Coupled node similarity learning for community detection in attributed networks

© 2018 by the authors. Attributed networks consist of not only a network structure but also node attributes. Most existing community detection algorithms only focus on network structures and ignore node attributes, which are also important. Although some algorithms using both node attributes and network structure information have been proposed in recent years, the complex hierarchical coupling relationships within and between attributes, nodes and network structure have not been considered. Such hierarchical couplings are driving factors in community formation. This paper introduces a novel coupled node similarity (CNS) to involve and learn attribute and structure couplings and compute the similarity within and between nodes with categorical attributes in a network. CNS learns and integrates the frequency-based intra-attribute coupled similarity within an attribute, the co-occurrence-based inter-attribute coupled similarity between attributes, and coupled attribute-to-structure similarity based on the homophily property. CNS is then used to generate the weights of edges and transfer a plain graph to a weighted graph. Clustering algorithms detect community structures that are topologically well-connected and semantically coherent on the weighted graphs. Extensive experiments verify the effectiveness of CNS-based community detection algorithms on several data sets by comparing with the state-of-the-art node similarity measures, whether they involve node attribute information and hierarchical interactions, and on various levels of network structure complexity

Construction and analysis of a suppression subtractive hybridization (SSH) library of genic multiple-allele inherited male-sterility in Chinese cabbage (Brassica campestris L. ssp. pekinensis)

Utilization of male sterility is a key method for producing crossbred Chinese cabbage (Brassica rapa L. ssp. pekinensis (Lour.) Olsson. In this study, suppression subtractive hybridization (SSH) was used to construct sterility and fertility cDNA libraries, which included differentially, expressed clones between fertile and sterile buds of the A/B line ‘AB01’. The positive clones were randomly selected by polymerase chain reaction amplification (PCR) and 25 high quality sequences (22 from the fertile-tester library and three from the sterile-tester libraries) were generated. The fragment lengths varied from 77 to 469 bp. Differential expression patterns between fertile and sterile buds were selected and verified using five expressed sequence tags (ESTs). Results indicated that, three ESTs were expressed only in fertile buds and two ESTs were down-regulated in sterile buds. According to the Basic Local Alignment Search Tool (BLAST) screening and functional annotation, the 25 ESTs were homologous to known sequences deposited in National Center for Biotechnology Information (NCBI). These genes had homology to known proteins such as flowers/buds development proteins, metabolic-related proteins, cell structure proteins, cell growth/division proteins and secondary metabolic-related proteins. The results suggested that, these proteins played a critical role in nuclear male sterility progression of genic multiple-allele inherited male-sterility in Chinese cabbage.Key words: Chinese cabbage, male sterility, suppression subtractive hybridization (SSH), expressed sequence tags (ESTs)

Entanglement, subsystem particle numbers and topology in free fermion systems

We study the relationship between bipartite entanglement, subsystem particle number and topology in a half-filled free fermion system. It is proposed that the spin-projected particle numbers can distinguish the quantum spin Hall state from other states, and can be used to establish a new topological index for the system. Furthermore, we apply the new topological invariant to a disordered system and show that a topological phase transition occurs when the disorder strength is increased beyond a critical value. It is also shown that the subsystem particle number fluctuation displays behavior very similar to that of the entanglement entropy. This provides a lower-bound estimation for the entanglement entropy, which can be utilized to obtain an estimate of the entanglement entropy experimentally.Comment: 14 pages, 6 figure

Pathways to folding, nucleation events and native geometry

We perform extensive Monte Carlo simulations of a lattice model and the Go potential to investigate the existence of folding pathways at the level of contact cluster formation for two native structures with markedly different geometries. Our analysis of folding pathways revealed a common underlying folding mechanism, based on nucleation phenomena, for both protein models. However, folding to the more complex geometry (i.e. that with more non-local contacts) is driven by a folding nucleus whose geometric traits more closely resemble those of the native fold. For this geometry folding is clearly a more cooperative process.Comment: Accepted in J. Chem. Phy

