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

DeepHistoClass: A novel strategy for confident classification of immunohistochemistry images using Deep Learning

© 2021 Elsevier Ltd. All rights reserved. This is the accepted manuscript version of the article. The final version is available online from Elsevier at: https://doi.org/10.1016/j.mcpro.2021.100140A multitude of efforts worldwide aim to create a single cell reference map of the human body, for fundamental understanding of human health, molecular medicine and targeted treatment. Antibody-based proteomics using immunohistochemistry (IHC) has proven to be an excellent technology for integration with large-scale single cell transcriptomics datasets. The golden standard for evaluation of IHC staining patterns is manual annotation, which is expensive and may lead to subjective errors. Artificial intelligence holds much promise for efficient and accurate pattern recognition, but confidence in prediction needs to be addressed. Here, the aim was to present a reliable and comprehensive framework for automated annotation of IHC images. We developed a multi-label classification of 7,848 complex IHC images of human testis corresponding to 2,794 unique proteins, generated as part of the Human Protein Atlas (HPA) project. Manual annotation data for eight different cell types was generated as a basis for training and testing a proposed Hybrid Bayesian Neural Network. By combining the deep learning model with a novel uncertainty metric; DeepHistoClass (DHC) confidence score; the average diagnostic performance improved from 86.9% to 96.3%. This metric not only reveals which images are reliably classified by the model, but can also be utilized for identification of manual annotation errors. The proposed streamlined workflow can be developed further for other tissue types in health and disease, and has important implications for digital pathology initiatives or large-scale protein mapping efforts such as the HPA project.Knut and Alice Wallenberg Foundation

Эпидемиологическая характеристика парвовирусной В19 инфекции у детей с гематологическими заболеваниями

ДЕТИ, СЛУЖБЫ ОХРАНЫ ЗДОРОВЬЯКРОВИ БОЛЕЗНИПАРВОВИРУСНЫЕ ИНФЕКЦИИЭПИДЕМИОЛОГИ

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

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

A phonon scattering assisted injection and extraction based terahertz quantum cascade laser

A novel lasing scheme for terahertz quantum cascade lasers, based on consecutive phonon-photon-phonon emissions per module, is proposed and experimentally demonstrated. The charge transport of the proposed structure is modeled using a rate equation formalism. An optimization code based on a genetic algorithm was developed to find a four-well design in the $\mathrm{GaAs/Al_{0.25}Ga_{0.75}As}$ material system that maximizes the product of population inversion and oscillator strength at 150 K. The fabricated devices using Au double-metal waveguides show lasing at 3.2 THz up to 138 K. The electrical characteristics display no sign of differential resistance drop at lasing threshold, which suggests - thanks to the rate equation model - a slow depopulation rate of the lower lasing state, a hypothesis confirmed by non-equilibrium Green's function calculations.Comment: 11 pages, 10 figure

Onset of main Phanerozoic marine radiation sparked by emerging Mid Ordovician icehouse

This is the final version. Available on open access from Springer Nature via the DOI in this recordThe Great Ordovician Biodiversification Event (GOBE) was the most rapid and sustained increase in marine Phanerozoic biodiversity. What generated this biotic response across Palaeozoic seascapes is a matter of debate; several intrinsic and extrinsic drivers have been suggested. One is Ordovician climate, which in recent years has undergone a paradigm shift from a text-book example of an extended greenhouse to an interval with transient cooling intervals - at least during the Late Ordovician. Here, we show the first unambiguous evidence for a sudden Mid Ordovician icehouse, comparable in magnitude to the Quaternary glaciations. We further demonstrate the initiation of this icehouse to coincide with the onset of the GOBE. This finding is based on both abiotic and biotic proxies obtained from the most comprehensive geochemical and palaeobiological dataset yet collected through this interval. We argue that the icehouse conditions increased latitudinal and bathymetrical temperature and oxygen gradients initiating an Early Palaeozoic Great Ocean Conveyor Belt. This fuelled the GOBE, as upwelling zones created new ecospace for the primary producers. A subsequent rise in δ(13)C ratios known as the Middle Darriwilian Isotopic Carbon Excursion (MDICE) may reflect a global response to increased bioproductivity encouraged by the onset of the GOBE.Our expeditions to Russia were mainly funded by the Carlsberg Foundation. C.M.Ø.R. and D.A.T.H. are particularly grateful to the Danish Council for Independent Research | Natural Sciences for their support of this specific project. C.M.Ø.R. further acknowledge support from the VILLUM Foundations Young Investigator Programme. A.L. was funded by the Royal Swedish Physiographic Society in Lund

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

A phonon scattering assisted injection and extraction based terahertz quantum cascade laser

A novel lasing scheme for terahertz quantum cascade lasers, based on consecutive phonon-photon-phonon emissions per module, is proposed and experimentally demonstrated. The charge transport of the proposed structure is modeled using a rate equation formalism. An optimization code based on a genetic algorithm was developed to find a four-well design in the $\mathrm{GaAs/Al_{0.25}Ga_{0.75}As}$ material system that maximizes the product of population inversion and oscillator strength at 150 K. The fabricated devices using Au double-metal waveguides show lasing at 3.2 THz up to 138 K. The electrical characteristics display no sign of differential resistance drop at lasing threshold, which suggests - thanks to the rate equation model - a slow depopulation rate of the lower lasing state, a hypothesis confirmed by non-equilibrium Green's function calculations.Comment: 11 pages, 10 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. Clinical Oral Implants Research, 18(5), 545-551. doi:10.1111/j.1600-0501.2007.01382.xYAMADA, M. K., & WATARI, F. (2003). Imaging and Non-Contact Profile Analysis of Nd: YAG Laser-Irradiated Teeth by Scanning Electron Microscopy and Confocal Laser Scanning Microscopy. Dental Materials Journal, 22(4), 556-568. doi:10.4012/dmj.22.55