Pair-Matching Digital 3D Models of Temporomandibular Fragments Using Mesh-To-Mesh Value Comparison and Implications for Commingled Human Remain Assemblages.

The mesh-to-mesh value comparison (MVC) method developed by Karell et al. (Int J Legal Med 130(5):1315-1322, 2016) facilitates the digital comparison of three-dimensional mesh geometries obtained from laser-scanned or computed tomography data of osteological materials. This method has been employed with great success to pair-matching geometries of intact skeletal antimeres, that is, left and right sides. However, as is frequently the case for archaeological materials, there are few circumstances which proffer complete skeletal remains and fewer still when considering contexts of commingling. Prior to the present research, there existed a paucity of sorting techniques for the diverse taphonomic conditions of skeletal materials found within commingled assemblages, especially regarding fragmentary remains. The present chapter details a study in which the MVC method was adapted to encompass comparisons of isolated components of bone in lieu of entire bone geometries in order to address this dearth. Using post-mortem computed tomography data from 35 individuals, three-dimensional models of 70 mandibular fossae and 69 mandibular condyles were created and then compared using Viewbox 4, to produce numerical mesh-to-mesh values which indicate the geometrical and spatial relationship between any two given models. An all-to-all comparison was used to determine if the MVC method, using an automated Trimmed Iterative Closest Point (TrICP) algorithm, could be utilized to (1) match corresponding bilateral pairs of condyles and fossae and (2) match same-sided articular correlates. The pair-matching of both the condyles and the fossae generally produced high sensitivity and specificity rates. However, the articulation results were much poorer and are not currently recommended.

Three-Dimensional Geometry of Phalanges as a Proxy for Pair-Matching: Mesh Comparison Using an ICP Algorithm.

Forensic anthropologists are frequently faced with the challenge of individualizing and sorting commingled remains in a variety of scenarios. A number of protocols have been proposed to standardize the methodological approach to individuating commingled remains, some of which are focused on pair-matching. A recent study by Karell et al. (2016) proposed a virtual method for pair-matching humeri using a semi-automatic procedure that gave encouraging results. With regards to the phalanges, there are only a handful of studies focusing on identifying and siding phalanges, as well as exploring their directional and functional asymmetry. Yet, they are still as important as every other bone when sorting commingled human remains in various situations, such as archaeological common burials and mass graves, commingled decomposed remains resulting from atrocities, accidents or natural disasters. This study investigates a new method for pair-matching, a common individualization technique, using digital three-dimensional models of bone: mesh-to-mesh value comparison (MVC) as proposed by Karell et al. (2016). The MVC method digitally compares the entire three-dimensional geometry of two bones using an iterative closest point (ICP) algorithm to produce a single value as a proxy for their similarity. The method is automated with the use of Viewbox software 4.1 beta for a simultaneous comparison of all possible pairs. For this study, 515 phalanges from 24 individuals of mixed ancestry were digitized using CT scans and the 3D modeling program AMIRA 5.3.3. The models were also hollowed (internal information of compact and trabecular bone removed) to test the method with simulated surface scan models. The subsequent data-over 73,000 comparisons-were assessed using sensitivity and specificity rates via ROC analysis to indicate how well the automated version of MVC pair-matched phalanges. The best bone in terms of pair-matching was the proximal phalanx of Digit 3 with 87.5% sensitivity and 92.4% specificity rates at a threshold value of 0.488 for the unhollowed bones. The specificity drops slightly (91.1%) when the hollowed models are compared. To compare the performance of the method in all phalanges, the specificity was set to 95%-allowing for a 5% acceptable error-and the adjusted sensitivity was compared. The highest sensitivity, namely 68.8%, was noted for Digit 2 proximal phalanx for both unhollowed and hollowed models. Thus far, our preliminary results indicate that the MVC method performs well when pair-matching phalanges, though it is less accurate than pair-matching other types of bones. The introduction of 95% specificity threshold allows for rejecting pairs in great confidence, which could, for instance, significantly reduce the number of DNA comparisons required for the remaining possible matches. In addition, the similar results obtained from hollowed and unhollowed models indicate that the internal information included in the unhollowed models adds little to the identification of true pairs. This means that if a CT scan is not available, the method could be applied to surface models produced by light and laser scanners as well. While additional work needs to be done to verify these preliminary results, this research has the potential to expand the repertoire of individualization methods.

