bluuebunny/crossref_metadata_2025_split huggingface dataset:
Emergent spectral properties of river network topology: an optimal channel network approach
Authors: Abed-Elmdoust Armaghan , Singh Arvind , Yang Zong-Liang 
Published: September 2017

AbstractCharacterization of river drainage networks has been a subject of research for many years. However, most previous studies have been limited to quantities which are loosely connected to the topological properties of these networks. In this work, through a graph-theoretic formulation of drainage river networks, we investigate the eigenvalue spectra of their adjacency matrix. First, we introduce a graph theory model for river networks and explore the properties of the network through its adjacency matrix. Next, we show that the eigenvalue spectra of such complex networks follow distinct patterns and exhibit striking features including a spectral gap in which no eigenvalue exists as well as a finite number of zero eigenvalues. We show that such spectral features are closely related to the branching topology of the associated river networks. In this regard, we find an empirical relation for the spectral gap and nullity in terms of the energy dissipation exponent of the drainage networks. In addition, the eigenvalue distribution is found to follow a finite-width probability density function with certain skewness which is related to the drainage pattern. Our results are based on optimal channel network simulations and validated through examples obtained from physical experiments on landscape evolution. These results suggest the potential of the spectral graph techniques in characterizing and modeling river networks.
Microbial diversity in the hypersaline Lake Meyghan, Iran
Authors: Naghoni Ali , Emtiazi Giti , Amoozegar Mohammad Ali , Cretoiu Mariana Silvia , Stal Lucas J. , Etemadifar Zahra , Shahzadeh Fazeli Seyed Abolhassan , Bolhuis Henk 
Published: September 2017

AbstractLake Meyghan is one of the largest and commercially most important salt lakes in Iran. Despite its inland location and high altitude, Lake Meyghan has a thalassohaline salt composition suggesting a marine origin. Inputs of fresh water by rivers and rainfall formed various basins characterized by different salinities. We analyzed the microbial community composition of three basins by isolation and culturing of microorganisms and by analysis of the metagenome. The basins that were investigated comprised a green ~50 g kg−1 salinity brine, a red ~180 g kg−1 salinity brine and a white ~300 g kg−1 salinity brine. Using different growth media, 57 strains of Bacteria and 48 strains of Archaea were isolated. Two bacterial isolates represent potential novel species with less than 96% 16S rRNA gene sequence identity to known species. Abundant isolates were also well represented in the metagenome. Bacteria dominated the low salinity brine, with Alteromonadales (Gammaproteobacteria) as a particularly important taxon, whereas the high salinity brines were dominated by haloarchaea. Although the brines of Lake Meyghan differ in geochemical composition, their ecosystem function appears largely conserved amongst each other while being driven by different microbial communities.
Enhanced paramagnetism of mesoscopic graphdiyne by doping with nitrogen
Authors: Zhang Mingjia , Wang Xiaoxiong , Sun Huijuan , Wang Ning , Lv Qing , Cui Weiwei , Long Yunze , Huang Changshui 
Published: September 2017

AbstractThe new two-dimensional graphitic material, graphdiyne, has attracted great interest recently due to the superior intrinsic semiconductor properties. Here we investigate the magnetism of pure graphdiyne material and find it demonstrating a remarkable paramagnetic characteristic, which can be attributed to the appearance of special sp-hybridized carbon atoms. On this basis, we further introduce nitrogen with 5.29% N/C ratio into graphdiyne followed by simply annealing in a dopant source and realize a twofold enhancement of saturation moment at 2 K. Associate with the density of states calculation, we investigate the influence of the nitrogen atom doping sites on paramagnetism, and further reveal the important role of doped nitrogen atom on benzene ring in improving local magnetic moment. These results can not only help us deeply understand the intrinsic magnetism of graphdiyne, but also open an efficient way to improve magnetism of graphdiyne by hetero atom doping, like nitrogen doping, which may promote the potential application of graphdiyne in spintronics.
DNA methylation profiling reveals common signatures of tumorigenesis and defines epigenetic prognostic subtypes of canine Diffuse Large B-cell Lymphoma
Authors: Ferraresso Serena , Aricò Arianna , Sanavia Tiziana , Da Ros Silvia , Milan Massimo , Cascione Luciano , Comazzi Stefano , Martini Valeria , Giantin Mery , Di Camillo Barbara , Mazzariol Sandro , Giannuzzi Diana , Marconato Laura , Aresu Luca 
Published: September 2017

