Distinct differences in community composition were found between 13C- and 12C-DNA-based communities and between two substrate-supplemented 13C-DNA-based communities; these differences distinctly varied with depth and site. In most cases, there were more genera with relative abundances of >0.1% in D-Glc-incorporating communities than in D-GlcN-incorporating communities. The Roseobacter clade was one of the prominent actively substrate-incorporating bacterial populations in all 13C-DNA-based communities. Vibrio was another prominent actively D-GlcN-incorporating bacterial population in most incubations. However notably, different OTUs dominated this clade or genus in different treatments at different depths. Altogether, these results suggested that there were taxa-specific differences in DOC assimilations and, moreover, their differences varied among the typical water masses, which could have been caused by the variant compositions of original bacterial communities from different hydrological environments. This implies that ecologically, the levels of labile or recalcitrance of DOC can be maintained only in a specific environmental context with specific bacterial community composition.To determine the adapted microbial populations to variant dissolved organic carbon (DOC) sources in the marine environment and improve the understanding of the interaction between microorganisms and marine DOC pool, field-based incubation experiments were carried out using supplemental  D-amino acid -AGAGTTTGATCMTGGCTCAG-3') and the unlabeled reverse primer 927R (5'-ACCGCTTGTGCGGGCCC-3') were used to amplify bacterial 16S rRNA genes [http://trex.biohpc.org/) [13C- and 12C-fractions were chosen for pyrosequencing.The 2g et al. . BrieflyNA genes , 35. PCRpc.org/) , 36 for 5'-AGAGTTTGATCCTGGCTCAG-3') and 534R (5'-ATTACCGCGGCTGCTGG-3'). In addition, a unique 10 bp barcode was used to tag each sample to enable multiplex sequencing. Each sample was amplified in triplicate to weaken the influence of specific amplification and with a negative control for each barcoded primer pair to verify samples were uncontaminated. Triplicate PCR products from each sample were combined, checked by electrophoresis on 1% agarose gel and purified with an agarose gel DNA purification kit . The quantity and quality of the combined products were checked using a NanoDrop device . Pyrosequencing was carried out on a 454 Genome Sequencer GS-FLX Titanium instrument  at the Chinese National Human Genome Center .PCR reaction mixtures and amplifying conditions for the V1–V3 region of bacterial 16S rRNA genes were in accordance with Zhang et al., using twww.mothur.org/wiki/Schloss_SOP) [screen.seqs” command was applied to remove those sequences whose lengths were outside the desired range and “filter.seqs” command applied to remove those columns with only gaps. Those sequences within 2 bp of difference to a more abundant sequence were merged with “pre.cluster” command for reducing sequencing error. Chimeras were identified and removed using “chimera.uchime” and “remove.seqs” commands, respectively. These processes avoided superfluous computations, as much as possible, for the following commands below. Finally, classification was carried out using the MOTHUR version of the “Bayesian” classifier with the SILVA reference sequences and taxonomic outline. The confidence cut-off was set to 60%. The sequences that were classified as “Cyanobacteria_Chloroplast” or “Mitochondria” or could not be classified at the kingdom level were removed from the data set.The criteria previously described  were useoss_SOP) . Brieflyoss_SOP)  using “aSequences were further clustered into Operational Taxonomic Units (OTUs) using the furthest-neighbor algorithm and the cutoff value set at 0.03 . All theRoseobacter and Vibrio in the present study) and its relative abundance was >1% of total reads in any 13C-DNA library were phylogenetically analyzed. Sequences were compared to known 16S rDNA sequences in the database using the BLASTN search (http://www.ncbi.nlm.nih.gov/BLAST/) to aid the selection of the closest reference sequences. Sequences were aligned and compiled using the MEGA5 program and neighbor-joining phylogenetic trees were constructed.Representative sequences from each OTU that fell in the most prominent actively substrate-incorporating bacterial populations  + 1.66.13C-DNA from incubations with 13C-labeled substrate supplementation peaked in the density range from 1.73 to 1.743 g∙mL-1, corresponding to the 4th–5th density fractions, while 12C-DNA peaked from 1.693 to 1.705 g∙mL-1, corresponding to the 10th–11th fractions  to 11th (light) density gradient fractions were analyzed with T-RFLP. In general, the community structure showed distinct differences between heavy and light fractions of each sample. In the 13C-D-GlcN supplemented seawater-incubation experiment at 0 m of site D001, for instance, the cluster analysis of communities from the 10 density gradient fractions revealed three distinct groups at 44.07% Bray-Curtis similarity level: heavy group , light group , and middle group  density ranges, the typical middle DNA  between them, and the extremely heavy DNA  were selected for 454 pyrosequencing and further analysis. The selected density fractions for each sample according to the same means are shown in 13C-labeled substrates, only the H2 fraction from each sample was selected and analyzed together with the light fraction.Among the 12 density gradient fractions, the 213C-labeled D-Glc at 0 m of site D001, were generally higher than heavy fractions (H2s) in each incubation  and from 74.4% to 94.5% , respectively. Diversity indexes  showed that the bacterial diversity of light fractions (L), except for the incubation with supplemental cubation  Tables. 13C-labeled substrates and light fractions representing populations not incorporating 13C-labeled substrates were analyzed with dendrogram. At the coastal site D001, 12C-DNA-based communities clustered together with in situ communities, there being two subclusters at 0–25 m and 70 m, respectively. In general, 13C-DNA-based communities clustered separately according to the two supplemented 13C-labeled substrates, but D-Glc-incorporating communities at 0 m separated from those at 25 and 70 m and D-GlcN-incorporating communities at 70 m separated from those at 0 and 25 m  where two 12C-DNA-based communities and the in situ community clustered together. In addition, 12C-DNA-based community at 200 m separated from 13C-DNA-based communities at 5 and 200 m within the D-Glc cluster; D-GlcN-incorporating communities at 5 m distinctly different from that at 200 m within the D-GlcN cluster  were the most abundant populations incorporating D-Glc at all three depths for site D001. Rhodobacteraceae Donghicola also accounted for >10% of 13C-DNA sequences at 0 and 25 m. For D-GlcN-incorporating organisms, the Roseobacter clade was a highly active population, accounting for >80% of total 13C-DNA sequences at 0 and 25 m and >15% at 70 m of site D001. Vibrio also accounted for >10% at 70 m. It was clear that there were more genera with relative abundances of >0.1% in D-Glc-incorporating communities than in the D-GlcN-incorporating communities  and many unclassified taxa belonging to Rhodobacteraceae (>10%) were the most abundant populations incorporating D-Glc at 5 and 200 m depths. However, for D-GlcN-incorporating organisms, Vibrio was the most abundant population  at the two depths. The Roseobacter clade and Thalassobius (>10%) were also relatively active at 5 m. There were more genera with relative abundances of >0.1% in D-Glc-incorporating communities than in D-GlcN-incorporating communities at 5 m, and on the contrary at 200 m  were used in incubation experiments for stimulating cellular growth. However, high substrate concentrations might lead to a fundamentally different metabolic characteristic of DOC incorporation compared with in situ or lower concentrations [12C-DNA-based communities showed relatively high similarities with their corresponding in situ communities after incubation suggesting that the results on differential incorporation of 12C vs. 13C into microbial community are reliable. In addition, the isotope fractionation effect in the incubation systems are neglectable in the concentrations of supplemented isotopic substrates. Secondly, the incubation time was set at 3 d, during which a cross-feeding effect might have occurred among the organisms. However, 3 d of incubation time has been normally used in seawater SIP experiments for obtaining sufficient 13C-labeled DNA [As sufficient trations , 44. Eveeled DNA , 44. In eled DNA , 31. How12C- than 13C-DNA-based communities in each incubation suggested that microbial populations that were adapted to the supplemented organic substrate accounted for only a small part of total bacterial community composition. Also, 12C-DNA-based communities showed relatively high similarities with their corresponding in situ communities and were distinctly separated from 13C-DNA-based communities. As revealed by the dendrograms, there were distinct differences in community composition between 13C-DNA-based communities in incubations supplemented with 13C-labeled D-Glc and D-GlcN  were found in D-Glc-incorporating communities than in D-GlcN-incorporating communities. The Roseobacter clade was one of the prominent actively substrate-incorporating bacterial populations in 13C-DNA-based communities. This result was consistent with the conclusion that Roseobacter dominates the incorporation of high concentration glucose and amino acids in the German Bay of the North Sea [Roseobacter must bloom when incubated because of a “bottle effect” [Roseobacter has revealed that they have versatile mechanisms for energy and carbon acquisition in various environments, behaving as an “ecological generalist” [Roseobacter thrived in all of the present incubations. It was clear that Roseobacter might have played an important role here in DOC transformation and the oceanic carbon cycle. However notably, different OTUs dominated this clade in different incubations from different depths.In most cases, there were more genera with relative abundances of >0.1% in orth Sea . Thus fa effect” . Genomiceralist” –48. ThisVibrio was another prominent actively D-GlcN-incorporating bacterial population, as expected. Vibrio is an important oceanic chitinolytic bacteria, depolymerizing chitin with cell surface hydrolases to GlcNAc for better use [Vibrio plays a significant role in oceanic nutrient cycling [Vibrio did not thrived at 0 and 25 m of site D001 among all 13C-D-GlcN supplemented incubations of the two sites. This could be caused by distinctly different original bacterial communities Click here for additional data file.S2 Table(DOC)Click here for additional data file.S3 Table(DOC)Click here for additional data file.