A novel method for pair-matching using three-dimensional digital models of bone: mesh-to-mesh value comparison.

The commingling of human remains often hinders forensic/physical anthropologists during the identification process, as there are limited methods to accurately sort these remains. This study investigates a new method for pair-matching, a common individualization technique, which uses digital three-dimensional models of bone: mesh-to-mesh value comparison (MVC). The MVC method digitally compares the entire three-dimensional geometry of two bones at once to produce a single value to indicate their similarity. Two different versions of this method, one manual and the other automated, were created and then tested for how well they accurately pair-matched humeri. Each version was assessed using sensitivity and specificity. The manual mesh-to-mesh value comparison method was 100 % sensitive and 100 % specific. The automated mesh-to-mesh value comparison method was 95 % sensitive and 60 % specific. Our results indicate that the mesh-to-mesh value comparison method overall is a powerful new tool for accurately pair-matching commingled skeletal elements, although the automated version still needs improvement.

PET-PCR method for the molecular detection of malaria parasites in a national malaria surveillance study in Haiti, 2011.

BACKGROUND: Recently, a real-time PCR assay known as photo-induced electron transfer (PET)-PCR which relies on self-quenching primers for the detection of Plasmodium spp. and Plasmodium falciparum was described. PET-PCR assay was found to be robust, and easier to use when compared to currently available real-time PCR methods. The potential of PET-PCR for molecular detection of malaria parasites in a nationwide malaria community survey in Haiti was investigated. METHODS: DNA from the dried blood spots was extracted using QIAGEN methodology. All 2,989 samples were screened using the PET-PCR assay in duplicate. Samples with a cycle threshold (CT) of 40 or less were scored as positive. A subset of the total samples (534) was retested using a nested PCR assay for confirmation. In addition, these same samples were also tested using a TaqMan-based real-time PCR assay. RESULTS: A total of 12 out of the 2,989 samples screened (0.4%) were found to be positive by PET-PCR (mean CT value of 35.7). These same samples were also found to be positive by the nested and TaqMan-based methods. The nested PCR detected an additional positive sample in a subset of 534 samples that was not detected by either PET-PCR or TaqMan-based PCR method. CONCLUSION: While the nested PCR was found to be slightly more sensitive than the PET-PCR, it is not ideal for high throughput screening of samples. Given the ease of use and lower cost than the nested PCR, the PET-PCR provides an alternative assay for the rapid screening of a large number of samples in laboratory settings.

Exploring the Functionality of Mesh-to-Mesh Value Comparison in Pair-Matching and Its Application to Fragmentary Remains.

Many cases encountered by forensic anthropologists involve commingled remains or isolated elements. Common methods for analysing these contexts are characterised by limitations such as high degrees of subjectivity, high cost of application, or low proven accuracy. This study sought to test mesh-to-mesh value comparison (MCV), a relatively new method for pair-matching skeletal elements, to validate the claims that the technique is unaffected by age, sex and pathology. The sample consisted of 160 three-dimensional clavicle models created from computed tomography (CT) scans of a contemporary Turkish population. Additionally, this research explored the application of MVC to match fragmented elements to their intact counterparts by creating a sample of 480 simulated fragments, consisting of three different types based on the region of the bone they originate from. For comparing whole clavicles, this resulted in a sensitivity value of 87.6% and specificity of 90.9% using ROC analysis comparing clavicles. For the fragment comparisons, each type was compared to the entire clavicles of the opposite side. The results included a range of sensitivity values from 81.3% to 87.6%. Overall results are promising and the MVC technique seems to be a useful technique for matching paired elements that can be accurately applied to a Modern Turkish sample.

Sex estimation of os coxae using DSP2 software: A validation study of a Greek sample.

