bluuebunny/crossref_metadata_2025_split huggingface dataset:
Optical patterning of trapped charge in nitrogen-doped diamond
Authors: Jayakumar Harishankar , Henshaw Jacob , Dhomkar Siddharth , Pagliero Daniela , Laraoui Abdelghani , Manson Neil B. , Albu Remus , Doherty Marcus W. , Meriles Carlos A. 
Published: August 2016

AbstractThe nitrogen-vacancy (NV) centre in diamond is emerging as a promising platform for solid-state quantum information processing and nanoscale metrology. Of interest in these applications is the manipulation of the NV charge, which can be attained by optical excitation. Here, we use two-colour optical microscopy to investigate the dynamics of NV photo-ionization, charge diffusion and trapping in type-1b diamond. We combine fixed-point laser excitation and scanning fluorescence imaging to locally alter the concentration of negatively charged NVs, and to subsequently probe the corresponding redistribution of charge. We uncover the formation of spatial patterns of trapped charge, which we qualitatively reproduce via a model of the interplay between photo-excited carriers and atomic defects. Further, by using the NV as a probe, we map the relative fraction of positively charged nitrogen on localized optical excitation. These observations may prove important to transporting quantum information between NVs or to developing three-dimensional, charge-based memories.
A social-ecological database to advance research on infrastructure development impacts in the Brazilian Amazon
Authors: Tucker Lima Joanna M. , Valle Denis , Moretto Evandro Mateus , Pulice Sergio Mantovani Paiva , Zuca Nadia Lucia , Roquetti Daniel Rondinelli , Beduschi Liviam Elizabeth Cordeiro , Praia Amanda Salles , Okamoto Claudia Parucce Franco , da Silva Carvalhaes Vinicius Leite , Branco Evandro Albiach , Barbezani Bruna , Labandera Emily , Timpe Kelsie , Kaplan David 
Published: August 2016

AbstractRecognized as one of the world’s most vital natural and cultural resources, the Amazon faces a wide variety of threats from natural resource and infrastructure development. Within this context, rigorous scientific study of the region’s complex social-ecological system is critical to inform and direct decision-making toward more sustainable environmental and social outcomes. Given the Amazon’s tightly linked social and ecological components and the scope of potential development impacts, effective study of this system requires an easily accessible resource that provides a broad and reliable data baseline. This paper brings together multiple datasets from diverse disciplines (including human health, socio-economics, environment, hydrology, and energy) to provide investigators with a variety of baseline data to explore the multiple long-term effects of infrastructure development in the Brazilian Amazon.
Data for evaluation of fast kurtosis strategies, b-value optimization and exploration of diffusion MRI contrast
Authors: Hansen Brian , Jespersen Sune Nørhøj 
Published: August 2016

AbstractHere we describe and provide diffusion magnetic resonance imaging (dMRI) data that was acquired in neural tissue and a physical phantom. Data acquired in biological tissue includes: fixed rat brain (acquired at 9.4 T) and spinal cord (acquired at 16.4 T) and in normal human brain (acquired at 3 T). This data was recently used for evaluation of diffusion kurtosis imaging (DKI) contrasts and for comparison to diffusion tensor imaging (DTI) parameter contrast. The data has also been used to optimize b-values for ex vivo and in vivo fast kurtosis imaging. The remaining data was obtained in a physical phantom with three orthogonal fiber orientations (fresh asparagus stems) for exploration of the kurtosis fractional anisotropy. However, the data may have broader interest and, collectively, may form the basis for image contrast exploration and simulations based on a wide range of dMRI analysis strategies.
Combinatory annotation of cell membrane receptors and signalling pathways of Bombyx mori prothoracic glands
Authors: Moulos Panagiotis , Samiotaki Martina , Panayotou George , Dedos Skarlatos G. 
Published: August 2016

