bluuebunny/crossref_metadata_2025_split huggingface dataset:
Application of 3-D Urbanization Index to Assess Impact of Urbanization on Air Temperature
Authors: Wu Chih-Da , Lung Shih-Chun Candice 
Published: April 2016

AbstractThe lack of appropriate methodologies and indicators to quantify three-dimensional (3-D) building constructions poses challenges to authorities and urban planners when formulating polices to reduce health risks due to heat stress. This study evaluated the applicability of an innovative three-dimensional Urbanization Index (3DUI), based on remote sensing database, with a 5 m spatial resolution of 3-D man-made constructions to representing intra-urban variability of air temperature by assessing correlation of 3DUI with air temperature from a 3-D perspective. The results showed robust high correlation coefficients, ranging from 0.83 to 0.85, obtained within the 1,000 m circular buffer around weather stations regardless of season, year, or spatial location. Our findings demonstrated not only the strength of 3DUI in representing intra-urban air-temperature variability, but also its great potential for heat stress assessment within cities. In view of the maximum correlation between building volumes within the 1,000 m circular buffer and ambient air temperature, urban planning should consider setting ceilings for man-made construction volume in each 2 × 2 km2 residential community for thermal environment regulation, especially in Asian metropolis with high population density in city centers.
Pulse-modulated multilevel data storage in an organic ferroelectric resistive memory diode
Authors: Lee Jiyoul , van Breemen Albert J. J. M. , Khikhlovskyi Vsevolod , Kemerink Martijn , Janssen Rene A. J. , Gelinck Gerwin H. 
Published: April 2016

AbstractWe demonstrate multilevel data storage in organic ferroelectric resistive memory diodes consisting of a phase-separated blend of P(VDF-TrFE) and a semiconducting polymer. The dynamic behaviour of the organic ferroelectric memory diode can be described in terms of the inhomogeneous field mechanism (IFM) model where the ferroelectric components are regarded as an assembly of randomly distributed regions with independent polarisation kinetics governed by a time-dependent local field. This allows us to write and non-destructively read stable multilevel polarisation states in the organic memory diode using controlled programming pulses. The resulting 2-bit data storage per memory element doubles the storage density of the organic ferroelectric resistive memory diode without increasing its technological complexity, thus reducing the cost per bit.
Low-Dimensional Network Formation in Molten Sodium Carbonate
Authors: Wilding Martin C. , Wilson Mark , Alderman Oliver L. G. , Benmore Chris , Weber J. K. R. , Parise John B. , Tamalonis Anthony , Skinner Lawrie 
Published: April 2016

AbstractMolten carbonates are highly inviscid liquids characterized by low melting points and high solubility of rare earth elements and volatile molecules. An understanding of the structure and related properties of these intriguing liquids has been limited to date. We report the results of a study of molten sodium carbonate (Na2CO3) which combines high energy X-ray diffraction, containerless techniques and computer simulation to provide insight into the liquid structure. Total structure factors (Fx(Q)) are collected on the laser-heated carbonate spheres suspended in flowing gases of varying composition in an aerodynamic levitation furnace. The respective partial structure factor contributions to Fx(Q) are obtained by performing molecular dynamics simulations treating the carbonate anions as flexible entities. The carbonate liquid structure is found to be heavily temperature-dependent. At low temperatures a low-dimensional carbonate chain network forms, at T = 1100 K for example ~55% of the C atoms form part of a chain. The mean chain lengths decrease as temperature is increased and as the chains become shorter the rotation of the carbonate anions becomes more rapid enhancing the diffusion of Na+ ions.
The first see-through frog created by breeding: description, inheritance patterns and dermal chromatophore structure
Authors: Sumida Masayuki , Islam Mohammed Mafizul , Igawa Takeshi , Kurabayashi Atsushi , Furukawa Yukari , Sano Naomi , Fujii Tamotsu , Yoshizaki Norio 
Published: April 2016

