3D Jigsaw Research Articles

Optical Ciphering Scheme for Cancellable Speaker Identification System

Most current security and authentication systems are based on personal biometrics. The security problem is a major issue in the field of biometric systems. This is due to the use in databases of the original biometrics. Then biometrics will forever be lost if these databases are attacked. Protecting privacy is the most important goal of cancelable biometrics. In order to protect privacy, therefore, cancelable biometrics should be non-invertible in such a way that no information can be inverted from the cancelable biometric templates stored in personal identification/verification databases. One methodology to achieve non-invertibility is the employment of non-invertible transforms. This work suggests an encryption process for cancellable speaker identification using a hybrid encryption system. This system includes the 3D Jigsaw transforms and Fractional Fourier Transform (FrFT). The proposed scheme is compared with the optical Double Random Phase Encoding (DRPE) encryption process. The evaluation of simulation results of cancellable biometrics shows that the algorithm proposed is secure, authoritative, and feasible. The encryption and cancelability effects are good and reveal good performance. Also, it introduces recommended security and robustness levels for its utilization for achieving efficient cancellable biometrics systems.

3D BRAIN TUMOR DETECTION

The efficacy of self-supervised learning techniques in a variety of application fields has helped them become more popular recently. In this work, we give 3D proxy tasks for five various self-supervised learning approaches using these principles. By enabling neural network feature learning from unlabelled 3D images, we hope to minimise the cost of expert annotation. The techniques include Relative 3D Patch Location, 3D Exemplar Networks, 3D Rotation Prediction, 3D Jigsaw Puzzles, and 3D Contrastive Predictive Coding. Our findings show that pretraining models using our 3D tasks generates more rich semantic representations and enables completing downstream tasks more accurately and quickly compared to training the models from scratch and pretraining them on 2D slices.

Synthesis of 3D jigsaw puzzles over freeform 2-manifolds

We present a simple algorithm for synthesizing 3D jigsaw puzzles from arbitrary 3D freeform 2-manifold geometric models represented with trimmed NURBS surfaces. The construction algorithm is based on a few conventional geometric operations on freeform curves and surfaces. In particular, we need to compute the offset of freeform NURBS surfaces (for thickening the 2-manifold surfaces) and the functional composition of a univariate curve representation to a bivariate rational surface (for breaking up a 3D model into curved jigsaw tiles). It is thus almost straightforward to convert the proposed algorithm to a practical system using standard tools available in B-rep based geometric modeling systems, that employ trimmed NURBS surfaces. We demonstrate the effectiveness of the proposed approach by fabricating several test sets of 3D jigsaw puzzles for freeform solids consisting of trimmed NURBS surface models.

Cancelable face and fingerprint recognition based on the 3D jigsaw transform and optical encryption

Biometric systems are widely used now for security applications. Two major problems are encountered in biometric systems: the security problem and the dependence on a single biometric for verification. The security problem arises from the utilization of the original biometrics in databases. So, if these databases are attacked, the biometrics are lost forever. Hence, there is a need to secure original biometrics by keeping them away from utilization in biometric databases. Cancelable biometrics is an emerging security trend in the field of biometric authentication. Cancelable biometric systems depend on the transformation of biometric features into new formats so that users can replace their biometric templates in the same or different systems. In this paper, we present a proposed cancelable face and fingerprint recognition algorithm based on the 3D jigsaw transform and optical encryption. The algorithm adopts the Fractional Fourier Transform (FRFT) in the optical encryption scheme with a single random phase mask. This structure can be implemented all optically with a single lens. The proposed cancelable biometric recognition algorithm employs an optical image encryption scheme that depends on two cascaded stages of 2D-FRFT with separable kernels in both dimensions. The two stages are separated with a random phase mask. A preceding bit plane permutation process is performed on the obtained biometrics prior to the FRFT operation to achieve a high level of security. To validate the proposed algorithm for cancelable biometric recognition, different sets of face and fingerprint images are used. A comparative study is presented between the proposed algorithm and the optical Double Random Phase Encoding (DRPE) algorithm. The simulations results obtained for performance evaluation show that the proposed algorithm is safe, reliable, and feasible. It has good encryption and cancelability that reveal good performance.