AbstractThe cells of prothoracic glands (PG) are the main site of synthesis and secretion of ecdysteroids, the biochemical products of cholesterol conversion to steroids that shape the morphogenic development of insects. Despite the availability of genome sequences from several insect species and the extensive knowledge of certain signalling pathways that underpin ecdysteroidogenesis, the spectrum of signalling molecules and ecdysteroidogenic cascades is still not fully comprehensive. To fill this gap and obtain the complete list of cell membrane receptors expressed in PG cells, we used combinatory bioinformatic, proteomic and transcriptomic analysis and quantitative PCR to annotate and determine the expression profiles of genes identified as putative cell membrane receptors of the model insect species, Bombyx mori, and subsequently enrich the repertoire of signalling pathways that are present in its PG cells. The genome annotation dataset we report here highlights modules and pathways that may be directly involved in ecdysteroidogenesis and aims to disseminate data and assist other researchers in the discovery of the role of such receptors and their ligands.
Inhibition of nuclear factor kappaB proteins-platinated DNA interactions correlates with cytotoxic effectiveness of the platinum complexes
Authors: Brabec Viktor , Kasparkova Jana , Kostrhunova Hana , Farrell Nicholas P. 
Published: August 2016

AbstractNuclear DNA is the target responsible for anticancer activity of platinum anticancer drugs. Their activity is mediated by altered signals related to programmed cell death and the activation of various signaling pathways. An example is activation of nuclear factor kappaB (NF-κB). Binding of NF-κB proteins to their consensus sequences in DNA (κB sites) is the key biochemical activity responsible for the biological functions of NF-κB. Using gel-mobility-shift assays and surface plasmon resonance spectroscopy we examined the interactions of NF-κB proteins with oligodeoxyribonucleotide duplexes containing κB site damaged by DNA adducts of three platinum complexes. These complexes markedly differed in their toxic effects in tumor cells and comprised highly cytotoxic trinuclear platinum(II) complex BBR3464, less cytotoxic conventional cisplatin and ineffective transplatin. The results indicate that structurally different DNA adducts of these platinum complexes exhibit a different efficiency to affect the affinity of the platinated DNA (κB sites) to NF-κB proteins. Our results support the hypothesis that structural perturbations induced in DNA by platinum(II) complexes correlate with their higher efficiency to inhibit binding of NF-κB proteins to their κB sites and cytotoxicity as well. However, the full generalization of this hypothesis will require to evaluate a larger series of platinum(II) complexes.
Hyperuricemia in acute gastroenteritis is caused by decreased urate excretion via ABCG2
Authors: Matsuo Hirotaka , Tsunoda Tomoyuki , Ooyama Keiko , Sakiyama Masayuki , Sogo Tsuyoshi , Takada Tappei , Nakashima Akio , Nakayama Akiyoshi , Kawaguchi Makoto , Higashino Toshihide , Wakai Kenji , Ooyama Hiroshi , Hokari Ryota , Suzuki Hiroshi , Ichida Kimiyoshi , Inui Ayano , Fujimori Shin , Shinomiya Nariyoshi 
Published: August 2016

AbstractTo clarify the physiological and pathophysiological roles of intestinal urate excretion via ABCG2 in humans, we genotyped ABCG2 dysfunctional common variants, Q126X (rs72552713) and Q141K (rs2231142), in end-stage renal disease (hemodialysis) and acute gastroenteritis patients, respectively. ABCG2 dysfunction markedly increased serum uric acid (SUA) levels in 106 hemodialysis patients (P = 1.1 × 10−4), which demonstrated the physiological role of ABCG2 for intestinal urate excretion because their urate excretion almost depends on intestinal excretion via ABCG2. Also, ABCG2 dysfunction significantly elevated SUA in 67 acute gastroenteritis patients (P = 6.3 × 10−3) regardless of the degree of dehydration, which demonstrated the pathophysiological role of ABCG2 in acute gastroenteritis. These findings for the first time show ABCG2-mediated intestinal urate excretion in humans, and indicates the physiological and pathophysiological importance of intestinal epithelium as an excretion pathway besides an absorption pathway. Furthermore, increased SUA could be a useful marker not only for dehydration but also epithelial impairment of intestine.
Knowledge discovery from high-frequency stream nitrate concentrations: hydrology and biology contributions
Authors: Aubert Alice H. , Thrun Michael C. , Breuer Lutz , Ultsch Alfred 
Published: August 2016