The adhesive system of geckos has inspired hundreds of synthetic adhesives. While this system has been used relentlessly as a source of inspiration, less work has been done in reverse, where synthetics are used to test questions and hypotheses about the natural system. Here we take such an approach. We tested shear adhesion of a mushroom-tipped synthetic gecko adhesive under conditions that produced perplexing results in the natural adhesive system. Synthetic samples were tested at two temperatures (12 °C and 32 °C) and four different humidity levels . Surprisingly, adhesive performance of the synthetic samples matched that of living geckos, suggesting that uncontrolled parameters in the natural system, such as surface chemistry and material changes, may not be as influential in whole-animal performance as previously thought. There was one difference, however, when comparing natural and synthetic adhesive performance. At 12 °C and 80% RH, adhesion of the synthetic structures was lower than expected based on the natural system’s performance. Our approach highlights a unique opportunity for both biologists and material scientists, where new questions and hypotheses can be fueled by joint comparisons of the natural and synthetic systems, ultimately improving knowledge of both. Principally known for strong, reversible, and dry adhesion134678910111213141516et al. tested whole animal shear adhesion of live geckos at two temperatures and a series of humidity levels3520and temperature, and this debate has been relatively quiet for years.One major challenge to fully resolving how geckos stick is also the most obvious: geckos are biological organisms and thus have inherent variability and complexity. Specifically, the biological adhesive system is likely adapted to work in multiple contexts and under a variety of circumstances, which may in turn mean that the system is not optimized to work maximally in any one condition. This versatility can be a useful property for synthetic adhesives, but can also be a central problem when designing tests to better elucidate the properties of the natural adhesive system. Take the case of capillary adhesion. The role of capillary adhesion has surfaced in the literature multiple times. In 2002, Autumn and colleagues dispelled the idea that capillary adhesion could be playing a significant role in gecko adhesion by showing that geckos were able to stick to both hydrophobic and hydrophilic substrates equally well during shear sliding27Using the capillary adhesion example, it is quite clear that the context in which adhesion occurs is critical. Load, sliding velocity, level of humidity, temperature, presence of water, dynamic surface groups, and other parameters can impact adhesion. Furthermore, whole animal studies are consistently different than those testing single spatula, setae, and setal arrays37383940et al. used for whole animal experiments, which consisted of measuring maximum shear adhesion of live geckos on a glass plate at two temperatures (12 °C and 32 °C) and four different humidity levels In this study, we tested shear adhesion of a high performing mushroom-tipped gecko-inspired synthetic and used it to probe the effect of humidity and temperature on a dry fibrillar adhesive. We replicated the conditions Niewiarowski 8,39 = 11.47, p < 0.0001; There was a significant effect of temperature and humidity on shear adhesion of the gecko-inspired synthetic microfibers . When investigating temperature and humidity independently, we found that the two temperatures tested had significantly different behavior , where samples tested at 32 °C had all three behavior types  and those tested at 12 °C only had two (SS and V). Humidity had no significant effect on adhesion behavior when considered independently .We defined three adhesion behavior types from the experimental force profiles. First, some force profiles exhibited a “U” shape (U), where maximum adhesion occurred at some point in a smooth “U” shaped curve. This profile suggests that sliding friction is greater than static friction. Second, some force profiles exhibited a “V” shape (V), where maximum adhesion occurred at the apex of the “V”. This profile implies static friction is stronger than sliding friction. Finally, the third type of force profile was “Stick-Slip” (SS), where maximum adhesion occurred during periodic stick-slip events. In this profile static and sliding fiction are intermittent and dynamic, where in periods of stick, static friction is dominant, and in periods of slip, sliding friction is dominant. Some samples showed multiple behaviors in one test, thus behavior was assigned based on where the maximum force value occurred. Examples of all three force profiles are shown in et al.Our work represents one of very few examples using a gecko-inspired synthetic microfiber array to probe questions about the natural gecko adhesive system. Results from both the natural system and the synthetic system are strikingly similar: adhesion only increases with increasing humidity at cool temperatures. In the biological system several hypotheses have been proposed, but not yet resolved, for the effect of humidity on adhesion. First, the reduction of setal modulus increases available contact area by allowing the setae to become more compliant and flexible, thus adhesion increases at high humidity (>80% RH). Second, surface restructuring causes an increase in adhesion in the presence of water . Finally, non-independent from the change in modulus hypothesis, material swelling may occur , causing an increase in contact area and therefore adhesion. Unfortunately, none of these hypotheses can be completely independently tested in the natural system , where temperature was the only significant effect driving this difference (p = 0.0007). Modulus at the 12 °C temperature set point was significantly higher than the modulus measured at 32 °C . This means that overall, temperature influences the synthetic modulus but humidity does not, suggesting that the temperature by humidity interaction observed in adhesion tests of the synthetic is not driven by changes in modulus. Furthermore, given the increase in modulus at 12 °C, we would expect the opposite adhesion results, where shear adhesion would reduce at cold temperatures rather than improve. It is important to note the modulus of gecko setae is higher than the synthetic (~2 GPa)The first, and most dominant hypothesis, is the reduction of setal modulus in high humidity (>80%)3536423,45 = 0.35, p = 0.7929), suggesting that no significant surface restructuring occurred in the synthetic adhesive. Contact angle for a smooth sheet of the fiber material yields a contact angle of 78.5 ± 1.4° at room temperature and humidity, which is within the range of what is expected for the natural system based on measurements and theoretical calculations (70–90°)19et al.Similar to the first hypothesis, we expected the second and third hypotheses (surface group restructuring and swelling) to have no major effect on adhesive performance of the synthetic. To test this, we again utilized the synthetic and investigated changes in contact angle and weight in high humidity to confirm that the synthetic material was stable during adhesion tests. To test the second hypothesis, we measured the contact angle of water on the smooth backing material in four of the eight treatments used in adhesion tests (12 °C and 32 °C at ~35% RH and 80% RH). Contact angle was averaged over three measurements per sample using ImageJ to analyze images from a custom goniometer. At least 10 samples were used per treatment and all were held in the test environment for at least 1 hour. We found no significant change in water contact angle across the treatments . One alternative may be to reconsider the influence of adsorbed water on shear adhesion. Water can influence shear adhesion by two main mechanisms. First, adsorbed water layers may lubricate the contact interface and reduce shear adhesion and friction. Secondly, capillary bridges may form between the contact elements and the substrate and increase normal adhesion. Both mechanisms can change as humidity increases, however, why increased shear adhesion of the natural and synthetic systems occurs only at cool temperatures is not explained completely by either mechanism. In whole animal experiments surface water on a hydrophilic glass surface, like the one used here, produced significantly reduced adhesion at room temperature484950While there are startling similarities between the natural and the synthetic systems, is also important to investigate where these two systems differ. One clear difference between the synthetic and natural system adhesion results is at 12 °C and 80% RH. In the natural system, adhesion was almost twice as high at 12 °C and 80% RH as compared to the low humidity trials at 12 °C and 35% RHFinally, this experiment also highlights the ability of a synthetic gecko-inspired mushroom-tipped adhesive to adhere in a variety of environmental conditions. Specifically, while temperature effects on pressure sensitive adhesives (PSAs) have been investigated previously53In summary, by comparing the natural and synthetic systems’ performance and adhesion behavior, we are able to offer a new perspective on experiments focusing on gecko adhesion at the whole animal scale. First, we found that several of the prevailing hypotheses about how geckos stick in humid environments may not be viable. Our results once again call into question the roles of capillary adhesion and interfacial water layers in the gecko adhesive system. Secondly, by investigating the particular temperature and humidity regime where the systems differ, our understanding of the natural adhesive system will improve, as well as produce ideas for design parameters that can increase synthetic performance in conditions where the natural system has higher performance. Thirdly, the stability of this adhesive in challenging environmental conditions, such as high temperature and humidity, has several applications to real-world adhesive use and commercialization. Finally, we hope our work inspires further investigations into how synthetic designs can improve the type of questions we ask about the natural adhesive system, creating an “idea feedback loop” between the natural and synthetic system, both of which have been generally tested independently.et al.2. Each sample was imaged independently both before and after experimental trials to check for defects and experimental damage. Samples were attached to a glass slide with mushroom caps facing upward using a cyanoacrylate gel adhesive that was slightly cured prior to attachment, making sure the gel adhesive did not cover the sample. A controlled weight (174.5 g) was placed on the sample before a protective backing layer was removed from the pillar caps. This pre-weight was used to ensure that the samples had been fully pressed into the glue and were horizontally level. No sample was used more than once and samples that had premature loading (prior to testing or during testing in a non-controlled way) were discarded.A polyurethane elastomer mushroom-tipped synthetic gecko-inspired adhesive was obtained from Carnegie Mellon University. Samples were manufactured using methods similar to those outlined by Murphy et al.et al. for a schematic). The weighted glass side was pulled across the sample in the shear direction for about 4 cm at a controlled rate. The glass slide was cleaned with ethanol and water after each sample and dried with a Kimwipe. Force was recorded over time and maximum force was determined from the force curve post-experiment. Adhesion behavior was also characterized post-experiment using the force curves. All experiments were conducted in an environmentally controlled walk-in chamber set to either 12 °C or 32 °C and all experiments were conducted within ±2 °C of this range. Humidity was controlled within ±2% of the following set points: 30%, 55%, 70% and 80% RH. Each of the four humidity set points were tested at the two temperature settings, totaling eight different treatments. All samples were equilibrated to the treatment temperature and humidity for at least 1 hour prior to experiments.Each sample slide was placed in a test arena as described in Badge Samples were tested semi-randomly. The effect of temperature, humidity, and their interaction on shear adhesion was tested using an analysis of covariance (ANCOVA) where area was used as a covariate. Individual comparisons across groups were done using a Tukey HSD test to control for multiple tests. To compare adhesion behavior across temperature and humidity we used a Pearson Chi-square test. Means are reported mean ±1 s.e.m.The raw data are provided in the How to cite this article: Stark, A. Y. et al. The effect of temperature and humidity on adhesion of a gecko-inspired adhesive: implications for the natural system. Sci. Rep.6, 30936; doi: 10.1038/srep30936 (2016).


