An In-Vitro Evaluation of Articulation Accuracy for Digitally Milled Models vs. Conventional Gypsum Casts

With the advent of a digital workflow in dentistry, the inter-occlusal articulation of digital models is now possible through various means. The Cadent iTero intraoral scanner uses a buccal scan in maximum intercuspation to record the maxillomandibular relationship. This in-vitro study compares the occlusion derived from conventionally articulated stone casts versus that of digitally articulated quadrant milled models. Thirty sets of stone casts poured from full arch polyvinyl siloxane impressions (Group A) and thirty sets of polyurethane quadrant models milled from digital impressions (Group B) were used for this study. The full arch stone casts were hand-articulated and mounted on semi-adjustable articulators, while the digitally derived models were pre-mounted from the milling center based on the data obtained from the buccal scanning procedure. A T-scan sensor was used to obtain a bite registration from each set of models in both groups. The T-scan data derived from groups A and B were compared to that from the master model to evaluate the reproducibility of the occlusion in the two groups. A statistically significant difference of the contact region surface area was found on #11 of the digitally articulated models compared to the master. An analysis of the force distribution also showed a tendency for a heavier distribution on the more anterior #11 tooth for the digitally articulated models. Within the limitations of this study, the use of a digitally articulated quadrant model system may result in a loss of accuracy, in terms of occlusion, the further anteriorly the tooth to be restored is located. Care must be taken to consider the sources of inaccuracies in the digital workflow to minimize them for a more efficient and effective restorative process.

Surface reconstruction post-processing method for 3D- scanned objects

3D scanning is widely used in multiple applications to obtain high precision / non-destructive documentation of real-life objects, which is especially important in Cultural Heritage (CH) preservation. However, some issues (in particular missing parts which are commonly known as “holes”) affect the accuracy of the obtained 3D model after the scanning procedure and requires time-consuming post-processing procedures, which include manual editing by highly-trained personnel. In this article an automatic method to reconstruct the obtained surface of 3D models is proposed, improving previously obtained results for high-density point clouds.

GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphs

Transcription factors (TFs) are proteins that promote or reduce the expression of genes by binding short genomic DNA sequences known as transcription factor binding sites (TFBS). While several tools have been developed to scan for potential occurrences of TFBS in linear DNA sequences or reference genomes, no tool exists to find them in pangenome variation graphs (VGs). VGs are sequence-labelled graphs that can efficiently encode collections of genomes and their variants in a single, compact data structure. Because VGs can losslessly compress large pangenomes, TFBS scanning in VGs can efficiently capture how genomic variation affects the potential binding landscape of TFs in a population of individuals. Here we present GRAFIMO (GRAph-based Finding of Individual Motif Occurrences), a command-line tool for the scanning of known TF DNA motifs represented as Position Weight Matrices (PWMs) in VGs. GRAFIMO extends the standard PWM scanning procedure by considering variations and alternative haplotypes encoded in a VG. Using GRAFIMO on a VG based on individuals from the 1000 Genomes project we recover several potential binding sites that are enhanced, weakened or missed when scanning only the reference genome, and which could constitute individual-specific binding events. GRAFIMO is available as an open-source tool, under the MIT license, at https://github.com/pinellolab/GRAFIMO and https://github.com/InfOmics/GRAFIMO.

Computational Diagnostics of Jacobi Unstable Dynamical Systems with the Use of Hybrid Algorithms of Global Optimization

The study focuses on the problems of restoration and analysis of free parameters of dynamical systems from indirect, approximately given information. In the context of the Kosambi --- Cartan --- Chern theory, a geometric description of the time-evolution of the system is introduced. Five geometric invariants are determined for the system under study. The eigenvalues of the second invariant estimate the Jacobi stability of the system. Such a study is of interest in practical applications, where it is required to identify the regions in which both Lyapunov stability and Jacobi stability occur simultaneously. The inverse problem of computational diagnostics of the system is formulated for approximately given eigenvalues of the second invariant. The solution to the regularized inverse problem is determined using an optimization approach. Scalar criterion functions are assumed to be continuous, multidimensional, locally Lipschitzian, and not necessarily everywhere differentiable. When searching for global solutions, we used new hybrid algorithms that integrate stochastic algorithms for scanning the space of variables and a deterministic local minimization procedure. The numerical scanning procedure is implemented with the use of two modified versions: quasi-opposition-based and rotation-based learning mechanisms. In the phase of local search, two-parameter smoothing approximations of criterion functions are introduced. Examples of solving problems of computational diagnostics of Jacobi unstable dynamical systems are given: the Lorentz system and a controllable elliptical pendulum