AbstractHigh-frequency, in-situ monitoring provides large environmental datasets. These datasets will likely bring new insights in landscape functioning and process scale understanding. However, tailoring data analysis methods is necessary. Here, we detach our analysis from the usual temporal analysis performed in hydrology to determine if it is possible to infer general rules regarding hydrochemistry from available large datasets. We combined a 2-year in-stream nitrate concentration time series (time resolution of 15 min) with concurrent hydrological, meteorological and soil moisture data. We removed the low-frequency variations through low-pass filtering, which suppressed seasonality. We then analyzed the high-frequency variability component using Pareto Density Estimation, which to our knowledge has not been applied to hydrology. The resulting distribution of nitrate concentrations revealed three normally distributed modes: low, medium and high. Studying the environmental conditions for each mode revealed the main control of nitrate concentration: the saturation state of the riparian zone. We found low nitrate concentrations under conditions of hydrological connectivity and dominant denitrifying biological processes, and we found high nitrate concentrations under hydrological recession conditions and dominant nitrifying biological processes. These results generalize our understanding of hydro-biogeochemical nitrate flux controls and bring useful information to the development of nitrogen process-based models at the landscape scale.
Emergence of metapopulations and echo chambers in mobile agents
Authors: Starnini Michele , Frasca Mattia , Baronchelli Andrea 
Published: August 2016

AbstractMulti-agent models often describe populations segregated either in the physical space, i.e. subdivided in metapopulations, or in the ecology of opinions, i.e. partitioned in echo chambers. Here we show how both kinds of segregation can emerge from the interplay between homophily and social influence in a simple model of mobile agents endowed with a continuous opinion variable. In the model, physical proximity determines a progressive convergence of opinions but differing opinions result in agents moving away from each others. This feedback between mobility and social dynamics determines the onset of a stable dynamical metapopulation scenario where physically separated groups of like-minded individuals interact with each other through the exchange of agents. The further introduction of confirmation bias in social interactions, defined as the tendency of an individual to favor opinions that match his own, leads to the emergence of echo chambers where different opinions coexist also within the same group. We believe that the model may be of interest to researchers investigating the origin of segregation in the offline and online world.
Identification of lead chemotherapeutic agents from medicinal plants against blood flukes and whipworms
Authors: Wangchuk Phurpa , Giacomin Paul R. , Pearson Mark S. , Smout Michael J. , Loukas Alex 
Published: August 2016

AbstractSchistosomiasis and trichuriasis are two of the most common neglected tropical diseases (NTD) that affect almost a billion people worldwide. There is only a limited number of effective drugs to combat these NTD. Medicinal plants are a viable source of parasiticides. In this study, we have investigated six of the 19 phytochemicals isolated from two Bhutanese medicinal plants, Corydalis crispa and Pleurospermum amabile, for their anthelmintic properties. We used the xWORM technique and Scanning Electron Microscope-based imaging to determine the activity of the compounds. Of the six compounds tested, isomyristicin and bergapten showed significant anthelmintic activity against Schistosoma mansoni and Trichuris muris with bergapten being the most efficacious compound one against both parasites (S. mansoni IC50 = 8.6 μg/mL and T. muris IC50 = 10.6 μg/mL) and also against the schistosomulum stage of S. mansoni. These two compounds induced tegumental damage to S. mansoni and affected the cuticle, bacillary bands and bacillary glands of T. muris. The efficacy against multiple phylogenetically distinct parasites and different life stages, especially the schistosomulum where praziquantel is ineffective, makes isomyristicin and bergapten novel scaffolds for broad-spectrum anthelmintic drug development that could be used for the control of helminths infecting humans and animals.
A novel inhibitory effect of oxazol-5-one compounds on ROCKII signaling in human coronary artery vascular smooth muscle cells
Authors: Al-Ghabkari Abdulhameed , Deng Jing-Ti , McDonald Paul C. , Dedhar Shoukat , Alshehri Mana , Walsh Michael P. , MacDonald Justin A. 
Published: August 2016

AbstractThe selectivity of (4Z)-2-(4-chloro-3-nitrophenyl)-4-(pyridin-3-ylmethylidene)-1,3-oxazol-5-one (DI) for zipper-interacting protein kinase (ZIPK) was previously described by in silico computational modeling, screening a large panel of kinases and determining the inhibition efficacy. Our assessment of DI revealed another target, the Rho-associated coiled-coil-containing protein kinase 2 (ROCKII). In vitro studies showed DI to be a competitive inhibitor of ROCKII (Ki, 132 nM with respect to ATP). This finding was supported by in silico molecular surface docking of DI with the ROCKII ATP-binding pocket. Time course analysis of myosin regulatory light chain (LC20) phosphorylation catalyzed by ROCKII in vitro revealed a significant decrease upon treatment with DI. ROCKII signaling was investigated in situ in human coronary artery vascular smooth muscle cells (CASMCs). ROCKII down-regulation using siRNA revealed several potential substrates involved in smooth muscle contraction (e.g., LC20, Par-4, MYPT1) and actin cytoskeletal dynamics (cofilin). The application of DI to CASMCs attenuated LC20, Par-4, LIMK and cofilin phosphorylations. Notably, cofilin phosphorylation was not significantly decreased with a novel ZIPK selective inhibitor (HS-38). In addition, CASMCs treated with DI underwent cytoskeletal changes that were associated with diminution of cofilin phosphorylation. We conclude that DI is not selective for ZIPK and is a potent inhibitor of ROCKII.
Theoretical Study of the ESIPT Process for a New Natural Product Quercetin
Authors: Yang Yunfan , Zhao Jinfeng , Li Yongqing 
Published: August 2016