Superpixel Soup: Monocular Dense 3D Reconstruction of a Complex Dynamic Scene.

This work addresses the task of dense 3D reconstruction of a complex dynamic scene from images. The prevailing idea to solve this task is composed of a sequence of steps and is dependent on the success of several pipelines in its execution. To overcome such limitations with the existing algorithm, we propose a unified approach to solve this problem. We assume that a dynamic scene can be approximated by numerous piecewise planar surfaces, where each planar surface enjoys its own rigid motion, and the global change in the scene between two frames is as-rigid-as-possible (ARAP). Consequently, our model of a dynamic scene reduces to a soup of planar structures and rigid motion of these local planar structures. Using planar over-segmentation of the scene, we reduce this task to solving a "3D jigsaw puzzle" problem. Hence, the task boils down to correctly assemble each rigid piece to construct a 3D shape that complies with the geometry of the scene under the ARAP assumption. Further, we show that our approach provides an effective solution to the inherent scale-ambiguity in structure-from-motion under perspective projection. We provide extensive experimental results and evaluation on several benchmark datasets. Quantitative comparison with competing approaches shows state-of-the-art performance.

Patient-specific puzzle implant preformed with 3D-printed rapid prototype model for combined orbital floor and medial wall fracture

The management of combined orbital floor and medial wall fractures involving the inferomedial strut is challenging due to absence of stable cornerstone. In this article, we proposed surgical strategies using customized 3D puzzle implant preformed with Rapid Prototype (RP) skull model. Retrospective review was done in 28 patients diagnosed with combined orbital floor and medial wall fracture. Using preoperative CT scans, original and mirror-imaged RP skull models for each patient were prepared and sterilized. In all patients, porous polyethylene-coated titanium mesh was premolded onto RP skull model in two ways; Customized 3D jigsaw puzzle technique was used in 15 patients with comminuted inferomedial strut, whereas individual 3D implant technique was used in each fracture for 13 patients with intact inferomedial strut. Outcomes including enophthalmos, visual acuity, and presence of diplopia were assessed and orbital volume was measured using OsiriX software preoperatively and postoperatively. Satisfactory results were achieved in both groups in terms of clinical improvements. Of 10 patients with preoperative diplopia, 9 improved in 6 months, except one with persistent symptom who underwent extraocular muscle rupture. 18 patients who had moderate to severe enophthalmos preoperatively improved, and one remained with mild degree. Orbital volume ratio, defined as volumetric ratio between affected and control orbit, decreased from 127.6% to 99.79% (p < 0.05) in comminuted group, and that in intact group decreased from 117.03% to 101.3% (p < 0.05). Our surgical strategies using the jigsaw puzzle and individual reconstruction technique provide accurate restoration of combined orbital floor and medial wall fractures.

Combinatorial design of textured mechanical metamaterials.

The structural complexity of metamaterials is limitless, but, in practice, most designs comprise periodic architectures that lead to materials with spatially homogeneous features. More advanced applications in soft robotics, prosthetics and wearable technology involve spatially textured mechanical functionality, which requires aperiodic architectures. However, a naive implementation of such structural complexity invariably leads to geometrical frustration (whereby local constraints cannot be satisfied everywhere), which prevents coherent operation and impedes functionality. Here we introduce a combinatorial strategy for the design of aperiodic, yet frustration-free, mechanical metamaterials that exhibit spatially textured functionalities. We implement this strategy using cubic building blocks-voxels-that deform anisotropically, a local stacking rule that allows cooperative shape changes by guaranteeing that deformed building blocks fit together as in a three-dimensional jigsaw puzzle, and three-dimensional printing. These aperiodic metamaterials exhibit long-range holographic order, whereby the two-dimensional pixelated surface texture dictates the three-dimensional interior voxel arrangement. They also act as programmable shape-shifters, morphing into spatially complex, but predictable and designable, shapes when uniaxially compressed. Finally, their mechanical response to compression by a textured surface reveals their ability to perform sensing and pattern analysis. Combinatorial design thus opens up a new avenue towards mechanical metamaterials with unusual order and machine-like functionalities.