Recently, quantum Hall state analogs in classical mechanics attract much attention from topological points of view. Topology is not only for mathematicians but also quite useful in a quantum world. Further it even governs the Newton’s law of motion. One of the advantages of classical systems over solid state materials is its clear controllability. Here we investigate mechanical graphene, which is a spring-mass model with the honeycomb structure as a typical mechanical model with nontrivial topological phenomena. The vibration spectrum of mechanical graphene is characterized by Dirac cones serving as sources of topological nontriviality. We find that the spectrum has dramatic dependence on the spring tension at equilibrium as a natural control parameter, i.e., creation and annihilation of the Dirac particles are realized as the tension increases. Just by rotating the system, the manipulated Dirac particles lead to topological transition, i.e., a jump of the “Chern number” occurs associated with flipping of propagating direction of chiral edge modes. This is a bulk-edge correspondence governed by the Newton’s law. A simple observation that in-gap edge modes exist only at the fixed boundary, but not at the free one, is attributed to the symmetry protection of topological phases. Graphene47891011131415161718192022In this paper, a honeycomb spring-mass model1827mR denotes a lattice point, and a is a sublattice index.Mechanical graphene consists of mass points with mass nts. See . Motion l is the length of the spring at that moment, In mechanical graphene, the elastic energy cost for finite η controls the relation between the restoring forces for with η. In contrast, the motion in parallel with the spring direction, which corresponds to a longitudinal mode, is not affected by η as far as good linearity of the springs is assumed, since with good linearity, the elastic energy has a constant second derivative with respect to the spring deformation.The physical meaning of the last statement is illustrated in Having this in mind and assuming the periodicity of the system, we introduce new dynamical variables where ω-spectrum is obtained by diagonalizing and nd . See . Practicη in a wide range in real graphene. Furthermore, the effective model for graphene phonon does not respect the “chiral symmetry”, which plays important roles in topological characterization. This is because if the vibration in graphene is modeled by a spring-mass model, it requires springs connecting the next nearest neighbor sites and more.Now, the problem is quite similar to the phonon problem in graphene30313233η dependence of the ω-spectrum [p-orbital honeycomb lattice modelω-dispersion for η becomes less than 2/3, two new Dirac cones other than those at the K- and K’- points appear on M-K lines. [See η approaches to zero. For small η where the new Dirac cones get close to the K- and K’-points, the dispersion relation looks like the one for bilayer graphene with trigonal warpingx- and y-direction decouple, which leads to the two-fold degeneracy.Now, we follow the spectrum . ThroughSee Ref. . Note thlat. At  , the gapnes. See . Due to  warping , the newThe transition at d is spatial dimension, where π for the spinless casewhere Therefore, the Herring number has an ability to detect the number of Dirac cones. This idea has been applied to the 2D organic Dirac fermion systems41at the M-point are indicated for each band. We notice that at Next, we see edge states using ribbon geometry with zigzag edges. In this case, the equation to be solved is similar to equation The difference in momenta along the edge is reflected in the oscillation pattern in the real space. In order to convince this expectation we perform a calculation using a rectangular system with long zigzag edges and short armchair edges. In ω-spectrum for nonuniform diagonal elements in In order to see the importance of the boundary condition, the Lastly, we break the time reversal symmetry by uniform rotation as a whole with angular frequency Ω, which brings two new forces, the centrifugal and the Coriolis force. For simplicity, only the Coriolis force, which is first order in Ω, is taken account of since the centrifugal force, which is second order in Ω, is negligible for small Ω. The equation of motion becomeswhereω-spectrum is obtained by evaluating ω, η less than It is no longer possible to reduce the problem to diagonalization of C asFor the topological analysis of this gap closing and opening, we define the Chern number C can be evaluated with a well established numerical methodη is reduced, the Chern number jumps from 1 to −2 at The summation is taken over In order to have a vivid view on this topological transition, we perform a calculation on a triangular system with zigzag edges. The Chern number for the mechanical system itself is not a physical observable but the corresponding edge states reflecting nontrivial bulk can be observed experimentallywhere and which is explicitly evaluated by diagonalizing The selected snapshots of the time evolution for Before closing, we make a comment on the effects of dissipation. Assuming that the frictional force is proportional to the velocity, the effects of friction are easily incorporated by slightly modifying To summarize, we first propose a simple and feasible way, uniform stretch of the system, to control the vibration spectrum of mechanical graphene. An interesting point of the proposed procedure is it does not involve symmetry breaking, but we observe generation, migration, and creation of Dirac cones. It is also shown that the transitions associated with the motion of Dirac cones are detected by observing real space pattern of the edge modes. For the case without the time reversal symmetry, an intimate relation between the bulk topological number and chiral edge modes in a mechanical system is established, which indicates universality of the bulk-edge correspondence, which is one of the most important concepts in the topological approach. In addition, the boundary condition dependence of the edge modes is explained in terms of the symmetry protection of the topological state, which reveals new aspect of the symmetry in classical mechanical systems.How to cite this article: Kariyado, T. and Hatsugai, Y. Manipulation of Dirac Cones in Mechanical Graphene. Sci. Rep.5, 18107; doi: 10.1038/srep18107 (2015).


We investigate the interactions between two identical magnetic impurities substituted into a graphene superlattice. Using a first-principles approach, we calculate the electronic and magnetic properties for transition-metal substituted graphene systems with varying spatial separation. These calculations are compared for three different magnetic impurities, manganese, chromium, and vanadium. We determine the electronic band structure, density of states, and Millikan populations (magnetic moment) for each atom, as well as calculate the exchange parameter between the two magnetic atoms as a function of spatial separation. We find that the presence of magnetic impurities establishes a distinct magnetic moment in the graphene lattice, where the interactions are highly dependent on the spatial and magnetic characteristic between the magnetic and carbon atoms, which leads to either ferromagnetic or antiferromagnetic behavior. Furthermore, through an analysis of the calculated exchange energies and partial density of states, it is determined that interactions between the magnetic atoms can be classified as an RKKY interaction. For the last century, the vast increase in technological capabilities has been largely governed by the ability of devices to manipulate and control charge in various materials. However, charge is not the only property of electrons that can be exploited for technological use. Within the last decade, there has been a surge in the number of devices and materials that work to control, not only charge, but also the electron spin degree of freedom. This evolution has brought about the area of spintronics1234567The use for spintronic devices varies dramatically due to the multitude of interesting phenomena they exhibit. This includes spin relaxation and transport that may be used for quantum computation671012The most popular example of a 2D material is that of graphene1517181920214914p-orbital (π) bondingK-point of the Brillouin zone  methods. The process of removing individual carbon atoms from the graphene lattice was recently demonstrated by Gomes In this article, we present a comparative computational study examining the changes in the electronic and magnetic properties of transition-metal substituted graphene. Starting from a 128-atom supercell of graphene, two carbon atoms are replaced with either vanadium (V), chromium (Cr), or manganese (Mn) impurities. The magnetic impurities are considered for various spatial separations of N carbon (C) atoms (N = 1–6) in between the magnetic atoms along the zig-zag chain direction in graphene. Using density functional calculations with a full geometry optimization and spin polarization, we performed calculations to determine the total energy ground state, electronic band structure, density of states (DOS), and magnetic moment for each spin configuration. Overall, it is determined that the presence of magnetic atoms induces a magnetic state in the graphene, where the partial density of states shows a distinct increase in electron mobility at the Fermi level producing a metallic state. Additionally, we map the magnetic moment for each atom in superlattice to examine the magnetic exchange (or super-exchange) interaction characteristics throughout the graphene layer. Overall, this study provides clarity on how the magnetic atoms are communicating through graphene layer as well as helps in the understanding of the super-exchange interactions between the impurity atoms.Furthermore, through an analysis of the calculated exchange energy between the magnetic atoms, we find that the interaction alternates between a ferromagnetic and antiferromagnetic state as the magnetic atoms are separated spatially. This, in combination with the metallic state in the carbon, illustrates and suggests the presence of an RKKY exchange interaction. An RKKY (Ruderman-Kittel-Kasuya-Yosida) interaction is an indirect exchange coupling that is governed through interaction of localized spin moment and conduction electrons3839We conducted simulations on magnetically-substituted graphene lattice to see how the presence of magnetic atoms would affect the electronic and magnetic structure in the system. Therefore, we replaced two carbon atoms with vanadium, chromium, or manganese in a symmetric dimer configuration. Through DFT simulation of the formation energy, it was determined that graphene with magnetic atom substitution is energy favorable over a pure graphene state. To examine the formation energy, we determined the total energy for a pure graphene sheet with a unbound magnetic atom  and compared that to a graphene sheet with a bound magnetic atom and a free carbon . Here, it is found that the magnetic substitution is energy