Somewhat surprisingly, basic residues like arginine, also played an equally or even stronger role during this process. The strong dispersion interactions between the sidechains of these solvent-exposed basic residues and the graphene surface provide the driving force for a tight binding of these basic residues. To the best of our knowledge, this is the first study with blood proteins to show that, in addition to the aromatic residues, the basic residues also play an important role in the formation of protein-graphene corona complexes.With its many unique properties, graphene has shown great potential in various biomedical applications, while its biocompatibility has also attracted growing concerns. Previous studies have shown that the formation of protein-graphene corona could effectively reduce its cytotoxicity; however, the underlying molecular mechanism remains not well-understood. Herein, we use extensive molecular dynamics simulations to demonstrate that blood proteins such as bovine fibrinogen (BFG) can absorb onto the graphene surface quickly and tightly to form a corona complex. Aromatic residues contributed significantly during this adsorption process due to the strong π−π stacking interactions between their aromatic rings and the graphene  Upon entry of the CBN into the microenvironment of bloodstream, massive biomolecules (such as proteins and lipids) quickly adsorb onto CBNs, forming the so-called corona complex3031α-helix chains. As shown in our previous studyα-helix tails act as tentacles, which can wrap along the CNTs and thus expose more inner residues to the CNT surfaces (and resulting in particularly strong effects in reducing the cytotoxicity of CNTs)3334In this study, all-atom molecular dynamics (MD) simulations were performed to examine the adsorption process of BFG and BSA onto the graphene surface. Both the largest (BFG) and smallest (BSA) protein among the four blood proteins were chosen for this study, with the BFG being the major target protein mainly because of its unique and special 3D topological structure with long-intertwining flexible σcc = 0.34 nm and a potential well depth of εcc = 0.3598 kJ mol−1. Carbon-carbon bond lengths and bond angles were maintained by harmonic potentials with spring constants of 392,460 kJ mol−1 nm−2 and 527 kJ mol−1rad−2 respectively.The coordinates of the graphene nanosheets used in the simulations were generated using the nanotube builder plugin of the VMD softwareα β and γ) d γ) see . The lenv-rescale thermostatSystem-1 consists of 612,464 atoms (with box size of 31.91 nm × 12.96 nm × 14.96 nm and graphene size of 25.66 nm × 9.90 nm) while system-2 consists of 621,358 atoms (with box size of 32.06 nm × 13.02 nm × 15.03 nm and graphene size of 25.66 nm × 9.90 nm). The distance between any heavy atom of the BFG and the graphene surface is greater than 1.0 nm in the initial configurations of the simulations. The solvated systems were then simulated with MD, which is widely used in the studies of both biomolecules4142434445462439484950ith residue (the first residue) and any heavy atom of another jth residue (j - i > 3) (the second residue) is shorter than 6.0 Å in the crystal structure of the protein. By definition, for the fully folded state, Q = 1, with decreasing Q as the instantaneous 3D structure of the protein resembles less the crystal structure.The adsorption process of BFG onto the graphene surface was interrogated by calculating the contact surface areas and the contact number between heavy atoms of the two molecules. As a measure to monitor the time evolution of the overall structure of BFG during the absorption process, the root mean square deviation (RMSD) of the heavy atoms of BFG compared with the crystal structure and the fraction of native contacts Q were also calculated. Here, an atom-atom pair contact is defined when the distance between any heavy atom of BFG and any carbon atom of graphene is smaller than 6.0 Å. Two residues are considered to have a native contact if the distance between any heavy atom of the γ-chain (cyan), the α-chain (pink) and the β-chain (yellow) (see The heavy atom contact number between BFG and graphene as a function of simulation time is shown in low) see .Q as function of simulation time for the protein and its three branched chains are shown in γ-chain, the α-chain and the β-chain, respectively  and Arg-108  in the γ-chain and Arg-110  in the α-chain. Later on, at about t = 16 ns, another round of moderate decrease in the vdW energy occurred for residues Val-111, Asn-106 and Arg-95 in the α-chain, with the largest decrease for Arg-95 by 10.77 ± 0.82 kcal/mol. Then, at about t = 23 ns, a new round of even more dramatic decrease in the vdW interaction energy occurred for residues Arg-91 in the β-chain, Arg-14, Phe-15 and Tyr-18 in the γ-chain with even the smallest decrease for Arg-91 in the β-chain by 12.95 ± 0.88 kcal/mol. The magnitude of the decrease in the vdW energy for each residue indicates how strongly it binds to the graphene surface. The more dramatic the decrease of the vdW energy, the tighter the binding of the residue to the graphene. Therefore, Arg-110 in the α-chain, Arg-91 in the β-chain, Arg-14, Phe-15, Tyr-18, Arg-391 and Arg-108 in the γ-chain played a very critical role in the binding of BFG to the graphene surface.To quantify the contribution of each residue to the adsorbing process, we computed the time evolution of the vdW (or dispersion) energy between each residue and graphene  of the identified key residues are basic in nature (arginine and lysine) see . AdditioTo clarify this puzzle, we carefully studied the detailed dynamics of some representative aromatic and basic residues in the adsorption process. We chose Arg-391 because it was found to play a very important role in the early adsorption of the head of protein. Similarly, we studied Tyr-18 since it was identified to be essential to anchor the protein tail onto the graphene surface. We monitored the time evolution of the heavy atom contact number between the side-chain of these residues and the graphene, and also computed the number of water molecules in the first solvation shell (FSS) of their side chains. Here, FSS is defined as the region within 5 Å to any heavy atom (non-hydrogen atom) of side chain.et al.The time evolution of the heavy atom contact number and the number of water molecules in the FFS for Arg-391 and Tyr-18 are shown in Considering the potentially favorable vdW interactions between Leu/Ile and graphene when they form close contact, it seems reasonable to expect that Leu/Ile should also play an equally or more important role than Arg/Lys in the adsorption of protein onto the graphene surface as they do not need to pay the desolvation penalty of the charged groups as Arg/Lys do. However, this argument ignores two important differences between Leu/Ile and Arg/Lys. First, the side chains of Arg/Lys are longer than Leu/Ile, making them more accessible to the graphene surface. Second, and more importantly, while Arg/Lys are usually exposed to solvent in the native structure of the protein, Leu/Ile are highly packed in the hydrophobic environment of the interior of the protein. Therefore, in contrary to Arg/Lys where the favorable vdW interactions between Arg/Lys and graphene compensate the relatively small desolvation penalty (water molecules in FSS only decreases from ~18 to ~15), the vdW interactions between Leu/Ile and graphene are not strong enough to compensate the loss of favorable interaction between Leu/Ile and its surroundings residues in the native structure of the protein. Consequently, Leu/Ile were not observed to have played as critical a role during this adsorption process.γ-chain, it was far away from graphene and fully solvated by water during the first 23 ns of the simulation  for the adsorption of BSA onto graphene. As shown in α-helix tails of BFG underwent large conformational changes, with some basic and aromatic residues that were originally in the interior now exposed to the graphene surface.Furthermore, as shown in both Finally, it should be noted that the π-π interactions essentially are the interactions between π-electron systems . The negatively charged and diffuse electron clouds of the π-systems exhibit an attractive interaction due to the London dispersion forces which are caused by favorable instantaneous multipole/induced multipole charge fluctuations. However, in molecular mechanics (MM) calculations of aromatic molecule and graphene interactions using modern classical force fields, the graphene carbon atoms are usually modeled as uncharged Lenard-Jones particles, thus the π-π stacking interactions simply reduce to vdW terms solely. Although not explicitly treated, the contribution of electrostatic interactions is well compensated by the vdW terms in these force fields. Our recent work, which combined both quantum mechanical-based dispersion corrected DFTB-D method and classical molecular mechanics-based MD simulations, has demonstrated that classical force fields can properly model the energetic strength of π-π stacking interaction between aromatic amino acid analogues and carbon-based nanomaterialsRecently, graphene has attracted increased attention in the biomedical field. Because of its unique electrical, mechanical and chemical properties, graphene has been applied to different drug delivery platforms or even as nanodrugs in both diagnostic and therapeutic endeavors. However, the detailed mechanisms about how graphene interacts with biomolecules, such as lipids, proteins, and nucleic acids, crucial for the study of the biocompatibility and cytotoxicity of graphene, are still not well understood7374In this study, we have investigated the underlying molecular mechanisms of the adsorption of blood proteins BFG and BSA (in particular BFG due to its unique 3D topology) onto the graphene surface through extensive large-scale all-atom MD simulations. We calculated the contact surface areas and the heavy atom contact number between blood proteins and the graphene surface during the adsorption process, and found a successive bursts-like adsorption pattern. The important intermediate states during the adsorption process have been carefully examined and key residues for the adsorption of both BFG and BSA onto the graphene surface have been identified by studying the time evolution of the vdW interaction energy and the contact probability of each residue with graphene.γ-chain, and a representative basic residue, Arg-391 in the γ-chain, as identified to have played an important role in the adsorption process, has been studied in detail. We found that while the π−π stacking interactions attract Tyr-18 to bind to the graphene surface, the strong vdW dispersion interactions between the long and relatively planar sidechain (guanidinium group) chain and the graphene provides the driving force for the adsorption of Arg-391. Those with equally long side chains and hydrophobic residues such as Leu/Ile were not found to play an important role during the adsorption process, because Leu/Ile are highly packed in the hydrophobic environment of the interior of the protein, while Arg/Lys are usually exposed to solvent in the native structure of the protein. These detailed systematic analyses provided a more complete molecular picture for the protein-graphene corona complex formation.To our surprise, in addition to aromatic residues, basic residues were also found to play a very important role. For example, in BFG, the dynamic process of a representative aromatic residue, Tyr-18 in the How to cite this article: Gu, Z. et al. The role of basic residues in the adsorption of blood proteins onto the graphene surface. Sci. Rep.5, 10873; doi: 10.1038/srep10873 (2015).