Computational analysis of physico-chemical properties and homology modeling of carbonic anhydrase from Cordyceps militaris

In the present study, the protein sequence of carbonic anhydrase enzyme from Cordyceps militaris (accession no. EGX89555.1) was retrieved from GenPept database and subjected to computation for various physico-chemical properties, transmembrane segment prediction, homology modeling, domain identification and structural alignment. Five potential transmembrane segments of various lengths were predicted by transmembrane prediction server. The 3D structure of this protein was determined by homology modeling using 3d jigsaw server. A single eukaryotic-type carbonic anhydrase domain belonging to Carb_anhydrases family domain was identified at two positions from 45 to 153 and 232 to 302 residues region. This modeled structure showed 100 % structural similarity with human carbonic anhydrase III (PDB ID: 1z93-A) in PDB database.

Restitution of Sculptural Groups Using 3D Scanners

Imagine for a moment that you have to solve a 3D jigsaw of which you have lost several pieces. You have also lost the original box-top showing the final picture, and as if that were not enough, some of the pieces you do have may belong to some other jigsaw. This is in essence the sort of challenge that we faced in the novel project that we shall be describing in this paper. The final aim of the project was, with the help of 3D scanners, to digitalize and reconstruct multi-piece classical sculptures. Particularly, we tackle the restitution of the so-called “Aeneas Group”, a famous iconographic reference during the Roman Empire. We have undertaken this ambitious project in collaboration with the research department of the Spanish National Museum of Roman Art (MNAR). This paper summarizes the real problems that arose and had to be solved, the innovations, and the main results of the work that we have carried out over these recent years.

Comparative structural modeling and docking studies of oxalate oxidase: Possible implication in enzyme supplementation therapy for urolithiasis

In humans oxalate is end product of protein metabolism, with no enzyme present to act on it. In conditions of its enhanced endogenous synthesis or increased absorption from the diet, oxalate accumulation leads to hyperoxaluria which can further lead to a number of pathological conditions including urolithiasis. Urolithiasis has been a perplexing problem due to its high incidence and rate of recurrence after treatment like Extracorporeal-shock wave lithotripsy (ESWL). Hence other prophylactic treatment becomes necessary. One of the newer approaches of curing such metabolic disorders is the enzyme supplementation therapy. Oxalate oxidase (OxOx) is a commonly occurring enzyme in plants, bacteria and fungi that catalyses oxidative cleavage of oxalate to CO2 with reduction of dioxygen to H2O2. Present study, used Hordeum vulgare OxOx crystal structure (PDB ID 2ET1A) as a template for constructing 3D models of OxOx from Triticum aestivum, Arabidopsis thaliana, Sclerotiana sclerotiarum. Similarly Homology models for isoforms Ceriporiopsis subvermispora 336, C. subvermispora 422 were constructed by using template Bacillus subtilis oxalate decarboxylase (Oxdc) (PDB ID 2UY8A) by comparative modeling approach in SWISS MODEL, MODELLER, 3D JIGSAW and GENO 3D program server. Based on overall stereochemical quality (PROCHECK, PROSA, VARIFY 3D), best models were selected, energy minimized, refined and characterized for active site in BioMed CaChe V 6.1 workspace. Selected models were further studied for structure function relationship with substrate (oxalate) and its analogue (glycolate) by using docking approach. Calculated interaction energy between the oxalate and constructed enzyme indicated that homology models for OxOx of T. aestivum, A. thaliana and S. sclerotiarum, can account for better regio-specificity of this enzyme towards oxalate. That supports the interested metabolism and thus may further implement in enzyme supplementation therapy for urolithiasis.

Virtual multi-fracture craniofacial reconstruction using computer vision and graph matching

The problem of computer vision-guided reconstruction of a fractured human mandible from a computed tomography (CT) image sequence exhibiting multiple broken fragments is addressed. The problem resembles 3D jigsaw puzzle assembly and hence is of general interest for a variety of applications dealing with automated reconstruction or assembly. The specific problem of automated multi-fracture craniofacial reconstruction is particularly challenging since the identification of opposable fracture surfaces followed by their pairwise registration needs to be performed expeditiously in order to minimize the operative trauma to the patient and also limit the operating costs. A polynomial time solution using graph matching is proposed. In the first phase of the proposed solution, the opposable fracture surfaces are identified using the Maximum Weight Graph Matching algorithm. The pairs of opposable fracture surfaces, identified in the first stage, are registered in the second phase using the Iterative Closest Point (ICP) algorithm. Correspondence for a given pair of fracture surfaces, needed for the Closest Set computation in the ICP algorithm, is established using the Maximum Cardinality Minimum Weight bipartite graph matching algorithm. The correctness of the reconstruction is constantly monitored by using constraints derived from a volumetric matching procedure guided by the computation of the Tanimoto Coefficient.

