Browsing by Author "Walsh, Susan"
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Item 3D Facial Matching by Spiral Convolutional Metric Learning and a Biometric Fusion-Net of Demographic Properties(IEEE, 2021) Mahdi, Soha Sadat; Nauwelaers, Nele; Joris, Philip; Bouritsas, Giorgos; Gong, Shunwang; Bokhnyak, Sergiy; Walsh, Susan; Shriver, Mark D.; Bronstein, Michael; Claes, Peter; Biology, School of ScienceFace recognition is a widely accepted biometric verification tool, as the face contains a lot of information about the identity of a person. In this study, a 2-step neural-based pipeline is presented for matching 3D facial shape to multiple DNA-related properties (sex, age, BMI and genomic background). The first step consists of a triplet loss-based metric learner that compresses facial shape into a lower dimensional embedding while preserving information about the property of interest. Most studies in the field of metric learning have only focused on 2D Euclidean data. In this work, geometric deep learning is employed to learn directly from 3D facial meshes. To this end, spiral convolutions are used along with a novel mesh-sampling scheme that retains uniformly sampled 3D points at different levels of resolution. The second step is a multi-biometric fusion by a fully connected neural network. The network takes an ensemble of embeddings and property labels as input and returns genuine and imposter scores. Since embeddings are accepted as an input, there is no need to train classifiers for the different properties and available data can be used more efficiently. Results obtained by a to-fold cross-validation for biometric verification show that combining multiple properties leads to stronger biometric systems. Furthermore, the proposed neural-based pipeline outperforms a linear baseline, which consists of principal component analysis, followed by classification with linear support vector machines and a Naïve Bayes-based score-fuser.Item 3D facial phenotyping by biometric sibling matching used in contemporary genomic methodologies(Public Library of Science, 2021-05-13) Hoskens, Hanne; Liu, Dongjing; Naqvi, Sahin; Lee, Myoung Keun; Eller, Ryan J.; Indencleef, Karlijne; White, Julie D.; Li, Jiarui; Larmuseau, Maarten H. D.; Hens, Greet; Wysocka, Joanna; Walsh, Susan; Richmond, Stephen; Shriver, Mark D.; Shaffer, John R.; Peeters, Hilde; Weinberg, Seth M.; Claes, Peter; Biology, School of ScienceThe analysis of contemporary genomic data typically operates on one-dimensional phenotypic measurements (e.g. standing height). Here we report on a data-driven, family-informed strategy to facial phenotyping that searches for biologically relevant traits and reduces multivariate 3D facial shape variability into amendable univariate measurements, while preserving its structurally complex nature. We performed a biometric identification of siblings in a sample of 424 children, defining 1,048 sib-shared facial traits. Subsequent quantification and analyses in an independent European cohort (n = 8,246) demonstrated significant heritability for a subset of traits (0.17-0.53) and highlighted 218 genome-wide significant loci (38 also study-wide) associated with facial variation shared by siblings. These loci showed preferential enrichment for active chromatin marks in cranial neural crest cells and embryonic craniofacial tissues and several regions harbor putative craniofacial genes, thereby enhancing our knowledge on the genetic architecture of normal-range facial variation.Item Advancements in forensic DNA-based identification(2017) Dembinski, Gina M.; Picard, Christine; Christie, Mark; Walsh, Susan; Randall, Stephen; Goodpaster, JohnModern DNA profiling techniques have increased in sensitivity allowing for higher success in producing a DNA profile from limited evidence sources. However, this can lead to the amplification of more DNA profiles that do not get a hit on a suspect or DNA database and more mixture profiles. The work here aims to address or improve these consequences of current DNA profiling techniques. Based on allele-specific PCR and quantitative color measurements, a 24-SNP forensic phenotypic profile (FPP) assay was designed to simultaneously predict eye color, hair color, skin color, and ancestry, with the potential for age marker incorporation. Bayesian Networks (BNs) were built for model predictions based on a U.S sample population of 200 individuals. For discrete pigmentation traits