of about 4.7 × 105, fast photoresponse, and at the same time extended spectral range (UV to vis) have been achieved in these hybrid flexible photodetectors as compared to their pure counterparts In2O3 and ZnO. Furthermore, these photodetectors have shown excellent photoresponsivity of 18.5 A W−1 with an external quantum efficiency 7.4 × 103% and a high detectivity of 1.7 × 1012 Jones under the excitation wavelength of 308 nm. A facile, tunable, and cost‐effective method has been employed to assemble these photodetectors by using well‐aligned electrospun nanobelts. The prepared UV–vis photodetectors have shown a high transparency >90% under visible light (400–700 nm) which demonstrates their applications in fully light exposure required devices. These transparent electrospun nanobelts with high aspect ratios can also be transferred to multiple substrates, which shows their applications in different environment as a freestanding nanobelt network for UV–vis photodetectors.
Metasurface Holograms for Holographic Imaging
Authors: Wan Weiwei , Gao Jie , Yang Xiaodong 
Published: September 2017

AbstractAs a revolutionary three‐dimensional (3D) optical imaging technique, optical holography has attracted wide attention for its capability of recording both the amplitude and phase information of light scattered from objects. Holograms are designed to transform an incident wave into a desired arbitrary wavefront in the far field, which requires ultimate complex phase control in each hologram pixel. Conventional holograms shape the wavefront via the phase accumulation effect during the wave propagation through bulky optical elements, suffering issues of low‐resolution imaging and high‐order diffraction. Recently, metasurfaces, 2D metamaterials with ultrathin thickness, have emerged as an important platform to reproduce computer‐generated holograms due to their advantages in manipulating light with well‐controlled amplitude, phase, and polarization. In this article, the latest research progress in various types of metasurface holograms is reviewed from their design principles to versatile functional applications. At the end, more potential applications of metasurface holograms are discussed and some future research directions are also provided.
Enzyme‐Catalysed Synthesis of Cyclohex‐2‐en‐1‐one cis‐Diols from Substituted Phenols, Anilines and Derived 4‐Hydroxycyclohex‐2‐en‐1‐ones
Authors: Boyd Derek R. , Sharma Narain D. , McIntyre Peter B. A. , Stevenson Paul J. , McRoberts W. Colin , Gohil Amit , Hoering Patrick , Allen Christopher C. R. 
Published: September 2017

AbstractToluene dioxygenase‐catalysed cis‐dihydroxylations of substituted aniline and phenol substrates, with a Pseudomonas putida UV4 mutant strain and an Escherichia coli pCL‐4t recombinant strain, yielded identical arene cis‐dihydrodiols, which were isolated as the preferred cyclohex‐2‐en‐1‐one cis‐diol tautomers. These cis‐diol metabolites were predicted by preliminary molecular docking studies, of anilines and phenols, at the active site of toluene dioxygenase. Further biotransformations of cyclohex‐2‐en‐1‐one cis‐diol and hydroquinone metabolites, using Pseudomonas putida UV4 whole cells, were found to yield 4‐hydroxycyclohex‐2‐en‐1‐ones as a new type of phenol bioproduct. Multistep pathways, involving ene reductase‐ and carbonyl reductase‐catalysed reactions, were proposed to account for the production of 4‐hydroxycyclohex‐2‐en‐1‐one metabolites. Evidence for the phenol hydrate tautomers of 4‐hydroxycyclohex‐2‐en‐1‐one metabolites was shown by formation of the corresponding trimethylsilyl ether derivatives.magnified image
Netrin‐1 Promotes Inflammation Resolution to Achieve Endothelialization of Small‐Diameter Tissue Engineering Blood Vessels by Improving Endothelial Progenitor Cells Function In Situ
Authors: Li Yanzhao , Wan Simin , Liu Ge , Cai Wang , Huo Da , Li Gang , Yang Mingcan , Wang Yuxin , Guan Ge , Ding Ning , Liu Feila , Zeng Wen , Zhu Chuhong 
Published: September 2017

AbstractThe transplant of small‐diameter tissue engineering blood vessels (small‐diameter TEBVs) (<6 mm) in vascular replacement therapy often fails because of early onset thrombosis and long‐standing chronic inflammation. The specific inflammation state involved in small‐diameter TEBVs transplants remains unclear, and whether promoting inflammation resolution would be useful for small‐diameter TEBVs therapy need study. The neural protuberant orientation factor 1 (Netrin‐1) is found present in endothelial cells of natural blood vessels and has anti‐inflammatory effects. This work generates netrin‐1‐modified small‐diameter TEBVs by using layer‐by‐layer self‐assembly to resolve the inflammation. The results show that netrin‐1 reprograms macrophages (MΦ) to assume an anti‐inflammatory phenotype and promotes the infiltration and subsequent efflux of MΦ from inflamed sites over time, which improves the local microenvironment and the function of early homing endothelial progenitor cells (EPCs). Small‐diameter TEBVs modified by netrin‐1 achieve endothelialization after 30 d and retain patency at 14 months. These findings suggest that promoting the resolution of inflammation in time is necessary to induce endothelialization of small‐diameter TEBVs and prevent early thrombosis and problems associated with chronic inflammation. Furthermore, this work finds that the MΦ‐derived exosomes can target and regulate EPCs, which may serve as a useful treatment for other inflammatory diseases.
Recent Progress in Semiconductor‐Based Nanocomposite Photocatalysts for Solar‐to‐Chemical Energy Conversion
Authors: Wang Feifan , Li Qi , Xu Dongsheng 
Published: September 2017

AbstractPhotocatalysis, which can directly convert solar energy into chemical energy and simultaneously accomplish solar energy conversion and storage objectives, is regarded as one of the most promising strategies to address the energy supply and environmental degradation issues. In recent decades, great efforts and encouraging achievements are performed in the field of semiconductor photocatalysts. Herein, this progress report summarizes the recent investigations and focuses on the advanced semiconductor‐based nanocomposite materials and structures and the novel mechanisms for the photocatalytic solar‐to‐chemical energy conversion. It begins with discussing basic principles for the establishment of an efficient photocatalysis system and illustrating recent studies on improving the elementary processes of photocatalysis, i.e., photophysics and surface/interface chemistry. Then, it demonstrates how the fundamental principles are utilized to enhance the important energy‐conversion‐related reactions, such as light‐driven water splitting, CO2 reduction, nitrogen fixation, organic photosynthesis, etc. Finally, the report concludes the topic on semiconductor‐based nanocomposite photocatalysis along with identifying crucial issues in fundamental studies, challenges in large‐scale industrializations, and perspectives in related research fields.