bluuebunny/crossref_metadata_2025_split huggingface dataset:
The anatomy of urban social networks and its implications in the searchability problem
Authors: Herrera-Yagüe C. , Schneider C. M. , Couronné T. , Smoreda Z. , Benito R. M. , Zufiria P. J. , González M. C. 
Published: June 2015

AbstractThe appearance of large geolocated communication datasets has recently increased our understanding of how social networks relate to their physical space. However, many recurrently reported properties, such as the spatial clustering of network communities, have not yet been systematically tested at different scales. In this work we analyze the social network structure of over 25 million phone users from three countries at three different scales: country, provinces and cities. We consistently find that this last urban scenario presents significant differences to common knowledge about social networks. First, the emergence of a giant component in the network seems to be controlled by whether or not the network spans over the entire urban border, almost independently of the population or geographic extension of the city. Second, urban communities are much less geographically clustered than expected. These two findings shed new light on the widely-studied searchability in self-organized networks. By exhaustive simulation of decentralized search strategies we conclude that urban networks are searchable not through geographical proximity as their country-wide counterparts, but through an homophily-driven community structure.
Comparative study reveals better far-red fluorescent protein for whole body imaging
Authors: Luker K.E. , Pata P. , Shemiakina I.I. , Pereverzeva A. , Stacer A.C. , Shcherbo D.S. , Pletnev V.Z. , Skolnaja M. , Lukyanov K.A. , Luker G.D. , Pata I. , Chudakov D.M. 
Published: June 2015

AbstractGenetically encoded far-red and near-infrared fluorescent proteins enable efficient imaging in studies of tumorigenesis, embryogenesis and inflammation in model animals. Here we report comparative testing of available GFP-like far-red fluorescent proteins along with a modified protein, named Katushka2S and near-infrared bacterial phytochrome-based markers. We compare fluorescence signal and signal-to-noise ratio at various excitation wavelength and emission filter combinations using transiently transfected cell implants in mice, providing a basis for rational choice of optimal marker(s) for in vivo imaging studies. We demonstrate that the signals of various far-red fluorescent proteins can be spectrally unmixed based on different signal-to-noise ratios in different channels, providing the straightforward possibility of multiplexed imaging with standard equipment. Katushka2S produced the brightest and fastest maturing fluorescence in all experimental setups. At the same time, signal-to-noise ratios for Katushka2S and near-infrared bacterial phytochrome, iRFP720 were comparable in their optimal channels. Distinct spectral and genetic characteristics suggest this pair of a far-red and a near-infrared fluorescent protein as an optimal combination for dual color, whole body imaging studies in model animals.
Nutrition regulation of male accessory gland growth and maturation in Tribolium castaneum
Authors: xu Jingjing , Anciro Ashlee L , Palli Subba Reddy 
Published: June 2015

AbstractInsulin/IGF-1 signaling (IIS) pathway is known to control growth, development and reproduction. Insulin-like peptide mediated body size plasticity in Drosophila melanogaster has been reported. Here, our studies showed that IIS pathway and nutrition regulate growth and maturation of the male accessory gland (MAG) in the red flour beetle, Tribolium castaneum. The size of MAG increased from day 1 to day 5 post-adult emergence (PAE). This increase in the size of MAG is contributed by an increase in cell size, but not cell number. The growth of MAG was impaired after double-stranded RNA (dsRNA)-mediated knockdown in the expression of genes coding for ILP3, InR, Chico, PI3k, AKT and GATA1 involved in IIS pathway. Interestingly, starvation showed similar effects on the growth and maturation of MAG. The phenotypes observed in animals where IIS signaling pathway genes were knocked down are similar to the phenotypes observed after starving beetles for 5 days PAE. These data suggest that nutrition signals working through IIS pathway regulate maturation of MAG by promoting the growth of MAG cells.
A Novel Characterization of Amalgamated Networks in Natural Systems
Authors: Barranca Victor J. , Zhou Douglas , Cai David 
Published: June 2015