favored by about 8 eV. This is most likely due to the number of electrons that can be shared by the magnetic atoms over the carbon.To examine the electronic and magnetic interactions, we started with two atoms separated by a single carbon atom, and then separating them by one carbon along the zig-zag chain of graphene until there were six carbon atoms between the magnetic atoms . This alThe presence of the magnetic atoms produce a distinct distortion in the graphene lattice. This distortion is shown in 21Focusing mainly on chromium, μB respectively. Here, μB is the Bohr magneton. μB, which is mainly produced by the vanadium atoms maintaining a constant ferromagnetism. However, the net magnetic moment of the entire lattice structure tends to fluctuate for chromium and manganese as the magnetic atoms flip between FM and AFM ground states. With respect to the electronic bandstructure, the competition between the interactions of the magnetic atoms and carbon atoms have distinct consequences on the presence of Dirac cone, which is the staple characteristic of pure graphene. It is clear that all of the odd carbon spacing , Mn4+ (high-spin state S = 3/2), and V4+ (S = 1/2) produced mainly from sharing three valance electrons with the graphene lattice. These spin states are minimum approximations for the local magnetic moments. The use of an on-site potential may increase these values. However, this shows that magnetic moment is shared with the surrounding carbon atoms.From Therefore, the addition of magnetic atoms produces a net magnetic moment in the graphene lattice around the atoms, which leads to better conduction and an overall super-exchange. This exchange can be quantified by examining the change in the total energy of the FM (↑↑) state and the AFM (↑↓) state. Using a standard Heisenberg Hamiltonian for an independent dimerSi is the quantum mechanical spin for sites i = 1, 2, it can be determined that the change in energy (ΔE) from the FM and AFM state is simply proportional to the exchange energy J42where JV−C (the exchange between vanadium and carbon) is dominant over JC−C (the exchange between carbon atoms). Therefore, vanadium is able to force the carbon moments into a configuration that works to maintain JV−V > 0.Depending on the coupling between the magnetic atoms and the carbons, magnetic frustration could be the cause of the variation between the FM and AFM characterization. As shown in JC−C seem to dominate JCr−C, since the JCr−Cr alternates through between FM and AFM, which is similar for manganese. These interactions seems to indicate the presence of an RKKY exchange through the graphene lattice. However, in order to have an RKKY interaction, the graphene needs to have a metallic DOS at the Fermi level, which is established in This effect is different for chromium  and manget al. using a standard exchange model with the spin-orbit couplingd transition-metal atoms, spin-orbit coupling can be assumed to be negligible. Therefore, we find that the presence of magnetic transition-metal atoms produces multiple electron bands at the Fermi level beyond the standard Dirac cone crossing, and that there are distinct correlations between magnetic atoms  and separated until there are six carbons in between (6C) the magnetic atoms. Using a generalized-gradient approximation density functional theory with a full geometry optimization and spin polarization, we performed calculations to determine the total energy ground state, electronic band structure, density of states (DOS), and magnetic moment for each configuration.Through an analysis of the total energy for the different magnetic configurations, the super-exchange interaction between magnetic atoms is shown to alternate between antiferromagnetic and ferromagnetic state as a function of impurity distance. Additionally, we examine the spatially dependent magnetic moment for each atom in the superlattice and discover that the carbon atoms within close proximity to the magnetic atoms gain a distinct magnetic moment. The magnetic carbon atoms produce a complex network of exchange interactions. Through an analysis of the partial density of states for the carbon atoms, a distinct increase in electron mobility at the Fermi level is shown. Therefore, the calculation of a variable super-exchange with spatial distance and the transition to a more metallic state for the carbons in between the magnetic atoms indicates the presence of an RKKY-like super-exchange interaction through the graphene atoms.in-situ substitution and induced magnetism in graphene shows the increased possibility of using graphene for spintronic materials. These calculations are meant as the motivation for the use of magnetically-doped graphene and other 2D materials for the possible advancement for spintronic devices and quantum computation.Further investigation is needed to understand the induced magnetic moment in carbon and the exchange network between the magnetic atoms. Given the advancements in STM and nanoscopic enhancements of atomic substitutions in graphene, experimental exploration of these interactions is a distinct possibility. The presence of variable magnetic exchange due to k-sampling was for purposes of computational time given that extent and number of calculations being performed. Geometry optimizations performed with the higher k-point sampling showed no significant difference.Using Atomistix Toolkit4546μeV with an energy cut off of 2 keV. As shown in Santos et al.We implemented initial spin states of up-up (↑↑), up-down (↑↓), and down-down (↓↓) configurations on the magnetically-substituted atoms and zero spin on the carbon atoms, which was established through non-substituted test runs on pure graphene. As expected, the configurations of ↑↑ and ↓↓ were found to be degenerate. In all, we perform calculations on 54 total configurations . The DFT calculations were run using a tolerance of 0.3 K point in the Brillouin zone, and we also map the induced magnetic moments for each atom to examine the interactions throughout the graphene supercell.In all, we calculated the total energy of each system to find the ground state configuration assuming collinear polarized spins and estimated the exchange parameters between the two magnetic atoms. Furthermore, we determined the electronic band structure and density of states (DOS) to investigate the magnetic effect on the graphene Dirac cone at the How to cite this article: Crook, C. B. et al. Proximity-induced magnetism in transition-metal substituted graphene. Sci. Rep.5, 12322; doi: 10.1038/srep12322 (2015).


We investigate the absorption properties of graphene-based anisotropic metamaterial structures where the metamaterial layer possesses an electromagnetic response corresponding to a near-zero permittivity. We find that through analytical and numerical studies, near perfect absorption arises over an unusually broad range of beam incidence angles. Due to the presence of graphene, the absorption is tunable via a gate voltage, providing dynamic control of the energy transmission. We show that this strongly enhanced absorption arises due to a coupling between light and a fast wave-mode propagating along the graphene/metamaterial hybrid. These artificial hybrid structures have been shown to allow propagation of electromagnetic (EM) waves through narrow369111214E) or magnetic (H) responses.With the refinement and advancement of fabrication techniques and theoretical methods, it is now possible to successfully create anisotropic metamaterial structures that have at least one vanishing principal component of the permeability EF. When EM waves interact with a graphene sheet, the gate voltage can tune the amount of energy that gets absorbed, depending on the relevant scattering processes, temperature, relaxation time, frequency of the incident beam and its polarization.These developments have led to a significant number of recent works devoted to studying graphene as a component in hybrid metamaterial designsε describing the anisotropic response has components that are near zeroBy placing graphene in contact with an anisotropic metamaterial that has vanishing principal components of the permittivity and permeability tensors over the frequencies of interest, one could expect the interplay between the two samples to present additional possibilities regarding the transmission of the light. More specifically, we pose the question if it is possible to utilize the dynamic and tunable conductivity of graphene to yield greater control over the way energy of EM waves is absorbed or reflected compared to when the materials are in isolation. Motivated by recent experimental and theoretical developments, we seek to establish if one may obtain tunable wide angle absorption in hybrid graphene/metamaterial layers where the tensor ε near-zero (ENZ) response, where the metamaterial has a vanishingly small value of the real part of ε. In contrast to numerous past works in the RF and visible light regime, we focus here on operational wavelengths that correspond to the less exploited THz regime, where many new technologies are emerging. To accurately determine the absorption as a function of the geometrical and material parameters that describe graphene and the metamaterial, Maxwell’s equations are solved using a transfer matrix approach that accounts for the presence of graphene through boundary conditions imposed on the magnetic field. We discuss the behavior of the absorption in terms of the energy flow throughout the entire structure.To this end, we consider here the absorption characteristics of a layered system, comprised of monolayer graphene overlaying a metamaterial slab that is connected to a perfectly conducting metal. In accordance with the discussion above, we will consider metamaterial structures that can possess an EF, we are able to determine experimentally relevant regimes where near perfect absorption can occur over an extremely wide range of incident angles for an ENZ metamaterial layer that has a small component of the permittivity tensor. We show that the enhanced absorption occurs due to coherent perfect absorption which couples light to a fast wave propagating along the graphene/ENZ hybrid.Our main result is that by tuning p-polarized incident light  ≠ 0. In the anisotropic medium (region 2), the nonzero components to the tensors are . It is backed by a perfect electric conductor (PEC) in region 1, where no electric or magnetic fields exist. The finite surface conductivity σ of graphene will be effectively taken into account in the boundary condition for the magnetic field H at the interface between air (region 3) and the anisotropic medium, whereThe principal coordinate axes are chosen so that both the permittivity and permeability tensor in the anisotropic medium are both diagonal. A diagram of our setup is shown in EF ≫ kBT, ħω, we have,When T of 300 K, and THz frequencies, we have kBT = 25 meV, and ħω ~ 1 meV, meaning doping levels should exceed EF = 100 meV when using EF is the Fermi energy, ω is the frequency of the EM wave, and trel is the relaxation time. For