Sex estimation methods based on skeletal remains vary on the selection of skeletal element, data acquisition and statistical approach resulting in variable classification accuracies that are highly dependent on the sample population. The only exception of this rule seems to be the os coxa, that appears to differ consistently between males and females across the globe. Currently sex estimation based on the os coxa can be easily estimated by taking ten measurements, inputting these in the DPS2 software and getting a sex estimate and the probability of correct group assessment. The performance of the software is highly reliable as confirmed by a validation study by Bruzek et al. (2017). Yet, there are still many populations not represented in the reference sample used to develop the software. The current study aimed to validate DPS2 using a sample from Crete, Greece. A total of 133 os coxae were measured following instructions on DSP2. Data were used to estimate sex with the software and to create population specific formulae for Greeks. DSP2 classified 117/133 (85.7%) of the sample with over 95% posterior probability (PP) of correct classification. Of the individuals classified with over 95% PP, only 3 were misclassified (2.6%).The best population specific formula only improved this percentage by 2.1% which indicates that DSP2 is a reliable tool for sex estimation in the Greek sample and it is recommended as method of choice in sex estimation of remains of unknown ancestry. If Greek ancestry is confirmed, population-specific formulae can be used in conjunction with DSP2 for a more reliable sex estimation.

Metric variation of the tibia in the Mediterranean: Implications in forensic identification.

Ancestry estimation from skeletal remains is a challenging task, but essential for the creation of a complete biological profile. As such, the study of human variation between populations is important for the fields of biological and forensic anthropology, as well as medicine. Cranial and dental morphological variation have traditionally been linked to geographic affinity resulting in several methods of ancestry estimation, while the postcranial skeleton has been systematically neglected. The current study explores metric variation of the tibia in six Mediterranean populations and its validity in estimating ancestry in the Mediterranean. The study sample includes 909 individuals (470 males and 439 females) from Cyprus, Greece, Italy, Spain, Portugal and Turkey. The sample was divided in two subsamples: a reference and a validation sample. Multinomial regression models were created based on the reference sample and then applied to validation sample. The first model used three variables and resulted in 57% and 56% accuracy for the two samples respectively, while the second model (6 variables) resulted in 80% and 74% respectively. Classification between groups ranged from 28% to 95% for the reference sample and from 15% to 91% for the validation sample. The highest classification accuracy was noted for the Greek sample (95% and 90% for the reference and validation sample respectively), followed by the Turkish sample (74% and 78% respectively). The Spanish, Portuguese and Italian samples presented greater morphological overlap which resulted in lower classification accuracies. The results indicate that although the tibia presents considerable variation amongst neighbour populations it is not suitable as a sole skeletal element to separate all groups successfully. A combination of different skeletal elements may be required in order to achieve the levels of reliability required for forensic applications.

Molecular diagnosis of malaria by photo-induced electron transfer fluorogenic primers: PET-PCR.

There is a critical need for developing new malaria diagnostic tools that are sensitive, cost effective and capable of performing large scale diagnosis. The real-time PCR methods are particularly robust for large scale screening and they can be used in malaria control and elimination programs. We have designed novel self-quenching photo-induced electron transfer (PET) fluorogenic primers for the detection of P. falciparum and the Plasmodium genus by real-time PCR. A total of 119 samples consisting of different malaria species and mixed infections were used to test the utility of the novel PET-PCR primers in the diagnosis of clinical samples. The sensitivity and specificity were calculated using a nested PCR as the gold standard and the novel primer sets demonstrated 100% sensitivity and specificity. The limits of detection for P. falciparum was shown to be 3.2 parasites/µl using both Plasmodium genus and P. falciparum-specific primers and 5.8 parasites/µl for P. ovale, 3.5 parasites/µl for P. malariae and 5 parasites/µl for P. vivax using the genus specific primer set. Moreover, the reaction can be duplexed to detect both Plasmodium spp. and P. falciparum in a single reaction. The PET-PCR assay does not require internal probes or intercalating dyes which makes it convenient to use and less expensive than other real-time PCR diagnostic formats. Further validation of this technique in the field will help to assess its utility for large scale screening in malaria control and elimination programs.