Practical RGB-to-XYZ Color Transformation Matrix Estimation under Different Lighting Conditions for Graffiti Documentation.

Color data are often required for cultural heritage documentation. These data are typically acquired via standard digital cameras since they facilitate a quick and cost-effective way to extract RGB values from photos. However, cameras' absolute sensor responses are device-dependent and thus not colorimetric. One way to still achieve relatively accurate color data is via camera characterization, a procedure which computes a bespoke RGB-to-XYZ matrix to transform camera-dependent RGB values into the device-independent CIE XYZ color space. This article applies and assesses camera characterization techniques in heritage documentation, particularly graffiti photographed in the academic project INDIGO. To this end, this paper presents COOLPI (COlor Operations Library for Processing Images), a novel Python-based toolbox for colorimetric and spectral work, including white-point-preserving camera characterization from photos captured under diverse, real-world lighting conditions. The results highlight the colorimetric accuracy achievable through COOLPI's color-processing pipelines, affirming their suitability for heritage documentation.

Low-dose xenogeneic mesenchymal stem cells target canine osteoarthritis through systemic immunomodulation and homing.

BACKGROUND: As current therapies for canine osteoarthritis (OA) provide mainly symptomatic improvement and fail to address the complex pathology of the disease, mesenchymal stem cells (MSCs) offer a promising biological approach to address both aspects of OA through their immunomodulatory properties. METHODS: This study aimed to investigate the safety and efficacy of xenogeneic MSCs in dogs with OA at different dose levels after intravenous injection. OA was surgically induced in the right stifle joint. Thirty-two male and female dogs were divided into three treatment groups and a control group. Regular general physical examinations; lameness, joint, radiographic, and animal caretaker assessments; pressure plate analyses; and blood analyses were performed over 42 days. At study end, joint tissues were evaluated regarding gross pathology, histopathology, and immunohistochemistry. In a follow-up study, the biodistribution of intravenously injected 99mTc-labeled equine peripheral blood-derived MSCs was evaluated over 24h in three dogs after the cruciate ligament section. RESULTS: The dose determination study showed the systemic administration of ePB-MSCs in a canine OA model resulted in an analgesic, anti-inflammatory, and joint tissue protective effect associated with improved clinical signs and improved cartilage structure, as well as a good safety profile. Furthermore, a clear dose effect was found with 0.3 × 106 ePB-MSCs as the most effective dose. In addition, this treatment was demonstrated to home specifically towards the injury zone in a biodistribution study. CONCLUSION: This model-based study is the first to confirm the efficacy and safety of systemically administered xenogeneic MSCs in dogs with OA. The systemic administration of a low dose of xenogeneic MSCs could offer a widely accessible, safe, and efficacious treatment to address the complex pathology of canine OA and potentially slow down the disease progression by its joint tissue protective effect.

Intravenous Injection of Equine Mesenchymal Stem Cells in Dogs with Articular Pain and Lameness: A Feasibility Study.

Osteoarthritis is a frequently occurring joint disorder in veterinary practice. Current treatments are focused on pain and inflammation; however, these are not able to reverse the pathological condition. Mesenchymal stem cells (MSCs) could provide an interesting alternative because of their immunomodulatory properties. The objective of this study was to evaluate the potential of a single intravenous (IV) injection of xenogeneic equine peripheral blood-derived MSCs (epbMSCs) as treatment for articular pain and lameness. Patients with chronic articular pain were injected intravenously with epbMSCs. They were evaluated at three time points (baseline and two follow-ups) by a veterinarian based on an orthopedic joint assessment and an owner canine brief pain inventory scoring. Thirty-five dogs were included in the safety and efficacy evaluation of the study. Results showed that the epbMSC therapy was well tolerated, with no treatment-related adverse events and no increase in articular heat or pain. A significant improvement in lameness, range of motion, joint effusion, pain severity, and interference scores was found 6 weeks post-treatment compared with baseline. This study demonstrates that future research on IV administration of epbMSCs is warranted to further explore its possible beneficial effects in dogs with chronic articular pain and lameness. Clinical Trial gov ID: EC_2018_002.

Author Correction: Development and performance of a targeted whole exome sequencing enrichment kit for the dog (Canis Familiaris Build 3.1).