We report on the integration of inkjet-printed graphene with a CMOS micro-electro-mechanical-system (MEMS) microhotplate for humidity sensing. The graphene ink is produced via ultrasonic assisted liquid phase exfoliation in isopropyl alcohol (IPA) using polyvinyl pyrrolidone (PVP) polymer as the stabilizer. We formulate inks with different graphene concentrations, which are then deposited through inkjet printing over predefined interdigitated gold electrodes on a CMOS microhotplate. The graphene flakes form a percolating network to render the resultant graphene-PVP thin film conductive, which varies in presence of humidity due to swelling of the hygroscopic PVP host. When the sensors are exposed to relative humidity ranging from 10–80%, we observe significant changes in resistance with increasing sensitivity from the amount of graphene in the inks. Our sensors show excellent repeatability and stability, over a period of several weeks. The location specific deposition of functional graphene ink onto a low cost CMOS platform has the potential for high volume, economic manufacturing and application as a new generation of miniature, low power humidity sensors for the internet of things. Over the years, a variety of transduction techniques has been reported for humidity sensors, including the use of surface acoustic wave (SAW)1248Sensors available on the market are typically bulky or usually have high power consumptioni.e. active area) compared to graphene produced by solution processing, a key requirement for sensing applications. Solution based strategies, such as ultrasonic assisted liquid phase exfoliation (UALPE) produces high quality, defect free, pristine graphene nanoflakes at room temperatureWith its 2-dimensional (2d) structure, high specific surface area and in particular, sensitivity of its electrical properties to environmental perturbations, graphene has attracted significant attention in various sensing applications including humidity19202122Here, we demonstrate resistive CMOS MEMS devices, fully integrated with an inkjet-printed chemically pristine graphene-polyvinyl pyrrolidone (PVP) composite sensing layer for humidity sensing. Our graphene ink formulation allows selective area deposition and room temperature curing after printing. The conductive graphene flakes, interspersed inside the insulating, hygroscopic PVP form a 3-dimensional (3d) percolating network that responds to adsorbed moisture by the polymer with a change in electrical resistivity, allowing humidity sensing.μHP) structure. Details of the μHP structure are reported elsewhere33μm Silicon on Insulator (SOI) CMOS process technology and fabricated in a commercial foundry, followed by deep reactive ion etching (DRIE) to release the thin membrane. The processing employs SOI wafers with 1 μm buried oxide, 0.25 μm SOI layer and 3 metallization layers. The μHP structure typically consists of an embedded, 0.3 μm thick, resistive tungsten microheater , 0.3 μm thick heat spreader plate , and a top gold layer for interdigitated sensing electrodes (IDEs). The diameters of the circular heater and membrane structures are 250 and 600 μm, respectively. The heater is fabricated during the CMOS process while the top gold electrodes and corresponding tracks are deposited as a post CMOS process in the same commercial foundry. The tungsten heater controls the operating temperature of the membrane and graphene-based sensing layer. The IDEs underneath the sensing layer are used to measure the change in resistance due to humidity exposure. Use of tungsten in the heater allows the device to operate at a very high temperature (up to 750 °C), if required, for example, when oxide-based sensing materials are used. Gold is used as the electrode material because of its chemical inertness  compared to commonly used aluminum in this SOI process. The silicon underneath the μHP is etched away, using the dioxide layer as the etch stopper, at a wafer level by DRIE technique. This forms a 4.5 μm silicon dioxide: SiO2 (4 μm)/silicon nitride: Si3N4 (0.5 μm) membrane structure onto which the microheater and electrodes are suspended. The membrane structure reduces DC power consumption of the sensing device to <5 mW when used for humidity sensing in this work. The heating temperature is uniformly confined over the microheater region, due to the buried heat spreaderA key component of our resistive humidity sensor is the CMOS MEMS based microhotplate . Two temperature coefficients of resistance  are calculated from the measured value using the relationship: α (2.05 × 10−3 K−1) and β (0.2 × 10−6 K−2) are very closely matched to the values provided by the CMOS foundry. A constant current is supplied to the The characteristic power versus temperature plot (up to 217 °C) of the 1/2, 1/2 and 1/2. N-methyl-2-pyrrolidone (NMP) is an example of such effective solvents1/2, 1/2 and 1/2 )−1) suitable for graphene typically poses a challenge for inkjet printing on low energy surfaces3N4 is estimated as ~40 mNm−1)The first step towards ink formulation is exfoliation of graphite into graphene flakes. UALPE starts with mixing bulk graphite crystals into a solvent. The ultrasound causes high-frequency pressure variations and formation of microcavities in the solvent. Collapse of these microcavities produces high shear forces, exfoliating mono-, bi- and few-layer flakes from the bulk crystals by overcoming the interlayer van der Waals forces1/2, 1/2 and 1/2) with graphene. Therefore, pure IPA based graphene dispersion cannot be used for inkjet printing. UALPE with ionic surfactants and nonionic polymers are commonly used strategies to stabilize graphene46494951It is thus required to develop graphene inks with low surface tension solvents to allow for good wetting. Alcohols, in particular, are attractive for this purpose. In addition, their low boiling point allows rapid drying of ink after deposition, ensuring uniform coating of graphene flakes. Indeed, they are commonly used as the primary or secondary solvent in the majority of graphics and functional inksg), sedimenting the unexfoliated graphite. The upper 70% of the dispersion, enriched with mono- and few-layer graphene nanoflakes, is decanted for analysis and experiment.We ultrasonicate 100 mg of graphite  with 1.5 mg PVP  in 10 mL IPA for 12 hours at ~15 °C. This starting PVP concentration enables stabilization as well as desired ink rheological properties specific to our inkjet printer nozzle discussed below. The resultant dispersion is centrifuged for 1 hour at 4,030 rpm (~1540 −1) and −1m−1) at wavelength αnm660  = 2460 Lg−1m−1 −1. We note that the graphene ink is stable, without forming any visible aggregation over several months.Optical absorption spectroscopy is used to estimate the concentration of the dispersed graphene using the Beer-Lambert law . The sample for AFM is prepared by dip-coating a Si/SiOμm diameter CMOS μm. The volume of individual droplets from this nozzle is ~10 pL. We achieve printing resolutions of ~100 μm with this set-up onto the IDEs without any surface modification. By controlling the number of droplets and the area of deposition, inkjet printing thus enables us to deposit a well defined volume of ink for humidity sensing only onto the IDEs.We next consider deposition of our graphene ink to form a graphene-PVP thin film composite as the active sensing layer over the IDEs of the 250 −1), −3), μm). As a rule of thumb, it is commonly accepted that Z value of our graphene ink, we use pendant drop measurement and parallel plate rheometry to measure −1 and −3. With a = 22 μm, we calculate Z ~ 9.48, falling into the recommended range for stable jetting. This indicates the formulated ink is suitable for inkjet printing. A stable jetting without the formation of satellite droplet or long filament is thus expected. This is experimentally confirmed by high speed jetting sequence images presented in A stable drop generation  and jetting of ink (avoiding deviation of droplet trajectory) is of primary importance for high quality inkjet printing. Otherwise, unstable jetting may lead to uncontrolled amount of ink deposition on to undesired locations. In inkjet printing, a figure of merit, The drying process of the deposited ink is critical to ensure uniform coverage after the carrier solvent is evaporated. After impacting the substrate, the wettability of the ink droplets carrying stably dispersed nanoparticles  formed from this graphene ink (c ~ 0.40 gL−1) is therefore predicted to be conductive. This is experimentally confirmed with resistance measurement between the IDEs at room temperature, 40 °C and 70 °C, as shown in where RH) levels inside a stainless steel chamber. Initially the sensors are kept in dry air before they are exposed to eight different humidity levels (10–80% The sensors are next tested using different relative humidity (RH) achieved from the sensor varies from 0.3%/%where To investigate the effect of temperature on the response, we have tested the sensors at three temperatures . The temperature rise is achieved by using the on-chip microheater. The result is plotted in –1 graphene concentration is prepared while keeping the PVP concentration constant. This gives the volume fraction v > 0.486, the deposited graphene-PVP composites after evaporation of IPA are predicated to be conductive. Sensors with these inks are then exposed to 40–60% To further investigate the influence of graphene volume fraction on the sensing layer, a series of 5 inks with 0.40, 0.32, 0.24, 0.16 and 0.08 gL−1 graphene ink exhibits the highest response and is used to further investigate typical response and recovery times . The response and recovery times measured at room temperature are reasonably fast, varying from ~6–16 s and ~60–300 s, respectively; The sensor with 0.40 gL−1 ink and are tested at room temperature. The reproducibility of response is demonstrated at 50% Reproducibility of a sensor at different sensing cycles and of sensing over a long period are also investigated. We measure response of different sensors with the same design to investigate performance variations between the devices. All the sensors use 0.40 gL+ and OH− ions at the edges of graphene, similar to what is observed for graphene oxide samples+ ions may tunnel from one water molecule to another through hydrogen bonding, reducing the overall electrical resistance of the sensing layerThe adsorbed water molecules on graphene surface may disassociate to HIn summary, we have integrated functional graphene inks with CMOS MEMS technology to fabricate a resistive humidity sensor. Our formulation of the ink using a blend of hygroscopic, electrically insulating polymer with chemically pristine, conducting graphene nanoflakes offers an ideal sensing layer for use with an economic, compact and low power CMOS sensing platform. Through 3d percolation theory, we show that our ink formulation produces a conductive sensing layer. Upon humidity exposure, reduction in percolating networks in the sensing layer leads to an increased resistivity for humidity sensing. The response of the sensors are reproducible, with a maximum of ~13% variation among sensors at different How to cite this article: Santra, S. et al. CMOS integration of inkjet-printed graphene for humidity sensing. Sci. Rep. 5, 17374; doi: 10.1038/srep17374 (2015).