3D Jigsaw Puzzle in Rotavirus Assembly

In this issue of Structure, Lu et al. (2008) report results of structural and functional analysis of rotavirus RNA-dependent RNA polymerase, VP1. Based on their analyses of VP1 in RNA free and bound forms, the authors propose a mechanism for coordinated genome packaging and replication.

PROTEUS2: a web server for comprehensive protein structure prediction and structure-based annotation

PROTEUS2 is a web server designed to support comprehensive protein structure prediction and structure-based annotation. PROTEUS2 accepts either single sequences (for directed studies) or multiple sequences (for whole proteome annotation) and predicts the secondary and, if possible, tertiary structure of the query protein(s). Unlike most other tools or servers, PROTEUS2 bundles signal peptide identification, transmembrane helix prediction, transmembrane β-strand prediction, secondary structure prediction (for soluble proteins) and homology modeling (i.e. 3D structure generation) into a single prediction pipeline. Using a combination of progressive multi-sequence alignment, structure-based mapping, hidden Markov models, multi-component neural nets and up-to-date databases of known secondary structure assignments, PROTEUS is able to achieve among the highest reported levels of predictive accuracy for signal peptides (Q2 = 94%), membrane spanning helices (Q2 = 87%) and secondary structure (Q3 score of 81.3%). PROTEUS2's homology modeling services also provide high quality 3D models that compare favorably with those generated by SWISS-MODEL and 3D JigSaw (within 0.2 Å RMSD). The average PROTEUS2 prediction takes ∼3 min per query sequence. The PROTEUS2 server along with source code for many of its modules is accessible a http://wishart.biology.ualberta.ca/proteus2.

Solving a 3D jigsaw puzzle

Solving a 3D jigsaw puzzle

An All-Atom Model of the Chromatin Fiber Containing Linker Histones Reveals a Versatile Structure Tuned by the Nucleosomal Repeat Length

In the nucleus of eukaryotic cells, histone proteins organize the linear genome into a functional and hierarchical architecture. In this paper, we use the crystal structures of the nucleosome core particle, B-DNA and the globular domain of H5 linker histone to build the first all-atom model of compact chromatin fibers. In this 3D jigsaw puzzle, DNA bending is achieved by solving an inverse kinematics problem. Our model is based on recent electron microscopy measurements of reconstituted fiber dimensions. Strikingly, we find that the chromatin fiber containing linker histones is a polymorphic structure. We show that different fiber conformations are obtained by tuning the linker histone orientation at the nucleosomes entry/exit according to the nucleosomal repeat length. We propose that the observed in vivo quantization of nucleosomal repeat length could reflect nature's ability to use the DNA molecule's helical geometry in order to give chromatin versatile topological and mechanical properties.

Reconstruction of human fossils

Paleoanthropologists rarely discover complete and undamaged vertebrate fossils. The original bones may have been torn apart by carnivores, and the fossils further broken down and scattered by geological processes and weathering. A thorough study of specimens generally requires reassembling the original fossil shape as accurately as possible from the broken pieces. Furthermore, since very few fossil fragments belong to a single individual, paleoanthropologists often make composite reconstructions, using pieces that come from many individuals. Thus, reconstructing damaged fossils is somewhat like solving a 3D jigsaw puzzle, in which many of the pieces are missing or deformed. The authors consider how the Computer-Assisted Anthropology system helps paleoanthropologists reconstruct fossils electronically by providing tools to display, manipulate, and measure fossil specimens on screen. The CAA system was built using IBM Visualization Data Explorer, a toolkit for analysis and visualization. Since the CAA system works with computed tomography (CT) scans of the fossils, it can extract embedded fragments nondestructively, using image processing to segment out the matrix.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>