frequencies in the THz region and lower, Thus, at a temperature p-polarized incident light and diagonal tensors, we obtain the following set of equations determining the components of the fields when the time-dependence is harmonic (et−iω):We now consider Maxwell’s equation (in SI units) in the incident air region and in the anisotropic medium, both having no free charges or currents. For kx is conserved due to translational invariance. The Methods section contains additional details of the numerical and analytical solutions of the above equations.These equations are solved with a plane-wave ansatz for the field components where A2 and B2 are associated with the transmitted and reflected electric field wave in region 2 whereas B3 ≡ r is the coefficient for the reflected wave in region 3. Since there is no transmission into the PEC layer, the absorbance r is obtained asOnce the equations have been solved, one may compute the absorption where we have definedB2 = −A2. We are now interested to see how the presence of the graphene layer modifies the absorption properties of the metamaterial, and in particular determine the influence of the gate-controlled Fermi level which is tunable in situ. The analytical expression for the reflection coefficient r allows us to estimate which order of magnitude EF should have in order to have any influence on the results. If the terms proportional to the conductivity σ are to be comparable in magnitude with the other terms, we see that e.g. εx,3ω ~ kz,3σ needs to be satisfied. Since we are considering an EM wave incident from air, εx,3 = εz,3 = ε0. Inserting the expression for σ, one finds that the above equation corresponds to a Fermi level in graphene ofThe coefficients for the other waves are given as: EF. We also note that when σ → ∞, r → 1 such that the absorption vanishes, S = E × H. We write E = E0et−iω and H = H0et−iω. For future use, we define the normalization constant for the power flow as the time-averaged incident power at z = τ: S0 = ε0c/(2 cos θ).For grazing incidence θ ~ π/2, the graphene layer thus has no influence for any realistic values of EF, graphene-dielectric stacks can exhibit a wavevector dispersion that traces out a hyperbolic contour at a given frequency21EF. Specifically, we focus on gate-tunable HMM structures in the ENZ limit, whereby the tensor components εx,2 and εz,2 are opposite in sign. We set μy,2 = μ0, and the relaxation time in graphene to τ = 10−13 s. For incident light in the THz regime, with EF = 100 meV and λ = 1.6 mm, this leads to a surface conductivity of graphene σ = (1.2 × 10−3 + 1.37i × 10−4) A ⋅ C/J.By appropriately tuning We first consider the standard Drude-like frequency response in the metamaterial, such thatz and f = 0.02, where λz is the characteristic wavelength, with λz = 1.6 mm. Designing a metamaterial within effective medium theory to possess the prescribed dielectric response in the THz regime can be challenging with current fabrication and materials capabilities. It may be possible however to design a multilayer dielectric structure or rod lattice56Here, α = λ/λz,2, determined by the frequency of the incident wave, and also its magnitude. We set x,2 → 0, the reflection coefficient simplifies toIt will also be of interest to see how the absorption properties depend on the sign of εr|2 = 1. However, when graphene is present (σ ≠ 0) an interesting opportunity arises. It is seen from the above equation that r = 0, meaning perfect absorptionIn the absence of graphene (σ = 0), we have zero absorption since |In the low THz regime and below (ω ≪ 10 THz), we have ω ≪ τ and full absorption takes place for angles Although this equation represents the criterium for 100% absorption, we show in the next section that the absorption in fact is close to 100% for an extremely wide range of incident angles.kx = β + iα to the complex plane and solve the pole dispersion equation (see the Methods section) for β and α (at a given ω). This dispersion equation admits four types of solutions for the complex wavevectorkx/k0 < 1, and ℑm(kx) = 0. These modes represent a coherent superposition of waves that propagate without loss along the surface. Indeed, only when the incident wave is incident at the perfect absorption angle, Sx/Sz), precisely coincide with the incident angle r to be single-valued, the appropriate branch cuts at the points ±k0 need to be made for kz,3. When examining the perfect absorption phenomena, we utilize a simple yet useful property of the reflection coefficient: r into its reciprocal:To establish how perfect absorption can be achieved, we discuss how the incident beam can couple to the intrinsic EM modes of the system. Our approach involves finding the poles of the reflection coefficient, kz,3 = k0 cos θ. This property simplifies the solution process since finding a complex pole, related to −kz,3, is equivalent to finding the perfect absorption modes for kz,359with x,2 > 0 and εz,2 < 0, or type II if εx,2 < 0 and εz,2 > 0. The operating wavelength of the incident beam is tuned around λz to control the sign of εz,2. The component of ε parallel to the interface always has the same magnitude, but can differ in sign according to εx,2 = (±4 + 0.1i)ε0.We now introduce more possibilities for enhanced absorption, and investigate anisotropic systems where the permittivity components perpendicular and parallel to the interfaces are of opposite sign. The corresponding HMM dispersion relations are then identified as either type I if εEF is seen to improve the absorption dramatically not only in magnitude, but also in terms of which angles of incidence that become absorbed. Remarkably, the absorption coefficient can be tuned to be nearly perfect, for an unusually broad range of angles. This is distinct from a scenario involving conventional dielectrics where isolated absorption peaks can appear at specific angles of incidence.Extremely wide-angle absorption for type-I and type-II anisotropic structures is demonstrated clearly in kx of the incident EM wave with the permitted EM modes of the graphene-based ENZ structure, the critical coupling responsible for perfect absorption can be identified. Since kx/k0 < 1, and ℑm(kx) = 0, we search for the allowed fast-wave EM modes (whereby the phase velocities exceed c) that the structure supportsR+ = 0 [kx, are converted to a critical coupling angle via θ = arcsin(kx/k0), giving the necessary incident beam angles for fast-wave mode coupling to occur. To illustrate this, in R+ = 0) are shown as a function of EF and θ. The wavelength considered λ = 1.01λz corresponds to a negative real part of εz,2 that is also near zero. In (a) εx,2 = (4 + 0.1i)ε0 corresponding to a type I HMM, while in (b) both permittivity components are of the same sign, since now εx,2 = (−4 + 0.1i)ε0. The dispersion curves are shown together with density plots of the absorption EF and θ. Clearly the fast-wave dispersion curves overlap with the regions of perfect absorption. A broader range of incident angles leading to perfect absorption is found in the graphene/HMM structure (a) compared to (b) where both kx below the light line. These modes are distinct from conventional guided wave modes that have kx/k0 > 1, and consequently the EM fields would be evanescent in the air region near the graphene layer. They also differ from leaky wave modesx since in that case, ℑm{kx} ≠ 0. Therefore, by coupling the incident beam to fast wave modes of the structure, the enhanced absorption features provided by the HMM in the ENZ regimeEF afforded by graphene, generates a broad range of angles for perfect absorption to arise.To pinpoint the mechanism of the observed perfect absorption, the mode characteristics of the system should be identified. By correlating the longitudinal wavevector component tsR+ = 0 , we findSx and Sz are shown within the air (z/τ > 1) and metamaterial (z/τ ≤ 1) regions for the structure considered in Sx and Sz are largest near the interfaces, except for near normal angles of incidence, whereby the energy flows along the metal backing. The flow of Sx in the metamaterial is opposite to the incident beam, demonstrating negative refraction that arises from the small negative permittivity component εz,2. The perfect absorption features seen in The behavior of the energy flow is exhibited in Ex and Ez take the same form in region j = 2, 3:We here provide some details for how to obtain the solution of the Maxwell equations in the presence of graphene. The wave-equations for j is then written: j which takes into account both transmitted and reflected waves:The dispersion relation then reads: j = kxεx,j/kz,jεz,j. Since the light is incident from air, we take A3 = 1. The magnetic field is obtained as where we defined κA2, B2, B3}. To do this, we need to specify the boundary conditions at the air/anisotropic medium interface (z = τ) and the anisotropic medium/PEC interface (z = 0). Since the tangential component of E is always continuous, it follows that H by writing the free current as Jf = σE: aM = b whereThere are three coefficients to be determined: {a = M−1b, which in turn fully determines E and H throughout the entire structure.where we defined We also provide an explicit expression for the time-averaged Poynting vector kz,3. The corresponding transcendental equation determines the allowed ω and kx pair that a source field can excite in the metamaterial system. From the many possible solutions, we consider only fast-waves corresponding to kx < k0, and ℑ{kx} = 0. The dispersion equation that must be solved is,To determine the fast-wave modes of the system, we solve Maxwell’s equations for the EM fields in the absence of an incident field, thereby effectively treating the structure as a waveguide. This is equivalent to finding the poles of the reflection coefficient for a given sign of kz,3 can be either positive or negative. When the system under consideration is isotropic, the transcendental equation for the modes in the ENZ limit , reduces to,where kx is converted into a coupling angle θc that the incident beam must be directed at in order for fast-wave modes to be excited: θc = arcsin(kx/k0). What constitutes a zero numerically in the root finding algorithm that solves The z is relatively close to 1. For large deviations from λ/λz = 1, a conventional scenario with isolated absorption peaks arises.For completeness, we also briefly show results for the spectral dependence of the absorbance, i.e. when moving away from the ENZ regime by varying the wavelength λ of the incident wave. This is shown in z,2, has a large imaginary component. Although the wide-angle absorption properties are seen to be reduced in the type-II case, the top panels (b) and (c) reveal that remarkably for the type-I HMM, wide-angle absorption remains intact when considerable losses are present.We also examine the effects of loss on the absorption properties of the graphene-based metamaterial. In How to cite this article: Linder, J. and Halterman, K. Graphene-based extremely wide-angle tunable metamaterial absorber. Sci. Rep.6, 31225; doi: 10.1038/srep31225 (2016).