Idiopathic pulmonary fibrosis (IPF) is an emerging problem in the western world, being related to increasing age and implying significant costs for the diagnosis and management of affected patients. The epidemiology of IPF is not well understood.To allow estimates of the problem and eventually to evaluate quality of the care of IPF patients in Sweden, a national IPF Registry was started in the autumn of 2014. Data on criteria used to diagnose IPF, demographics, lung function, and quality of life  were reported directly to the registry, based at the coordinating centre  via a web-based platform.During the first year, the registry was implemented in 11 (33%) of the 33 respiratory units in the country. Seventy-one patients were registered between October 2014 and October 2015, 50 (70.4%) males and 21 (29.6%) females. Median age was 70 (range 47–86). The mean K-BILD score at the first inclusion in the registry was 54.3+9.5.The main features of IPF patients in this first Swedish cohort were consistent with data published in the literature in main multinational randomized controlled trials. The K-BILD questionnaire showed that quality of life of patients with IPF and their perception of the disease are quite poor at the time of inclusion in the registry. Idiopathic pulmonary fibrosis (IPF) is defined as a specific form of chronic, progressive fibrosis of unknown cause, occurring primarily in older adults, and limited to the lungs, with a survival of about 3–5 years from the diagnosis . A multiThe Swedish Guidelines for IPF , publishTwo drugs (pirfenidone and nintedanib) are now registered based on large randomised clinical trials –11 and aTo provide a platform to address these questions, a national quality registry for IPF was started in Sweden in September 2014.The main objective of this paper is to demonstrate the feasibility of the implementation of a web-based IPF registry in Sweden and to report the results of the first year of activity of the Swedish IPF-Registry.A web-based platform, already in use in Finland , was chosen and adapted to Swedish healthcare and regulatory standards. The platform allowed the registration of demographics, lung function, radiology, quality of life ) , ongoingTo be included in the registry, patients had to fulfil the diagnostic criteria for the diagnosis of IPF according to national and international guidelines –7. Tablet-test was used when appropriate, with level of significance at p<0.05.A cross-sectional analysis of the data reported at the time of inclusion in the registry between September 2014 and October 2015 is presented. Continuous variables are presented as mean±standard deviation of the mean or median and range. Categorical variables are presented as proportions of the total population. Single sample, paired The study was approved in August 2014 by the Stockholm's Regional Ethical Committee (Ref. No. 2014/1202-31/4). All patients needed to be informed by the case manager at his/her hospital about the aim of the project and to sign a written consent before inclusion in the registry.The web-based platform was activated at the Karolinska University Hospital, Stockholm, Sweden, and made available for all participating centres in September 2014. The Karolinska University Hospital assumed the role of leading and legally responsible institution for the implementation of the project.The initiative was made public with annual presentations at the Swedish Respiratory Society Congresses in Malmoe 2014)  and in G14  and iDuring the study period, 14 of the 33 (42%) Swedish respiratory disease units were connected to the registry and 11 (33%) started to report data from patients with IPF in the first year of activity of the Swedish IPF-Registry. The hospitals participating in the data collection and the relative number of patients registered for each centre during the study period are reported in A total of 71 patients with IPF were recorded in the Swedish IPF-Registry during the first year of activity. Demographics and main features of the patients at the time of registration in the IPF-registry are reported in The diagnosis of IPF was based on clinical–radiological features in 52 (72%) patients, while 10 (14%) underwent a lung biopsy and 14 (20%) received a diagnosis after a multidisciplinary conference.2 during or just after the test compared to the value at rest .Thirty-one (44%) of the patients underwent a 6-min walking test at the time of inclusion in the registry; most of them presented a much lower SaOThe mean value of the K-BILD score was 54.3±9.5, demonstrating a relatively low quality of life at the time of inclusion in the registry.Our report shows that web-based tools can rapidly be implemented and used to address important questions in healthcare at national level. Our experience reinforces previous reports from Australia, showing that technological tools can greatly improve the understanding of rare disease at a national level and overcome quite easily geographical distances and logistic problems .The implementation process is crucial to the success of the project, and many practical and technical issues need to be promptly addressed while connecting the participating centres: to secure that data are correctly entered and timely reported is important to secure accuracy and completeness of the registry; on the other hand, the staff of the respiratory units involved in the project had already a clinical burden of everyday chores to perform in their hospitals. Part of the success of the initial implementation of the Swedish IPF-Registry was to identify committed doctors and motivated staff in the respiratory units. Support of a registry coordinator making regular visits to the participating centres to solve technical and practical issues was crucial to ensure engagement of the users and registered data of high quality. Users were constantly involved in a discussion on how to ease the registration of data, and the national guidelines on IPF served as a valuable source of definitions. Technical, IT, and practical issues  were continuously discussed with the registry coordinator and addressed with the IT company.The patient cohort presented in this manuscript cannot be considered representative of the whole population of IPF patients in Sweden. Data on the epidemiology of IPF in Sweden are simply not available. One of the aims of starting an IPF-registry was in fact to provide estimates on this disease in Sweden, but this will be possible only if the registry covers at least 80% of the country. This goal might be reasonably reached in 2018.The main features of the patients recorded in the Swedish IPF-Registry seem to resemble the clinical presentation of IPF as reported in multinational multicentre randomised controlled trials –11.Males seem to be more affected than females, as shown in previous studies, as well as the high prevalence of ex-smokers among IPF-patients .The diagnosis was mostly based on clinical–radiological features  , 7, and Interestingly, most of our patients were affected by a mild or moderate form of IPF according to the forced vital capacity (FVC) value. Nevertheless, most of them reported a relatively poor quality of life, with a mean K-BILD of 54.8; this finding supports an ongoing discussion questioning the value of FVC in the assessment and follow-up of patients with IPF. Perhaps total lung capacity and diffusion capacity for carbon monoxide might better correlate to quality of life, but further studies on large cohorts are needed to confirm this hypothesis. Data from the Australian IPF registry, presented at the latest European Respiratory Society Congress in Amsterdam in September 2015, showed no correlation between the decrease of FVC and the changes in quality of life recorded with the Saint George Respiratory Questionnaire . Larger Thanks to a grant from the Swedish Heart and Lung Foundation (Ref. No. 20130706). We thank the Karolinska University Hospital, the Karolinska Institutet and the Quality-Registry-Centre Stockholm (QRC-Stockholm) for the technical support, and the Department of Respiratory Medicine and Allergy at the Karolinska University Hospital for supporting the project by providing resources to hire the registry coordinator. Boheringer Ingelheim contributed with a supporting grant in 2015 and Intermune/Roche supported the translation in Swedish of the K-BILD questionnaire. We thank Dr. Surrinder Birring for allowing the use of K-BILD and for the technical help he offered in implementing K-BILD in our registry. A special thanks to Helène Blomqvist, Margitha Dahl, Gunnel de Forest, Henrik Ryftenius, and Lise-Lotte Ladenfelt Gestrè for their help in the implementation of the registry at the headquarter of Karolinska University Hospital, Solna, Sweden.The Swedish Idiopathic Pulmonary Fibrosis Registry Group: Stockholm: Giovanni Ferrara, Magnus Sköld, Lisa Carlson, Maria Diakopoulou, Valentyna Yasinska, Henrik Ryftenius, Lise-Lott Landenfelt Gestré, Gunnel de Forest, Margitha Dahl, Helene Blomqvist, Ingrid Gerhardsson, Olov Andersson. Göteborg: Anders Thylen, Kärstin Byström; Umeå: Kenneth Nilsson, Lena Granbom, Ala Muala. Uppsala: Shumi Omar, Carl-Axel Karlsson, Inger Dahlen. Gävle: Andreas Palm, Anna Svensson, Kristina Forsberg, Anna Bergengren, Carl Blomberg, Eva Branden, Johan Isaksson, Hirsh Koyi, Johanna Roos, Stefan Soneberg. Falun: Pierre Sobrino, Anders Pettersson, Anders Birkehag, Jon Goenechea, Wolfgang Greger, Gabriel Lundberg, Saba Raouf. Helsingborg: Rolf Rosin, Charlotta Berling, Lars Danielsson, Lena Eldh, Mats Lagerstedt. Lund: Jonas Einarsson, Helena Jonsson, Hillevi Larsson. Linköping: Lennart Persson, Ewa Petterstedt, Christel Bergström, Antje Kuhlman, Maria Sege. Sunderby: Dirk Albrecht, Christos Belias, Cecilia Olivesten. Östersund: Per-Olof Rydström, Nikolai Stenfors, Cristina Cretu, Jan Starlander. Örebro: Lennart Nilholm, Josefin Sundh. Kristianstad: Lars Andersson, Håkan Leksell, Anna Collen Kandell. Skövde: Anders Planck, Synnöve Alves, Gudrun Hemeren, Åke Johansson, Savvas Papadopoulos, Akos Somoskovi, Per Torstensson. Trollhättan: Bo Pedersen, Lars Johansson, Ulla Waxne, Milena Ymefors.


