bluuebunny/crossref_metadata_2025_split huggingface dataset:
Estimator of Surface Ozone Using Formaldehyde and Carbon Monoxide Concentrations Over the Eastern United States in Summer
Authors: Cheng Ye , Wang Yuhang , Zhang Yuzhong , Crawford James H. , Diskin Glenn S. , Weinheimer Andrew J. , Fried Alan 
Published: July 2018

AbstractStrong correlations of O3‐CH2O, O3‐CO and CO‐CH2O were observed during the Deriving Information on Surface Conditions from Column and Vertically Resolved Observations Relevant to Air Quality (DISCOVER‐AQ) aircraft experiment in July 2011 over the Washington‐Baltimore area. The linear regression slopes of observed O3‐CH2O, O3‐CO, and CO‐CH2O do not vary significantly with time (11 a.m. to 4 p.m.) or altitude in the boundary layer. These observed relationships are simulated well by a regional chemical transport model. Using tagged‐tracer simulations, we find that biogenic isoprene oxidation makes the largest contribution to the regression slope of O3‐CH2O across much of the eastern United States, providing a good indicator for O3 enhanced by biogenic isoprene oxidation. In contrast, the regression slope of O3‐CO is controlled by both anthropogenic and biogenic emissions. Therefore, we use the CO‐CH2O relationship to separate biogenic from anthropogenic contributions to CO. By combining these regressions, we can track the contributions to surface O3 by anthropogenic and biogenic factors and build a fast‐response ozone estimator using near‐surface CH2O and CO concentrations as inputs. We examine the quality of O3 estimator by increasing or decreasing anthropogenic emissions by up to 50%. The estimated O3 distribution is in reasonably good agreement with the full‐model simulations (R2 > 0.77 in the range of −30% to +50% of anthropogenic emissions). The analysis provides the basis for using high‐quality geostationary satellites with UV, thermal infrared, or near‐infrared instruments for observing CH2O and CO to improve surface O3 distribution monitoring. The estimation model can also be applied to derive observation‐derived regional metrics to evaluate and improve full‐fledged 3‐D air quality models.
Cancer cell specific inhibition of Wnt/β-catenin signaling by forced intracellular acidification
Authors: Melnik Svitlana , Dvornikov Dmytro , Müller-Decker Karin , Depner Sofia , Stannek Peter , Meister Michael , Warth Arne , Thomas Michael , Muley Tomas , Risch Angela , Plass Christoph , Klingmüller Ursula , Niehrs Christof , Glinka Andrey 
Published: July 2018

AbstractUse of the diabetes type II drug Metformin is associated with a moderately lowered risk of cancer incidence in numerous tumor entities. Studying the molecular changes associated with the tumor-suppressive action of Metformin we found that the oncogene SOX4, which is upregulated in solid tumors and associated with poor prognosis, was induced by Wnt/β-catenin signaling and blocked by Metformin. Wnt signaling inhibition by Metformin was surprisingly specific for cancer cells. Unraveling the underlying specificity, we identified Metformin and other Mitochondrial Complex I (MCI) inhibitors as inducers of intracellular acidification in cancer cells. We demonstrated that acidification triggers the unfolded protein response to induce the global transcriptional repressor DDIT3, known to block Wnt signaling. Moreover, our results suggest that intracellular acidification universally inhibits Wnt signaling. Based on these findings, we combined MCI inhibitors with H+ ionophores, to escalate cancer cells into intracellular hyper-acidification and ATP depletion. This treatment lowered intracellular pH both in vitro and in a mouse xenograft tumor model, depleted cellular ATP, blocked Wnt signaling, downregulated SOX4, and strongly decreased stemness and viability of cancer cells. Importantly, the inhibition of Wnt signaling occurred downstream of β-catenin, encouraging applications in treatment of cancers caused by APC and β-catenin mutations.
Large-scale gene losses underlie the genome evolution of parasitic plant Cuscuta australis
Authors: Sun Guiling , Xu Yuxing , Liu Hui , Sun Ting , Zhang Jingxiong , Hettenhausen Christian , Shen Guojing , Qi Jinfeng , Qin Yan , Li Jing , Wang Lei , Chang Wei , Guo Zhenhua , Baldwin Ian T. , Wu Jianqiang 
Published: July 2018