There has been a significant increase in the popularity of Web-based question-and-answer (Q&A) services that provide health care information for consumers. Large amounts of Q&As have been archived in these online communities, which form a valuable knowledge base for consumers who seek answers to their health care concerns. However, due to consumers’ possible lack of professional knowledge, it is still very challenging for them to find Q&As that are closely relevant to their own health problems. Consumers often repeatedly ask similar questions that have already been answered previously by other users.In this study, we aim to develop efficient informatics methods that can retrieve similar Web-based consumer health questions using syntactic and semantic analysis.We propose the “SimQ” to achieve this objective. SimQ is an informatics framework that compares the similarity of archived health questions and retrieves answers to satisfy consumers’ information needs. Statistical syntactic parsing was used to analyze each question’s syntactic structure. Standardized Unified Medical Language System (UMLS) was employed to annotate semantic types and extract medical concepts. Finally, the similarity between sentences was calculated using both semantic and syntactic features.We used 2000 randomly selected consumer questions to evaluate the system’s performance. The results show that SimQ reached the highest precision of 72.2%, recall of 78.0%, and F-score of 75.0% when using compositional feature representations.We demonstrated that SimQ complements the existing Q&A services of Netwellness, a not-for-profit community-based consumer health information service that consists of nearly 70,000 Q&As and serves over 3 million users each year. SimQ not only reduces response delay by instantly providing closely related questions and answers, but also helps consumers to improve the understanding of their health concerns. Web-based health-related question and answering (Q&A) services are becoming more and more popular. Some consumer health websites receive millions of page views each year, such as NetWellness, WebMed, and EverydayHealth. Thousands of users visit these websites to search for answers related to their health problems . Many ofThe service model of community-based Q&A platforms has several unique advantages. First, users keep their identity anonymous, which protects the users’ privacy and encourages information sharing. For example, many people who feel too stressed or embarrassed to ask certain types of questions during face-to-face physician consultations  can seek help from the online community. Second, the Q&A platform can serve as an information source for acquiring new knowledge. It enhances a user’s understanding of health care on many different topics, such as nutrition, patient care, or disease management. Third, compared to face-to-face physician consultation, a community-based service normally provides a quicker response and a wider range of perspectives. For example, a user who asks a question about “children nutrition” may receive answers from both child-care experts and nutritionists. Finally, the online community provides a platform for consumers to share their health concerns and wellness interests. This creates an environment that not only shares new knowledge, but also provides emotional support for health care consumers. Therefore, a community based Q&A is an excellent way of delivering health care information to a wide range of public users. It could help reduce the time and cost of information delivery, such as those services provided by MIMIR  and YahoDespite the fact that an online community-based health information service has many advantages, there are still many challenging problems that need to be addressed to improve the service’s quality and accessibility . ConsumeMany community-based service platforms have now archived thousands of Q&As, which creates a valuable knowledge base. Berland et al published a study  on evalusemantic similarity analysis method to support the need for retrieving similar questions from NetWellness, that complements existing services, and that enables efficient reuse of the accumulated Q&A knowledge , NP (noun phrase), and VP (verb phrase). The syntactic tree is expanded until all leaves contain a single constituent. Unlike standard syntactic parsing that treats each of the words as a constituent, our method uses the semantic annotation results and treats the UMLS recognizable entities as syntactic constituents. This last step enabled us to retrieve relationships between the identified named entities.To analyze the linguistic structure and the constituents of consumer questions, we parsed the question sentences into syntactic trees. The AQUA parser  was exteWe constructed dependency grammars  from theQ1 and Q2 that are generated from two different consumer questions, we can then calculate the DC and CS similarity scores through the formulas in Dice coefficient and cosine similarity are the algorithms that are employed for calculating similarity in this paper. Dice coefficient (DC) and cosine similarity (CS) see  were useWe use binary representation for both syntactic and semantic features. If a feature appears to a consumer in a question, then it has a value of 1; otherwise, the value is 0. From the binary representation, we can generate vectors containing both syntactic and semantic features to compare the similarity between these two questions as indicated in formulas 1 and 2 in F-score were measured. Also, we created an illustration for the aggregated semantic type patterns of the “Diet and Nutrition” category, which contained 2335 questions (see We applied our method (SimQ) to the consumer questions posted on the Netwellness website, which has archived over 70,000 Q&As and more than 600 health information articles that were written by domain experts. All of the Q&As and articles were categorized into 121 health topics. The performance of the proposed SimQ method was then evaluated by using 2000 random selected NetWellness questions. The precision, recall, and ions see .To evaluate the performance of the SimQ method, 12 seed consumer questions were selected from Yahoo Answers as input questions. These questions were selected from different categories, such as women’s health, diseases and conditions, and mental health. Two biomedical informaticians, who were independent to this project, were recruited to generate a gold standard to evaluate the results of the SimQ question retrieval engine. They were asked to manually select Netwellness questions that were closely similar to the seed questions. A total of 2000 randomly selected Netwellness questions were used as the candidate pool. In total, 246 consumer questions were selected by the evaluators as the positive gold standard to evaluate SimQ’s retrieval performance. The initial agreement between the two evaluators was 83%. However, they were allowed to discuss and reach a final unanimous agreement on all the similar consumer questions, which were then used as the gold standard.We also compared the performance of similarity analysis using different feature representations. F-score, 72.2% precision, and 78.0% recall.In Syntactic parsing is used to facilitate the identification of named entities and to support the construction of semantic features . Part-ofTo demonstrate the use of SimQ, we developed an application that complemented the existing Q&A services on the NetWellness website. This new application enhances the workflow through semantic similarity analysis see , Step 1.At present, one of the most common ways to find health information online is through search engines. Search engines use keyword-based information retrieval techniques , which rThe SimQ method is related to but fundamentally different than Question Answering Machines (QAMs) ,26. QAMsWe observed two types of errors from the SimQ retrieval results: false positive results and false negative results. False positive results, which are incorrectly included questions, were often created by questions with small but important differences. For example, SimQ retrieves the query, “How can I lose weight in one month?” for the question, “How I can gain weight quickly”, because both “lose weight” and “gain weight” have the same semantic type, Findings. Both questions contain the same semantic types, Patient Group and Temporal Concept. The only major difference is seen in the concepts of “lose weight (CUI:C0043096)” and “gain weight (CUI:C0043094)”. One potential solution for this type of error is to incorporate concept importance ranking into the similarity analysis. When generating feature vectors, important concepts have higher weights for calculating the similarity score, which can improve the retrieval results. False negative results (incorrectly excluded questions) are often caused by complex questions. For example, the question “I have a breast lump, could it be a lymph node or tumor?” is semantically close to “Is swelling breast a sign of breast cancer?” by human standards. However, the SimQ similarity score is not very high. To address this problem, we need to add concept reasoning ability to the similarity analysis. In this example, the concept “breast lump (CUI:C0424849)” is a descendent of the concept “swelling (CUI:C0038999)”, and “breast cancer (CUI:C0006142)” is a descendent of “tumor (CUI:C0027651)”.Short ambiguous questions can also lead to both false negative and false positive errors. For example, when analyzing the question, “Vitamin B6 deficiency”, SimQ retrieved the false positive result “Vitamin B12 deficiency?” and the false negative result “What are the symptoms of Vitamin B6 deficiency?” We believe that potential methods to address errors created by short ambiguous questions include weighting the question elements by importance and/or applying a query expansion technique. For example, an intuitive way to expand the question for Netwellness is to include previous answers from similarity analysis. However, the answers usually are much more complex and longer than the question, so it is still challenging to achieve a good result, especially since real-time retrieval response is needed. Integrating both questions and answers to improve retrieval results will be examined in subsequent studies that we plan to undertake.SimQ uses UMLS as a standardized semantic knowledge source. In the future, we plan to exploit other medical knowledge sources for semantic annotation, which could provide finer granularity of the semantic assignment and improve semantic analysis. Additionally, some researchers have pointed out that Consumer Health Vocabularies (CHV)  may faciF-score of 75.0%. We demonstrated a use case application by designing a new Q&A pipeline for the NetWellness website, which retrieves previous Q&As similar to the user’s health care. We designed a new Q&A pipeline for NetWellness, which retrieves previous Q&As similar to the user’s health care question. Then we demonstrated by using a particular case how the additional features of SimQ would be applied to a health consumer’s inquiry and integrated into the existing system to improve the service quality of the Q&A workflow. Therefore, we have shown that SimQ not only reduces response delay by instantly providing closely related question and answers, but also helps consumers improve the understanding of their health concerns.Similarity analysis of consumer health questions can significantly improve the quality and accessibility of online community-based question answering (Q&A) services. In this study, we proposed a new application called SimQ, which analyzes the semantic similarity of consumer health questions by combining natural language processing and semantic pattern techniques. The evaluation results show that our approach effectively retrieves similar questions on NetWellness. The results show that SimQ reached the highest precision of 72.2%, recall of 78.0%, and