Isonymy measures and surname distances have been computed for, and between, the 47 mainland Spanish provinces and compared to a numerical classification of corresponding language varieties spoken in Spain. The comparison of the two bootstrap consensus trees, representing surname and linguistic variability, suggests a similar picture; major clusters are located in the east , and in the north of the country . Remaining regions appear to be considerably homogeneous. We interpret this pattern as the long-lasting effect of the surname and linguistic normalization actively led by the Christian kingdoms of the north (Reigns of Castilla y León and Aragón) during and after the southwards reconquest (Reconquista) of the territories ruled by the Arabs from the 8th century to the late 15th century, that is when surnames became transmitted in a fixed way and when Castilian linguistic varieties became increasingly prestigious and spread out. The geography of contemporary surname and linguistic variability in Spain corresponds to the political geography at the end of the Middle-Ages. The synchronicity between surname adoption and the political and cultural effects of the Reconquista have permanently forged a Spanish identity that subsequent migrations, internal or external, did not deface.To assess whether the present-day geographical variability of Spanish surnames mirrors historical phenomena occurred at the times of their introduction (13 Llegando el autor desta grande historia a contar lo que en este capítulo cuenta, dice que quisiera pasarle en silencio, temeroso de que no había de ser creído […]. Finalmente, aunque con este miedo y recelo, las escribió de la misma manera que él las hizo, sin añadir ni quitar a la historia un átomo de la verdad, sin dársele nada por objeciones que podían ponerle de mentiroso; y tuvo razón, porque la verdad adelgaza y no quiebra, y siempre anda sobre la mentira, como el aceite sobre el agua…. But after all, though still under the same fear and apprehension, he has recorded it without adding to the story or leaving out a particle of the truth, and entirely disregarding the charges of falsehood that might be brought against him; and he was right, for the truth may run fine but will not break, and always rises above falsehood as oil above water…]Miguel de Cervantes Saavedra, Don Quixote, second part, chapter X.Fifty years have passed since the seminal study on the relation between surname diversity and inbreeding by Crow and Mange  and, todth century. Initially they were a simple way to identify a family or a person, like a designation or nickname that could vary over the time and the generations , while later, for the administrative need to identify a lineage without ambiguities, they became progressively fixed in meaning and spelling. The geographic diversity of the naming practices, the influence of regional languages, the political asset of a region, contributed to the diversity of initial surnames that remain, several centuries after their introduction, a marker of regional diversity. Analyzing Spanish surnames as markers of population diversity, or homogeneity, is the purpose of this research.In many Europeans countries, surnames started to develop in the early Middle Ages and became stable, generation after generation, towards the 16th century. They became progressively inherited from the 13th to the 15th century, which is during the growing expansion of the Reign of Castilla and the Reconquista of the territories ruled by the Arabs in the preceding centuries. Isabel I, queen of Castilla y León, and her husband Ferdinand II of Aragón (known as the Catholic Majesties) completed the reconquest and gave stability to their respective reigns in a process of large political integration that officially ended, with a unique crown, in 1714 . At the time, religion was also a political instrument and the Spanish Inquisition  contributed to the castillanization and normalization of surnames (a process that lasted until 1870), ultimately leading to a considerable loss of surname diversity. Newly adopted surnames  were often ending with the suffix—ez, a typical Castillan patronymic form . This process corresponds to the growing of the Castilian kingdom, when Aragónese, Asturian-Leonese and Basque names were Castilianized. This is particularly the case for Aragónese and Asturian-Leonese family names. A confirmation that records were generally written in Castilian, and therefore the surnames, comes from the Spanish surnames existing in Latin America, a major destination of historical Spanish emigration, that are generally in this form. The process of Castilianization, together with the use of a double surname-system , largely explains why Spain has a lower number of surname variants than other European countries [In Spain, the use of surnames started with the 10ountries , 10, 11.th century, the prescriptions of the Ecumenical Council of the Roman Catholic Church  made mandatory the use of vertically transmitted surnames, stable generation after generation, in order to keep exhaustive birth and marriage records in all parishes (death and census records became compulsory in 1614).Castilianized forms lasted because, in the 16Arab and Jewish surnames, two large communities in the Spain of that time, did not escape the “normalization” described above, meaning that a large proportion of the Arab and Jewish family names existing nowadays in Spain corresponds to later immigration, and not to the descendants of the medieval population.By using the national telephone directory as source of data, the Spanish surname corpus has been studied at least three times , 13, 14,corpora, the family names that are historically typical (“autochthonous”) of given regions, that is those that better describe the Middle-Ages population stock in geographical terms. In this article we adopt the opposite approach by avoiding any surname selection in the analysis of the Padrón municipal, the largest available register of the Spanish population. The Padrón municipal is a national census of all residents, listed regardless of their age and nationality. It also includes all the immigrants whose administrative status has not been decided yet. This database is less conservative than telephone directories or voters’ lists that have a lower sample size and do not represent all social groups, particularly immigrants .The robustness of the surname classification has been tested by bootstrap . In factPadrón municipal  of the year 2008 has been obtained from the Spanish National Institute of Statistics . We processed the 45,593,365 personal records corresponding to the 47 mainland official provinces and to 15 regions  and the second one is inherited from the mother (-Diaz). At each generation the surname of the mother is lost, only the one of the father being constantly listed in the first position (recent laws now enable to swap their order or to keep only one surname of choice). Paternal and maternal surnames constantly mix in a double form that is not stable over the time and just depends on the random process of mating. This is why we decided to process them as separate tokens corresponding to single surname types  and not to individuals (Rodríguez Diaz). For computational ease, we kept only the surnames having a frequency higher than 20 occurrences  have been developed over the time. They are often based on isonymy, that is the probability that two surnames, randomly extracted, are identical. This probability is computed for all the different surnames in the database and depends on their frequency. In short, if two areas do not share any common surname, the measure of isonymy will be null; in the opposite extreme case, when the two areas are inhabited by individuals all having the same identical surname frequency, isonymy will be equal to 1. Mathematically isonymy is computed as:Isonymy was originally developed to estimate inbreeding in marriage registers by computing the number of same-surname marriages, that often correspond to marriages between first-cousins. Since this application, the computation of isonymy, as a probability, has been extended to large databases.From isonymy, several similar measures of diversity can be computed, for instance Hedrick’s , Nei’s , Lasker’darlu@mnhn.fr.We ended by having two 47 x 47 distance matrices (according to formulas 4 and 5) accounting for the 47 mainland Spanish provinces. The computations were run on the DISNEI program, written by P. Darlu. The software is available upon request to Each surname has a peculiar frequency distribution in space. Any new subset of a surname database, once analyzed, leads to a distance matrix that is each time different, the differences being determined by the random presence or absence of given surnames.Instead of computing a single distance matrix on the whole dataset, we preferred to resample original data to obtain 100 subsets and, from them, 100 different pairwise distance matrices. Then, from each matrix, we computed a separate Neighbor Joining (NJ) tree . From thThe Linguistic Atlas of the Iberian Peninsula (ALPI)  is consti.e. the Catalan zone, the Castilian-speaking area and the Galician-Portuguese area. The Basque varieties have not been recorded and the islands have not been fully sampled . When the Spanish Civil War started (1936–1939) the fieldwork had almost been completed, but Navarro Tomás went in exile and took all the materials with him. The notebooks were returned to Spain in 1951, and remaining surveys were completed between 1947 and 1954. Manuel Sanchis Guarner coordinated with Lorenzo Rodríguez Castellano and Aníbal Otero the painstaking work of preparing the materials for publication, which yielded to the only available volume of the Atlas [http://westernlinguistics.ca/alpi/more_info.phpThe project was started in 1914 by the Spanish philologist Ramón Menéndez Pidal  and was supervised by his student Tomás Navarro Tomás. Three teams of fieldworkers covered the Iberian Peninsula, he Atlas . Shortlyrelativer Identitätswert, RIW [RIW measures the similarity between two basilectal varieties as the percentage of items on which the two varieties agree. This is an accepted method to measure differences between dialects and close languages. A description of the computational work is reported in [A dialectometric analysis of the first volume started in 2009 in the laboratory of Hans Goebl . Dialectometry is the subfield of dialectology aimed at mathematically measuring the differences between dialect variants. Original data have been analyzed by Goebl to identify phonetic, morphologic, syntactical and lexical features. Each feature has been processed separately in 375 working maps corresponding to 532 sampling points. Goebl sent us the final 532 x 532 similarity matrix computed according to the relative identity value . Thorted in .To compare the linguistic similarity of Spain to its surname diversity, we have selected a subset of 44 sample points out of the 532 ones listed in the ALPI . We keptAs we wanted to analyze linguistic diversity in terms of distance matrices, we applied the transformation:As with surnames, tiny differences in the selection of the features that are aggregated in a linguistic database can lead to unstable results . As we had no access to the dataset of linguistic features reported in , we coulPadrón municipal) because we added the paternal and the maternal surnames to the database separately  occurring 51,419,788 times. This quantity exceeds the number of individuals constituting the Spanish population in 2008 . Very large deviations from this reasonable pattern concern the provinces of Barcelona and Madrid, and, to a lesser extent, the province of Valencia . It turns out that the measures of isonymy, and the clustering derived from them, remain very similar to the ones presented in this paper (f ≥ 20). This is not surprising, because the mathematical definition of isonymy (and related distance measures) gives a low weight to infrequent surnames. While there is a systematic bias linked to the number of municipalities that compose each province, it does not seem to significantly influence our results because, after all, the classification of Valencia, Madrid and Barcelona . Further analyses (not shown), restricted to the Castilian speaking area only, have confirmed its really low differentiation.The linguistic tree  is extreWhen distance (or similarity) matrices concerning the same elements are available, is it common practice to compute Mantel test correlations . We compReconquista have defaced a large part of its surname and linguistic variability. Our point, here, is to show that Mantel correlations are often insufficient to describe a phenomenon that concerns only a part of the pair-wise elements.According to the Mantel test, while linguistic and surname measures are correlated with geographic distances, they are not cross correlated . This reth–16th century), or if internal migration and international immigration have defaced them. Our analyses may be unrepresentative of the surnames (often