Infant and Child MRI: A Review of Scanning Procedures

Magnetic resonance imaging (MRI) is a safe method to examine human brain. However, a typical MR scan is very sensitive to motion, and it requires the subject to lie still during the acquisition, which is a major challenge for pediatric scans. Consequently, in a clinical setting, sedation or general anesthesia is often used. In the research setting including healthy subjects anesthetics are not recommended for ethical reasons and potential longer-term harm. Here we review the methods used to prepare a child for an MRI scan, but also on the techniques and tools used during the scanning to enable a successful scan. Additionally, we critically evaluate how studies have reported the scanning procedure and success of scanning. We searched articles based on special subject headings from PubMed and identified 86 studies using brain MRI in healthy subjects between 0 and 6 years of age. Scan preparations expectedly depended on subject’s age; infants and young children were scanned asleep after feeding and swaddling and older children were scanned awake. Comparing the efficiency of different procedures was difficult because of the heterogeneous reporting of the used methods and the success rates. Based on this review, we recommend more detailed reporting of scanning procedure to help find out which are the factors affecting the success of scanning. In the long term, this could help the research field to get high quality data, but also the clinical field to reduce the use of anesthetics. Finally, we introduce the protocol used in scanning 2 to 5-week-old infants in the FinnBrain Birth Cohort Study, and tips for calming neonates during the scans.

Some features of linear scanning of the chemical composition of mineral aggregates using LA-ICP-MS: the modes and limits of the method

A routine linear and 2D scanning procedure using the inductively coupled plasma mass spectrometry with laser ablation (LA-ICP-MS) is often used when studying the composition of zonal and polyphase solid objects (crystals, rocks, alloys, etc.). However, the proper interpretation of the data necessitates taking into account the features inherent to the procedure. One of the most important features of the results obtained for the objects contrasting in composition is the asymmetry of the concentration profile of elements when going from high to low and, to a lesser extent, when going from low to high contents. Physical processes accompanying the analysis of rocks with the aforementioned features are considered. The duration of the time of signal distortion upon change of one crystal phase to another at large differences in the content of elements is estimated. To obtain the correct data for linear and 2D scanning using LA-ICP-MS, the scanning should be performed point by point: to avoid the influence of crater effects, points should be spaced 1.5 – 2.0 laser beam diameter apart. The goal of obtaining of reliable results requires also keeping the time intervals between measurements of at least 2 – 5 sec.

Role of T2 Mapping Sequences using MR Imaging in Evaluation of Knee Joint Articular Cartilage

Background: Cartilage mapping using Magnetic Resonance Imaging T2 is a functional scanning procedure without invasion delivering cartography of the cartilage T2 relaxation time without using of any contrast. It is tissue anisotropy sensitive, and compositional data on the collagen network of cartilage, content of water and concentration of proteoglycans are provided by it. This study used MR scanning technique to assess the T2 mapping sequence role in diagnosis of articular cartilage lesions of knee joint. Patients and Methods: This prospective trial was done to utilize sagittal T2 mapping sequence for assessment of articular cartilage of knee joint on 1.5 T MR. The material of this study included thirty (30) patients. The study included 24/30 cases presented by knee pain, 6/30 cases presented by knee pain following trauma, 10/30 cases presented by limitation of movement and 7/30 cases presented by knee swelling. As each patient had a single conventional MRI examination of the knee followed by a single sagittal T2 maps, 30 MRI examinations and 30 corresponding T2 maps were analyzed. Results: The addition of sagittal T2 maps to standard views improved accuracy in diagnosing cartilage affection in early osteoarthritis. there are 69 (57.5%) lesions diagnosed as grade 0 by MRI only VS 24 (20%) lesions diagnosed as grade 0 by MRI with T2 mapping sequence and 34 (28.3%) lesions diagnosed as grade 1 by MRI only VS 77 (64.2%) lesions diagnosed as grade 1 by MRI with T2 mapping sequence. there is 46 (38.3%) lesions diagnosed as grade 1a by MRI with T2 mapping sequence which diagnosed grade 0 by MRI only. Conclusions: This imaging plane seems to provide a useful addition to standard MR imaging when osteoarthritis is suspected specially among the young population.