AbstractDensely-connected networks are prominent among natural systems, exhibiting structural characteristics often optimized for biological function. To reveal such features in highly-connected networks, we introduce a new network characterization determined by a decomposition of network-connectivity into low-rank and sparse components. Based on these components, we discover a new class of networks we define as amalgamated networks, which exhibit large functional groups and dense connectivity. Analyzing recent experimental findings on cerebral cortex, food-web and gene regulatory networks, we establish the unique importance of amalgamated networks in fostering biologically advantageous properties, including rapid communication among nodes, structural stability under attacks and separation of network activity into distinct functional modules. We further observe that our network characterization is scalable with network size and connectivity, thereby identifying robust features significant to diverse physical systems, which are typically undetectable by conventional characterizations of connectivity. We expect that studying the amalgamation properties of biological networks may offer new insights into understanding their structure-function relationships.
GPS tracking for mapping seabird mortality induced by light pollution
Authors: Rodríguez Airam , Rodríguez Beneharo , Negro Juan J. 
Published: June 2015

AbstractLight pollution and its consequences on ecosystems are increasing worldwide. Knowledge on the threshold levels of light pollution at which significant ecological impacts emerge and the size of dark refuges to maintain natural nocturnal processes is crucial to mitigate its negative consequences. Seabird fledglings are attracted by artificial lights when they leave their nest at night, causing high mortality. We used GPS data-loggers to track the flights of Cory’s shearwater Calonectris diomedea fledglings from nest-burrows to ground and to evaluate the light pollution levels of overflown areas on Tenerife, Canary Islands, using nocturnal, high-resolution satellite imagery. Birds were grounded at locations closer than 16 km from colonies in their maiden flights and 50% were rescued within a 3 km radius from the nest-site. Most birds left the nests in the first three hours after sunset. Rescue locations showed radiance values greater than colonies and flight distance was positively related to light pollution levels. Breeding habitat alteration by light pollution was more severe for inland colonies. We provide scientific-based information to manage dark refuges facilitating that fledglings from inland colonies reach the sea successfully. We also offer methodological approaches useful for other critically threatened petrel species grounded by light pollution.
Urokinase-type Plasminogen Activator Resulting from Endometrial Carcinogenesis Enhances Tumor Invasion and Correlates with Poor Outcome of Endometrial Carcinoma Patients
Authors: Huang Chia-Yen , Chang Ming-Cheng , Huang Wei-Yun , Huang Ching-Ting , Tang Yu-Chien , Huang Hsien-Da , Kuo Kuan-Ting , Chen Chi-An , Cheng Wen-Fang 
Published: June 2015

AbstractThe purpose of this study was to identify the dysregulated genes involved in the tumorigenesis and progression of endometrial endometrioid adenocarcinoma (EEC) and their possible mechanisms. Endometrial specimens including normal endometrial tissues, atypical endometrial hyperplasia and EEC were analyzed. The expression profiles were compared using GeneChip Array. The gene expression levels were determined by real-time RT-PCR in the training and testing sets to correlate the clinico-pathological parameters of EEC. Immunoblotting, in vitro cell migration and invasion assays were performed in human endometrial cancer cell lines and their transfectants. In microarray analysis, seven dysregulated genes were identified. Only the levels of urokinase-type plasminogen activator (uPA) were higher in EEC with deep myometrial invasion, positive lympho-vascular space invasion, lymph node metastasis and advanced stages. After multivariate analysis, uPA was the only independent poor prognostic factor for disease-free survival in the EEC patients (hazard ratio: 4.65, p = 0.03). uPA may enhance the migratory and invasive capabilities of endometrial tumor cells by the phosphorylation of ERK1/2, Akt and p38 molecules. uPA is a dysregulated gene involved in the tumorigenesis, bio-pathological features and outcomes of EEC. uPA may be a potential molecule and target for the detection and treatment of EEC.
Three-dimensional digital microfluidic manipulation of droplets in oil medium
Authors: Hong Jiwoo , Kim Young Kwon , Won Dong-Joon , Kim Joonwon , Lee Sang Joon 
Published: June 2015

