3D Sets Research Articles

3D Cocultures of Osteoblasts and Staphylococcus aureus on Biomimetic Bone Scaffolds as a Tool to Investigate the Host-Pathogen Interface in Osteomyelitis.

Osteomyelitis (OM) is an infectious disease of the bone primarily caused by the opportunistic pathogen Staphylococcus aureus (SA). This Gram-positive bacterium has evolved a number of strategies to evade the immune response and subvert bone homeostasis, yet the underlying mechanisms remain poorly understood. OM has been modeled in vitro to challenge pathogenetic hypotheses in controlled conditions, thus providing guidance and support to animal experimentation. In this regard, traditional 2D models of OM inherently lack the spatial complexity of bone architecture. Three-dimensional models of the disease overcome this limitation; however, they poorly reproduce composition and texture of the natural bone. Here, we developed a new 3D model of OM based on cocultures of SA and murine osteoblastic MC3T3-E1 cells on magnesium-doped hydroxyapatite/collagen I (MgHA/Col) scaffolds that closely recapitulate the bone extracellular matrix. In this model, matrix-dependent effects were observed in proliferation, gene transcription, protein expression, and cell–matrix interactions both of the osteoblastic cell line and of bacterium. Additionally, these had distinct metabolic and gene expression profiles, compared to conventional 2D settings, when grown on MgHA/Col scaffolds in separate monocultures. Our study points to MgHA/Col scaffolds as biocompatible and bioactive matrices and provides a novel and close-to-physiology tool to address the pathogenetic mechanisms of OM at the host–pathogen interface.

Negligibility of haptotaxis effect in a chemotaxis–haptotaxis model

In this work, we rigorously study chemotaxis effect versus haptotaxis effect on boundedness, blow-up and asymptotical behavior of solutions for a chemotaxis-haptotaxis model in 2D settings. It is well-known that the corresponding Keller–Segel chemotaxis-only model possesses a striking feature of critical mass blowup phenomenon, namely, subcritical mass ensures boundedness, whereas, supercritical mass induces the existence of blow-ups. Herein, we show that this critical mass blow-up phenomenon stays almost the same in the full chemotaxis-haptotaxis model and that any global-in-time haptotaxis solution component vanishes exponentially and the other two solution components converge exponentially to that of chemotaxis-only model in a global sense for suitably large chemo-sensitivity and in the usual sense for suitably small chemo-sensitivity. Therefore, haptotaixs is neither good nor bad than chemotaxis, showing negligibility of haptotaxis effect in the underlying chemotaxis-haptotaxis model.

Cone beam computed tomography (CBCT) assessment of incisor root resorption (IRR) associated with impacted maxillary canines (IMC). Literature review

CBCT assessment of impacted canine improves canine localization to adjacent teeth and provides higher level of confidence in the treatment plan compared to 2D images. However, there is conflicting evidence to support using CBCT as a routine first-line imaging method in patients with impacted maxillary canine and incisor root resorption. Consequently, there are doubts regarding difference in diagnostic and treatment planning between the use of conventional 2D and CBCT sets. Therefore, the present review will attempt to summarize the new aspects regarding the benefits of three-dimensional (3D) diagnostic techniques (cone-beam computed tomography, CBCT), including the accuracy of localization of impacted canine and the detection of the degree and location of root resorption of maxillary incisors.

MI-UNet: Multi-Inputs UNet Incorporating Brain Parcellation for Stroke Lesion Segmentation From T1-Weighted Magnetic Resonance Images.

Stroke is a serious manifestation of various cerebrovascular diseases and one of the most dangerous diseases in the world today. Volume quantification and location detection of chronic stroke lesions provide vital biomarkers for stroke rehabilitation. Recently, deep learning has seen a rapid growth, with a great potential in segmenting medical images. In this work, unlike most deep learning-based segmentation methods utilizing only magnetic resonance (MR) images as the input, we propose and validate a novel stroke lesion segmentation approach named multi-inputs UNet (MI-UNet) that incorporates brain parcellation information, including gray matter (GM), white matter (WM) and lateral ventricle (LV). The brain parcellation is obtained from 3D diffeomorphic registration and is concatenated with the original MR image to form two-channel inputs to the subsequent MI-UNet. Effectiveness of the proposed pipeline is validated using a dataset consisting of 229 T1-weighted MR images. Experiments are conducted via a five-fold cross-validation. The proposed MI-UNet performed significantly better than UNet in both 2D and 3D settings. Our best results obtained by 3D MI-UNet has superior segmentation performance, as measured by the Dice score, Hausdorff distance, average symmetric surface distance, as well as precision, over other state-of-the-art methods.