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Surfaces from the Visual Past: Recovering High-Resolution Terrain Data from Historic Aerial Imagery for Multitemporal Landscape Analysis.

Historic aerial images are invaluable sources of aid to archaeological research. Often collected with large-format photogrammetric quality cameras, these images are potential archives of multidimensional data that can be used to recover information about historic landscapes that have been lost to modern development. However, a lack of camera information for many historic images coupled with physical degradation of their media has often made it difficult to compute geometrically rigorous 3D content from such imagery. While advances in photogrammetry and computer vision over the last two decades have made possible the extraction of accurate and detailed 3D topographical data from high-quality digital images emanating from uncalibrated or unknown cameras, the target source material for these algorithms is normally digital content and thus not negatively affected by the passage of time. In this paper, we present refinements to a computer vision-based workflow for the extraction of 3D data from historic aerial imagery, using readily available software, specific image preprocessing techniques and in-field measurement observations to mitigate some shortcomings of archival imagery and improve extraction of historical digital elevation models (hDEMs) for use in landscape archaeological research. We apply the developed method to a series of historic image sets and modern topographic data covering a period of over 70 years in western Sicily (Italy) and evaluate the outcome. The resulting series of hDEMs form a temporal data stack which is compared with modern high-resolution terrain data using a geomorphic change detection approach, providing a quantification of landscape change through time in extent and depth, and the impact of this change on archaeological resources.

Intraobserver and interobserver agreement on the radiographical diagnosis of canine cranial cruciate ligament rupture.

Even though radiography is one of the most frequently used imaging techniques for orthopaedic disorders, it has been demonstrated that the interpretation can vary between assessors. As such, the purpose of this study was to examine the intraobserver and interobserver agreement and the influence of level of expertise on the interpretation of radiographs of the stifle in dogs with and without cranial cruciate ligament rupture (CCLR). Sixteen observers, divided in four groups according to their level of experience, evaluated 30 radiographs (15 cases with CCLR and 15 control stifles) twice. Each observer was asked to evaluate joint effusion, presence and location of degenerative joint disease, joint instability and whether CCLR was present or absent. Overall, intraobserver and interobserver agreement ranged from fair to almost perfect with a trend towards increased agreement for more experienced observers. Additionally, it was found that stifles that were classified with high agreement have either overt disease characteristics or no disease characteristics at all, in comparison to the ones that are classified with a low agreement. Overall, the agreement on radiographic interpretation of CCLR was high, which is important, as it is the basis of a correct diagnosis and treatment.

COMPUTED TOMOGRAPHIC FINDINGS IN CANINE ELBOWS ARTHROSCOPICALLY DIAGNOSED WITH EROSION OF THE MEDIAL COMPARTMENT: AN ANALYTICAL METHOD COMPARISON STUDY.

Medial compartment erosion is an advanced stage of medial coronoid disease, an important cause of elbow lameness in dogs, with treatment and the expected prognosis depending on the extent of the cartilage lesions. The identification of specific computed tomographic (CT) findings might facilitate the nonsurgical diagnosis and add to treatment decision making. Aims of this retrospective, analytical, method comparison study were to describe CT findings in elbows of dogs arthroscopically diagnosed with medial compartment erosion and to compare CT vs. arthroscopic findings. A total of 56 elbows met inclusion criteria. Elbows with focal (n = 13), diffuse (n = 11), and complete (n = 32) erosion were compared. Prevalence findings for CT lesions were as follows: periarticular osteophytosis (100%), abnormal shape of the medial coronoid process of the ulna (96.4%), and subchondral bone defect of the medial part of the humeral condyle (MHC; 96.4%). The three groups significantly differed for presence of medial coronoid process fragmentation, radial head subchondral bone sclerosis, and widening of the humeroulnar joint space. No significant agreement was found between CT and arthroscopy for presence of a subchondral bone defect of the MHC. A significant agreement was found between CT and arthroscopy for presence of fragmentation of the medial coronoid process. However, some of the calcified body/fragment(s) visualized on CT in the region of the medial coronoid process could not be identified via arthroscopy. Findings indicated that an accurate estimation of the extent of the elbow cartilage lesions still requires arthroscopic joint inspection.