AbstractDodders (Cuscuta spp., Convolvulaceae) are root- and leafless parasitic plants. The physiology, ecology, and evolution of these obligate parasites are poorly understood. A high-quality reference genome of Cuscuta australis was assembled. Our analyses reveal that Cuscuta experienced accelerated molecular evolution, and Cuscuta and the convolvulaceous morning glory (Ipomoea) shared a common whole-genome triplication event before their divergence. C. australis genome harbors 19,671 protein-coding genes, and importantly, 11.7% of the conserved orthologs in autotrophic plants are lost in C. australis. Many of these gene loss events likely result from its parasitic lifestyle and the massive changes of its body plan. Moreover, comparison of the gene expression patterns in Cuscuta prehaustoria/haustoria and various tissues of closely related autotrophic plants suggests that Cuscuta haustorium formation requires mostly genes normally involved in root development. The C. australis genome provides important resources for studying the evolution of parasitism, regressive evolution, and evo-devo in plant parasites.
An intercross population study reveals genes associated with body size and plumage color in ducks
Authors: Zhou Zhengkui , Li Ming , Cheng Hong , Fan Wenlei , Yuan Zhengrong , Gao Qiang , Xu Yaxi , Guo Zhanbao , Zhang Yunsheng , Hu Jian , Liu Hehe , Liu Dapeng , Chen Weihuang , Zheng Zhuqing , Jiang Yong , Wen Zhiguo , Liu Yongming , Chen Hua , Xie Ming , Zhang Qi , Huang Wei , Wang Wen , Hou Shuisheng , Jiang Yu 
Published: July 2018

AbstractComparative population genomics offers an opportunity to discover the signatures of artificial selection during animal domestication, however, their function cannot be directly revealed. We discover the selection signatures using genome-wide comparisons among 40 mallards, 36 indigenous-breed ducks, and 30 Pekin ducks. Then, the phenotypes are fine-mapped based on resequencing of 1026 ducks from an F2 segregating population generated by wild × domestic crosses. Interestingly, the two key economic traits of Pekin duck are associated with two selective sweeps with fixed mutations. A novel intronic insertion most possibly leads to a splicing change in MITF accounted for white duck down feathers. And a putative long-distance regulatory mutation causes continuous expression of the IGF2BP1 gene after birth which increases body size by 15% and feed efficiency by 6%. This study provides new insights into genotype–phenotype associations in animal research and constitutes a promising resource on economically important genes in fowl.
Discovery of a drug candidate for GLIS3-associated diabetes
Authors: Amin Sadaf , Cook Brandoch , Zhou Ting , Ghazizadeh Zaniar , Lis Raphael , Zhang Tuo , Khalaj Mona , Crespo Miguel , Perera Manuradhi , Xiang Jenny Zhaoying , Zhu Zengrong , Tomishima Mark , Liu Chengyang , Naji Ali , Evans Todd , Huangfu Danwei , Chen Shuibing 
Published: July 2018

AbstractGLIS3 mutations are associated with type 1, type 2, and neonatal diabetes, reflecting a key function for this gene in pancreatic β-cell biology. Previous attempts to recapitulate disease-relevant phenotypes in GLIS3−/− β-like cells have been unsuccessful. Here, we develop a “minimal component” protocol to generate late-stage pancreatic progenitors (PP2) that differentiate to mono-hormonal glucose-responding β-like (PP2-β) cells. Using this differentiation platform, we discover that GLIS3−/− hESCs show impaired differentiation, with significant death of PP2 and PP2-β cells, without impacting the total endocrine pool. Furthermore, we perform a high-content chemical screen and identify a drug candidate that rescues mutant GLIS3-associated β-cell death both in vitro and in vivo. Finally, we discovered that loss of GLIS3 causes β-cell death, by activating the TGFβ pathway. This study establishes an optimized directed differentiation protocol for modeling human β-cell disease and identifies a drug candidate for treating a broad range of GLIS3-associated diabetic patients.
Collective molecular switching in hybrid superlattices for light-modulated two-dimensional electronics
Authors: Gobbi Marco , Bonacchi Sara , Lian Jian X. , Vercouter Alexandre , Bertolazzi Simone , Zyska Björn , Timpel Melanie , Tatti Roberta , Olivier Yoann , Hecht Stefan , Nardi Marco V. , Beljonne David , Orgiu Emanuele , Samorì Paolo 
Published: July 2018

