Measuring degree-degree association in networks

The Pearson correlation coefficient is commonly used for quantifying the global level of degree-degree association in complex networks. Here, we use a probabilistic representation of the underlying network structure for assessing the applicability of different association measures to heavy-tailed degree distributions. Theoretical arguments together with our numerical study indicate that Pearson's coefficient often depends on the size of networks with equal association structure, impeding a systematic comparison of real-world networks. In contrast, Kendall-Gibbons' $\tau_{b}$ is a considerably more robust measure of the degree-degree association

Investigations of a Cretaceous limestone with spectral induced polarization and scanning electron microscopy

Characterization of varying bedrock properties is a common need in various contexts, ranging from large infrastructure pre-investigations to environmental protection. A direct current resistivity and time domain induced polarization (IP) survey aiming to characterize properties of a Cretaceous limestone was carried out in the Kristianstad basin, Sweden. The time domain IP data was processed with a recently developed method in order to suppress noise from the challenging urban setting in the survey area. The processing also enabled extraction of early decay times resulting in broader spectra of the time decays and inversion for Cole-Cole parameters. The aims of this study is to investigate if large-scale geoelectrical variations as well as small-scale structural and compositional variations exist within the Kristianstad limestone, and to evaluate the usefulness of Cole-Cole inverted IP data in early time ranges for bedrock characterization. The inverted sections showed variations within the limestone that could be caused by variations in texture and composition. Samples from a deep drilling in the Kristianstad basin were investigated with scanning electron microscopy and energy dispersive X-ray spectroscopy, and the results showed that varying amounts of pyrite, glauconite and clay matrix were present at different levels in the limestone. The local high IP anomalies in the limestone could be caused by these minerals otherwise the IP responses were generally weak. There were also differences in the texture of the limestone at different levels, governed by fossil shapes and composition, proportions of calcareous cement and matrix as well as amount of silicate grains. Textural variations may have implications on the variation in Cole-Cole relaxation time and frequency factor. However, more research is needed in order to directly connect microgeometrical properties in limestone to spectral IP responses. The results from this study show that it is possible to recover useable spectral information from early decay times. We also show that under certain conditions (e.g. relatively short relaxation times in the subsurface), it is possible to extract spectral information from time domain IP data measured with on-off times as short as 1 s

The Bivariate Normal Copula

We collect well known and less known facts about the bivariate normal distribution and translate them into copula language. In addition, we prove a very general formula for the bivariate normal copula, we compute Gini's gamma, and we provide improved bounds and approximations on the diagonal.Comment: 24 page

Transfer Functions for Protein Signal Transduction: Application to a Model of Striatal Neural Plasticity

We present a novel formulation for biochemical reaction networks in the context of signal transduction. The model consists of input-output transfer functions, which are derived from differential equations, using stable equilibria. We select a set of 'source' species, which receive input signals. Signals are transmitted to all other species in the system (the 'target' species) with a specific delay and transmission strength. The delay is computed as the maximal reaction time until a stable equilibrium for the target species is reached, in the context of all other reactions in the system. The transmission strength is the concentration change of the target species. The computed input-output transfer functions can be stored in a matrix, fitted with parameters, and recalled to build discrete dynamical models. By separating reaction time and concentration we can greatly simplify the model, circumventing typical problems of complex dynamical systems. The transfer function transformation can be applied to mass-action kinetic models of signal transduction. The paper shows that this approach yields significant insight, while remaining an executable dynamical model for signal transduction. In particular we can deconstruct the complex system into local transfer functions between individual species. As an example, we examine modularity and signal integration using a published model of striatal neural plasticity. The modules that emerge correspond to a known biological distinction between calcium-dependent and cAMP-dependent pathways. We also found that overall interconnectedness depends on the magnitude of input, with high connectivity at low input and less connectivity at moderate to high input. This general result, which directly follows from the properties of individual transfer functions, contradicts notions of ubiquitous complexity by showing input-dependent signal transmission inactivation.Comment: 13 pages, 5 tables, 15 figure

Post-extraction mesio-distal gap reduction assessment by confocal laser scanning microscopy - a clinical 3-month follow-up study