rare) corresponding to international immigration, because we processed only a subset of the Padron Municipal  appears several times in the Padrón Municipal, thus making possible their inclusion in our working database.Our initial research question was to assess whether the present-day geographical variability of Spanish surnames mirrors historical phenomena occurred at the times of surname introduction , North African Muslims and other groups largely present in Spain until the reconquest, is still found in the Spanish population, as a comprehensive Y-chromosome study has recently shown [ly shown . If specly shown , conductEven if the historical signal is well preserved in contemporary Spanish surname data, some features of the classification  are likeReconquista, as the consequence of a long-lasting process of Christianization and castillanization together with the increase of the Castilian prestige. The other way round, the lower levels of isonymy in Cataluña, Valencia, Aragón and Navarra can be interpreted by a lower degree of surname Castilianization (these regions were part of the reign of Aragón that maintained separate administrative systems until 1714 CE) and by the specific language context  that acted as a source of surname diversity. To these structural aspects, we should add the effect of internal migrations, from all Spain, to the wealthy province of Valencia and to the region of Cataluña , with a recent increase in their surname diversity. The reverse probably happened in provinces having very high levels of isonymy . Interestingly, and as a partial explanation deserving more research, none of the provinces listed has, or had, a special economical attractiveness. We note that isonymy also depends on the population size at the time of surnames introduction, and it is likely that high levels of isonymy reflect a sparse population during the Middle-Ages .Isonymy levels at the provincial level ; Fig 7C,As a general conclusion, isonymy cannot be readily attributed to a single cause and multidisciplinary research, involving historians and historical demographers, would be of help to assess the magnitude of each single factor. What is clear is that the east/west divide in the pattern of isonymy  perfectlWe found no statistical support for the inverse correlation between consanguinity values (computed from isonymy) and the density of the population per province  reportedThe data contained in the Linguistic Atlas of the Iberian Peninsula (ALPI)  are abouThe clusters yielded by the computational linguistics analysis of the ALPI  largely Before the Arab invasion, the linguistic landscape of Spain consisted of local varieties resulting from the adoption of Latin by populations that previously spoke Celtic and Iberian languages. Latin varieties evolved for about a thousand years, from the Roman conquest of the Iberian peninsula (started in 218 BCE) to the Arab take-over (started in 711 CE), when a progressive linguistic arabization started.The length of the Arab domination, and its influence on the language, differ geographically, having lasted a couple of centuries in the North of Spain and about eight centuries in the very South. During the progressive reconquest of the peninsula by the Christian kingdoms of the North and the growing expansion of the reigns of Castilla y León and Aragón , northerBy looking at the forces here at play in the forge of a distinctive Spanish linguistic identity, we can understand how strong must have been the Castilianization of Spanish surnames.


While active LINE-1 (L1) elements possess the ability to mobilize flanking sequences to different genomic loci through a process termed transduction influencing genomic content and structure, an approach for detecting polymorphic germline non-reference transductions in massively-parallel sequencing data has been lacking.Here we present the computational approach TIGER (Transduction Inference in GERmline genomes), enabling the discovery of non-reference L1-mediated transductions by combining L1 discovery with detection of unique insertion sequences and detailed characterization of insertion sites. We employed TIGER to characterize polymorphic transductions in fifteen genomes from non-human primate species , as well as in a human genome. We achieved high accuracy as confirmed by PCR and two single molecule DNA sequencing techniques, and uncovered differences in relative rates of transduction between primate species.By enabling detection of polymorphic transductions, TIGER makes this form of relevant structural variation amenable for population and personal genome analysis.The online version of this article (doi:10.1186/s12864-016-2670-x) contains supplementary material, which is available to authorized users. Alu, L1 and SVA [The completion of the human and of non-human primate reference genome sequences showed that nearly half of the genome is derived from various transposable sequences –4. Due t and SVA , 12. Upo and SVA . This pr and SVA –17. In a and SVA .reference transductions (i.e. elements present in the reference genome) have reported that transductions are relatively abundant, with estimates that around 10 % of L1 and SVA insertions detectable in the human reference assembly exhibit 3′ transduction events [non-reference transductions and consequently there is little knowledge on transduction-mediated sequences polymorphic in the population. Kidd and co-authors, prior to the widespread application of next generation sequencing (NGS), identified several polymorphic L1-transductions through a fosmid library-based Sanger sequencing approach in nine HapMap samples [Retrotransposition can contribute to diseases , 19 and n events , 23, 27. samples  and MacF samples . Further samples , Paterso samples  and two  samples , 33 – whhttp://www.korbel.embl.de/software), makes a relevant class of structural variation amendable for personal genome analysis.Here we describe a computational approach suitable for the discovery of non-reference polymorphic (or monomorphic) mobile element transduction events – termed TIGER for Transduction Inference in Germline genomes – based on Illumina NGS data. We applied TIGER to the detection of L1 mediated 3′-transductions, the most abundant class of mobile element transductions , 16, in Using TIGER we analyzed previously published chimpanzee, orangutan and macaque whole-genome sequencing (WGS) data  from fivTIGER uses a combination of 1) non-reference L1 insertions – in this study discovered by a modified version of TEA , includi non-refeAll predicted L1-mediated transduction insertion regions were filtered for overlap with corresponding segmental duplications  as wellTo assess which subfamily class drives L1 insertions as well as L1-mediated transductions, consensus sequences for all full-length (>6 kb) primate L1s were constructed from multiple reference elements  characteristic hallmarks of mobile element insertions (MEIs), including non-reference polyA tails and TSDs, which are retrieved from the Transposable Element Analyzer (TEA) algorithm ; (2) abe charactein silico simulations  . An examTo verify the accuracy of TIGER, we performed validation experiments on 51 randomly chosen 3′ transduction calls , using PCR followed by capillary sequencing Table . This vaTIGER can be used for estimation of the size of the transduced sequence – however, this capability is strongly dependent on read length and insert-size of the paired-end NGS library, with short NGS reads being only of limited use for detecting the boundaries of the L1 element’s 3′ and the transduced sequence’s 5′ at target loci. In our analyses, sizes of computationally inferred transduction sequence lengths varied between 90–260 bp in chimpanzee, 74–437 bp in orangutan and 64–361 bp in macaque. This suggests that TIGER’s minimal sequence requirement for reliably inferring transductions in Illumina sequencing data is ~50–60 bp.Both short NGS reads and Sanger sequencing reads do not typically fully span the target locus, which complicates the characterization of transduction events. We reasoned that third generation long-read single molecule DNA sequencing technologies may help overcome this challenge, by fully recovering the complete sequence and structure of the combined insertion. Hence, we employed both Pacific Biosciences (PacBio) sequencing  Fig. 4aa4a and cWe first employed TIGER to discover transduction events in the human HapMap DNA sample NA12878 (down-sampled to a similar coverage as the primate data ), which Second, we obtained similar validation results for all three non-human primate species, through Oxford Nanopore sequencing data which we generated as part of the MinION Early-Access Programme, following long-range PCR amplification of candidate loci . For example, MinION reads spanning the rhesus macaque L1 transduction candidate locus on chromosome 3 (chr3:85520263-85520279) verified the presence of a ~1.2 kb insertion Fig. , and furFacilitated by the generated long read sequencing data we examined the length distribution of the inserted L1 elements and of the transduced sequences, observing transduction sequence lengths ranging from 51 to 1570 bp  for chimpanzee, 8.8 % ± 1.4 for orangutan, and 5.5 % ± 1.2 for macaque, , chimpanzee-macaque (P = 0.000073) and orangutan-macaque (P = 0.0003), Table To calculate the rate of transductions per species, we divided the number of high confidence TIGER transduction calls by the total number of non-reference L1 insertions (including solo L1s and transducing L1s) identified using TEA  or TIGERWe further tested whether the observed difference in transduction rates among species could reflect underlying differences in the efficacy of selection among non-human primates with different effective population sizes. We observed no evidence that selective constraints varied substantially among these primate species, and obtained little evidence for an impact of effective population size on the efficacy of selection  with annotated functional regions of the genome, considering all events identified in this study. The majority of transduction sequences were derived from intergenic regions (205/280) and a similar fraction also inserted into intergenic regions. Approximately a third (90/280) inserted into intronic regions, where some may have an effect on gene regulation , 35, 44 in trans , which mWe further investigated the source-donor L1 relationship with a focus on transduced sequences. Among three out of the six transduction calls observed in humans, we obtained evidence for a full-length reference L1  element immediately upstream of the predicted transduction source locus , albeit not nominally significant, whereby L1CER-3 associated transductions showed depletion relative to solo L1s (P = 0.026). By comparison, in orangutan L1PA2 elements exhibited an increased rate of transductions relative to solo L1s (P = 0.001), whereby in chimpanzee too few L1 transductions with reliable subfamily annotation were identified to allow for robust statistics.Finally, we investigated L1 subfamilies responsible for transductions to evaluate whether L1 subfamily specificity may explain the differential rate at which L1 elements are accompanied by transduced sequences in different species  is slightly lower when compared to previous studies reporting ~10 % , 17, 49,.5 % is sIt is possible that an improved FDR of TIGER may be achieved in conjunction with higher confidence MEI calls. In this regard, our FDR estimate for TIGER (15.7 %) is well in line with a recent FDR estimate (16–24 %) for the TEA mobile element discover algorithm  used forAlthough TIGER should in principle be capable of identifying 3′ and 5′ transductions accompanying L1 insertions, we have not observed a single 5′ transduction event driven by an alternative upstream promoter in our data. 5′ transduction events were shown to be extremely rare in human genomes with only few cases reported , 42, 43.Alu-mediated transductions have so far not been reported in the literature and thus were not a target of our study. In principle, while we chose to work with the TEA algorithm to identify L1 input signals, TIGER can be used in conjunction with other MEI discovery algorithms, including Tangram [Our study focused on the inference of polymorphic L1 transductions, with L1 elements belonging to the autonomous retrotransposition-competent mobile element class commonly mobilizing non-repetitive sequences. While SVA elements are also capable of transducing unique DNA sequences  and ther Tangram , Mobster Tangram , TE-Trac Tangram  and Retr Tangram , augmentWe developed TIGER for identifying non-reference retrotransposon-mediated transductions in the germline using NGS data. TIGER, which can be used in conjunction with a number of translocation and non-reference retrotransposon discovery tools, will enhance variant analysis pipelines, and offers access to an as yet under-explored type of germline genetic variation.Not applicable.Not applicable.All data presented in this study is either a part of the manuscript or supplementary files listed below.