AbstractMolecular switches enable the fabrication of multifunctional devices in which an electrical output can be modulated by external stimuli. The working mechanism of these devices is often hard to prove, since the molecular switching events are only indirectly confirmed through electrical characterization, without real-space visualization. Here, we show how photochromic molecules self-assembled on graphene and MoS2generate atomically precise superlattices in which a light-induced structural reorganization enables precise control over local charge carrier density in high-performance devices. By combining different experimental and theoretical approaches, we achieve exquisite control over events taking place from the molecular level to the device scale. Unique device functionalities are demonstrated, including the use of spatially confined light irradiation to define reversible lateral heterojunctions between areas possessing different doping levels. Molecular assembly and light-induced doping are analogous for graphene and MoS2, demonstrating the generality of our approach to optically manipulate the electrical output of multi-responsive hybrid devices.
Systemic control of immune cell development by integrated carbon dioxide and hypoxia chemosensation in Drosophila
Authors: Cho Bumsik , Spratford Carrie M. , Yoon Sunggyu , Cha Nuri , Banerjee Utpal , Shim Jiwon 
Published: July 2018

AbstractDrosophila hemocytes are akin to mammalian myeloid blood cells that function in stress and innate immune-related responses. A multi-potent progenitor population responds to local signals and to systemic stress by expanding the number of functional blood cells. Here we show mechanisms that demonstrate an integration of environmental carbon dioxide (CO2) and oxygen (O2) inputs that initiate a cascade of signaling events, involving multiple organs, as a stress response when the levels of these two important respiratory gases fall below a threshold. The CO2 and hypoxia-sensing neurons interact at the synaptic level in the brain sending a systemic signal via the fat body to modulate differentiation of a specific class of immune cells. Our findings establish a link between environmental gas sensation and myeloid cell development in Drosophila. A similar relationship exists in humans, but the underlying mechanisms remain to be established.
Tools for engineering coordinated system behaviour in synthetic microbial consortia
Authors: Kylilis Nicolas , Tuza Zoltan A. , Stan Guy-Bart , Polizzi Karen M. 
Published: July 2018

AbstractAdvancing synthetic biology to the multicellular level requires the development of multiple cell-to-cell communication channels that propagate information with minimal signal interference. The development of quorum-sensing devices, the cornerstone technology for building microbial communities with coordinated system behaviour, has largely focused on cognate acyl-homoserine lactone (AHL)/transcription factor pairs, while the use of non-cognate pairs as a design feature has received limited attention. Here, we demonstrate a large library of AHL-receiver devices, with all cognate and non-cognate chemical signal interactions quantified, and we develop a software tool that automatically selects orthogonal communication channels. We use this approach to identify up to four orthogonal channels in silico, and experimentally demonstrate the simultaneous use of three channels in co-culture. The development of multiple non-interfering cell-to-cell communication channels is an enabling step that facilitates the design of synthetic consortia for applications including distributed bio-computation, increased bioprocess efficiency, cell specialisation and spatial organisation.
An in vitro paradigm to assess potential anti-Aβ antibodies for Alzheimer’s disease
Authors: Jin Ming , O’Nuallain Brian , Hong Wei , Boyd Justin , Lagomarsino Valentina N. , O’Malley Tiernan T. , Liu Wen , Vanderburg Charles R. , Frosch Matthew P. , Young-Pearse Tracy , Selkoe Dennis J. , Walsh Dominic M. 
Published: July 2018

AbstractAlthough the amyloid β-protein (Aβ) is believed to play an initiating role in Alzheimer’s disease (AD), the molecular characteristics of the key pathogenic Aβ forms are not well understood. As a result, it has proved difficult to identify optimal agents that target disease-relevant forms of Aβ. Here, we combined the use of Aβ-rich aqueous extracts of brain samples from AD patients as a source of human Aβ and live-cell imaging of iPSC-derived human neurons to develop a bioassay capable of quantifying the relative protective effects of multiple anti-Aβ antibodies. We report the characterization of 1C22, an aggregate-preferring murine anti-Aβ antibody, which better protects against forms of Aβ oligomers that are toxic to neurites than do the murine precursors of the clinical immunotherapeutics, bapineuzumab and solanezumab. These results suggest further examination of 1C22 is warranted, and that this bioassay maybe useful as a primary screen to identify yet more potent anti-Aβ therapeutics.
The impact of stimulus size and orientation on individual face coding in monkey face-selective cortex
Authors: Taubert Jessica , Van Belle Goedele , Vogels Rufin , Rossion Bruno 
Published: July 2018