BIM – AN APPLICATION IN GEOTECHNICAL ENGINEERING

BIM model represents a significant step forward within the frame of the overall process of construction. This new approach goes from the assumption that up to date praxis, which is represented by different sets of 2D or 3D drawings of drawings, technical reports and calculations does not cover all problems of the above mentioned overall process of construction. Basic principles of BIM will be discussed, not only from the view of 3D models of the structure design. The utilization of the BIM model during life time structure expectancy will be stressed - from the initial phase (investigation, design) via the phase of structure execution, maintenance and ending with structure demolition at the end of life time expectancy. Specificity of the geotechnical engineering is in this entire process fundamental, as each construction is in the interaction with ground. 3D model of the ground (geotechnical model) is therefore one of the basic individual parametric elements from which BIM model consist. Ground model is time dependant as geological profile and geotechnical properties are refinement during each phase of ground investigation as well during geotechnical structure construction. Final 3D Ground model together with 3D model of geotechnical structure represents a first significant step of the overall BIM model. In the case of underground or earth structures such output can be primordial element of the BIM model with parametric elements around it. Finally some other possibilities or practical applications are mentioned.

New set of non-separable 2D and 3D invariant moments for image representation and recognition

The extraction of feature vectors of the images is the most important step in image recognition, because it allows a good description of the forms to be recognized. This step is an operation that makes it possible to convert an image into a vector of real or complex values that can serve as a signature for this image. For an accurate recognition system, the used feature vector must be invariant to the three image transformations (translation, rotation and scale), which means that, the descriptor vectors of the image and the transformed image by translation, rotation or scale must be equal. Given the importance of moments and their invariants in pattern recognition and imaging, based on Newton’s binomial and trinomial formulas and the normalized central moments, we construct in this paper four new series of moments for 2D and 3D image recognition, which are invariant to translation, scaling and rotation (TSR): the first is a set of non-orthogonal moment invariants for 2D images (2dMIs), the second is a set of orthogonal moment invariants for 2D images (2dOMIs), the third is a set of non-orthogonal moment invariants for 3D images (3dMIs) and the fourth is a set of orthogonal moment invariants for 3D images (3dOMIs). Using the proposed invariant moments (2dMIs), (2dOMIs), (3dMIs) and (3dOMIs), we construct two types of image descriptor vectors for 2D images and two types for 3D images, which are invariant to translation, rotation and scale. A series of experiments is performed to validate this new set of invariant moments and compare its performance with the existing invariants moments. The obtained results ensure the superiority of the proposed moments over all existing moments in image recognition. Experiments on processing time show that the proposed method is faster than the existing orthogonal invariant moments.

Analysis of phase waves in the ECoG data

Subdural ECoG data recorded from the matrix of electrodes during syllable pronunciation are analyzed by the method of circular-linear regression. Phase waves in 1D electrode arrays and in the whole 2D set of electrodes are detected, and their spatial organization and temporal evolution are studied. Phase portraits of wave vectors indicate the presence of sources, sinks, and saddle points. The analysis of temporal evolution of phase portraits shows that they changed more at the beginning of syllable pronunciation. Furthermore, wave sources were more stable in their localization during the pronunciation. Overall, in spite of large variability of phase portraits, they represent some characterization of the dynamics of electric potential in the cerebral cortex.

A feature-aware SPH for isotropic unstructured mesh generation

In this paper, we present a feature-aware SPH method for the concurrent and automated isotropic unstructured mesh generation. Two additional objectives are achieved with the proposed method compared to the original SPH-based mesh generator (Fu et al., 2019). First, a feature boundary correction term is introduced to address the issue of incomplete kernel support at the boundary vicinity. The mesh generation of feature curves, feature surfaces and volumes can be handled concurrently without explicitly following a dimensional sequence. Second, a two-phase model is proposed to characterize the mesh-generation procedure by a feature-size-adaptation phase and a mesh-quality-optimization phase. By proposing a new error measurement criterion and an adaptive control system with two sets of simulation parameters, the objectives of faster feature-size adaptation and local mesh-quality improvement are merged into a consistent framework. The proposed method is validated with a set of 2D and 3D numerical tests with different complexities and scales. The results demonstrate that high-quality meshes are generated with a significant speedup of convergence.