Production of whey protein-based aggregates under ohmic heating

Formation of whey protein isolate protein aggregates under the influence of moderate electric fields upon ohmic heating (OH) has been monitored through evaluation of molecular protein unfolding, loss of its solubility, and aggregation. To shed more light on the microstructure of the protein aggregates produced by OH, samples were assayed by transmission electron microscopy (TEM). Results show that during early steps of an OH thermal treatment, aggregation of whey proteins can be reduced with a concomitant reduction of the heating chargeby reducing the come-up time (CUT) needed to reach a target temperatureand increase of the electric field applied (from 6 to 12 V cm1). Exposure of reactive free thiol groups involved in molecular unfolding of -lactoglobulin (-lg) can be reduced from 10 to 20 %, when a CUT of 10 s is combined with an electric field of 12 V cm1. Kinetic and multivariate analysis evidenced that the presence of an electric field during heating contributes to a change in the amplitude of aggregation, as well as in the shape of the produced aggregates. TEM discloses the appearance of small fibrillar aggregates upon the influence of OH, which have recognized potential in the functionalization of food protein networks. This study demonstrated that OH technology can be used to tailor denaturation and aggregation behavior of whey proteins due to the presence of a constant electric field together with the ability to provide a very fast heating, thus overcoming heat transfer limitations that naturally occur during conventional thermal treatments.The authors thank the Portuguese Foundation for Science and Technology (FCT) strategic project UID/BIO/04469/2013 unit, the project RECI/BBB-EBI/0179/2012 (FCOMP-01-0124FEDER-027462), and the project BBioInd - Biotechnology and Bioengineering for improved Industrial and Agro-Food processes^ REF. NORTE-07-0124-FEDER-000028 co-funded by the Programa Operacional Regional do Norte(ON.2–O Novo Norte), QREN, FEDER. The authors would like to acknowledge Rui Fernandes from the Institute for Molecular and Cell Biology (IBMC), University of Porto, for the assistance in taking the TEM pictures. The authors Ricardo N. Pereira and Oscar L. Ramos also acknowledge FCT for their post-doctoral grants with references SFRH/BPD/81887/2011 and SFRH/BPD/80766/2011, respectively

Doping Effect of Nano-Diamond on Superconductivity and Flux Pinning in MgB2

Doping effect of diamond nanoparticles on the superconducting properties of MgB2 bulk material has been studied. It is found that the superconducting transition temperature Tc of MgB2 is suppressed by the diamond-doping, however, the irreversibility field Hirr and the critical current density Jc are systematically enhanced. Microstructural analysis shows that the diamond-doped MgB2 superconductor consists of tightly-packed MgB2 nano-grains (~50-100 nm) with highly-dispersed and uniformly-distributed diamond nanoparticles (~10-20 nm) inside the grains. High density of dislocations and diamond nanoparticles may take the responsibility for the enhanced flux pinning in the diamond-doped MgB2.Comment: 16 pages, 6 figure

Influence of moderate electric fields on gelation of whey protein isolate

Proteins are one of the food constituents most affected by heating, and some of the changes involve their unfolding, denaturation and gelation. Ohmic heating has often been claimed to improve the quality of foodstuffs due to its uniform heating and (putative) presence of a moderate electric field (MEF). However, this is still subject to discussion, so it is important to determine the effect of ohmic heating and of its MEF upon food constituents. Hence, the aim of this work was to evaluate the effects of MEF on denaturation, aggregation and viscoelastic properties of whey protein isolate (WPI), and compare them with those obtained via conventional heating under identical treatment conditions (up to 30 min at 85 °C). Results have shown that MEF interferes with whey protein unfolding and aggregation pathways at relatively high temperatures. MEF treatments have resulted in WPI solutions possessing more 8 and 10% of native β-Lactoglobulin and α-Lactalbumin, respectively, after 30 s of heating at 85 °C, when compared with a conventional heating method. Protein aggregates from MEF-treated WPI solutions presented a maximum increase in size of 78 nm, whereas conventional heating produced an increase of 86 nm. Unlike in conventional heating, aggregation of whey proteins during MEF was not sufficiently strong to form a true elastic gel network, since decreases in both storage and loss modulus were observed following MEF treatment. Our results suggest that MEF may provide a novel method for production of a whey protein matrix with distinctive gel-forming properties.Ricardo N. Pereira and Oscar L. Ramos gratefully acknowledge their Post-Doctoral grants (SFRH/BPD/81887/2011 and SFRH/BPD/80766/2011, respectively) by Fundacao para a Ciencia e Tecnologia (FCT, Portugal). The authors thank the FCT Strategic Project PEst-OE/EQB/LA0023/2013 and the project "BioInd - Biotechnology and Bioengineering for improved Industrial and Agro-Food processes", REF. NORTE-07-0124-FEDER-000028 Co-funded by the Programa Operacional Regional do Norte (ON.2 - O Novo Norte), QREN, FEDER

Stress acts cumulatively to precipitate Alzheimer’s disease-like tau pathology and cognitive deficits