[EN] AimThe aim of this 3-month follow-up study is to quantify the reduction in the mesio-distal gap dimension (MDGD) that occurs after tooth extraction through image analysis of three-dimensional images obtained with the confocal laser scanning microscopy (CLSM) technique. Materials and MethodsFollowing tooth extraction, impressions of 79 patients 1month and 72 patients 3months after tooth extraction were obtained. Cast models were processed by CLSM, and MDGD changes between time points were measured. ResultsThe mean mesio-distal gap reduction 1month after tooth extraction was 343.4m and 3months after tooth extraction was 672.3m. The daily mean gap reduction rate during the first term (between baseline and 1month post-extraction measurements) was 10.3m/day and during the second term (between 1 and 3months) was 5.4m/day. ConclusionsThe mesio-distal gap reduction is higher during the first month following the extraction and continues in time, but to a lesser extent. When the inter-dental contacts were absent, the mesio-distal gap reduction is lower. When a molar tooth is extracted or the distal tooth to the edentulous space does not occlude with an antagonist, the mesio-distal gap reduction is larger. The consideration of mesio-distal gap dimension changes can help improve dental treatment planning.The authors would like to express their gratitude to MEC (contract grant number AP2008-01653), to FEDER, to the Generalitat Valenciana for its help in the CLSM acquisition (MY08/ISIRM/S/100), to the Universitat Politecnica de Valencia (PAID-05-12) and to Dr. Asuncion Jaime for her translation assistance.García-Herraiz, A.; Silvestre, FJ.; Leiva García, R.; Crespo Abril, F.; Garcia-Anton, J. (2017). Post-extraction mesio-distal gap reduction assessment by confocal laser scanning microscopy - a clinical 3-month follow-up study. Journal Of Clinical Periodontology. 44(5):548-555. https://doi.org/10.1111/jcpe.12706S548555445Aguilar, M. L., Elias, A., Vizcarrondo, C. E. T., & Psoter, W. J. (2010). Analysis of three-dimensional distortion of two impression materials in the transfer of dental implants. The Journal of Prosthetic Dentistry, 103(4), 202-209. doi:10.1016/s0022-3913(10)60032-7Amit, G., JPS, K., Pankaj, B., Suchinder, S., & Parul, B. (2012). Periodontally accelerated osteogenic orthodontics (PAOO) - a review. Journal of Clinical and Experimental Dentistry, e292-296. doi:10.4317/jced.50822Armitage, G. C. (1999). Development of a Classification System for Periodontal Diseases and Conditions. Annals of Periodontology, 4(1), 1-6. doi:10.1902/annals.1999.4.1.1Belli, R., Pelka, M., Petschelt, A., & Lohbauer, U. (2009). In vitro wear gap formation of self-adhesive resin cements: A CLSM evaluation. Journal of Dentistry, 37(12), 984-993. doi:10.1016/j.jdent.2009.08.006Belli, R., Rahiotis, C., Schubert, E. W., Baratieri, L. N., Petschelt, A., & Lohbauer, U. (2011). Wear and morphology of infiltrated white spot lesions. Journal of Dentistry, 39(5), 376-385. doi:10.1016/j.jdent.2011.02.009Brauchli, L. M., Baumgartner, E.-M., Ball, J., & Wichelhaus, A. (2011). Roughness of enamel surfaces after different bonding and debonding procedures. Journal of Orofacial Orthopedics / Fortschritte der Kieferorthopädie, 72(1), 61-67. doi:10.1007/s00056-010-0002-3Chen, S. Y., Liang, W. M., & Chen, F. N. (2004). Factors affecting the accuracy of elastometric impression materials. Journal of Dentistry, 32(8), 603-609. doi:10.1016/j.jdent.2004.04.002Christou, P., & Kiliaridis, S. (2007). Three-dimensional changes in the position of unopposed molars in adults. The European Journal of Orthodontics, 29(6), 543-549. doi:10.1093/ejo/cjm036Craddock, H. L., Youngson, C. C., Manogue, M., & Blance, A. (2007). Occlusal Changes Following Posterior Tooth Loss in Adults. Part 2. Clinical Parameters Associated with Movement of Teeth Adjacent to the Site of Posterior Tooth Loss. Journal of