AbstractWe have succeeded in creating see-through frogs from natural color mutants of the Japanese brown frog Rana japonica, which usually possesses an ochre or brown back; this coloration enables the organs, blood vessels and eggs to be observed through the skin without performing dissection. We crossed two kinds of recessive color mutant (black-eyed and gray-eyed) frogs through artificial insemination and F2 offspring produced frogs whose skin is translucent throughout the life cycle. Three kinds of dermal chromatophores—xanthophores, iridophores and melanophores—are observed in a layered arrangement in the skin of wild-type frogs, but few chromatophores were present in the skin of the see-through frogs. The translucent skin enables observation of organ growth and cancer formation and progression in the animal, which can be monitored over its entire life without the need for dissection. See-through frogs thus provide a useful animal model for environmental, medical and biological research.
Structural basis of DNA sequence recognition by the response regulator PhoP in Mycobacterium tuberculosis
Authors: He Xiaoyuan , Wang Liqin , Wang Shuishu 
Published: April 2016

AbstractThe transcriptional regulator PhoP is an essential virulence factor in Mycobacterium tuberculosis, and it presents a target for the development of new anti-tuberculosis drugs and attenuated tuberculosis vaccine strains. PhoP binds to DNA as a highly cooperative dimer by recognizing direct repeats of 7-bp motifs with a 4-bp spacer. To elucidate the PhoP-DNA binding mechanism, we determined the crystal structure of the PhoP-DNA complex. The structure revealed a tandem PhoP dimer that bound to the direct repeat. The surprising tandem arrangement of the receiver domains allowed the four domains of the PhoP dimer to form a compact structure, accounting for the strict requirement of a 4-bp spacer and the highly cooperative binding of the dimer. The PhoP-DNA interactions exclusively involved the effector domain. The sequence-recognition helix made contact with the bases of the 7-bp motif in the major groove, and the wing interacted with the adjacent minor groove. The structure provides a starting point for the elucidation of the mechanism by which PhoP regulates the virulence of M. tuberculosis and guides the design of screening platforms for PhoP inhibitors.
Spontaneous bidirectional ordering of CH3NH3+ in lead iodide perovskites at room temperature: The origins of the tetragonal phase
Authors: Deretzis Ioannis , Di Mauro Bruno N. , Alberti Alessandra , Pellegrino Giovanna , Smecca Emanuele , La Magna Antonino 
Published: April 2016

AbstractCH3NH3PbI3 is a hybrid organic-inorganic material with a perovskite structure and a temperature-dependent polymorphism whose origins are still unclear. Here we perform ab initio molecular dynamics simulations in order to investigate the structural properties and atom dynamics of CH3NH3PbI3 at room temperature. Starting from different initial configurations, we find that a single-crystalline system undergoes a spontaneous ordering process which brings the "Equation missing" ions to alternately point towards the center of two out of the six faces of the cubic "Equation missing" framework, i.e. towards the 〈100〉 and 〈010〉 directions. This bidirectional ordering gives rise to a preferential distortion of the inorganic lattice on the a-b plane, shaping the observed tetragonal symmetry of the system. The process requires tens of picoseconds for CH3NH3PbI3 supercells with just eight "Equation missing" ions.
Stratification of Digestive Cancers with Different Pathological Features and Survival Outcomes by MicroRNA Expression
Authors: Tang Senwei , Wu William K. K. , Li Xiangchun , Wong Sunny H. , Wong Nathalie , Chan Matthew T. V. , Sung Joseph J. Y. , Yu Jun 
Published: April 2016

AbstractMicroRNAs (miRNAs) are aberrantly expressed in virtually all cancer types, including digestive cancers. Herein, we aggregated and systematically analyzed miRNA expression profiles of 1765 tumor samples, including esophageal, gastric, liver, pancreatic, colon and rectal cancers, obtained through small RNA sequencing by The Cancer Genome Atlas. We found that digestive cancers of different tissue origins could be differentiated according to their miRNA expression profiles. In particular, esophageal squamous cell carcinoma and esophageal adenocarcinoma exhibited distinct miRNA expression patterns. Thirteen (e.g. miR-135b, miR-182) and sixteen (e.g. miR-139, miR-133a-1, miR-490) miRNAs were commonly upregulated and downregulated in more than four cancer types, respectively. Pertinent to pathological features, low miR-181d expression was associated with microsatellite instability in colon and gastric cancers whereas low miR-106a expression was associated with hepatitis B virus infection in hepatocellular carcinoma. Progression in colon cancer could also be predicted by low let-7f-2 and high miR-106a expression. Molecular subtypes with distinct prognostic outcomes independent of tumor-node-metastasis staging were identified in hepatocellular carcinoma and colon cancer. In total, 4 novel and 6 reported associations between specific miRNAs and patients’ survival were identified. Collectively, novel miRNA markers were identified to stratify digestive cancers with different pathological features and survival outcomes.
The Parkinson Disease gene SNCA: Evolutionary and structural insights with pathological implication
Authors: Siddiqui Irum Javaid , Pervaiz Nashaiman , Abbasi Amir Ali 
Published: April 2016