AbstractEpigenetic deregulation is a hallmark of cancer characterized by frequent acquisition of new DNA methylation in CpG islands. To gain insight into the methylation changes of canine DLBCL, we investigated the DNA methylome in primary DLBCLs in comparison with control lymph nodes by genome-wide CpG microarray. We identified 1,194 target loci showing different methylation levels in tumors compared with controls. The hypermethylated CpG loci included promoter, 5′-UTRs, upstream and exonic regions. Interestingly, targets of polycomb repressive complex in stem cells were mostly affected suggesting that DLBCL shares a stem cell-like epigenetic pattern. Functional analysis highlighted biological processes strongly related to embryonic development, tissue morphogenesis and cellular differentiation, including HOX, BMP and WNT. In addition, the analysis of epigenetic patterns and genome-wide methylation variability identified cDLBCL subgroups. Some of these epigenetic subtypes showed a concordance with the clinical outcome supporting the hypothesis that the accumulation of aberrant epigenetic changes results in a more aggressive behavior of the tumor. Collectively, our results suggest an important role of DNA methylation in DLBCL where aberrancies in transcription factors were frequently observed, suggesting an involvement during tumorigenesis. These findings warrant further investigation to improve cDLBCL prognostic classification and provide new insights on tumor aggressiveness.
Toll-like receptor 2 induced cytotoxic T-lymphocyte-associated protein 4 regulates Aspergillus-induced regulatory T-cells with pro-inflammatory characteristics
Authors: Raijmakers Ruud P. H. , Sprenkeler Evelien G. G. , Aleva Floor E. , Jacobs Cor W. M. , Kanneganti Thirumala-Devi , Joosten Leo A. B. , van de Veerdonk Frank L. , Gresnigt Mark S. 
Published: September 2017

AbstractPatients with cystic fibrosis, chronic obstructive pulmonary disease, severe asthma, pre-existing pulmonary lesions, and severely immunocompromised patients are susceptible to develop infections with the opportunistic pathogenic fungus Aspergillus fumigatus, called aspergillosis. Infections in these patients are associated with persistent pro-inflammatory T-helper (TH)2 and TH17 responses. Regulatory T-cells, natural suppressor cells of the immune system, control pro-inflammatory T-cell responses, but can also contribute to disease by shifting to a pro-inflammatory TH17-like phenotype. Such a shift could play an important role in the detrimental immunopathology that is seen in aspergillosis. Our study demonstrates that Aspergillus fumigatus induces regulatory T-cells with a TH17-like phenotype. We also demonstrate that these regulatory T-cells with a pro-inflammatory TH17-like phenotype can be reprogrammed to their “classical” anti-inflammatory phenotype by activating Toll-like receptor 2 (TLR2), which regulates the induction of cytotoxic T-lymphocyte-associated protein 4 (CTLA4). Similarly, soluble CTLA4 could reverse the pro-inflammatory phenotype of Aspergillus-induced regulatory T-cells. In conclusion, our results suggest a role for regulatory T-cells with a pro-inflammatory TH17-like phenotype in Aspergillus-associated immunopathology, and identifies key players, i.e. TLR2 and CTLA4, involved in this mechanism.
CScape: a tool for predicting oncogenic single-point mutations in the cancer genome
Authors: Rogers Mark F. , Shihab Hashem A. , Gaunt Tom R. , Campbell Colin 
Published: September 2017

AbstractFor somatic point mutations in coding and non-coding regions of the genome, we proposeCScape, an integrative classifier for predicting the likelihood that mutations are cancer drivers. Tested on somatic mutations,CScapetends to outperform alternative methods, reaching 91% balanced accuracy in coding regions and 70% in non-coding regions, while even higher accuracy may be achieved using thresholds to isolate high-confidence predictions. Positive predictions tend to cluster in genomic regions, so we apply a statistical approach to isolate coding and non-coding regions of the cancer genome that appear enriched for high-confidence predicted disease-drivers. Predictions and software are available athttp://CScape.biocompute.org.uk/.
Interference-exact radiative transfer equation
Authors: Partanen Mikko , Häyrynen Teppo , Oksanen Jani 
Published: September 2017