Prosthodontics, 16(6), 495-501. doi:10.1111/j.1532-849x.2007.00223.xFaria, A. C. L., Rodrigues, R. C. S., Macedo, A. P., Mattos, M. da G. C. de, & Ribeiro, R. F. (2008). Accuracy of stone casts obtained by different impression materials. Brazilian Oral Research, 22(4), 293-298. doi:10.1590/s1806-83242008000400002García-Herraiz, A., Leiva-García, R., Cañigral-Ortiz, A., Silvestre, F. J., & García-Antón, J. (2011). Confocal laser scanning microscopy for the study of the morphological changes of the postextraction sites. Microscopy Research and Technique, 75(4), 513-519. doi:10.1002/jemt.21085Gragg, K. L., Shugars, D. A., Bader, J. D., Elter, J. R., & White, B. A. (2001). Movement of Teeth Adjacent to Posterior Bounded Edentulous Spaces. Journal of Dental Research, 80(11), 2021-2024. doi:10.1177/00220345010800111401LINDSKOG-STOKLAND, B., HANSEN, K., TOMASI, C., HAKEBERG, M., & WENNSTRÖM, J. L. (2011). Changes in molar position associated with missing opposed and/or adjacent tooth: a 12-year study in women. Journal of Oral Rehabilitation, 39(2), 136-143. doi:10.1111/j.1365-2842.2011.02252.xLove, W. D., & Adams, R. L. (1971). Tooth movement into edentulous areas. The Journal of Prosthetic Dentistry, 25(3), 271-278. doi:10.1016/0022-3913(71)90188-0Nishikawa, T., Masuno, K., Mori, M., Tajime, Y., Kakudo, K., & Tanaka, A. (2006). Calcification at the Interface Between Titanium Implants and Bone: Observation With Confocal Laser Scanning Microscopy. Journal of Oral Implantology, 32(5), 211-217. doi:10.1563/799.1Pereira, J. R., Murata, K. Y., Valle, A. L. do, Ghizoni, J. S., & Shiratori, F. K. (2010). Linear dimensional changes in plaster die models using different elastomeric materials. Brazilian Oral Research, 24(3), 336-341. doi:10.1590/s1806-83242010000300013Schilling, T., Müller, M., Minne, H. W., & Ziegler, R. (1998). Influence of Inflammation-Mediated Osteopenia on the Regional Acceleratory Phenomenon and the Systemic Acceleratory Phenomenon During Healing of a Bone Defect in the Rat. Calcified Tissue International, 63(2), 160-166. doi:10.1007/s002239900508Scivetti, M., Pilolli, G. P., Corsalini, M., Lucchese, A., & Favia, G. (2007). Confocal laser scanning microscopy of human cementocytes: Analysis of three-dimensional image reconstruction. Annals of Anatomy - Anatomischer Anzeiger, 189(2), 169-174. doi:10.1016/j.aanat.2006.09.009SHUGARS, D. A., BADER, J. D., PHILLIPS, S. W., WHITE, B. A., & BRANTLEY, C. F. (2000). THE CONSEQUENCES OF NOT REPLACING A MISSING POSTERIOR TOOTH. The Journal of the American Dental Association, 131(9), 1317-1323. doi:10.14219/jada.archive.2000.0385Thalmair, T., Fickl, S., Schneider, D., Hinze, M., & Wachtel, H. (2013). Dimensional alterations of extraction sites after different alveolar ridge preservation techniques - a volumetric study. Journal of Clinical Periodontology, 40(7), 721-727. doi:10.1111/jcpe.12111Thongthammachat, S., Moore, B. K., Barco, M. T., Hovijitra, S., Brown, D. T., & Andres, C. J. (2002). Dimensional accuracy of dental casts: Influence of tray material, impression material, and time. Journal of Prosthodontics, 11(2), 98-108. doi:10.1053/jopr.2002.125192Van der Weijden, F., Dell’Acqua, F., & Slot, D. E. (2009). Alveolar bone dimensional changes of post-extraction sockets in humans: a systematic review. Journal of Clinical Periodontology, 36(12), 1048-1058. doi:10.1111/j.1600-051x.2009.01482.xWeinstein, S. (1967). Minimal forces in tooth movement. American Journal of Orthodontics, 53(12), 881-903. doi:10.1016/0002-9416(67)90163-7Windisch, S. I., Jung, R. E., Sailer, I., Studer, S. P., Ender, A., & Hämmerle, C. H. F. (2007). A new optical method to evaluate three-dimensional volume changes of alveolar contours: a methodological in vitro study. 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Conformational effects on the Circular Dichroism of Human Carbonic Anhydrase II: a multilevel computational study