using an ancestry influenced pigmentation prediction model, AUC values were greater than 0.65 for the eye, hair, and skin color categories considered. For ancestry using an all SNPs prediction model, AUC values were greater than 0.88 for the 5 continental ancestry categories considered. Quantitative pigmentation models were also built with prediction output as RGB values; the average amount of error was approximately 7% for eye color, 12% for hair color, and 8% for skin color. A novel sequencing method, methyl-RADseq, was developed to aid in the discovery of candidate age-informative CpG sites to incorporate into the FPP assay. There were 491 candidate CpG sites found that either increased or decreased with age in three forensically relevant xii fluids with greater than 70% correlation: blood, semen, and saliva. The effects of exogenous microbial DNA on human DNA profiles were analyzed by spiking human DNA with differing amounts of microbial DNA using the Promega PowerPlex® 16 HS kit. Although there were no significant effects to human DNA quantitation, two microbial species, B. subtilis and M. smegmatis, amplified an allelic artifact that mimics a true allele (‘5’) at the TPOX locus in all samples tested, interfering with the interpretation of the human profile. Lastly, the number of contributors of theoretically generated 2-, 3-, 4-, 5-, and 6-person mixtures were evaluated via allele counting with the Promega PowerPlex® Fusion 6C system, an amplification kit with the newly expanded core STR loci. Maximum allele count in the number of contributors for 2- and 3-person mixtures was correct in 99.99% of mixtures. It was less accurate in the 4-, 5-, and 6-person mixtures at approximately 90%, 57%, and 8%, respectively. This work provides guidance in addressing some of the limitations of current DNA technologies.Item Ancient genomes indicate population replacement in Early Neolithic Britain(Springer Nature, 2019-05) Brace, Selina; Diekmann, Yoan; Booth, Thomas J.; van Dorp, Lucy; Faltyskova, Zuzana; Rohland, Nadin; Mallick, Swapan; Olalde, Iñigo; Ferry, Matthew; Michel, Megan; Oppenheimer, Jonas; Broomandkhoshbacht, Nasreen; Stewardson, Kristin; Martiniano, Rui; Walsh, Susan; Kayser, Manfred; Charlton, Sophy; Hellenthal, Garrett; Armit, Ian; Schulting, Rick; Craig, Oliver E.; Sheridan, Alison; Parker Pearson, Mike; Stringer, Chris; Reich, David; Thomas, Mark G.; Barnes, Ian; Biology, School of ScienceThe roles of migration, admixture and acculturation in the European transition to farming have been debated for over 100 years. Genome-wide ancient DNA studies indicate predominantly Aegean ancestry for continental Neolithic farmers, but also variable admixture with local Mesolithic hunter-gatherers. Neolithic cultures first appear in Britain circa 4000 BC, a millennium after they appeared in adjacent areas of continental Europe. The pattern and process of this delayed British Neolithic transition remain unclear. We assembled genome-wide data from 6 Mesolithic and 67 Neolithic individuals found in Britain, dating 8500-2500 BC. Our analyses reveal persistent genetic affinities between Mesolithic British and Western European hunter-gatherers. We find overwhelming support for agriculture being introduced to Britain by incoming continental farmers, with small, geographically structured levels of hunter-gatherer ancestry. Unlike other European Neolithic populations, we detect no resurgence of hunter-gatherer ancestry at any time during the Neolithic in Britain. Genetic affinities with Iberian Neolithic individuals indicate that British Neolithic people were mostly descended from Aegean farmers who followed the Mediterranean route of dispersal. We also infer considerable variation in pigmentation levels in Europe by circa 6000 BC.Item Automated 3D Landmarking of the Skull: A Novel Approach for Craniofacial Analysis(bioRxiv, 2024-02-12) Wilke, Franziska; Matthews, Harold; Herrick, Noah; Dopkins, Nichole; Claes, Peter; Walsh, Susan; Biology, School of ScienceAutomatic dense 3D surface registration is a powerful technique for comprehensive 3D shape analysis that has found a successful application in human craniofacial morphology research, particularly within the mandibular and cranial vault regions. However, a notable gap exists when exploring the frontal aspect of the human skull, largely due to the intricate and unique nature of its cranial anatomy. To better examine this region, this study introduces