AbstractFace-selective neurons in the monkey temporal cortex discharge at different rates in response to pictures of different individual faces. Here we tested whether this pattern of response across single neurons in the face-selective area ML (located in the middle Superior Temporal Sulcus) tolerates two affine transformations; picture-plane inversion, known to decrease the average response of face-selective neurons and the other, stimulus size. We recorded the response of 57 ML neurons in two awake and fixating monkeys. Face stimuli were presented at two sizes (10 and 5 degrees of visual angle) and two orientations (upright and inverted). Different faces elicited distinct patterns of activity across ML neurons that were reliable (i.e., predictable with a classifier) within a specific size and orientation condition. Despite observing a reduction in the average response magnitude of face-selective neurons to inverted faces, compared to upright faces, classifier performance was above chance for both upright and inverted faces. While decoding was largely preserved across changes in stimulus size, a classifier trained with one orientation condition and tested on the other did not lead to performance above chance level. We conclude that different individual faces can be decoded from patterns of responses in the monkey area ML regardless of orientation or size, but with qualitatively different patterns of responses for upright and inverted faces.
Evolutionary and expression analysis of CAMTA gene family in Nicotiana tabacum yielded insights into their origin, expansion and stress responses
Authors: Kakar Kaleem U. , Nawaz Zarqa , Cui Zhouqi , Cao Peijian , Jin Jingjing , Shu Qingyao , Ren Xueliang 
Published: July 2018

AbstractCalmodulin-binding transcription activators (CAMTAs) represent the novel gene family of transcriptional regulators, which play important biological functions. Though, the first ever plant CAMTA gene was evidenced in Nicotiana tabacum in 2002. But, the systematic identification, origin and function of this gene family has not been performed due to the lack of reference genome information until now. Here, we identified 29 CAMTA genes in four Nicotiana species, including thirteen NtabCAMTAs, six NsylCAMTAs, and five NtomCAMTAs and NbenCAMTAs. These CAMTA families were classified into five phylogenetic groups (I-V), among which, the group-IV CAMTAs probably emerged the earliest. The NtabCAMTA family genes have diverse structures, and are randomly localized on five chromosomes and scaffolds. N. tabacum acquired 11 copies of homolog CAMATA genes from the parental genomes of N. tomentosiformis and N. sylvestris, followed by expansion through polyploidization and duplication. The NtabCAMTA genes were differentially expressed in different plant parts, and showed sensitivity towards different abiotic and biotic stresses. Co-expression network analysis revealed that some NtabCAMTA subunits interact with each other, and co-expressed. The current study is the first report presenting a comprehensive overview of Nicotiana CAMTA families, and opens a new avenue for the improvement of the cultivated tobacco.
A subduction and mantle plume origin for Samoan volcanism
Authors: Strak Vincent , Schellart Wouter P. 
Published: July 2018

AbstractThe origin of Samoan volcanism in the southwest Pacific remains enigmatic. Whether mantle melting is solely caused by a mantle plume is questionable because some volcanism, here referred to as non-hotspot volcanism, defies the plume model and its linear age-progression trend. Indeed, non-hotspot volcanism occurred as far as 740 km west of the predicted Samoan hotspot after 5 Ma. Here we use fully-dynamic laboratory subduction models and a tectonic reconstruction to show that the nearby Tonga-Kermadec-Hikurangi (TKH) subduction zone induces a broad mantle upwelling around the northern slab edge that coincides with the non-hotspot volcanic activity after 5 Ma. Using published potential mantle temperatures for the ambient mantle and Samoan mantle plume, we find that two geodynamic processes can explain mantle melting responsible for intraplate volcanism in the Samoan region. We propose that before 5 Ma, the volcanism is consistent with the plume model, whereas afterwards non-hotspot volcanism resulted from interaction between the Subduction-Induced Mantle Upwelling (SIMU) and Samoan mantle plume material that propagated west from the hotspot due to the toroidal component of slab rollback-induced mantle flow. In this geodynamic scenario, the SIMU drives decompression melting in the westward-swept plume material, thus producing the non-hotpot volcanism.
Voltage-Controlled Magnetic Anisotropy in Fe1−xCox/Pd/MgO system
Authors: Shukla Amit Kumar , Goto Minori , Xu Xiandong , Nawaoka Kohei , Suwardy Joko , Ohkubo Tadakatsu , Hono Kazuhiro , Miwa Shinji , Suzuki Yoshishige 
Published: July 2018