Circular Dichroism (CD) spectroscopy is a powerful method for investigating conformational changes in proteins and therefore has numerous applications in structural and molecular biology. Here a computational investigation of the CD spectrum of the Human Carbonic Anhydrase II (HCAII), with main focus on the near-UV CD spectra of the wild-type enzyme and it seven tryptophan mutant forms, is presented and compared to experimental studies. Multilevel computational methods (Molecular Dynamics, Semiempirical Quantum Mechanics, Time-Dependent Density Functional Theory) were applied in order to gain insight into the mechanisms of interaction between the aromatic chromophores within the protein environment and understand how the conformational flexibility of the protein influences these mechanisms. The analysis suggests that combining CD semi empirical calculations, crystal structures and molecular dynamics (MD) could help in achieving a better agreement between the computed and experimental protein spectra and provide some unique insight into the dynamic nature of the mechanisms of chromophore interactions

Reflection seismic imaging to unravel subsurface geological structures of the Zinkgruvan mining area, central Sweden

The Zinkgruvan mining area is located on the south-eastern part of the Bergslagen district, one of the three major mineral producing regions in Sweden. In this study, we present the results from three (P1, P2 and P8) reflection seismic profiles each approximately 3000 m-long crossing the Zinkgruvan Zn-Pb-Ag-(Cu) mining area. P1 was acquired using cabled geophones with 10 m receiver and source interval and crossed major geological features. The other two profiles (P2 and P8) were acquired by wireless recorders with 20 m receiver and 10 m source interval and ran perpendicular to P1. Through a special data processing workflow adapted to this dataset, good quality seismic sections were obtained along these profiles, although a high noise level due to high voltage electric power lines was present. The interpretations were constrained by (1) seismic P-wave velocity and density data from a series of downhole logging measurements, (2) 3D forward reflection traveltime modelling in both pre- and post-stack domains, and (3) other geophysical and geological observations available from the site. Despite the notably complex geology, the processed seismic sections clearly reveal a series of horizontal to gently dipping reflections associated with known geological formations. Results indicate that most structures and lithological contacts dip or plunge to the northeast, including the targeted Zinkgruvan Formation. The results from this seismic survey are encouraging regarding the potential of the seismic method for base-metal exploration in Sweden and in particular in the Bergslagen district. It shows the high resolving power of the reflection seismic methods for imaging complex geological structures in a cost-effective and environmentally-friendly way.EIT-RawMaterials is gratefully thanked for funding this up-scaling project 17024.Peer reviewe

Lack of effects of typical and atypical antipsychotics in DARPP-32 and NCS-1 levels in PC12 cells overexpressing NCS-1

<p>Abstract</p> <p>Background</p> <p>Schizophrenia is the major psychiatry disorder, which the exact cause remains unknown. However, it is well known that dopamine-mediated neurotransmission imbalance is associated with this pathology and the main target of antipsychotics is the dopamine receptor D₂. Recently, it was described alteration in levels of two dopamine signaling related proteins in schizophrenic prefrontal cortex (PFC): Neuronal Calcium Sensor-1 (NCS-1) and DARPP-32. NCS-1, which is upregulated in PFC of schizophrenics, inhibits D₂internalization. DARPP-32, which is decreased in PFC of schizophrenics, is a key downstream effector in transducing dopamine signaling. We previously demonstrated that antipsychotics do not change levels of both proteins in rat's brain. However, since NCS-1 and DARPP-32 levels are not altered in wild type rats, we treated wild type PC12 cells (PC12 WT) and PC12 cells stably overexpressing NCS-1 (PC12 Clone) with antipsychotics to investigate if NCS-1 upregulation modulates DARPP-32 expression in response to antipsychotics treatment.</p> <p>Results</p> <p>We chronically treated both PC12 WT and PC12 Clone cells with typical (Haloperidol) or atypical (Clozapine and Risperidone) antipsychotics for 14 days. Using western blot technique we observed that there is no change in NCS-1 and DARPP-32 protein levels in both PC12 WT and PC12 Clone cells after typical and atypical antipsychotic treatments.</p> <p>Conclusions</p> <p>Because we observed no alteration in NCS-1 and DARPP-32 levels in both PC12 WT and Clone cells treated with typical or atypical antipsychotics, we suggest that the alteration in levels of both proteins in schizophrenic's PFC is related to psychopathology but not with antipsychotic treatment.</p

Comparison between Bipolar Hemiarthroplasty and Total Hip Arthroplasty for Unstable Intertrochanteric Fractures in Elderly Osteoporotic Patients

The present study was conducted to compare bipolar hemiarthroplasty (BA) with total hip arthroplasty (THA) in treatment of unstable intertrochanteric fractures in elderly osteoporotic patients. The THA group included 14 males and 26 females with a mean age of 73.4 years, and the BA group included 27 males and 45 females with a mean age of 76.5 years. Significant difference existed between the two groups in operation time, blood loss, transfusion volume and cost of hospitalization, while no remarkable difference was identified in hospitalization period, general complications, joint function, pain, rate of revision and mortality. No dislocation was observed in BA group while 3 occurred in THA group. The results indicated that for unstable intertrochanteric fractures in elderly osteoporotic patients, BA seems to be a better or more reasonable choice compared with THA for the reason of less blood loss, shorter operation time, lower cost and no dislocation