A finite-strain model for incomplete damage in elastoplastic materials

We address a three-dimensional model capable of describing coupled damage and plastic effects in solids at finite strains. Formulated within the variational setting of generalized standard materials, the constitutive model results from the balance of conservative and dissipative forces. Material response is rate-independent and associative and damage evolution is unidirectional. We assess the model features and performance on both uniaxial and non-proportional biaxial tests.The constitutive model is then complemented with the quasistatic equilibrium system and initial and boundary conditions. We produce numerical simulations with the help of the multiphysics finite element software NETGEN/NGSolve. We show the flexibility of the implementation and run simulations for various 2D and 3D settings under different choices of boundary conditions and possibly in presence of pre-damaged regions.

Study of Electronic Effects on Normal vs. Abnormal Tetrazol-5-ylidenes at DFT

We present electronic effects on stability (ΔES-T), nucleophilicity (N), global electrophilicity (ω), and band gaps (ΔEHOMO-LUMO) of 36 novel 1,4- and 1,3-tetrazole-5-ylidenes, 1 and 2, respectively. A union of three sets of normal 1W,W, 1D,D, and 1D,W are compared to another union of four sets of abnormal 2W,W, 2D,D, 2D,W and 2W,D NHCs, electron-withdrawing substituents (W) and electron-donating ones (D). Every 1 is more stable and shows a larger bandgap than its corresponding 2. In addition, philicities, N and ω, of every 2 appear larger than that of the corresponding 1 isomer. Carbenes with W groups increase electrophilicity while D ones increase nucleophilicity and in pull-push groups, W groups in carbene center increase electrophilicity. All our NHCs give doubly bonded head-to-head dimers except for 5 species.

Identification of the actual excess excavation ratio (Stakhanovskaya street – Nizhegorodskaya street site)

Introduction. Redundant strain arises in buildings and structures in areas of construction work influence caused by the deep bore tunneling performed by tunnel boring machines. The strain analysis must include an excess excavation ratio that depends on the structural features of the shield, the technology of grouting mixture injection outside the lining, the counterweight pressure applied to the shield face and geotechnical conditions so that excessive settlement could be taken account of. The purpose of the article is to identify actual values of the excess excavation ratio to raise excavation and determine the values of standard averaged excess excavation to be further applied in design.
 Materials and methods. This paper focuses on tunnel driving between “Stakhanovskaya Street” and “Nizhegorodskaya Street” stations. The project excess excavation ratio was applied pursuant to the regulatory documents in order to perform the analysis using PLAXIS 2D and PLAXIS 3D software packages. The method of sequential iteration was applied to identify the value of excess excavation in line with the actual settlement of buildings and structures obtained by means of monitoring.
 Results. The analysis has shown that the actual excess excavation ratio varies between 0.1 and 1.2 % for this construction site which is below the values required by the regulatory documents. As for the 3D setting, the values of actual excess excavation ratios are 2 to 4 times higher than those obtained for the 2D setting, although the value of the actual building settlement remains the same.
 Conclusions. Since the actual building settlement is smaller than the projected one, the cost of deep bored tunneling can be reduced by cutting the cost of protection of nearby buildings and structures within the area of tunneling influence without violating any safety requirements and also by reducing the number of buildings withing the projected area of influence, and respectively, by reducing the cost of geodetic monitoring over their displacements.

Targeting Telomerase with an HLA Class II-Restricted TCR for Cancer Immunotherapy

T cell receptor (TCR)-engineered T cell therapy is a promising cancer treatment approach. Human telomerase reverse transcriptase (hTERT) is overexpressed in the majority of tumors and a potential target for adoptive cell therapy. We isolated a novel hTERT-specific TCR sequence, named Radium-4, from a clinically responding pancreatic cancer patient vaccinated with a long hTERT peptide. Radium-4 TCR-redirected primary CD4+ and CD8+ T cells demonstrated in vitro efficacy, producing inflammatory cytokines and killing hTERT+ melanoma cells in both 2D and 3D settings, as well as malignant, patient-derived ascites cells. Importantly, T cells expressing Radium-4 TCR displayed no toxicity against bone marrow stem cells or mature hematopoietic cells. Notably, Radium-4 TCR+ T cells also significantly reduced tumor growth and improved survival in a xenograft mouse model. Since hTERT is a universal cancer antigen, and the very frequently expressed HLA class II molecules presenting the hTERT peptide to this TCR provide a very high (>75%) population coverage, this TCR represents an attractive candidate for immunotherapy of solid tumors.