AbstractVoltage-controlled magnetic anisotropy (VCMA) in an epitaxially grown Fe/Fe1−xCox/Pd/MgO system was investigated using spin-wave spectroscopy. The spin-wave resonant frequency linearly depended on the bias-voltage. The resonant-frequency shift increased with the Co fraction in Fe1−xCox/Pd. We achieved a VCMA of approximately 250 fJ/Vm at the Co/Pd/MgO region.
Effects of collagen-derived bioactive peptides and natural antioxidant compounds on proliferation and matrix protein synthesis by cultured normal human dermal fibroblasts
Authors: Edgar Suzanne , Hopley Blake , Genovese Licia , Sibilla Sara , Laight David , Shute Janis 
Published: July 2018

AbstractNutraceuticals containing collagen peptides, vitamins, minerals and antioxidants are innovative functional food supplements that have been clinically shown to have positive effects on skin hydration and elasticityin vivo. In this study, we investigated the interactions between collagen peptides (0.3–8 kDa) and other constituents present in liquid collagen-based nutraceuticals on normal primary dermal fibroblast function in a novel, physiologically relevant, cell culture model crowded with macromolecular dextran sulphate. Collagen peptides significantly increased fibroblast elastin synthesis, while significantly inhibiting release of MMP-1 and MMP-3 and elastin degradation. The positive effects of the collagen peptides on these responses and on fibroblast proliferation were enhanced in the presence of the antioxidant constituents of the products. These data provide a scientific, cell-based, rationale for the positive effects of these collagen-based nutraceutical supplements on skin properties, suggesting that enhanced formation of stable dermal fibroblast-derived extracellular matrices may follow their oral consumption.
Mapping the Dynamic Functions and Structural Features of AcrB Efflux Pump Transporter Using Accelerated Molecular Dynamics Simulations
Authors: Jamshidi Shirin , Sutton J. Mark , Rahman Khondaker Miraz 
Published: July 2018

AbstractMultidrug efflux pumps confer resistance to their bacterial hosts by pumping out a diverse range of compounds, including most antibiotics. Being more familiar with the details of functional dynamics and conformations of these types of pumps could help in discovering approaches to stop them functioning properly. Computational approaches, particularly conventional molecular dynamics simulations followed by diverse post simulation analysis, are powerful methods that help researchers by opening a new window to study phenomena that are not detectable in as much detailin vitroorin vivoas they arein silico. In this study, accelerated molecular dynamics simulations were applied to study the dynamics of AcrB efflux pump transporters in interaction with PAβN and tetracycline as an inhibitor and a substrate, respectively, to compare the differences in the dynamics and consequently the mechanism of action of the pump. The different dynamics for PAβN -bound form of AcrB compared to the TET-bound form is likely to affect the rotating mechanism typically observed for AcrB transporter. This shows the dynamics of the active AcrB transporter is different in a substrate-bound state compared to an inhibitor-bound state. This advances our knowledge and helps to unravel the mechanism of tripartite efflux pumps.
Fatty liver is associated with blood pathways of inflammatory response, immune system activation and prothrombotic state in Young Finns Study
Authors: Taipale Tuukka , Seppälä Ilkka , Raitoharju Emma , Mononen Nina , Lyytikäinen Leo-Pekka , Illig Thomas , Waldenberger Melanie , Juonala Markus , Hutri-Kähönen Nina , Oksala Niku , Kähönen Mika , Raitakari Olli , Lehtimäki Terho 
Published: July 2018

AbstractFatty liver (FL) disease is the most common type of chronic liver disease. We hypothesized that liver’s response to the process where large droplets of triglyceride fat accumulate in liver cells is reflected also in gene pathway expression in blood. Peripheral blood genome wide gene expression analysis and ultrasonic imaging of liver were performed for 1,650 participants (316 individuals with FL and 1,334 controls) of the Young Finns Study. Gene set enrichment analysis (GSEA) was performed for the expression data. Fourteen gene sets were upregulated (false discovery rate, FDR < 0.05) in subjects with FL. These pathways related to extracellular matrix (ECM) turnover, immune response regulation, prothrombotic state and neural tissues. After adjustment for known risk factors and biomarkers of FL, we found i) integrin A4B1 signaling, ii) leukocyte transendothelial migration, iii) CD40/CD40L and iv) netrin-1 signaling pathways to be upregulated in individuals with FL (nominal p < 0.05). From these all but not ii) remained significantly upregulated when analyzing only subjects without history of heavy alcohol use. In conclusion, FL was associated with blood gene sets of ECM turnover, inflammatory response, immune system activation and prothrombotic state. These may form a systemic link between FL and the development of cardiovascular diseases.