AbstractWe here develop a three-dimensional DMF (3D DMF) platform with patterned electrodes submerged in an oil medium to provide fundamental solutions to the technical limitations of 2D DMF platforms and water–air systems. 3D droplet manipulation on patterned electrodes is demonstrated by programmably controlling electrical signals. We also demonstrate the formation of precipitates on the 3D DMF platform through the reaction of different chemical samples. A droplet containing precipitates, hanging on the top electrode, can be manipulated without adhesion of precipitates to the solid surface. This method could be a good alternative strategy to alleviate the existing problems of 2D DMF systems such as cross-contamination and solute adsorption. In addition, we ascertain the feasibility of temperature-controlled chemical reaction on the 3D DMF platform by introducing a simple heating process. To demonstrate applicability of the 3D DMF system to 3D biological process, we examine the 3D manipulation of droplets containing mouse fibroblasts in the 3D DMF platform. Finally, we show detachment of droplets wrapped by a flexible thin film by adopting the electro-elasto-capillarity (EEC). The employment of the EEC may offer a strong potential in the development of 3D DMF platforms for drug encapsulation and actuation of microelectromechanical devices.
Tuning Organic Carbon Dioxide Absorbents for Carbonation and Decarbonation
Authors: Rajamanickam Ramachandran , Kim Hyungsoo , Park Ji-Woong 
Published: June 2015

AbstractThe reaction of carbon dioxide with a mixture of a superbase and alcohol affords a superbase alkylcarbonate salt via a process that can be reversed at elevated temperatures. To utilize the unique chemistry of superbases for carbon capture technology, it is essential to facilitate carbonation and decarbonation at desired temperatures in an easily controllable manner. Here, we demonstrate that the thermal stabilities of the alkylcarbonate salts of superbases in organic solutions can be tuned by adjusting the compositions of hydroxylic solvent and polar aprotic solvent mixtures, thereby enabling the best possible performances to be obtained from the various carbon dioxide capture agents based on these materials. The findings provides valuable insights into the design and optimization of organic carbon dioxide absorbents.
Somatic expression of unc-54 and vha-6 mRNAs declines but not pan-neuronal rgef-1 and unc-119 expression in aging Caenorhabditis elegans
Authors: Adamla Frauke , Ignatova Zoya 
Published: June 2015

AbstractAging is a highly controlled biological process characterized by a progressive deterioration of various cellular activities. One of several hallmarks of aging describes a link to transcriptional alteration, suggesting that it may impact the steady-state mRNA levels. We analyzed the mRNA steady-state levels of polyCAG-encoding transgenes and endogenous genes under the control of well-characterized promoters for intestinal (vha-6), muscular (unc-54, unc-15) and pan-neuronal (rgef-1, unc-119) expression in the nematode Caenorhabditis elegans. We find that there is not a uniform change in transcriptional profile in aging, but rather a tissue-specific difference in the mRNA levels of these genes. While levels of mRNA in the intestine (vha-6) and muscular (unc-54, unc-15) cells decline with age, pan-neuronal tissue shows more stable mRNA expression (rgef-1, unc-119) which even slightly increases with the age of the animals. Our data on the variations in the mRNA abundance from exemplary cases of endogenous and transgenic gene expression contribute to the emerging evidence for tissue-specific variations in the aging process.
Regulation of transcription factors on sexual dimorphism of fig wasps
Authors: Sun Bao-Fa , Li Yong-Xing , Jia Ling-Yi , Niu Li-Hua , Murphy Robert W. , Zhang Peng , He Shunmin , Huang Da-Wei 
Published: June 2015

AbstractFig wasps exhibit extreme intraspecific morphological divergence in the wings, compound eyes, antennae, body color and size. Corresponding to this, behaviors and lifestyles between two sexes are also different: females can emerge from fig and fly to other fig tree to oviposit and pollinate, while males live inside fig for all their lifetime. Genetic regulation may drive these extreme intraspecific morphological and behavioral divergence. Transcription factors (TFs) involved in morphological development and physiological activity may exhibit sex-specific expressions. Herein, we detect 865 TFs by using genomic and transcriptomic data of the fig wasp Ceratosolen solmsi. Analyses of transcriptomic data indicated that up-regulated TFs in females show significant enrichment in development of the wing, eye and antenna in all stages, from larva to adult. Meanwhile, TFs related to the development of a variety of organs display sex-specific patterns of expression in the adults and these may contribute significantly to their sexual dimorphism. In addition, up-regulated TFs in adult males exhibit enrichment in genitalia development and circadian rhythm, which correspond with mating and protandry. This finding is consistent with their sex-specific behaviors. In conclusion, our results strongly indicate that TFs play important roles in the sexual dimorphism of fig wasps.
Constructing three-dimensional (3D) nanocrystalline models of Li4SiO4 for numerical modeling and simulation
Authors: Shen Yanhong , Gao Tao , Tian Xiaofeng , Chen Xiaojun , Xiao ChengJian , Lu Tiecheng 
Published: June 2015