AbstractThe Purcell effect, i.e., the modification of the spontaneous emission rate by optical interference, profoundly affects the light-matter coupling in optical resonators. Fully describing the optical absorption, emission, and interference of light hence conventionally requires combining the full Maxwell’s equations with stochastic or quantum optical source terms accounting for the quantum nature of light. We show that both the nonlocal wave and local particle features associated with interference and emission of propagating fields in stratified geometries can be fully captured by local damping and scattering coefficients derived from the recently introduced quantized fluctuational electrodynamics (QFED) framework. In addition to describing the nonlocal optical interference processes as local directionally resolved effects, this allows reformulating the well known and widely used radiative transfer equation (RTE) as a physically transparent interference-exact model that extends the useful range of computationally efficient and quantum optically accurate interference-aware optical models from simple structures to full optical devices.
Impacts of light limitation on corals and crustose coralline algae
Authors: Bessell-Browne Pia , Negri Andrew P. , Fisher Rebecca , Clode Peta L. , Jones Ross 
Published: September 2017

AbstractTurbidity associated with elevated suspended sediment concentrations can significantly reduce underwater light availability. Understanding the consequences for sensitive organisms such as corals and crustose coralline algae (CCA), requires an understanding of tolerance levels and the time course of effects. Adult colonies of Acropora millepora and Pocillopora acuta, juvenile P. acuta, and the CCA Porolithon onkodes were exposed to six light treatments of ~0, 0.02, 0.1, 0.4, 1.1 and 4.3 mol photons m−2 d−1, and their physiological responses were monitored over 30 d. Exposure to very low light (<0.1 mol photons m-2 d-1) caused tissue discoloration (bleaching) in the corals, and discolouration (and partial mortality) of the CCA, yielding 30 d EI10 thresholds (irradiance which results in a 10% change in colour) of 1.2–1.9 mol photons m−2 d−1. Recent monitoring studies during dredging campaigns on a shallow tropical reef, have shown that underwater light levels very close (~500 m away) from a working dredge routinely fall below this value over 30 d periods, but rarely during the pre-dredging baseline phase. Light reduction alone, therefore, constitutes a clear risk to coral reefs from dredging, although at such close proximity other cause-effect pathways, such as sediment deposition and smothering, are likely to also co-occur.
Mitigating Motor Neuronal Loss in C. elegans Model of ALS8
Authors: Zhang Wendy , Colavita Antonio , Ngsee Johnny K. 
Published: September 2017

AbstractALS8 is a late-onset familial autosomal dominant form of Amyotrophic Lateral Sclerosis (ALS) caused by a point mutation (P56S) in the VAPB gene (VAMP associated protein isoform B). Here, we generated two C. elegans models of the disease: a transgenic model where human VAPB wild-type (WT) or P56S mutant was expressed in a subset of motor neurons, and a second model that targeted inducible knockdown of the worm’s orthologue, vpr-1. Overexpression of human VAPB in DA neurons caused a backward locomotion defect, axonal misguidance, and premature neuronal death. Knockdown of vpr-1 recapitulated the reduction in VAPB expression associated with sporadic cases of human ALS. It also caused backward locomotion defects as well as an uncoordinated phenotype, and age-dependent, progressive motor neuronal death. Furthermore, inhibiting phosphatidylinositol-4 (PtdIns 4)-kinase activity with PIK-93 reduced the incidence of DA motor neuron loss and improved backward locomotion. This supports the loss of VAPB function in ALS8 pathogenesis and suggests that reducing intracellular PtdIns4P might be an effective therapeutic strategy in delaying progressive loss of motor neurons.
Antimutagenic and antioxidant activity of the essential oils of Citrus sinensis and Citrus latifolia
Authors: Toscano-Garibay J. D. , Arriaga-Alba M. , Sánchez-Navarrete J. , Mendoza-García M. , Flores-Estrada J. J. , Moreno-Eutimio M. A. , Espinosa-Aguirre J. J. , González-Ávila M. , Ruiz-Pérez N. J. 
Published: September 2017