AbstractAfter Alzheimer, Parkinson’s disease (PD) is the second most common neurodegenerative disorder. Alpha synuclein (SNCA) is deemed as a major component of Lewy bodies, a neuropathological feature of PD. Five point mutations in SNCA have been reported so far, responsible for autosomal dominant PD. This study aims to decipher evolutionary and structural insights of SNCA by revealing its sequence and structural evolutionary patterns among sarcopterygians and its paralogous counterparts (SNCB and SNCG). Rate analysis detected strong purifying selection on entire synuclein family. Structural dynamics divulges that during the course of sarcopterygian evolutionary history, the region encompassed 32 to 58 of N-terminal domain of SNCA has acquired its critical functional significance through the epistatic influence of the lineage specific substitutions. In sum, these findings provide an evidence that the region from 32 to 58 of N-terminal lipid binding alpha helix domain of SNCA is the most critical region, not only from the evolutionary perspective but also for the stability and the proper conformation of the protein as well as crucial for the disease pathogenesis, harboring critical interaction sites.
Tongue Coating and the Salivary Microbial Communities Vary in Children with Halitosis
Authors: Ren Wen , Xun Zhe , Wang Zicheng , Zhang Qun , Liu Xuenan , Zheng Hui , Zhang Qian , Zhang Yifei , Zhang Linshuang , Wu Chunyan , Zheng Shuguo , Qin Nan , Ehrlich S. Dusko , Li Yihong , He Xuesong , Xu Tao , Chen Ting , Chen Feng 
Published: April 2016

AbstractHalitosis is a common symptom mainly caused by microbial activities in the oral cavity. Here, we used 16S rRNA gene pyrosequencing and metagenomic sequencing to examine oral microbial compositions and their functional variations in children with halitosis. We found that the tongue coating of subjects with halitosis had greater bacterial richness than those of healthy subjects. The relative abundance and prevalence of Leptotrichia wadei and Peptostreptococcus stomatis were higher in tongue coating samples from children with halitosis than those from children without halitosis; Prevotella shahii had higher relative abundance and prevalence in saliva samples from children with halitosis. We present the first comprehensive evaluation of the co-occurrence networks of saliva and tongue coating communities under healthy and halitosis conditions and investigated patterns of significant differences between these communities. Moreover, we observed that bacterial genes associated with responses to infectious diseases and terpenoid and polyketide metabolism were enriched in subjects with halitosis, but not in healthy subjects. Hydrogen sulphide (H2S)-related metabolic pathways suggested that there was higher microbial production and less usage of H2S in subjects with halitosis. Thus, the mechanism of halitosis was implied for the first time via metagenomic sequencing.
INaP selective inhibition reverts precocious inter- and motorneurons hyperexcitability in the Sod1-G93R zebrafish ALS model
Authors: Benedetti Lorena , Ghilardi Anna , Rottoli Elsa , De Maglie Marcella , Prosperi Laura , Perego Carla , Baruscotti Mirko , Bucchi Annalisa , Del Giacco Luca , Francolini Maura 
Published: April 2016