The increasing number of open-access ontologies and their key role in several applications such as decision-support systems highlight the importance of their validation. Human expertise is crucial for the validation of ontologies from a domain point-of-view. However, the growing number of ontologies and their fast evolution over time make manual validation challenging.We propose a novel semi-automatic approach based on the generation of natural language (NL) questions to support the validation of ontologies and their evolution. The proposed approach includes the automatic generation, factorization and ordering of NL questions from medical ontologies. The final validation and correction is performed by submitting these questions to domain experts and automatically analyzing their feedback. We also propose a second approach for the validation of mappings impacted by ontology changes. The method exploits the context of the changes to propose correction alternatives presented as Multiple Choice Questions.This research provides a question optimization strategy to maximize the validation of ontology entities with a reduced number of questions. We evaluate our approach for the validation of three medical ontologies. We also evaluate the feasibility and efficiency of our mappings validation approach in the context of ontology evolution. These experiments are performed with different versions of SNOMED-CT and ICD9.The obtained experimental results suggest the feasibility and adequacy of our approach to support the validation of interconnected and evolving ontologies. Results also suggest that taking into account RDFS and OWL entailment helps reducing the number of questions and validation time. The application of our approach to validate mapping evolution also shows the difficulty of adapting mapping evolution over time and highlights the importance of semi-automatic validation. As multiple ontologies can describe the same domain, semantic mappings are often defined to link ontology elements that refer to the same real-world entity but belong to different domain-related ontologies } where semanticTypei∈{≡,≤,≥,≈} such that Relalternatives to formulate the question in the revision of MR category. The alternative relations are proposed from the most precise one to the more general one .Revising the semantic relation We selected a set of ontologies and mappings and designed a series of experiments to evaluate the proposed methods. In this article, we considered medical ontologies and mappings in English language, but our approaches can be applied to other languages as well. We present the obtained results in Sections “Caries Ontology (CO). CO was developed manually by a dentistry expert in our company.Disease-Treatment Ontology (DTO). We constructed an OWL translation of the ontology proposed by Khoo et al. .Mental Diseases Ontology (MDO). This ontology is publicly available.We tested our ontology validation approach on three different medical ontologies that cover different aspects of the medical domains  and constructed using different methods: For the first step of the experiment, Table i.e. more invalid elements), the number of deleted questions will increase.The number of generated questions depends on the ontology size and shows the importance of question ranking and optimization. The results indicate that the optimization method works better in case of ontologies with many instances. For the CO ontology, this strategy helps minimizing the number of submitted questions from 290 to 283 questions with only four NO answers. For the MDO ontology, our method allows asking 239 questions instead of 243 with only two NO answers. In case of ontologies with more NO answers , other methods should be used to optimize the presentation and reduce the time needed to answer the questions. For example, the following presentation methods can be studied: (i) question factorization according to an ontology element  and (ii) logical chaining . Such organization can be effective in helping medical experts understand and answer the questions more quickly.9 (SCT) and ICD-9-CM10 (ICD9) including different versions of official mappings established between them.We evaluate the NL quality of the questions generated automatically to validate mappings. We use two biomedical ontologies SNOMED-CTWe aim to investigate to which degree it is possible to generate NL sentences that can adequately describe mappings. For this purpose, we evaluate the generated questions according to three standard measures in NL generation: grammaticality, fluency and meaning preservation. Since our approach aims to facilitate human intervention in mapping adaptation, we assume that it is relevant to assess the NL quality of the automatically-generated questions.We presented the generated questions to three different human assessors who were asked to associate a score value between 1 and 10 for each dimension and each question. Assessors were ontology experts and familiar with the biomedical domain. We evaluated the approach for the validation of 20 randomly-selected adapted mappings generated from the evolution of mappings between SCT and ICD9.κ measure defined in , [4..6], [7..10]. We use these intervals as categories in the calculation of the κ measure, which corresponds to: We measure the Inter-Assessor Agreement (IAA) for grammaticality, fluency and meaning preservation. IAA corresponds to the average fined in . The κ mP(a) refers to the observed inter-assessor agreement and P(c) is the probability of a chance agreement. κ values range from -1 to 1  the number of returned answer-types for the set of 20 questions according to the different question types and (ii) the number of validation/invalidation according to the observed adapted mappings  , which provides a positive test on the reliability of the assessors’ ratings. In short-term perspectives, further tests will be made with a correlation-based approach to have a more precise view on the levels of agreement.The overall assessment of the generated initial Boolean Questions   or also NO for a specific kind of patient, or under a specific condition. In our experiments the experts answered NO for such cases. Therefore, it would be interesting to give to the expert the possibility to specify a contextual element or an additional condition to their YES/NO answers. A possible solution can be to integrate factual questions as possible question type, which will also contribute to enrich the ontology during the validation process.The experiments on ontology validation showed the need to add other specific types of questions and answer types. In some observed cases an answer can be i.e. concepts with the largest number of links).On the other hand, even if our optimization method may allow significantly reducing the number of questions, it is still challenging to validate very large ontologies with natural language questions. In this context, advanced content selection techniques such as summarization can play an important role. As suggested by Sure et al. , a summaTo validate huge ontologies, we are considering approaches based on summarization. A possible solution can be by using the Key Concepts Extraction (KCE) algorithm which automatically extracts the most representative classes of an ontology. More particularly, summarization can be adapted to the validation task by taking into account several features such as the number of questions needed to validate a given extract or summary and the number of key concepts.On the level of Mapping Validation, the conducted literature survey indicated that the generation of NL questions for mapping validation was not investigated. Our proposal originally evaluated the quality of generated NL questions to help human experts judge the quality of correspondences under evolution. The proposed method uses the context of the source concept to select similar concepts as alternatives in case of invalidated mappings.Are other eye disorders more specific than family history degenerative disorder of macula?”The heterogeneity and length of the literal attributes that led to some inadequacies with the conceived patterns, e.g., “Is other more specific than mechanical complication of suprapubic catheter?”.Errors in the concepts’ attributes (mainly labels), e.g. “ In the conducted experiments on mapping validation, the analysis of quality-deficient Boolean questions produced by the NL generation system highlighted to two main error causes: These observations show the importance of evaluating the linguistic quality of the ontology literals beforehand. This issue is particularly discussed in , where aThe methods for automatic ontology construction have highlighted the problems of validation of ontologies and mappings. Research efforts and interests have grown more and more, but mostly at a formal level. In this article, we addressed the problem of ontology validation including mappings from a conceptual and a semantic point of view.We proposed novel semi-automatic approaches based on the generation of questions and answers interpretation to facilitate the communication with domain experts. The defined methods generates natural language questions from medical ontologies and mappings and uses the answers from the expert to update/correct them.Our approach implementing automatic methods might guide domain experts in the validation process. Relying on domain experts to monitor the validation can lead to various benefits, ensuring reliable communication between heterogeneous systems.We evaluated the proposed methods based on several real datasets from different releases of biomedical ontologies and their associated mappings. The achieved results underscored the feasibility of our general approach for the validation of ontologies and mappings, and its relevant role in the completion of the their adequate evolution over time.1http://ihtsdo.org/snomed-ct/2http://ncit.nci.nih.gov/3http://bioportal.bioontology.org/4http://www.chu-rouen.fr/cismef/5 An international workshop is also held on question generation since 2008.6http://nlp.stanford.edu/software/lex-parser.shtml7http://www.w3.org/TR/rdf-mt/#RDFSRules8 Free textual explanation is considered for future perspectives and is not used in this work.9www.nlm.nih.gov/research/umls/licensedcontent/snomedctarchive.html10www.cdc.gov/nchs/icd/icd9cm.htm


Amongst birds, a single order, Dinornithiformes, comprising the extinct wingless moa of New Zealand, are unique in having no skeletal evidence of forelimb-like structures.The forelimb-specific gene tbx5 in moa, we used a range of PCR-based techniques on ancient DNA to retrieve all nine tbx5 exons and splice sites from the giant moa, Dinornis. Moa Tbx5 is identical to chicken Tbx5 in being able to activate the downstream promotors of fgf10 and ANF. In addition we show that missexpression of moa tbx5 in the hindlimb of chicken embryos results in the formation of forelimb features, suggesting that Tbx5 was fully functional in wingless moa. An alternatively spliced exon 1 for tbx5 that is expressed specifically in the forelimb region was shown to be almost identical between moa and ostrich, suggesting that, as well as being fully functional, tbx5 is likely to have been expressed normally in moa since divergence from their flighted ancestors, approximately 60 mya.To determine the sequence of tbx5 is necessary for the induction of forelimbs, but is not sufficient for their outgrowth. Moa Tbx5 may have played an important role in the development of moa’s remnant forelimb girdle, and may be required for the formation of this structure. Our results further show that genetic changes affecting genes other than tbx5 must be responsible for the complete loss of forelimbs in moa.The results suggests that, as in mice, moa  Limb loss by regressive evolution is common in nature with well-known examples being whales, some salamanders, and snakes. Amongst birds, the loss of forelimbs is best represented amongst ratites, with a general reduction in wing size evident in the rhea and ostrich, and a more severe truncation of wings shown in emu, cassowary, kiwi, and elephant bird. Surprisingly, phylogenetically, New Zealand’s moa group with the fully winged and flighted tinamou , despitetbx5, a highly conserved Tbox motif-containing transcription factor known to be essential for forelimb initiation in nearly all animals. Tbx5 is an essential member of a