a simplified single-surface craniofacial bone mask comprising 9,999 quasi-landmarks, which can aid in the classification and quantification of variation over human facial bone surfaces. Automatic craniofacial bone phenotyping was conducted on a dataset of 31 skull scans obtained through cone-beam computed tomography (CBCT) imaging. The MeshMonk framework facilitated the non-rigid alignment of the constructed craniofacial bone mask with each individual target mesh. To gauge the accuracy and reliability of this automated process, 20 anatomical facial landmarks were manually placed three times by three independent observers on the same set of images. Intra- and inter-observer error assessments were performed using root mean square (RMS) distances, revealing consistently low scores. Subsequently, the corresponding automatic landmarks were computed and juxtaposed with the manually placed landmarks. The average Euclidean distance between these two landmark sets was 1.5mm, while centroid sizes exhibited noteworthy similarity. Intraclass coefficients (ICC) demonstrated a high level of concordance (>0.988), and automatic landmarking showing significantly lower errors and variation. These results underscore the utility of this newly developed single-surface craniofacial bone mask, in conjunction with the MeshMonk framework, as a highly accurate and reliable method for automated phenotyping of the facial region of human skulls from CBCT and CT imagery. This craniofacial template bone mask expansion of the MeshMonk toolbox not only enhances our capacity to study craniofacial bone variation but also holds significant potential for shedding light on the genetic, developmental, and evolutionary underpinnings of the overall human craniofacial structure.Item Automatic Landmark Placement for Large 3D Facial Image Dataset(IEEE, 2019-12) Wang, Jerry; Fang, Shiaofen; Fang, Meie; Wilson, Jeremy; Herrick, Noah; Walsh, Susan; Computer and Information Science, School of ScienceFacial landmark placement is a key step in many biomedical and biometrics applications. This paper presents a computational method that efficiently performs automatic 3D facial landmark placement based on training images containing manually placed anthropological facial landmarks. After 3D face registration by an iterative closest point (ICP) technique, a visual analytics approach is taken to generate local geometric patterns for individual landmark points. These individualized local geometric patterns are derived interactively by a user's initial visual pattern detection. They are used to guide the refinement process for landmark points projected from a template face to achieve accurate landmark placement. Compared to traditional methods, this technique is simple, robust, and does not require a large number of training samples (e.g. in machine learning based methods) or complex 3D image analysis procedures. This technique and the associated software tool are being used in a 3D biometrics project that aims to identify links between human facial phenotypes and their genetic association.Item Characterization of Simple Sequence Repeats in Phormia Regina Miegen (Diptera: Callphoridae)(2024-08) Waletzko, Cassandra; Picard, Christine; Walsh, Susan; Owings, CharityPhormia regina Meigen is a forensically relevant species of blow fly, common in North America and used to estimate the minimum postmortem interval in forensic casework. It is also possible to use blow flies to survey the environment for biotic and abiotic information drawn from both larval and adult stages. There are both forensic and environmental uses for genetic analysis of blow flies. Blow fly kinship is especially useful for detecting postmortem movement of a corpse or to assess abundance of carrion in a given location. To test genetic relationships between individuals, discriminatory loci such as microsatellites, or polymorphic tandemly repeated sequences of DNA are necessary. Here, we characterize novel microsatellites generated from the genome of P. regina. Thirty-four candidate polymorphic loci with conserved flanking regions, have been isolated. To date, seven are heterozygous and polymorphic testing in two lab populations and one wild population. The simple sequence repeats characterized here complement existing loci (N = 6) for greater discrimination for testing relationships between individual flies.Item Decoding the Human Face: Progress and Challenges in Understanding the