Colorful Helly-type theorems for the volume of intersections of convex bodies

We prove the following Helly-type result. Let C1,…,C3d be finite families of convex bodies in Rd. Assume that for any colorful selection of 2d sets, Cik∈Cik for each 1≤k≤2d with 1≤i1<…<i2d≤3d, the intersection ⋂k=12dCik is of volume at least 1. Then there is an 1≤i≤3d such that ⋂C∈CiC is of volume at least d−O(d2).

A fast and accurate computation of 2D and 3D generalized Laguerre moments for images analysis

In this paper, we will present a new set of 2D and 3D continuous orthogonal moments based on generalized Laguerre orthogonal polynomials (GLPs) for 2D and 3D image analysis. However, the computation of the generalized Laguerre orthogonal moments (GLMs) is limited by the problems of discretization of the continuous space of the polynomials, approximation of the integrals by finite sums and of too high computation time. To remedy these problems, we will propose a new method for the fast and the precise computation of 2D and 3D GLMs. This method is based on the development of an exact calculation of the double and triple integrals which define the 2D and 3D GLMs, and on the matrix calculation to accelerate the processing time of the images instead of the direct calculation. In addition to the theoretical results obtained, several experiments are carried out to validate the efficiency of the 2D and 3D GLMs descriptors in terms of computation precision and accuracy and in terms of acceleration of computation time and 2D/3D image reconstruction. The experimental results clearly show the advantages and the effectiveness of GLMs compared to the continuous orthogonal moments of Legendre, Chebyshev, Gegenbauer and Gaussian-Hermite.

Doxorubicin Improves Cancer Cell Targeting by Filamentous Phage Gene Delivery Vectors.

Merging targeted systemic gene delivery and systemic chemotherapy against cancer, chemovirotherapy, has the potential to improve chemotherapy and gene therapy treatments and overcome cancer resistance. We introduced a bacteriophage (phage) vector, named human adeno-associated virus (AAV)/phage or AAVP, for the systemic targeting of therapeutic genes to cancer. The vector was designed as a hybrid between a recombinant adeno-associated virus genome (rAAV) and a filamentous phage capsid. To achieve tumor targeting, we displayed on the phage capsid the double-cyclic CDCRGDCFC (RGD4C) ligand that binds the alpha-V/beta-3 (αvβ3) integrin receptor. Here, we investigated a combination of doxorubicin chemotherapeutic drug and targeted gene delivery by the RGD4C/AAVP vector. Firstly, we showed that doxorubicin boosts transgene expression from the RGD4C/AAVP in two-dimensional (2D) cell cultures and three-dimensional (3D) tumor spheres established from human and murine cancer cells, while preserving selective gene delivery by RGD4C/AAVP. Next, we confirmed that doxorubicin does not increase vector attachment to cancer cells nor vector cell entry. In contrast, doxorubicin may alter the intracellular trafficking of the vector by facilitating nuclear accumulation of the RGD4C/AAVP genome through destabilization of the nuclear membrane. Finally, a combination of doxorubicin and RGD4C/AAVP-targeted suicide gene therapy exerts a synergistic effect to destroy human and murine tumor cells in 2D and 3D tumor sphere settings.

A Variational Multiscale method with immersed boundary conditions for incompressible flows.

This paper presents a new stabilized form of incompressible Navier-Stokes equations for weak enforcement of Dirichlet boundary conditions at immersed boundaries. The boundary terms are derived via the Variational Multiscale (VMS) method which involves solving the fine-scale variational problem locally within a narrow band along the boundary. The fine-scale model is then variationally embedded into the coarse-scale form that yields a stabilized method which is free of user defined parameters. The derived boundary terms weakly enforce the Dirichlet boundary conditions along the immersed boundaries that may not align with the inter-element edges in the mesh. A unique feature of this rigorous derivation is that the structure of the stabilization tensor which emerges is naturally endowed with the mathematical attributes of area-averaging and stress-averaging. The method is implemented using 4-node quadrilateral and 8-node hexahedral elements. A set of 2D and 3D benchmark problems is presented that investigate the mathematical attributes of the method. These test cases show that the proposed method is mathematically robust as well as computationally stable and accurate for modeling boundary layers around immersed objects in the fluid domain.