Magnetism in graphene has been found to originate from various defects, e.g., vacancy, edge formation, add-atoms etc. Here, we discuss about an alternate route of achieving magnetism in graphene via grain boundary. During chemical vapor deposition of graphene, several graphene nucleation centers grow independently and face themselves with unusual bonding environment, giving rise to the formation of grain boundaries. We investigate the origin of magnetism in such grain boundaries within first-principles calculations, by letting two nucleation centers interact with each other at their interface. We observe formation of unprecedented point defect, consisting of fused three-membered and larger carbon rings, which induces net magnetization to graphene quantum dots. In case of periodic lattices, the appearance of array of point defects leads to the formation of magnetic grain boundaries. The net magnetization on these defects arises due to the deviation from bipartite characteristics of pristine graphene. We observe magnetic grain boundary induced dispersion less flat bands near Fermi energy, showing higher localization of electrons. These flat bands can be accessed via small doping, leading to enhanced magnetism. Moreover, the grain boundaries can induce asymmetric spin conduction behavior along the cross boundary direction. These properties can be exploited for sensor and spin-filtering applications. A ≠ NB introduces net magnetic moment. Being a bipartite lattice, this theorem is valid in case of graphene as well. The graphene unitcell consists of two sublattice points, A and B that prefer opposite spin occupancies, making the over all net magnetization zero  with active carbon atoms of unsatisfied valencies. Now, the structural relaxation results in merging of two domains with or without defects. Here defect refers to the formation of non-hexagonal carbon rings. Since, we consider quantum dot like small segments in During diffusive growth of graphene on some substrate, there is formation of several nucleation centers that grow independently until they merge finally at their interface with smooth or mismatched crystallographic angle4750Note that, we have not considered the underlying substrate explicitly in our calculations. However, we believe that, the simulation technique of surface diffusion of carbon atoms as adopted here can mimic the CVD growth of graphene on Cu surface535453S / C atom) for all the relaxed structures, which have been calculated by the following equation,We perform structural relaxations with several starting geometries varying the position and number of carbon atoms at the interface of two quantum dot like graphene segments and present four representative structures, namely S1, S2, S3 and S4. Our calculations always result in planar structures with varying geometry and bonding at the interface, as depicted by the shaded region in Total, EC and EH are the energies of the relaxed structures , one carbon atom and one hydrogen atom, respectively and NC NH is the number of carbon (hydrogen) atoms in the system. Note that, the stabilization energy of S2 as shown in where, EA and NB becomes impossible. That may lead to asymmetric distribution of up and down spins and may induce net magnetization. Although, the appearance of magnetization is not always obvious as observed in case of Stone-Well’s defect, i.e., the fused 5 and 7 membered rings, which does not prefer any local spin moments57585960A ≠ NB. Rather, it results due to the collapse of the bipartite nature over the PD. Moreover, the observed magnetization does not appear only due to the presence of zigzag edges. Although, the appearance of local spin moments at zigzag edges has been observed in S3’, their contribution is far too less compared to the local spin moment over the PD and cannot be seen within the considered isovalue in Now it is obvious that, the bipartite nature of pristine graphene collapses at such defects and discrimination of NThe appearance of localized states in case of zigzag edge graphene nanoribbons has been explored in great extent in the existing literature and observed experimentally as well19202326A ≠ NB. Moreover, in spite of even number of carbon atoms in the supercell of D3, the appearance of localized spin moments over the GB proves our argument of unusual bonding induced magnetization. Note that, these magnetic GBs contain four-eight and four-ten membered fused rings, respectively.That is why, we next consider the periodic supercells with two graphene grains facing each other with zigzag and Klein edges, as can be seen in 5354552 network. Now, before entering the electronic properties of these GBs, we first discuss about the modified Brillouin zone in All these GBs are less stable compared to the pristine graphene in , as can However, in case of GB formation in D1, D2 and D3, the linear dispersion completely disappears with appearance of metallic density of states (DOS) at Fermi energy, as can be seen from 57585960Furthermore, we explore the behavior of these magnetic GBs in presence of graphene edges. Before discussing about their electronic properties, we first present the much-studied zigzag graphene nanoribbon system in absence of any defect and show its spin density and electronic properties in 24252728When we create similar interfacial environment (as in D2 and D3) in case of ribbons, we obtain identical GBs after geometrical relaxation, as can be seen in In conclusion, we have observed the formation of magnetic point defects and grain boundaries during the CVD growth of graphene within ab-initio framework. The simulation procedure of defect formation via allowing two graphene segments to interact with each other, as adopted in this study is simple but unprecedented. Moreover, for the first time we detect the possibility of a point defect of three-membered carbon ring with surrounding larger rings that can induce net magnetization to the graphene sample through the spin polarized localized states. The observation of stable three-membered carbon ring is interesting from fundamental chemistry viewpoint and can be detected via scanning tunneling microscope (STM) experiment due to higher charge localization. In case of periodic systems, however the magnetic GBs are built by the fusion of four membered rings with larger carbon rings. These observations lead to the conclusion that, the existence of smaller rings in the defect indulges the formation of larger rings which localize the non-bonding electrons to give rise to net magnetization. As a whole, this phenomenon arises due to the deviation from the graphene bipartite nature at the defect. The electronic properties show the possibilities of doping induced magnetic excitations and asymmetric spin transports across the GBs. Therefore, these unprecedented magnetic defects can be useful for sensor and spin-filtering applications. Note that, the geometrical aspects of PDs and GBs can be completely stochastic depending on the interfacial environment within graphene grains during CVD growth. But, our argument that, the formation of localized states will always give rise to magnetism, remains generalized. There exist a vast room for exploration of these defects with potential application possibilities. Our present study is just the first step towards the understanding of the GB induced magnetism in a purely carbon system.ab-initio level of calculations as implemented in SIESTAFor the structural relaxation of CVD grown graphene and for the investigation of the electronic properties of the same in presence of PDs and GBs, we adopt How to cite this article: Dutta, S. and Wakabayashi, K. Magnetization due to localized states on graphene grain boundary. Sci. Rep.5, 11744; doi: 10.1038/srep11744 (2015).