Diffusion Spectrum Imaging of Corticospinal Tracts in Idiopathic Normal Pressure Hydrocephalus

Purpose: The purpose of this study was to measure the diffusion spectrum imaging (DSI) parameters of corticospinal tracts (CSTs) and evaluate diffusional changes in CSTs in patients with idiopathic normal pressure hydrocephalus (iNPH) by DSI.Methods: Twenty-three iNPH patients and twenty-one healthy controls (HCs) were involved in this study. Brain DSI data for all participants were collected through the same MR scanning procedure. The diffusion parameters measured and analyzed included quantitative anisotropy (QA), the isotropic diffusion component (ISO), general fractional anisotropy (GFA), fractional anisotropy (FA), mean diffusivity (MD), axial diffusivity (AD), and radial diffusivity (RD) of corticospinal tracts.Results: The QA and ISO values of corticospinal tracts in iNPH patients were significantly lower than those in HCs (PLQA = 0.008, PRQA = 0.016, PLISO = 0.024, PRISO = 0.016). The mean MD, AD, and RD values in iNPH patients were significantly higher than those in HCs (PMD = 0.032, PAD = 0.032, PRD = 0.048,). No significant differences in GFA and FA values were noted between iNPH patients and HCs.Conclusion: Decreased QA and ISO values of corticospinal tracts were found in iNPH patients. Quantitative CST evaluation using DSI may lead to information that can improve the present understanding of the disease mechanism.

GRAFIMO: variant and haplotype aware motif scanning on pangenome graphs

Transcription factors (TFs) are proteins that promote or reduce the expression of genes by binding short genomic DNA sequences known as transcription factor binding sites (TFBS). While several tools have been developed to scan for potential occurrences of TFBS in linear DNA sequences or reference genomes, no tool exists to find them in pangenome variation graphs (VGs). VGs are sequence-labelled graphs that can efficiently encode collections of genomes and their variants in a single, compact data structure. Because VGs can losslessly compress large pangenomes, TFBS scanning in VGs can efficiently capture how genomic variation affects the potential binding landscape of TFs in a population of individuals. Here we present GRAFIMO (GRAph-based Finding of Individual Motif Occurrences), a command-line tool for the scanning of known TF DNA motifs represented as Position Weight Matrices (PWMs) in VGs. GRAFIMO extends the standard PWM scanning procedure by considering variations and all the alternative haplotypes encoded in a VG. Using GRAFIMO on a VG based on individuals from the 1000 Genomes project we recover several potential binding sites that are enhanced, weakened or missed when scanning only the reference genome, and which could constitute individualspecific binding events. GRAFIMO is available as an open-source tool, under the MIT license, at https://github.com/pinellolab/GRAFIMO and https://github.com/InfOmics/GRAFIMO.Author summaryTranscription factors (TFs) are key regulatory proteins and mutations occurring in their binding sites can alter the normal transcriptional landscape of a cell and lead to disease states. Pangenome variation graphs (VGs) efficiently encode genomes from a population of individuals and their genetic variations. GRAFIMO is an open-source tool that extends the traditional PWM scanning procedure to VGs. By scanning for potential TBFS in VGs, GRAFIMO can simultaneously search thousands of genomes while accounting for SNPs, indels, and structural variants. GRAFIMO reports motif occurrences, their statistical significance, frequency, and location within the reference or alternative haplotypes in a given VG. GRAFIMO makes it possible to study how genetic variation affects the binding landscape of known TFs within a population of individuals.

A framework for prioritising present and potentially invasive mammal species for a national list

The European Union (EU) has recently adopted a regulation on invasive alien species that foresees the possibility of developing lists of species of National Concern. We developed a prioritisation process for alien mammals already established in Italy, but not yet included in the EU list (n = 6 species) and a systematic horizon-scanning procedure to obtain ranked lists for those species that are already introduced worldwide or traded in Italy (n = 213). Experts were asked to score these species, by evaluating their likelihood of establishment and spread and the magnitude of their potential impacts on biodiversity, economy, human-health and society. The manageability of each species was also evaluated, both for the proritisation and the horizon-scanning processes. We produced five lists that ranked species according to their potential spread and impacts and their manageability. These will allow policy-makers to select outputs according to a balance between risk assessment and risk management, establishing priorities for alien species management at the national level.