AbstractThe pathogenic role ofSOD1mutations in amyotrophic lateral sclerosis (ALS) was investigated using a zebrafish disease model stably expressing the ALS-linked G93R mutation. In addition to the main pathological features of ALS shown by adult fish, we found remarkably precocious alterations in the development of motor nerve circuitry and embryo behavior, and suggest that these alterations are prompted by interneuron and motor neuron hyperexcitability triggered by anomalies in the persistent pacemaker sodium current INaP. The riluzole-induced modulation of INaPreduced spinal neuron excitability, reverted the behavioral phenotypes and improved the deficits in motor nerve circuitry development, thus shedding new light on the use of riluzole in the management of ALS. Our findings provide a valid phenotype-based tool for unbiasedin vivodrug screening that can be used to develop new therapies.
Optically controlled spin-polarization memory effect on Mn delta-doped heterostructures
Authors: Balanta M. A. G. , Brasil M. J. S. P. , Iikawa F. , Mendes Udson C. , Brum J. A. , Danilov Yu. A. , Dorokhin M. V. , Vikhrova O. V. , Zvonkov B. N. 
Published: April 2016

AbstractWe investigated the dynamics of the interaction between spin-polarized photo-created carriers and Mn ions on InGaAs/GaAs: Mn structures. The carriers are confined in an InGaAs quantum well and the Mn ions come from a Mn delta-layer grown at the GaAs barrier close to the well. Even though the carriers and the Mn ions are spatially separated, the interaction between them is demonstrated by time-resolved spin-polarized photoluminescence measurements. Using a pre-pulse laser excitation with an opposite circular-polarization clearly reduces the polarization degree of the quantum-well emission for samples where a strong magnetic interaction is observed. The results demonstrate that the Mn ions act as a spin-memory that can be optically controlled by the polarization of the photocreated carriers. On the other hand, the spin-polarized Mn ions also affect the spin-polarization of the subsequently created carriers as observed by their spin relaxation time. These effects fade away with increasing time delays between the pulses as well as with increasing temperatures.
Suppression of B function strongly supports the modified ABCE model in Tricyrtis sp. (Liliaceae)
Authors: Otani Masahiro , Sharifi Ahmad , Kubota Shosei , Oizumi Kanako , Uetake Fumi , Hirai Masayo , Hoshino Yoichiro , Kanno Akira , Nakano Masaru 
Published: April 2016

AbstractB class MADS-box genes play important roles in petal and stamen development. Some monocotyledonous species, including liliaceous ones, produce flowers with petaloid tepals in whorls 1 and 2. A modified ABCE model has been proposed to explain the molecular mechanism of development of two-layered petaloid tepals. However, direct evidence for this modified ABCE model has not been reported to date. To clarify the molecular mechanism determining the organ identity of two-layered petaloid tepals, we used chimeric repressor gene-silencing technology (CRES-T) to examine the suppression of B function in the liliaceous ornamental Tricyrtis sp. Transgenic plants with suppressed B class genes produced sepaloid tepals in whorls 1 and 2 instead of the petaloid tepals as expected. In addition, the stamens of transgenic plants converted into pistil-like organs with ovule- and stigma-like structures. This report is the first to describe the successful suppression of B function in monocotyledonous species with two-layered petaloid tepals, and the results strongly support the modified ABCE model.
Soil ionomic and enzymatic responses and correlations to fertilizations amended with and without organic fertilizer in long-term experiments
Authors: Feng Xumeng , Ling Ning , Chen Huan , Zhu Chen , Duan Yinghua , Peng Chang , Yu Guanghui , Ran Wei , Shen Qirong , Guo Shiwei 
Published: April 2016

AbstractTo investigate potential interactions between the soil ionome and enzyme activities affected by fertilization with or without organic fertilizer, soil samples were collected from four long-term experiments over China. Irrespective of variable interactions, fertilization type was the major factor impacting soil ionomic behavior and accounted for 15.14% of the overall impact. Sampling site was the major factor affecting soil enzymatic profile and accounted for 34.25% of the overall impact. The availabilities of Pb, La, Ni, Co, Fe and Al were significantly higher in soil with only chemical fertilizer than the soil with organic amendment. Most of the soil enzyme activities, including α-glucosidase activity, were significantly activated by organic amendment. Network analysis between the soil ionome and the soil enzyme activities was more complex in the organic-amended soils than in the chemical fertilized soils, whereas the network analysis among the soil ions was less complex with organic amendment. Moreover, α-glucosidase was revealed to generally harbor more corrections with the soil ionic availabilities in network. We concluded that some of the soil enzymes activated by organic input can make the soil more vigorous and stable and that the α-glucosidase revealed by this analysis might help stabilize the soil ion availability.
Effects of Frequency Drift on the Quantification of Gamma-Aminobutyric Acid Using MEGA-PRESS
Authors: Tsai Shang-Yueh , Fang Chun-Hao , Wu Thai-Yu , Lin Yi-Ru 
Published: April 2016