The sensor has been designed and fabricated through a standard 0.35 µm CMOS process technology and post-CMOS micromachining technique has been successfully implemented to release the MEMS structures. The sensor is operated in the dynamic mode using electrothermal actuation and the output signal measured using a piezoresistive (PZR) sensor connected in a Wheatstone bridge circuit. The output voltage of the humidity sensor increases from 0.585 mV to 30.580 mV as the humidity increases from 35% RH to 95% RH. The output voltage is found to be linear from 0.585 mV to 3.250 mV as the humidity increased from 35% RH to 60% RH, with sensitivity of 0.107 mV/% RH; and again linear from 3.250 mV to 30.580 mV as the humidity level increases from 60% RH to 95% RH, with higher sensitivity of 0.781 mV/% RH. On the other hand, the sensitivity of the humidity sensor increases linearly from 0.102 mV/% RH to 0.501 mV/% RH with increase in the temperature from 40 °C to 80 °C and a maximum hysteresis of 0.87% RH is found at a relative humidity of 80%. The sensitivity is also frequency dependent, increasing from 0.500 mV/% RH at 2 Hz to reach a maximum value of 1.634 mV/% RH at a frequency of 12 Hz, then decreasing to 1.110 mV/% RH at a frequency of 20 Hz. Finally, the CMOS-MEMS humidity sensor showed comparable response, recovery, and repeatability of measurements in three cycles as compared to a standard sensor that directly measures humidity in % RH.This paper reports on the fabrication and characterization of a Complementary Metal Oxide Semiconductor-Microelectromechanical System (CMOS-MEMS) device with embedded microheater operated at relatively elevated temperatures (40 °C to 80 °C) for the purpose of relative humidity measurement. The sensing principle is based on the change in amplitude of the device due to adsorption or desorption of humidity on the active material layer of titanium dioxide (TiO Humidity is the amount of water vapor in the air compared with the amount of vapor needed to make the air saturated at its current temperature. Humidity sensors can be used in many applications such as medical equipment, agriculture, heating, ventilation and air conditioning (HVAC) systems, the automobile and semiconductor industry, intelligent control of the living environment in buildings, hygrometers and consumer goods, and cooking food control for microwave ovens . Fenner et al.  reported2) and titanium dioxide (TiO2) are very popular sensing materials for these types of humidity sensors. Polymer-based sensors have also been used for humidity detection for a very long time [Traditional humidity sensors depend on changes in electrical properties of thin films of various materials; these changes can be estimated by measuring either a resistance ,4,5,6,7 ong time ,18,19.Humidity sensors of these types are fabricated using standard CMOS process with some form of post-CMOS micromachining or other additional post-CMOS processes to complete the sensor design. These process technologies provide enhancement in the size and cost due to the possibility of batch fabrication. These types of humidity sensors may be divided into two categories: CMOS- and CMOS-MEMS-based humidity sensors.Miniaturization trends have necessitated the fabrication of resistive or capacitive MOS- or polymer-based humidity sensors using CMOS process technology and some additional post-CMOS steps such as drop-coating or deposition of sensitive materials on the CMOS die. Their working principle is similar to MOS- and polymer-based sensors in that they convert information about the humidity level in the air into electrical signals . The opeMEMS is a technology that integrates mechanical elements, sensors, actuators, and electrical and electronic components on a common silicon substrate with feature sizes ranging from millimeters to micrometers. The most significant advantage of MEMS is their ability to communicate easily with electrical elements in semiconductor chips. Furthermore, there are many other advantages for MEMS such as small size, low power consumption, low cost, easy integration into systems, and possibility of use for array fabrication. The scaling down of micromechanical to micromechanical devices provides an improvement in several areas as demonstrated in applications such as inertial sensors, ink-jet printers, RF communications, satellites, smart phones, pressure sensors, accelerometers, gyroscopes, bio-medical devices, military systems, and chemical sensors ,22,23,24Some of the primary mechanical elements utilized in the development of CMOS-MEMS devices included micro-sized cantilevers and membranes or plates. Such devices are often used in sensing or actuation technologies and are generally based upon the changes in physical properties such as mass or stress of the device due to absorption/adsorption of gas species at the surface. Mass changes can be detected by monitoring frequency changes of the resonating structure or observing the deflection of the micromechanical structure due to mass loading and surface stress changes (static mode) . Mass-seet al. [Many of the current CMOS-MEMS resonant microstructures used as humidity sensors have a sensitive layer of polymer coating and are usually operated at room temperature. However, the humidity absorbed in the detection process in many instances adheres onto the polymer and cannot be easily desorbed. These characteristics cause problems in real-time measurement where humidity levels are changing and results in hysteresis when measurements are done in an environment with increasing and decreasing humidity levels. Many studies have been conducted to investigate hysteresis and reported hysteresis as high as 6.6% RH at 25 °C ambient temperature, while aet al. . TherefoThis paper reports the fabrication and characterization of a CMOS-MEMS humidity sensor with embedded microheater element that is employed for electrothermal actuation of the device as well as for maintaining the device plate at a moderately elevated temperature of 40 °C to 80 °C in order to improve reversibility, stability, and hysteresis in humidity detection.2) is used as the dielectric layer and tungsten is used for the vias. The sensor device is fabricated using standard 0.35 µm CMOS process technology and post-CMOS micromachining through a multiple project wafer (MPW). The CMOS process technology consists of two polysilicon, three metal, several dielectric layers, and two vias. All metal layers are aluminum (Al), whereas silicon dioxide (SiO2 using Reactive Ion Etching (RIE), while After completion of the CMOS process, before the dry etching step, the eight-inch wafer is back-grinded to a thickness of 350 µm from the initial thickness of 750 µm, as shown in the cross section view in z direction. These vibrations produce stress at the anchor points of the four supporting beams and this stress changes the resistance of the PZRs, which can be measured using a Wheatstone bridge circuit. In the initial experimental setup on which the results of this paper are based, a single longitudinal PZRLR (where the subscript LR stands for the lower right hand side of the device) is connected to three external resistors, 1R, 2R, and 3R of the same values as those of the PZR to construct a Wheatstone bridge circuit configuration. One of the three external resistors, 3R, is a variable resistor to adjust the Wheatstone bridge circuit. LR, while LR to voltage output outV and is biased using a DC voltage input inV of 3 V.The CMOS-MEMS device is operated in the dynamic mode using electrothermal actuation by applying an AC-current through the embedded microheater as shown in pp. The relative humidity inside the chamber is increased and decreased from 35% RH to 95% RH in steps of 5% RH while keeping the ambient temperature constant at 27 °C to observe hysteresis. The time for a 5% RH step increase in humidity is set to 7 min and, in between each step, the humidity is maintained constant for 3 min before increasing it to the next level in another 7 min; the output voltage is measured using PASCO interface card (PS-2124A) connected to a computer, as shown in The sensor device that was bonded and packaged in a commercial dual in line package (DIP) as shown in pp corresponding to different operating temperatures of 40, 50, 60, 70 and 80 °C, respectively, as determined from Temperature Coefficient of Resistance (TCR) measurements [pp for the same range of relative humidity from 60% RH to 95% RH. In order to understand the influence of temperature, the device is driven in the dynamic mode by applying a 2 Hz AC signal with different applied voltages of 2, 3, 4, 5 and 6 Vurements , while tpp and the relative humidity inside the chamber was programmed to change from ambient humidity of 68% RH to 95% RH. Once the humidity inside the chamber reaches the 95% RH set point, the chamber door is then abruptly opened, resulting in an abrupt drop in humidity level from 95% RH to the ambient humidity. Next, the chamber was closed again and the humidity inside the chamber allowed to increase from the ambient to 95% RH. These experimental steps were repeated three times in order to observe the response, recovery, repeatability, and stability of the sensor and the data was continuously recorded in a computer.The response, recovery, and repeatability of the sensor in the chamber were also measured together with a standard humidity sensor (PASPORT Humidity/Temp/Dew Point Sensor PS-2124A) that is used for validation of the results. The device was again operated in the dynamic mode by applying a 2 Hz AC signal with amplitude of 5 V2 paste successfully deposited on its plate using a drop-coating method; 2 patch on the plate showing the porous distribution of nanoparticles of TiO2; and 2. The carbon peak observed in the EDX spectrum is from the binder material used to form the paste. The porous structure of TiO2 on the plate increases its surface area and thus is expected to enhance its sensitivity in the adsorption/desorption reaction of H2O on its surface.pp, corresponding to a temperature on the plate of 80 °C. The maximum hysteresis is found to be 0.87% RH at 80% RH, indicating comparatively low hysteresis, which gives the device a high advantage for use in real-time measurements. The output voltage of the humidity sensor increases from 0.585 mV to 30.580 mV as the humidity is increased from 35% RH to 95% RH. It was observed to be linear from 0.585 mV to 3.250 mV as the humidity increases from 35% RH to 60% RH with sensitivity of 0.107 mV/% RH as shown in pp to 6 Vpp (corresponding to different operating temperatures from 40 °C to 80 °C) at a constant frequency of 2 Hz. It is observed that the output voltage of the device increases with increasing humidity for different operating temperatures. The slopes of the graph indicate that the sensitivity improves at higher temperatures, as indicated in 2O in humidity detection on the TiO2 surface is enhanced with increase in temperature. At higher temperatures more gaseous species desorb from the sensor surface, resulting in an overall decrease in the mass of the plate and TiO2 and thus an increase in the amplitude of the vibrating structure.pp at relative humidity from 60% RH to 95% RH. It is observed that the sensitivity of the device increases from 0.500 mV/% RH to reach a maximum value of 1.634 mV/% RH at a frequency of 12 Hz, then decreases to 1.110 mV/% RH at frequency of 20 Hz. The observed maximum at the frequency of 12 Hz is assumed to be due to the effect of air damping, which increases as the frequency increases. This increase in air damping affects the driving force, which results in decreased amplitude after a certain optimal frequency is reached (about 12 Hz in this case). pp and the relative humidity varied from ambient humidity of 68% RH to 95% RH for three cycles of measurement. It is observed that the output voltage of the CMOS-MEMS humidity sensor follows the standard sensor that directly measures humidity in % RH with a good comparable response, recovery, and stable repeatability. 