AbstractThe investigation of excited-state intramolecular proton transfer (ESIPT) has been carried out via the density functional theory (DFT) and the time-dependent density functional theory (TDDFT) method for natural product quercetin in dichloromethane (DCM) solvent. For distinguishing different types of intramolecular interaction, the reduced density gradient (RDG) function also has been used. In this study, we have clearly clarified the viewpoint that two kinds of tautomeric forms (K1, K2)originated from ESIPT processconsist inthe first electronic excited state (S1). The phenomenon of hydrogen bonding interaction strengtheninghas been proved by comparing the changes of infrared (IR) vibrational spectra and bond parameters of the hydrogen bonding groups in the ground state with that in the first excited state. The frontier molecular orbitals (MOs)provided visual electron density redistribution have further verified the hydrogen bond strengthening mechanism. It should be noted that the ESIPT process of the K2form is easier to occur than that of the K1form via observing the potential energy profiles. Furthermore, the RDG isosurfaces has indicated that hydrogen bonding interaction of the K2form is stronger than that of the K1formin the S1state, which is also the reason why the ESIPT process of the K2form is easier to occur.
MicroRNA393 is involved in nitrogen-promoted rice tillering through regulation of auxin signal transduction in axillary buds
Authors: Li Xiang , Xia Kuaifei , Liang Zhen , Chen Kunling , Gao Caixia , Zhang Mingyong 
Published: August 2016

AbstractRice tillering has an important influence on grain yield, and is promoted by nitrogen (N) fertilizer. Several genes controlling rice tillering, which are regulated by poor N supply, have been identified. However, the molecular mechanism associated with the regulation of tillering based on N supply is poorly understood. Here, we report that rice microRNA393 (OsmiR393) is involved in N-mediated tillering by decreasing auxin signal sensitivity in axillary buds. Expression analysis showed that N fertilizer causes up-regulation of OsmiR393, but down-regulation of two target genes (OsAFB2 and OsTB1). In situ expression analysis showed that OsmiR393 is highly expressed in the lateral axillary meristem. OsmiR393 overexpression mimicked N-mediated tillering in wild type Zhonghua 11 (ZH11). Mutation of OsMIR393 in ZH11 repressed N-promoted tillering, which simulated the effects of limited N, and this could not be restored by supplying N fertilizer. Western blot analysis showed that OsIAA6 was accumulated in both OsmiR393-overexpressing lines and N-treated wild type rice, but was reduced in the OsMIR393 mutant. Therefore, we deduced that N-induced OsmiR393 accumulation reduces the expression of OsTIR1 and OsAFB2, which alleviates sensitivity to auxin in the axillary buds and stabilizes OsIAA6, thereby promoting rice tillering.
High Mobility Group Box Protein 1 Boosts Endothelial Albumin Transcytosis through the RAGE/Src/Caveolin-1 Pathway
Authors: Shang Dan , Peng Tao , Gou Shanmiao , Li Yiqing , Wu Heshui , Wang Chunyou , Yang Zhiyong 
Published: August 2016