AbstractThe three-dimensional (3D) nanocrystalline models of lithium silicates with the log-normal grain size distribution are constructed by constrained Voronoi tessellation. During evolution process, the algorithm is improved. We proposed a new algorithm idea by combining Genetic Algorithm (GA) with Least Square (LS) method to make up for the disadvantages of traditional genetic algorithm which may be easily trapped in local optimal solution. In the process of modeling, it is the first time, to the best of our knowledge, that we keep the whole sample showing the charge neutrality by deleting the excess atoms on the polyhedron boundary during the modeling. By using the molecular-dynamics method, the relaxation procedure of nanostructured Li4SiO4 is carried out. The results show that the average mass density of the sample is slightly lower than the experimental data of the perfect crystal after relaxation process. In addition, boundary component proportion (BCP) and density reduction proportion (DRP) of the sample is obtained, respectively. The present results display a significantly reduced BCP but an increased DRP when increasing the mean grain size of the sample.
The protective effect of lactoferrin on ventral mesencephalon neurons against MPP+ is not connected with its iron binding ability
Authors: Wang Jun , Bi Mingxia , Liu Huiying , Song Ning , Xie Junxia 
Published: June 2015

AbstractLactoferrin (Lf) can bind to lactoferrin receptor (LfR), leading to iron transport through the plasma membrane. Besides iron transportation, Lf also has antioxidant and anti-inflammatory properties. In the brain, Lf is only synthesized by activated microglia. LfR is present in blood vessels and nigral dopaminergic neurons. Both nigral iron accumulation and microglia activation is believed to be involved in Parkinson’s disease (PD), moreover, increased Lf and LfR in dopaminergic neurons were found in PD cases and MPTP-intoxicated mice. How iron influences microglia to release Lf? Does Lf tend to transport iron to dopaminergic neurons leading to cell death or to protect dopaminergic neuron from neurotoxin? In this study, we observed that iron increased Lf synthesis in activated microglia. In ventral mesencephalon neurons, both iron-free Lf (apo-Lf) and iron-saturated Lf (holo-Lf) exerted neuroprotective effects against MPP+ by mechanisms, believed to enhance the mitochondrial transmembrane potential, improve Cu/Zn-superoxide dismutase activity, increase Bcl-2 expression. Although apo-Lf but not holo-Lf chelated cellular iron, there was no difference between the two types of Lf in the neuroprotection. Our data indicate that iron overload increases the activated microglia releasing Lf. Lf plays protective role on ventral mesencephalon neurons against MPP+, which is iron-chelating independent.
Direct growth of freestanding GaN on C-face SiC by HVPE
Authors: Tian Yuan , Shao Yongliang , Wu Yongzhong , Hao Xiaopeng , Zhang Lei , Dai Yuanbin , Huo Qin 
Published: June 2015

AbstractIn this work, high quality GaN crystal was successfully grown on C-face 6H-SiC by HVPE using a two steps growth process. Due to the small interaction stress between the GaN and the SiC substrate, the GaN was self-separated from the SiC substrate even with a small thickness of about 100 μm. Moreover, the SiC substrate was excellent without damage after the whole process so that it can be repeatedly used in the GaN growth. Hot phosphoric acid etching (at 240 °C for 30 min) was employed to identify the polarity of the GaN layer. According to the etching results, the obtained layer was Ga-polar GaN. High-resolution X-ray diffraction (HRXRD) and electron backscatter diffraction (EBSD) were done to characterize the quality of the freestanding GaN. The Raman measurements showed that the freestanding GaN film grown on the C-face 6H-SiC was stress-free. The optical properties of the freestanding GaN layer were determined by photoluminescence (PL) spectra.
Pannexin1 channels dominate ATP release in the cochlea ensuring endocochlear potential and auditory receptor potential generation and hearing
Authors: Chen Jin , Zhu Yan , Liang Chun , Chen Jing , Zhao Hong-Bo 
Published: June 2015