2 paste was deposited on the plate of the CMOS-MEMS humidity sensor as the active sensing element. Results showed that the output voltage of the humidity sensor increased from 0.585 mV to 30.580 mV as the humidity increased from 35% RH to 95% RH. It was observed that the output voltage was linear from 35% RH to 60% RH with sensitivity of 0.107 mV/% RH, and from 60% RH to 95% RH with a higher sensitivity of 0.781 mV/% RH; the maximum hysteresis was found to be 0.87% RH at 80% RH. Furthermore, the sensitivity of the humidity sensor increased linearly from 0.102 mV/% RH to 0.501 mV/% RH with an increase in the temperature from 40 °C to 80 °C; it was also found to be dependent on the frequency of driving voltage with a maximum sensitivity observed at the frequency of 12 Hz. Finally, the CMOS-MEMS humidity sensor showed a comparable response, recovery, and repeatability of measurements as compared to a standard sensor that directly measures humidity in % RH. A CMOS-MEMS device with embedded microheater for relative humidity sensing via amplitude change, due to mass loading, has been fabricated and characterized. The device was designed and fabricated using 0.35 µm CMOS process technology and post-CMOS micromachining. The device was operated in dynamic mode using electrothermal actuation and piezoresistive sensing was used to measure the output voltage via a Wheatstone bridge circuit. Nanostructured TiO


It was found that the graphene films present excellent electrical conductivity with high transparency. The conductivity is up to 1,240 S/cm, the sheet resistance is lower than 1 kΩ/sq, and the transparency is well over 85% in the visible wavelength range of 400 to 800 nm, showing that the graphene films have very low resistivity and superior transparency and completely satisfy the need for transparent conductors. These properties can be used in many applications, such as transparent conductor films for touch panels.We present a study on the transparent conducting characteristics of graphene-based films prepared by means of rapid chemical vapor deposition. The graphene films were grown on quartz slides with a CH61.48.+c, 78.67.Pt, 68.37.Hk, 68.65.Ac A transparent conducting (TC) electrode is a key component in various optoelectronic devices, such as liquid crystal displays (LCDs), solar cells, organic solar cells, organic light-emitting diodes (OLEDs), etc. -4. Indiu2 and other transparent insulators in fabricating optoelectronic device architectures, graphene films on Ni or Cu must be transferred to SiO2 and other transparent insulator substrates, which may perplex the preparation process and technique of devices. In this work, the objective of our research was to fabricate large-area graphene films on SiO2 substrates and investigate their conductivity and transparency. Graphene on SiO2 can be easily used to make optoelectronic devices and freely transferred to other substrates by etching the SiO2 layer using HF. It is especially interesting for the purpose of constructing electrodes. Herein, we describe a simple and reproducible method to uniformly deposit a few layers of graphene films grown by CVD. We investigated the influence of deposition time and thickness on the transparent conducting characteristics: conductivity, sheet resistance, and transparency, of graphene films. It was found that the deposited large-scale, conductive, and highly transparent graphene films are suitable for use as constructing electrodes.In using graphene as a TC electrode, it is very important to deposit a large-scale uniform graphene film on Si and other substrates. Graphene has been deposited in various approaches, such as chemical vapor deposition (CVD) , metal-b3 were cleaned ultrasonically with a sequence of acetone, ethanol, and deionized water, and then they were blown with N2 to dry them and placed at the center of the furnace. Prior to deposition, the furnace was pumped to 10-2 Pa and heated to 300°C for 10 min to remove any water moisture. High-purity CH4 gas (99.999%) and Ar gas with a volume ratio of 1:10 were introduced into the reactive chamber at the same temperature (950°C). In the graphene deposition process, CH4 was initially decomposed to give a mixture of C and H2, and the C atoms were condensed on the quartz substrates to form graphene films while the working pressure was kept at 50 Pa. The growth process was carried out for 1 ~ 5 min, and then the samples were annealed at 1,000°C for 20 min. Finally, when the system had cooled down to room temperature, the samples were removed.The graphene films were fabricated on quartz crystalline slides by a rapid CVD process. The growth system was composed of a large horizontal quartz tube furnace, a vacuum system, a gas meter, and an automatic temperature controller. Quartz crystalline substrates with a size of 15 × 15 × 2 mmThe morphology and structure of the samples were characterized by atomic force microscopy (AFM). The structure was analyzed by Raman spectroscopy, and the optical transparency was investigated by UV–vis spectroscopy . Finally, the conducting characteristics of the graphene films were evaluated by Hall effect measurement .Pictures of the obtained graphene films on quartz substrates under different times are shown in Figure -1 and a G band peak at 1,580 cm-1. It is well known that the G band indicates a sound graphite carbon structure (sp2) whereas the 2D band is a typical band of graphene [-1) was not seen in the first-order Raman spectra. The intensity ratio of D band (ID) to G band (IG) can be used as an indication of defect quantity: a low ID/IG corresponds to a small defect quantity. The absent D band in the Raman spectra shows that the deposited graphene in our samples has high quality. The sharp 2D peak in graphene is roughly three times (the largest intensity ratio of I2D/IG = 2.8) more intense than the G peak, suggesting that the quality of the deposited graphene is comparable to that of graphene grown on foils [2 with a good quality may be attributed to carbon atoms from pyrolysis of CH4 in the self-assembly adsorption process. Sun et al. [sp2-hybridized graphitic layers forming nanographene on a high-temperature substrate. The second mechanism is the promotion of oxygen. Since the reactive chamber has a low ultimate vacuum pressure (about 10-2 Pa) in our experiment, the remaining oxygen in the tube and the high substrate temperature will promote adsorption of carbon atoms onto the quartz slide. Chen et al. [x fragments through C-O and H-O binding and thus provides more opportunities for C-C coupling and graphene nucleation. Moreover, during deposition of graphene films on SiO2, we placed some nanoscaled Ni powder on the Si substrates in the tube to measure the electrical junction properties of graphene/Si. A few Ni nanoparticles on the Si substrates were carried on the quartz surface by CH4 and Ar gases, which accelerated the carbon atoms adhering and growing on the quartz, similar to that of graphene grown on Cu but not to graphene grown on Ni which occurs by a C segregation or precipitation process [Figure graphene . The dison foils . The main et al.  reportedn et al.  found th process .The visible light transmission rate of the graphene samples is shown in Figure I-V) behaviors of the 1, 3, and 5 min graphene films were measured by means of Hall effect measurement, as shown in Figure I-V behaviors between the four points are not a characteristic of a linear relation, but of a nonlinear property. Especially, I-Vbc and I-Vcd lines were largely shifted from the linear relation. This is because the graphene on quartz does not form a continuous film but islands by a short time. With deposition time increasing to 3 and 5 min, the graphene islands collected each other to become a continuous film, and then the I-V properties become linear, as shown in Figure I-Vda in Figure I-V behaviors in Figure I-V relations of the graphene surface show films with good conductivity.The surface current–voltage (2, 5.1 × 104, and 9.5 × 104 cm2/V/s for 1, 3, and 5 min samples, respectively. The latter two values are very close to the known ideal value of 2 × 105 cm2/V/s [I-V behaviors. For a low thickness value, the graphene does not form a continuous film but many islands, which collect and fuse each other with deposition time, leading to the mobility and conductivity increasing linearly and then up to their ultimate values. The conductivity of the graphene film with a 7-nm thickness is about 1,240 S/cm, superior to that of Levendorf et al. [2 S/cm for the same thickness. The sheet resistance Rs in Figure Rs drops from 105 to 103 Ω/sq as the thickness increases from 2 to 7 nm. The typical Rs of the ITO film is 103 ~ 106 Ω/sq. Hence, the Rs of about 103 Ω/sq shows that the deposited graphene has very low resistivity, satisfying the need for transparent conducting films. This value is about two times smaller than that of Wang et al. [2[The thickness of the graphene films with deposition time is shown in Figure g et al.  who repoet al. [2. Wu et aet al. [2 reported3 Ω/sq. These properties are much superior to those of GO films as transparent conductors. The high performance is attributed to the CVD technique that produced compact, large-area, uniform, and high-purity graphene films.The graphene sample deposited for 5 min has a high transparency of over 85% in the visible wavelength range of 400 to 800 nm and a sheet resistance of 104 in the CVD technique. The transmission rate of the graphene films decreases with the thickness of the film, which is over 85% for the film of about 5 to 7 nm. The mobility and conductivity were found to rapidly increase up to their saturation values with the thickness of the film. The sheet resistance rapidly drops from 105 to 103 Ω/sq as the film thickness increases from 2 to 7 nm. The largest conductivity is up to 1,240 S/cm and the minimum sheet resistance is about 103 Ω/sq, showing that the graphene films have very low resistivity and completely satisfy the need for transparent conducting films.The transparent conducting properties of graphene films with different thicknesses were investigated. Ultrathin graphene films were deposited on quartz substrates by controlling a very low reactive flow rate and pressure of CHThe authors declare that they have no competing interests.XM designed the structure of the graphene transistor, analyzed the results, and wrote the manuscript. HZ participated in the fabrication of the graphene films on the substrates. Both authors read and approved the final manuscript.