Stressful life experiences are likely tiological factors in sporadic forms of Alzheimer’s disease (AD). Many AD patients hypersecrete glucocorticoids (GCs), and their GC levels correlate with the rate of cognitive impairment and extent of neuronal atrophy. Severity of cognitive deficits in AD correlates strongly with levels of perphosphorylated forms of the cytoskeletal protein TAU, an essential mediator of the actions of amyloid Beta (ABeta ), another molecule with a key pathogenic role in AD. Our objective was to investigate the sequential interrelationships between these various pathogenic elements, in particular with respect to the mechanisms through which stress might precipitate cognitive decline. We thus examined whether stress, through the mediation of GCs, influences TAU hyperphosphorylation, a critical and early event in the cascade of processes leading to AD pathology. Results from healthy, wild-type, middle-aged rats show that chronic stress and GC induce abnormal hyperphosphorylation of TAU in the hippocampus and prefrontal cortex (PFC), with contemporaneous impairments of hippocampus- and PFC-dependent behaviors. Exogenous GC potentiated the ability of centrally infused ABeta to induce hyperphosphorylation of TAU epitopes associated with AD and cytoplasmic accumulation of TAU, while previous exposure to stress aggravated the biochemical and behavioral effects of GC in ABeta-infused animals. Thus, lifetime stress/GC exposure may have a cumulative impact on the onset and progress of AD pathology, with TAU hyperphosphorylation serving to transduce the negative effects of stress and GC on cognition.Marie Curie Training FellowshipsEU CRESCENDO Consortium contract FP6-018652University College, London.Max Planck Society and European Union (EU) German-Portuguese Luso-Alemas Program and the EU CRESCENDO Consortium (Contract FP6-018652).German-Portuguese Luso-Alemas Progra

The role of humic substances in drinking water in Kashin-Beck disease in China.

We conducted in vitro and in vivo assays in a selenium-deficient system to determine if organic matter (mainly fulvic acid; FA) is involved in a free radical mechanism of action for Kashin-Beck disease. Cartilage cell culture experiments indicated that the oxy or hydroxy functional groups in FA may interfere with the cell membrane and result in enhancement of lipid peroxidation. Experiments with rats demonstrated that toxicity from FA was reduced when the hydroxy group was blocked. Induction of lipid peroxidation by FA in liver and blood of rats was similar to that exhibited by acetyl phenyl hydrazine. FA accumulated in bone and cartilage, where selenium rarely concentrates. In addition, selenium supplementation in rats' drinking water inhibited the generation of oxy-free radicals in bone. We hypothesized that FA in drinking water is an etiological factor of Kashin-Beck disease and that the mechanism of action involves the oxy and hydroxy groups in FA for the generation of free radicals. Selenium was confirmed to be a preventive factor for Kashin-Beck disease

SN 2016coi/ASASSN-16fp: An example of residual helium in a type Ic supernova?

The optical observations of Ic-4 supernova (SN) 2016coi/ASASSN-16fp, from $\sim 2$ to $\sim450$ days after explosion, are presented along with analysis of its physical properties. The SN shows the broad lines associated with SNe Ic-3/4 but with a key difference. The early spectra display a strong absorption feature at $\sim 5400$ \AA\ which is not seen in other SNe~Ic-3/4 at this epoch. This feature has been attributed to He I in the literature. Spectral modelling of the SN in the early photospheric phase suggests the presence of residual He in a C/O dominated shell. However, the behaviour of the He I lines are unusual when compared with He-rich SNe, showing relatively low velocities and weakening rather than strengthening over time. The SN is found to rise to peak $\sim 16$ d after core-collapse reaching a bolometric luminosity of Lp $\sim 3\times10^{42}$ \ergs. Spectral models, including the nebular epoch, show that the SN ejected $2.5-4$ \msun\ of material, with $\sim 1.5$ \msun\ below 5000 \kms, and with a kinetic energy of $(4.5-7)\times10^{51}$ erg. The explosion synthesised $\sim 0.14$ \msun\ of 56Ni. There are significant uncertainties in E(B-V)host and the distance however, which will affect Lp and MNi. SN 2016coi exploded in a host similar to the Large Magellanic Cloud (LMC) and away from star-forming regions. The properties of the SN and the host-galaxy suggest that the progenitor had $M_\mathrm{ZAMS}$ of $23-28$ \msun\ and was stripped almost entirely down to its C/O core at explosion.Comment: Accepted for publication in MNRAS. Updated to reflect the published version, minor typographical changes onl