AbstractThe MEGA-PRESS method is the most common method used to measure γ-aminobutyric acid (GABA) in the brain at 3T. It has been shown that the underestimation of the GABA signal due to B0 drift up to 1.22 Hz/min can be reduced by post-frequency alignment. In this study, we show that the underestimation of GABA can still occur even with post frequency alignment when the B0 drift is up to 3.93 Hz/min. The underestimation can be reduced by applying a frequency shift threshold. A total of 23 subjects were scanned twice to assess the short-term reproducibility and 14 of them were scanned again after 2–8 weeks to evaluate the long-term reproducibility. A linear regression analysis of the quantified GABA versus the frequency shift showed a negative correlation (P < 0.01). Underestimation of the GABA signal was found. When a frequency shift threshold of 0.125 ppm (15.5 Hz or 1.79 Hz/min) was applied, the linear regression showed no statistically significant difference (P > 0.05). Therefore, a frequency shift threshold at 0.125 ppm (15.5 Hz) can be used to reduce underestimation during GABA quantification. For data with a B0 drift up to 3.93 Hz/min, the coefficients of variance of short-term and long-term reproducibility for the GABA quantification were less than 10% when the frequency threshold was applied.
Soil radon measurements as a potential tracer of tectonic and volcanic activity
Authors: Neri Marco , Ferrera Elisabetta , Giammanco Salvatore , Currenti Gilda , Cirrincione Rosolino , Patanè Giuseppe , Zanon Vittorio 
Published: April 2016

AbstractIn Earth Sciences there is a growing interest in studies concerning soil-radon activity, due to its potential as a tracer of numerous natural phenomena. Our work marks an advance in the comprehension of the interplay between tectonic activity, volcanic eruptions and gas release through faults. Soil-radon measurements, acquired on Mt. Etna volcano in 2009–2011, were analyzed. Our radon probe is sensitive to changes in both volcanic and seismic activity. Radon data were reviewed in light of the meteorological parameters. Soil samples were analyzed to characterize their uranium content. All data have been summarized in a physical model which identifies the radon sources, highlights the mechanism of radon transport and envisages how such a mechanism may change as a consequence of seismicity and volcanic events. In the NE of Etna, radon is released mainly from a depth of <1400 m, with an ascent speed of >50 m/day. Three periods of anomalous gas release were found (February 2010, January and February 2011). The trigger of the first anomaly was tectonic, while the second and third had a volcanic origin. These results mark a significant step towards a better understanding of the endogenous mechanisms that cause changes in soil-radon emission at active volcanoes.
Lipopolysaccharide (LPS) disrupts particle transport, cilia function and sperm motility in an ex vivo oviduct model
Authors: O’Doherty A. M. , Di Fenza M. , Kölle S. 
Published: April 2016

AbstractThe oviduct functions in the transportation of gametes to the site of fertilization (the ampulla) and is the site of early embryonic development. Alterations of this early developmental environment, such as the presence of sexually transmitted pathogens, may affect oviduct function leading to reduced fertilization rates and contribute to compromised embryonic development. In this study, sperm interactions, particle transport speed (PTS) and cilia beat frequency (CBF) in the ampulla following exposure to lipopolysaccharide (LPS), a constituent of the sexually transmitted pathogens Chlamydia trachomatis and Chlamydia abortus, was investigated. Three complementary experiments were performed to analyse; (1) bound sperm motility and cilia function (2) transport velocity in the oviduct and (3) the expression of genes related to immune function and inflammatory response (CASP3, CD14, MYD88, TLR4 and TRAF6). The motility of bound sperm was significantly lower in ampullae that were exposed to LPS. CBF and PTS significantly increased after treatment with LPS for 2 hours. Finally, gene expression analysis revealed that CASP3 and CD14 were significantly upregulated and TLR4 trended towards increased expression following treatment with LPS. These findings provide an insight on the impact of LPS on the oviduct sperm interaction, and have implications for both male and female fertility.