AbstractThe essential oils of Citrus sinensis and Citrus latifolia showed antimycotic activity against Candida spp. isolated from the oral cavity; they are neither mutagenic on the Ames test nor cytotoxic. Their main components are R-(+)-limonene, β-thujene, α-myrcene and γ-terpinene. The aim of this work was to evaluate their antimutagenic and antioxidant capacities. Antimutagenic properties were evaluated against MNNG and ENNG on S. typhimurium TA100; against 2AA on strain TA98 and in front of 4NQO and NOR on strain TA102. Both were antimutagenic against MNNG (p < 0.001) but only C. latifolia was antimutagenic against ENNG (p < 0.001). Both presented antimutagenic activity against 2AA (p < 0.001). They were antioxidant against the ROS-generating compound 4NQO (p < 0.001) and the antibiotic NOR (p < 0.001). In the antioxidant evaluation, the activity in DPPH assay was in a range of 6–23% for C. sinensis and of 22–71% for C. latifolia. Both were antioxidant compared with BHT in β-carotene bleaching assay and were able to decreased apoptosis in HaCat cells stimulated with H2O2. The levels of intracellular superoxide ion were lower in the presence of both oils. In conclusion, the essential oils of C. sinensis and C. latifolia are antimutagenic against at least three types of mutagens and have antioxidants properties.
Polarization-independent, wide-incident-angle and dual-band perfect absorption, based on near-field coupling in a symmetric metamaterial
Authors: Tung Bui Son , Khuyen Bui Xuan , Kim Young Ju , Lam Vu Dinh , Kim Ki Won , Lee YoungPak 
Published: September 2017

AbstractWe numerically and experimentally investigated a dual-band metamaterial perfect absorber (MPA), utilizing the near-field coupling of double split-ring resonators (DSRRs). Owing to the near-field coupling between resonators, two arms in each DSRR resonate in different phases, leading to a dual-band perfect absorption. The proposed MPA also exhibits polarization-insensitive behavior and maintains the high absorption above 90% up to a wide range of incident angle more than 45°. Finally, to further consolidate our approach, a multi-band absorption is also studied by exploiting the near-field coupling among a larger number of DSRRs. Our work is expected to be applied to future broadband devices using MPA.
Secretory phospholipase A2-IIA overexpressing mice exhibit cyclic alopecia mediated through aberrant hair shaft differentiation and impaired wound healing response
Authors: Chovatiya Gopal L. , Sarate Rahul M. , Sunkara Raghava R. , Gawas Nilesh P. , Kala Vineet , Waghmare Sanjeev K. 
Published: September 2017

AbstractSecretory phospholipase A2 Group-IIA (sPLA2-IIA) is involved in lipid catabolism and growth promoting activity. sPLA2-IIA is deregulated in many pathological conditions including various cancers. Here, we have studied the role of sPLA2-IIA in the development of cyclic alopecia and wound healing response in relation to complete loss of hair follicle stem cells (HFSCs). Our data showed that overexpression of sPLA2-IIA in homozygous mice results in hyperproliferation and terminal epidermal differentiation followed by hair follicle cycle being halted at anagen like stage. In addition, sPLA2-IIA induced hyperproliferation leads to complete exhaustion of hair follicle stem cell pool at PD28 (Postnatal day). Importantly, sPLA2-IIA overexpression affects the hair shaft differentiation leading to development of cyclic alopecia. Molecular investigation study showed aberrant expression of Sox21, Msx2 and signalling modulators necessary for proper differentiation of inner root sheath (IRS) and hair shaft formation. Further, full-thickness skin wounding on dorsal skin of K14-sPLA2-IIA homozygous mice displayed impaired initial healing response. Our results showed the involvement of sPLA2-IIA in regulation of matrix cells differentiation, hair shaft formation and complete loss of HFSCs mediated impaired wound healing response. These novel functions of sPLA2-IIA may have clinical implications in alopecia, cancer development and ageing.
Strong coupling of magnons in a YIG sphere to photons in a planar superconducting resonator in the quantum limit
Authors: Morris R. G. E. , van Loo A. F. , Kosen S. , Karenowska A. D. 
Published: September 2017