Arthroscopic, Computed Tomography, and Radiographic Findings in 25 Dogs With Lameness After Arthroscopic Treatment of Medial Coronoid Disease.

OBJECTIVE: To describe the radiographic, computed tomography (CT), and arthroscopic findings in the elbow of dogs admitted for elbow lameness after previous arthroscopic treatment of medial coronoid disease (MCD). STUDY DESIGN: Retrospective case series. ANIMALS: Client-owned dogs (n = 25) admitted for elbow lameness after arthroscopic treatment. METHODS: Clinical records (2005-2009), including radiographs, CT images, and arthroscopic findings, from the first and second presentation of dogs diagnosed with medial coronoid disease were searched and reviewed. RESULTS: Twenty-nine joints were included in this study. The mean age at first treatment was 2.2 years. Second presentation was at a mean of 2.7 years later and progressive osteoarthritis and cartilage damage was noticed in all joints. Arthroscopic findings included a calcified body in 11/29 joints (38%), multiple small calcified bodies in 1/29 joint (3%), loose scar tissue in 12/29 joints (42%), and immobile scar tissue in 2/29 joints (7%). Three of 29 joints (10%) did not have any calcified body or loose scar tissue found but had erosion of the medial compartment as the only pathology diagnosed in the coronoid region. Characteristics of flexor enthesopathy were identified in 9/29 joints (31%). CONCLUSION: Arthroscopic treatment of MCD, even with limited cartilage lesions, may not resolve lameness in some dogs. Calcified bodies or loose scar tissue near the medial coronoid process are a frequent followup finding in these joints.

An heuristic filtering tool to identify phenotype-associated genetic variants applied to human intellectual disability and canine coat colors.

BACKGROUND: Identification of one or several disease causing variant(s) from the large collection of variants present in an individual is often achieved by the sequential use of heuristic filters. The recent development of whole exome sequencing enrichment designs for several non-model species created the need for a species-independent, fast and versatile analysis tool, capable of tackling a wide variety of standard and more complex inheritance models. With this aim, we developed "Mendelian", an R-package that can be used for heuristic variant filtering. RESULTS: The R-package Mendelian offers fast and convenient filters to analyze putative variants for both recessive and dominant models of inheritance, with variable degrees of penetrance and detectance. Analysis of trios is supported. Filtering against variant databases and annotation of variants is also included. This package is not species specific and supports parallel computation. We validated this package by reanalyzing data from a whole exome sequencing experiment on intellectual disability in humans. In a second example, we identified the mutations responsible for coat color in the dog. This is the first example of whole exome sequencing without prior mapping in the dog. CONCLUSION: We developed an R-package that enables the identification of disease-causing variants from the long list of variants called in sequencing experiments. The software and a detailed manual are available at https://github.com/BartBroeckx/Mendelian.

Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes.

By limiting sequencing to those sequences transcribed as mRNA, whole exome sequencing is a cost-efficient technique often used in disease-association studies. We developed two target enrichment designs based on the recently released annotation of the canine genome: the exome-plus design and the exome-CDS design. The exome-plus design combines the exons of the CanFam 3.1 Ensembl annotation, more recently discovered protein-coding exons and a variety of non-coding RNA regions (microRNAs, long non-coding RNAs and antisense transcripts), leading to a total size of ≈ 152 Mb. The exome-CDS was designed as a subset of the exome-plus by omitting all 3' and 5' untranslated regions. This reduced the size of the exome-CDS to ≈ 71 Mb. To test the capturing performance, four exome-plus captures were sequenced on a NextSeq 500 with each capture containing four pre-capture pooled, barcoded samples. At an average sequencing depth of 68.3x, 80% of the regions and well over 90% of the targeted base pairs were completely covered at least 5 times with high reproducibility. Based on the performance of the exome-plus, we estimated the performance of the exome-CDS. Overall, these designs provide flexible solutions for a variety of research questions and are likely to be reliable tools in disease studies.

TTA Rapid: Description of the Technique and Short Term Clinical Trial Results of the First 50 Cases.