AbstractPannexin1 (Panx1) is a gap junction gene in vertebrates whose proteins mainly function as non-junctional channels on the cell surface. Panx1 channels can release ATP under physiological conditions and play critical roles in many physiological and pathological processes. Here, we report that Panx1 deficiency can reduce ATP release and endocochlear potential (EP) generation in the cochlea inducing hearing loss. Panx1 extensively expresses in the cochlea, including the cochlear lateral wall. We found that deletion of Panx1 in the cochlear lateral wall almost abolished ATP release under physiological conditions. Positive EP is a driving force for current through hair cells to produce auditory receptor potential. EP generation requires ATP. In the Panx1 deficient mice, EP and auditory receptor potential as measured by cochlear microphonics (CM) were significantly reduced. However, no apparent hair cell loss was detected. Moreover, defect of connexin hemichannels by deletion of connexin26 (Cx26) and Cx30, which are predominant connexin isoforms in the cochlea, did not reduce ATP release under physiological conditions. These data demonstrate that Panx1 channels dominate ATP release in the cochlea ensuring EP and auditory receptor potential generation and hearing. Panx1 deficiency can reduce ATP release and EP generation causing hearing loss.
Spatial analysis of the effect of the 2010 heat wave on stroke mortality in Nanjing, China
Authors: Chen Kai , Huang Lei , Zhou Lian , Ma Zongwei , Bi Jun , Li Tiantian 
Published: June 2015

AbstractTo examine the spatial variation of stroke mortality risk during heat wave, we collected 418 stroke mortality cases with permanent addresses for a severe heat wave (July 28–August 15, 2010) and 624 cases for the reference period (July 29–August 16, 2009 and July 27–August 14, 2011) in Nanjing, China. Generalized additive models were used to explore the association between location and stroke mortality risk during the heat wave while controlling individual-level risk factors. Heat wave vulnerability was then applied to explain the possible spatial variations of heat-wave-related mortality risk. The overall risk ratio (95% confidence intervals) of stroke mortality due to the heat wave in Nanjing was 1.34 (1.21 to 1.47). Geolocation was found to be significantly associated with the heat-wave-related stroke mortality risk. Using alternative reference periods generated similar results. A district-level risk assessment revealed similar spatial patterns. The highest stroke mortality risk observed in Luhe district was due to the combination of high heat exposure and high vulnerability. Our findings provide evidence that stroke mortality risk is higher in rural areas during heat waves and that these areas require future interventions to reduce vulnerability.
Probing the Effect of Two Heterozygous Mutations in Codon 723 of SLC26A4 on Deafness Phenotype Based on Molecular Dynamics Simulations
Authors: Yao Jun , Qian Xuli , Bao Jingxiao , Wei Qinjun , Lu Yajie , Zheng Heng , Cao Xin , Xing Guangqian 
Published: June 2015

AbstractA Chinese family was identified with clinical features of enlarged vestibular aqueduct syndrome (EVAS). The mutational analysis showed that the proband (III-2) had EVAS with bilateral sensorineural hearing loss and carried a rare compound heterozygous mutation of SLC26A4 (IVS7-2A>G, c.2167C>G), which was inherited from the same mutant alleles of IVS7-2A>G heterozygous father and c.2167C>G heterozygous mother. Compared with another confirmed pathogenic biallelic mutation in SLC26A4 (IVS7-2A>G, c.2168A>G), these two biallelic mutations shared one common mutant allele and the same codon of the other mutant allele, but led to different changes of amino acid (p.H723D, p.H723R) and both resulted in the deafness phenotype. Structure-modeling indicated that these two mutant alleles changed the shape of pendrin protein encoded by SLC26A4 with increasing randomness in conformation and might impair pendrin’s ability as an anion transporter. The molecular dynamics simulations also revealed that the stability of mutant pendrins was reduced with increased flexibility of backbone atoms, which was consistent with the structure-modeling results. These evidences indicated that codon 723 was a hot-spot region in SLC26A4 with a significant impact on the structure and function of pendrin and acted as one of the genetic factors responsible for the development of hearing loss.