AbstractWe report measurements made at millikelvin temperatures of a superconducting coplanar waveguide resonator (CPWR) coupled to a sphere of yttrium-iron garnet. Systems hybridising collective spin excitations with microwave photons have recently attracted interest for their potential quantum information applications. In this experiment the non-uniform microwave field of the CPWR allows coupling to be achieved to many different magnon modes in the sphere. Calculations of the relative coupling strength of different mode families in the sphere to the CPWR are used to successfully identify the magnon modes and their frequencies. The measurements are extended to the quantum limit by reducing the drive power until, on average, less than one photon is present in the CPWR. Investigating the time-dependent response of the system to square pulses, oscillations in the output signal at the mode splitting frequency are observed. These results demonstrate the feasibility of future experiments combining magnonic elements with planar superconducting quantum devices.
Treatment with Caffeic Acid and Resveratrol Alleviates Oxidative Stress Induced Neurotoxicity in Cell and Drosophila Models of Spinocerebellar Ataxia Type3
Authors: Wu Yu-Ling , Chang Jui-Chih , Lin Wei-Yong , Li Chien-Chun , Hsieh Mingli , Chen Haw-Wen , Wang Tsu-Shing , Liu Chin-San , Liu Kai-Li 
Published: September 2017

AbstractSpinocerebellar ataxia type 3 (SCA3) is caused by the expansion of a polyglutamine (polyQ) repeat in the protein ataxin-3 which is involved in susceptibility to mild oxidative stress induced neuronal death. Here we show that caffeic acid (CA) and resveratrol (Res) decreased reactive oxygen species (ROS), mutant ataxin-3 and apoptosis and increased autophagy in the pro-oxidant tert-butyl hydroperoxide (tBH)-treated SK-N-SH-MJD78 cells containing mutant ataxin-3. Furthermore, CA and Res improved survival and locomotor activity and decreased mutant ataxin-3 and ROS levels in tBH-treated SCA3 Drosophila. CA and Res also altered p53 and nuclear factor-κB (NF-κB) activation and expression in tBH-treated cell and fly models of SCA3, respectively. Blockade of NF-κB activation annulled the protective effects of CA and Res on apoptosis, ROS, and p53 activation in tBH-treated SK-N-SH-MJD78 cells, which suggests the importance of restoring NF-κB activity by CA and Res. Our findings suggest that CA and Res may be useful in the management of oxidative stress induced neuronal apoptosis in SCA3.
Bed bug aggregation on dirty laundry: a mechanism for passive dispersal
Authors: Hentley William T. , Webster Ben , Evison Sophie E. F. , Siva-Jothy Michael T. 
Published: September 2017

AbstractBed bugs have shown a recent and rapid global expansion that has been suggested to be caused by cheap air travel. How a small, flightless and anachoretic insect that hides within its host’s sleeping area manages to travel long distances is not yet clear. Bed bugs are attracted to the odour of sleeping humans and we suggest that soiled clothing may present a similarly attractive cue, allowing bed bugs to ‘hitch-hike’ around the world after aggregating in the laundry bags of travellers. We show that (1) soiled clothing is significantly more attractive than clean clothing to active bed bugs moving within a bedroom sized arena and (2) elevation of CO2 to a level that simulates human occupancy in the same arena appears to initiate search behaviour rather than direct it. Our results show, for the first time, how leaving worn clothing exposed in sleeping areas when travelling can be exploited by bed bugs to facilitate passive dispersal.
Inhibition of fucosylation by 2-fluorofucose suppresses human liver cancer HepG2 cell proliferation and migration as well as tumor formation
Authors: Zhou Ying , Fukuda Tomohiko , Hang Qinglei , Hou Sicong , Isaji Tomoya , Kameyama Akihiko , Gu Jianguo 
Published: September 2017

AbstractCore fucosylation is one of the most important glycosylation events in the progression of liver cancer. For this study, we used an easily handled L-fucose analog, 2-fluoro-L-fucose (2FF), which interferes with the normal synthesis of GDP-fucose, and verified its potential roles in regulating core fucosylation and cell behavior in the HepG2 liver cancer cell line. Results obtained from lectin blot and flow cytometry analysis clearly showed that 2FF treatment dramatically inhibited core fucosylation, which was also confirmed via mass spectrometry analysis. Cell proliferation and integrin-mediated cell migration were significantly suppressed in cells treated with 2FF. We further analyzed cell colony formation in soft agar and tumor xenograft efficacy, and found that both were greatly suppressed in the 2FF-treated cells, compared with the control cells. Moreover, the treatment with 2FF decreased the core fucosylation levels of membrane glycoproteins such as EGF receptor and integrin β1, which in turn suppressed downstream signals that included phospho-EGFR, -AKT, -ERK, and -FAK. These results clearly described the roles of 2FF and the importance of core fucosylation in liver cancer progression, suggesting 2FF shows promise for use in the treatment of hepatoma.