OBJECTIVE: To (1) describe a modified technique for tibial tuberosity advancement (TTA) in dogs with cranial cruciate ligament (CCL) rupture and (2) report short term outcome and complications. STUDY DESIGN: Prospective clinical study. ANIMALS: Dogs with unilateral CCL rupture (n = 50). METHODS: TTA was performed with a novel implant to achieve advancement of the tibial crest. The technical protocol, specific implants and instrumentation, and the short term outcome are described. RESULTS: Various breeds (mean ± SD weight, 31.9 ± 13.3 kg) were included. Mean age at treatment was 64 ± 30.6 months. Minor complications occurred in 30% and major complications in 4% of the cases. Forty-eight (96%) dogs had a good to excellent outcome 3 months after surgery. CONCLUSION: The modified technique is a viable alternative to other osteotomy techniques.

Intra- and interobserver agreement on radiographic phenotype in the diagnosis of canine hip dysplasia.

OBJECTIVE: To investigate the repeatability and reproducibility of the presence of a circumferential femoral head osteophyte (CFHO), a curvilinear caudolateral osteophyte (CCO), osteosclerosis of the cranial acetabular edge (Scler CrAE), degenerative joint disease (DJD), and the diagnosis of suspected canine hip dysplasia (CHD) in different groups of experienced observers. STUDY DESIGN: Cross-sectional study. SAMPLE POPULATION: Standard hip extended radiographs (n = 50). METHODS: Nine experienced observers were divided into 3 groups: surgeons (DECVS), radiologists (DECVDI), and non-board certified observers (NBC) and 2 subgroups (academics and non-academics). Cohen's kappa (κ) was calculated for CFHO, CCO, Scler CrAE, DJD, and suspected CHD, and weighted κ was calculated for DJD score to determine inter- and intraobserver agreement. RESULTS: Intraobserver agreement on CFHO, CCO, Scler CrAE, DJD, and suspected CHD ranged from slight to almost perfect, but was not significantly different between NBC, DECVS, and DECVDI. Radiologists and non-board certified observers had a more uniform scoring than surgeons on the overall DJD score, as did academics versus non-academics. Interobserver agreement for NBC was more uniform than that of radiologists and surgeons on CCO and DJD. NBC and radiologists scored more uniformly than surgeons on CFHO, and radiologists scored more uniformly than NBC and surgeons on Scler CrAE. Academics scored more uniformly than non-academics, but only significantly for Scler CrAE. CONCLUSIONS: Recognition of specific radiographic markers is only fairly reliable within and between experienced observers. Therefore, care must be taken to apply these traits in official screening, surgical decision-making and scientific research.

Development and performance of a targeted whole exome sequencing enrichment kit for the dog (Canis Familiaris Build 3.1).

Whole exome sequencing is a technique that aims to selectively sequence all exons of protein-coding genes. A canine whole exome sequencing enrichment kit was designed based on the latest canine reference genome (build 3.1.72). Its performance was tested by sequencing 2 exome captures, each consisting of 4 pre-capture pooled, barcoded Illumina libraries on an Illumina HiSeq 2500. At an average sequencing depth of 102x, 83 to 86% of the target regions were completely sequenced with a minimum coverage of five and 90% of the reads mapped on the target regions. Additionally, it is shown that the reproducibility within and between captures is high and that pooling four samples per capture is a valid option. Overall, we have demonstrated the strong performance of this WES enrichment kit and are confident it will be a valuable tool in future disease association studies.

The prevalence of nine genetic disorders in a dog population from Belgium, the Netherlands and Germany.

The objective of this study was to screen a dog population from Belgium, the Netherlands and Germany for the presence of mutant alleles associated with hip dysplasia (HD), degenerative myelopathy (DM), exercise-induced collapse (EIC), neuronal ceroid lipofuscinosis 4A (NCL), centronuclear myopathy (HMLR), mucopolysaccharidosis VII (MPS VII), myotonia congenita (MG), gangliosidosis (GM1) and muscular dystrophy (Duchenne type) (GRMD). Blood samples (K3EDTA) were collected for genotyping with Kompetitive Allele Specific PCR (n = 476). Allele and genotype frequencies were calculated in those breeds with at least 12 samples (n = 8). Hardy-Weinberg equilibrium was tested. Genetic variation was identified for 4 out of 9 disorders: mutant alleles were found in 49, 15, 3 and 2 breeds for HD, DM, EIC and NCL respectively. Additionally, mutant alleles were identified in crossbreeds for both HD and EIC. For HD, DM, EIC and NCL mutant alleles were newly discovered in 43, 13, 2 and 1 breed(s), respectively. In 9, 2 and 1 breed(s) for DM, EIC and NCL respectively, the mutant allele was detected, but the respective disorder has not been reported in those breeds. For 5 disorders (HMLR, MPS VII, MG, GM1, GRMD), the mutant allele could not be identified in our population. For the other 4 disorders (HD, DM, EIC, NCL), prevalence of associated mutant alleles seems strongly breed dependent. Surprisingly, mutant alleles were found in many breeds where the disorder has not been reported to date.