tightly regulated gene network that includes the Hox genes , characterized by reduction of the forelimbs and associated heart anomalies )D. novaezealandiae, D. robustus, E. curtus, E. crassus, and M. didinus  according to the manufacturers instructions. Genomic DNA was recovered from extant ratite blood by standard phenol/chloroform extraction and ethanol precipitation . AncientApproximately 5 ug of total RNA was reverse transcribed at 41°C for 60 min in 20 ul volumes with random 7-mer or oligodT primers and purified by phenol:chloroform extraction and ethanol precipitation.tbx5 intron/exon boundaries required to allow primer design for moa amplification. These included: Single primer PCR - A single primer was used in a standard PCR reaction at low annealing temperatures for one cycle to allow random priming and then amplified for ~35 cycles with the annealing temperature set at the primer’s Tm. Hairpin primer ligation PCR - hairpin primers containg a PstI compatible overhang were ligated to PstI-digested DNA before standard PCRs were carried out using the hairpin primer and a tbx5-specific primer. Medium range PCR - amplification across the smaller tbx5 introns was carried out usng Elongase® (Invitrogen) or Expand Long Template PCR System (Roche) as outlined by the manufacturer. Inverse PCR - Inverse PCR was carried out to obtain intron sequences directly from moa. Biefly, moa aDNA was denatured, then dephosphorylated with shrimp alkaline phosphatase (SAP) before fresh phosphates were added with T4 Polynucleotide Kinase. The aDNA was then circularised with CircligaseTM ssDNA Ligase (Epicentre®) and subjected to rolling circle amplification using TemplifyTM (Amersham). The amplified aDNA was then subjected to standard PCR using inverse primers.DNA was amplified from approximately 1–20 ng of DNA as outlined in . A numbetbx5 sequences we initially obtained full-length tbx5 cDNA sequences for kiwi and ostrich. Comparison with the chicken genome identified the intron/exon boundaries and primers were then designed to recover moa tbx5 exon sequences. To obtain moa tbx5 intron/exon boundaries, these boundaries were first isolated from kiwi. Primers were then designed to kiwi tbx5 intron sequences and conserved ostrich/kiwi/chicken tbx5 exon sequences to obtain moa tbx5 intron/exon boundary sequences. Most primers designed to kiwi tbx5 intron sequences successfully amplified from moa aDNA. For a few introns however, primers successful for amplification from moa required additional intron sequences from rhea, and/or ostrich.To isolate moa 20) and ex2R2 (5’- GGTGAGCGACTTGCTGGTG), followed by H5F (5’- AATCGGACAAACTGGTCCTTGCAAC) and ex2R3 (5’- CAAAGCCTTCCTCCGTAT). Amplified products were TA cloned into pGEM®T-Easy (Promega) and sequenced with m13F (5’-TGTAAAACGACGGCCAGT) or m13R (5’-CAGGAAACAGCTATGACC). Full-length forelimb-specific exon 1 transcripts were then obtained by cDNA walking using primers designed to conserved upstream regions of the chicken genome.Total RNA isolated from embryonic ostrich and kiwi forelimb and kiwi heart were A-tailed with terminal transferase (Invitrogen) and amplified with H5FdT (5’- AATCGGACAAACTGGTCCTTGCAACdTTM 5.0 (Gene Codes Corporation).PCR products were purified by centrifugation through dry Sephacryl S200HR, sequenced using ABI BigDye® Terminator v3.1 chemistry, then analysed and aligned in SequencherIn accordance with criteria suggested for the verification of aDNA sequences , a numbefgf10 and ANF promoters was determined using a luciferase assay. HEK293T cells were seeded into 24-well plates at a density of 5 × 104 cells/well twenty four hours before transfection. The following vectors were transfected into HEK293T cells using XtremeGENE HP (Roche); 6 kb of mouse sequence immediately upstream of fgf10.Supporting tables and figure are available as additional files. The authors declare that they have no competing interests.LH, TS, TO, YW, and SM carried out the molecular genetic studies. LH, DML, CDM, CS, and MH helped conceive the study and participated in its design and coordination, and helped to draft the manuscript. All authors read and approved the final manuscript.Moa tbx5; materials, methods and sequences. Detailed descriptions of materials and methods used, nucleotide and amino acid sequences.Click here for file


One intriguing feature of the human communication system is the interactional infrastructure it builds on. In both dyadic and multi-person interactions, conversation is highly structured and organized according to set principles  Foundations of turn-taking, (2) Signals and mechanisms for prediction and timing, (3) Planning next turns in conversation, (4) Effects of context and function on timing, (5) Turn-taking in signed languages, and (6) Development of turn-taking skills.Levinson and Torreira review behavioral and cognitive findings specifying the parameters of the processes underlying the human turn-taking system. This empirical evidence is synthesized into a model claiming that intention ascription and response planning begin as early as possible during the incoming turn, running through all the serial stages of speech production à la Levelt . These become available to listeners as turns unfold in conversation and often allow next speakers to predict the content of ongoing turns. Himbert et al. throw light on yet another source of information that speakers in interaction may use for timing their turns: their analysis demonstrates that interlocutors adapt their turn-taking rhythms to one another, which they argue is facilitated by the alignment of semantic and syntactic processes.One of the central debates on the cognitive processes involved in turn-taking focuses on the role played by prediction. Part of this debate is the issue of which kinds of cues adults may use for predicting the end of turns, allowing them to come in on time. The article by Roberts et al. explore the value of both psycholinguistic factors  and conversational structures  as explanatory factors when modeling the timing of turns in conversation. Their results show that both sets of factors significantly contribute to explaining variation in turn timing. Torreira et al. study pre-answer in-breaths in a dialogue setting using insights from acoustic and inductive plethysmography recordings. They demonstrate that the occurrence of an in-breath is dependent on the length of an answer, suggesting that answers are planned prior to these in-breaths. Since the pre-answer in-breaths in their data were launched close to the end of question turns, the data provide evidence for the concurrence of comprehension and next utterance planning.The contributions in this section explore some of the cognitive processes involved in preparing next turns in conversation. Applying a cutting edge statistical approach (“random forests”) to data from a large conversational corpus, Kendrick shows that turns dealing with problems of speaking, hearing, and understanding  are governed by different timing principles and can thus break the common pattern of minimal gaps between turns. As the analysis reveals, the longer gaps characteristic of repair sequences tend to be used by participants as opportunities to either allow the producer of the trouble source to resolve the issue before repair is initiated, to allow themselves to resolve their problems in understanding before initiating repair, or to signal problems in understanding through visual displays  before initiating repair verbally. The article by Gardner and Mushin provides evidence from Garrwa, an indigenous Australian language, for turns that are followed by substantially longer gaps than one would ordinarily expect based on prior work on English conversations. In these cases, however, it is not repair that drives the longer turn transition times; the environment in which they occur is slow-paced conversation, appearing to reduce the pressure for gap minimization. Stevanovic and Peräkylä discuss perspectives on the intersection of two different systems of temporal organization, that of turns at talk and that of emotional reciprocity—the former favoring sequential organization, the latter affording simultaneity and immediate uptake through emotional contagion and mimicry.Three articles investigate the interplay of turn-taking rules with other principles shaping human behavior in specific conversational contexts. De Vos et al. analyze the timing of turns in Sign Language of the Netherlands (NGT), showing that the timing of turns in signed conversation looks remarkably similar to that of spoken interaction  when considering not simply onset and offset of manual movements but individual movement phases . Girard-Groeber examines turn-taking principles in multi-party conversations in Swiss German Sign Language (DSGS), focusing on the occurrence of overlaps. She, too, finds striking similarities with spoken interactions: the examples provided illustrate a strong orientation to the “one at a time” principle, an orientation of participants toward points of possible completion in the sign stream, and a set of principles that appear to determine deviations from this rule (such as repair initiations or strong disagreements). Manrique and Enfield focus on a particular type of turn transition environment—other-initiated-repair—in Argentine Sign Language (LSA), thus complementing Kendrick's work on repair in spoken interaction (this volume). However, their focus is on how repair is elicited in visual question-answer sequences rather than on the timing of turns in the repair environment, revealing the frequent use of a visual display form termed the “freeze-look.” Next to clearly unique features, the three articles point toward some striking similarities regarding the timing and organization of turns in spoken and signed languages.The research presented in this section investigates the principles of turn-taking and sequence organization in signed languages where communication is constrained to the visual modality. Gratier et al. demonstrate that already at 8–21 weeks babies are active participants in, as well as initiators of, turn-taking sequences, but also that at this early stage of development mothers play a core role in the timing of turns by adapting their behavior to the infant. Hilbrink et al. provide a longitudinal study showing that turn-timing skills continue to develop continuously from 3 to 18 months, with some regressive slowing down as language comprehension kicks in around the “9 month revolution”  verbal and gestural responses to questions. The pattern they find nicely fits with the temporal slowing down in vocal turn-timing caused by the challenge of having to master language—while verbal responses often occurred with long delays, the child frequently produced gestural responses preceding speech. The following two articles examine children's use of linguistic cues for anticipating upcoming next turns when observing dyadic conversations. Keitel and Daum find that three but not 1 year olds are able to make use of intonational cues for predicting upcoming next turns. In line with this, Lammertink et al. find that 2 year olds make use of prosodic cues for predicting upcoming next turns, but that they make use of lexicosyntactic cues, too, even weighing these more strongly—just like adults do.Convergent findings regarding principles governing turn-taking across languages in different modalities hint at the possibility of a shared cognitive infrastructure underlying all human communicative interaction. This cognitive infrastructure may also account for the ease with which young children appear to acquire the necessary skills to interact with others. The contributions included in this section focus on the acquisition of turn-taking in very young infants and in children as they start to master spoken language. The first two articles suggest that temporal turn-taking skills are learned early on in infancy. The authors were supported through the Max Planck Gesellschaft and European Research Council (Advanced grant #269484 INTERACT awarded to SCL) during the preparation of the editorial and the research topic as a whole.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.