Genetics of Craniofacial Morp(Annual Reviews, 2022) Naqvi, Sahin; Hoskens, Hanne; Wilke, Franziska; Weinberg, Seth M.; Shaffer, John R.; Walsh, Susan; Shriver, Mark D.; Wysocka, Joanna; Claes, Peter; Biology, School of ScienceVariations in the form of the human face, which plays a role in our individual identities and societal interactions, have fascinated scientists and artists alike. Here, we review our current understanding of the genetics underlying variation in craniofacial morphology and disease-associated dysmorphology, synthesizing decades of progress on Mendelian syndromes in addition to more recent results from genome-wide association studies of human facial shape and disease risk. We also discuss the various approaches used to phenotype and quantify facial shape, which are of particular importance due to the complex, multipartite nature of the craniofacial form. We close by discussing how experimental studies have contributed and will further contribute to our understanding of human genetic variation and then proposing future directions and applications for the field.Item DNA Testing Reveals the Putative Identity of JB55, a 19th Century Vampire Buried in Griswold, Connecticut(MDPI, 2019-08-22) Daniels-Higginbotham, Jennifer; Gorden, Erin M.; Farmer, Stephanie K.; Spatola, Brian; Damann, Franklin; Bellantoni, Nicholas; Gagnon, Katie S.; de la Puente, Maria; Xavier, Catarina; Walsh, Susan; Parson, Walther; McMahon, Timothy P.; Marshall, Charla; Biology, School of ScienceIn 1990 in Griswold, Connecticut, archaeologists excavated a burial found in a "skull and crossbones" orientation. The lid of the 19th century coffin had brass tacks that spelled "JB55", the initials of the person lying there and age at death. JB55 had evidence of chronic pulmonary infection, perhaps tuberculosis. It is possible that JB55 was deemed a vampire due to his disease, and therefore had to be "killed" by mutilating his corpse. In an attempt to reveal the identity of JB55, DNA testing was performed. Ancestry informative single nucleotide polymorphism (SNP) analysis using the Precision ID Ancestry Panel indicated European ancestry. A full Y-chromosomal short tandem repeat (Y-STR) profile was obtained, belonging to haplogroup R1b. When the Y-STR profile was searched in the publicly accessible FamilyTreeDNA R1b Project website, the two closest matches had the surname "Barber". A search of historical records led to a death notice mentioning John Barber, whose son Nathan Barber was buried in Griswold in 1826. The description of Nathan Barber closely fits the burial of "NB13," found near JB55. By applying modern forensic DNA tools to a historical mystery, the identity of JB55 as John Barber, the 19th century Connecticut vampire, has been revealed.Item Effects of Male Facial Masculinity on Perceived Attractiveness(Springer Nature, 2021) Ekrami, Omid; Claes, Peter; Shriver, Mark D.; Weinberg, Seth M.; Marazita, Mary L.; Walsh, Susan; Van Dongen, Stefan; Biology, School of ScienceStudies suggest that high levels of masculinity in men can be a signal of 'better genes' as well as low parental investment. It is the trade-off between these two qualities that has led to the hypothesis that women's preferences for male masculinity are condition-dependent, yet, not all studies support this hypothesis. In addition, there is evidence that more average faces would be perceived as more attractive. Here we study the variation in masculinity preferences of a cohort of heterosexual women (n=769), using manipulated 3D faces of male subjects. We used linear mixed models to test for effects of various covariates such as relationship status, use of hormonal contraception, sociosexual orientation and self-perceived attractiveness on preference for masculinity. Our results show that women's sociosexual orientation has a positive correlation with masculinity preference while using hormonal contraception decreases this preference. None of the other covariates displayed any significant effect on masculinity preference. The initial level of masculinity of the faces (very low, low, average, high and very high) was also shown to affect this preference, where we found a significant preference for higher masculinity in the very low and average group, while no preference was found in the other groups. Our findings support the notion that condition-dependent variables have very small effects, if any, on women's preference for masculinity in men.