Worldwide screening for canine hip dysplasia: where are we now?

OBJECTIVE: To critically review the different screening systems used for canine hip dysplasia (CHD) and their impact on the prevalence of the disease. STUDY DESIGN: Critical literature review. METHODS: Literature search through PubMed (November 1959-October 2011) and the Orthopedic Foundation for Animals (OFA), Fédération Cynologique Internationale (FCI), British Veterinary Association/Kennel Club (BVA/KC), and Pennsylvania Hip Improvement Program (PennHIP) websites. RESULTS: The OFA, FCI, and BVA/KC screening methods, which use the hip-extended radiographic projection, have had relatively minor success on CHD prevalence. These screening approaches are prone to conflicting data regarding interobserver agreement. The PennHIP and Dorsolateral Subluxation (DLS) systems, both distraction methods, have not reported on prevalence but seem to be important heritable traits in genomic screening of dysplastic dogs. CONCLUSION: A shift towards genome screening yields a promising future combating CHD, although further investigation towards fine-mapping in the search for genes, responsible for CHD, is necessary.

The effect of a technical quality assessment of hip-extended radiographs on interobserver agreement in the diagnosis of canine hip dysplasia.

Experienced and inexperienced observers evaluated the assessability of 50 radiographs (25 dogs) and determined the hip status (dysplasia/nondysplasia and final scoring according Fédération Cynologique Internationale [FCI]-criteria) individually. A radiographic technical quality assessment was performed in a separate reading session. Interobserver agreement in determining dysplasia/nondysplasia and FCI-scoring did not significantly increase with the increasing quality of a radiograph, irrespective whether these observers are experienced or not. There was a significant agreement between the technical quality assessment and assessability (P < 0.0005). Despite the effort to objectify radiographic quality and to present high-quality radiographs to observers, interobserver agreement on dysplasia/nondysplasia and final scoring, remains low, even in the experienced group. Although increased radiographic quality narrows the range of scoring, the range remains unacceptably high.

Interobserver agreement on the assessability of standard ventrodorsal hip-extended radiographs and its effect on agreement in the diagnosis of canine hip dysplasia and on routine FCI scoring.

Insufficient agreement on scoring hip quality might be caused by differences in the assessability of a radiograph (exposure, contrast, positioning, and diagnostic quality). We studied the agreement in assessability of standard ventrodorsal hip-extended radiographs by experienced (nine) and inexperienced (21) observers, using the standard subjective method of quality control, currently applied in screening programs. The effect of assessability on the agreement of scoring hip quality [dysplastic vs. nondysplastic and the final Federation Cinologique International (FCI) score] was also investigated. There was a significant difference (P < 0.0001) in agreement on assessability between the experienced and inexperienced observers. In 68% of evaluations, experienced observers stated that the radiograph was assessable. Inexperienced observers evaluated the radiographs as being assessable in only 46.5% of evaluations. Increased interobserver agreement on assessability of a radiograph did not increase the overall interobserver agreement in the diagnosis of hip dysplasia, nor did it result in consistent scoring of the hip status from that radiograph, despite a significant (P < 0.05) increase in agreement of FCI scoring with an increasing agreement on assessability at a one to five ratio in the experienced group. The inconsistent evaluation of radiographic quality, as well as the inconsistent evaluation of the hip quality, caused differences in diagnosing hip dysplasia and FCI scoring in the same dog ranging from excellent hips to moderate hip dysplasia. Therefore, the credibility of the FCI screening method for canine hip dysplasia, using the standard hip-extended radiographic view, as currently applied in most European countries, is questionable.