Improving the immunosuppressive potential of articular chondroprogenitors in a three-dimensional culture setting

Cartilage repair in osteoarthritic patients remains a challenge. Identifying resident or donor stem/progenitor cell populations is crucial for augmenting the low intrinsic repair potential of hyaline cartilage. Furthermore, mediating the interaction between these cells and the local immunogenic environment is thought to be critical for long term repair and regeneration. In this study we propose articular cartilage progenitor/stem cells (CPSC) as a valid alternative to bone marrow-derived mesenchymal stem cells (BMMSC) for cartilage repair strategies after trauma. Similar to BMMSC, CPSC isolated from osteoarthritic patients express stem cell markers and have chondrogenic, osteogenic, and adipogenic differentiation ability. In an in vitro 2D setting, CPSC show higher expression of SPP1 and LEP, markers of osteogenic and adipogenic differentiation, respectively. CPSC also display a higher commitment toward chondrogenesis as demonstrated by a higher expression of ACAN. BMMSC and CPSC were cultured in vitro using a previously established collagen-chondroitin sulfate 3D scaffold. The scaffold mimics the cartilage niche, allowing both cell populations to maintain their stem cell features and improve their immunosuppressive potential, demonstrated by the inhibition of activated PBMC proliferation in a co-culture setting. As a result, this study suggests articular cartilage derived-CPSC can be used as a novel tool for cellular and acellular regenerative medicine approaches for osteoarthritis (OA). In addition, the benefit of utilizing a biomimetic acellular scaffold as an advanced 3D culture system to more accurately mimic the physiological environment is demonstrated.

Angular super-resolution retrieval in small-angle X-ray scattering

Small-angle X-ray scattering (SAXS) techniques enable convenient nanoscopic characterization for various systems and conditions. Unlike synchrotron-based setups, lab-based SAXS systems intrinsically suffer from lower X-ray flux and limited angular resolution. Here, we develop a two-step retrieval methodology to enhance the angular resolution for given experimental conditions. Using minute hardware additions, we show that translating the X-ray detector in subpixel steps and modifying the incoming beam shape results in a set of 2D scattering images, which is sufficient for super-resolution SAXS retrieval. The technique is verified experimentally to show superior resolution. Such advantages have a direct impact on the ability to resolve finer nanoscopic structures and can be implemented in most existing SAXS apparatuses both using synchrotron- and laboratory-based sources.

A modified hybrid finite‐element method for a semi‐implicit mass‐based non‐hydrostatic kernel

AbstractA hybrid finite‐element vertical discretization method for a semi‐implicit mass‐based non‐hydrostatic kernel is a feasible high‐order discretization approach which combines the advantages of both finite‐differential and finite‐element methods. In this article, we put forward a modified version of the existing hybrid finite‐element method to reduce computation load and improve precision. A key feature of our modified method is the presence, in the enlarging step, of new levels which are not equally spaced, but rather based on Gaussian quadrature. A higher‐order accuracy may be thus achieved with less enlarged levels by virtue of the properties of Gaussian quadrature. The modified method is also designed to fulfil the constraints required by the dynamic kernel, which themselves are crucial to ensure stability. A set of 2D and 3D test cases are conducted so as to confirm the accuracy and the stability of the new method.

Soliton formation and stability under the interplay between parity-time-symmetric generalized Scarf-II potentials and Kerr nonlinearity

We present an alternative type of parity-time (PT)-symmetric generalized Scarf-II potentials, which makes possible for non-Hermitian Hamiltonians in the classical linear Schrödinger system to possess fully real spectra with unique features such as the multiple PT-symmetric breaking behaviors and to support one-dimensional (1D) stable PT-symmetric solitons of power-law waveform, namely power-law solitons, in focusing Kerr-type nonlinear media. Moreover, PT-symmetric high-order solitons are also derived numerically in 1D and 2D settings. Around the exactly obtained nonlinear propagation constants, families of 1D and 2D localized nonlinear modes are also found numerically. The majority of fundamental nonlinear modes can still keep steady in general, whereas the 1D multipeak solitons and 2D vortex solitons are usually susceptible to suffering from instability. Likewise, similar results occur in the defocusing Kerr-nonlinear media. The obtained results will be useful for understanding the complex dynamics of nonlinear waves that form in PT-symmetric nonlinear media in other physical contexts.