AbstractHigh-mobility group box protein 1 (HMGB1), an inflammatory mediator, has been reported to destroy cell-cell junctions, resulting in vascular endothelial hyperpermeability. Here, we report that HMGB1 increases the endothelial transcytosis of albumin. In mouse lung vascular endothelial cells (MLVECs), HMGB1 at a concentration of 500 ng/ml or less did not harm cell-cell junctions but rapidly induced endothelial hyperpermeability to 125I-albumin. HMGB1 induced an increase in 125I-albumin and AlexaFluor 488-labeled albumin internalization in endocytosis assays. Depletion of receptor for advanced glycation end products (RAGE), but not TLR2 or TLR4, suppressed HMGB1-induced albumin transcytosis and endocytosis. Genetic and pharmacological destruction of lipid rafts significantly inhibited HMGB1-induced albumin endocytosis and transcytosis. HMGB1 induced the rapid phosphorylation of caveolin (Cav)-1 and Src. Either RAGE gene silencing or soluble RAGE suppressed Cav-1 Tyr14 phosphorylation and Src Tyr418 phosphorylation. The Src inhibitor 4-amino-5-(4-chlorophenyl)-7-(t-butyl) pyrazolo[3,4-d] pyrimidine (PP2) blocked HMGB1-induced Cav-1 Tyr14 phosphorylation. PP2 and overexpression of Cav-1 with a T14F mutation significantly inhibited HMGB1-induced transcytosis and albumin endocytosis. Our findings suggest that HMGB1 induces the transcytosis of albumin via RAGE-dependent Src phosphorylation and Cav-1 phosphorylation. These studies revealed a new mechanism of HMGB1-induced endothelial hyperpermeability.
Mammalian non-CG methylations are conserved and cell-type specific and may have been involved in the evolution of transposon elements
Authors: Guo Weilong , Zhang Michael Q. , Wu Hong 
Published: August 2016

AbstractAlthough non-CG methylations are abundant in several mammalian cell types, their biological significance is sparsely characterized. We gathered 51 human and mouse DNA methylomes from brain neurons, embryonic stem cells and induced pluripotent stem cells, primordial germ cells and oocytes. We utilized an unbiased sub-motif prediction method and reported CW as the representative non-CG methylation context, which is distinct from CC methylation in terms of sequence context and genomic distribution. A two-dimensional comparison of non-CG methylations across cell types and species was performed. Unambiguous studies of sequence preferences and genomic region enrichment showed that CW methylation is cell-type specific and is also conserved between humans and mice. In brain neurons, it was found that active long interspersed nuclear element-1 (LINE-1) lacked CW methylations but not CG methylations. Coincidentally, both human Alu and mouse B1 elements preferred high CW methylations at specific loci during their respective evolutionary development. Last, the strand-specific distributions of CW methylations in introns and long interspersed nuclear elements are also cell-type specific and conserved. In summary, our results illustrate that CW methylations are highly conserved among species, are dynamically regulated in each cell type, and are potentially involved in the evolution of transposon elements.
Spatial limitations in averaging social cues
Authors: Florey Joseph , Clifford Colin W. G. , Dakin Steven , Mareschal Isabelle 
Published: August 2016

AbstractThe direction of social attention from groups provides stronger cueing than from an individual. It has previously been shown that both basic visual features such as size or orientation and more complex features such as face emotion and identity can be averaged across multiple elements. Here we used an equivalent noise procedure to compare observers’ ability to average social cues with their averaging of a non-social cue. Estimates of observers’ internal noise (uncertainty associated with processing any individual) and sample-size (the effective number of gaze-directions pooled) were derived by fitting equivalent noise functions to discrimination thresholds. We also used reverse correlation analysis to estimate the spatial distribution of samples used by participants. Averaging of head-rotation and cone-rotation was less noisy and more efficient than averaging of gaze direction, though presenting only the eye region of faces at a larger size improved gaze averaging performance. The reverse correlation analysis revealed greater sampling areas for head rotation compared to gaze. We attribute these differences in averaging between gaze and head cues to poorer visual processing of faces in the periphery. The similarity between head and cone averaging are examined within the framework of a general mechanism for averaging of object rotation.
Novel facile method for obtaining CdSe/polyaniline/C60 composite materials
Authors: Rusen Edina , Diacon Aurel , Mocanu Alexandra , Nistor Leona Cristina 
Published: August 2016

AbstractThis study presents a novel method for the oxidative polymerization of aniline (ANI) by employing fullerene C60/cadmium selenide (CdSe) quantum dots, as promoting agent of the polymerization system. The polymerization initiation mechanism is based on the difference between the HOMO-LUMO energy levels of the components which permits the formation of a continuous donor-acceptor exchange. Both the polymerization reaction evolution and the molecular weights of the obtained polymers have been characterized. The novelty of the paper consists in the synthesis of a novel nano-composite material through a novel polymerization technique. The resulting material containing PANI, CdSe quantum dots and C60 has been characterized by UV-Vis, NIR, fluorescence, TEM and GPC analyses.