Automatic Landmark Placement for Large 3D Facial Image Dataset

Facial 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

Association between convalescent plasma treatment and mortality in COVID-19: a collaborative systematic review and meta-analysis of randomized clinical trials.

Funder: laura and john arnold foundationBACKGROUND: Convalescent plasma has been widely used to treat COVID-19 and is under investigation in numerous randomized clinical trials, but results are publicly available only for a small number of trials. The objective of this study was to assess the benefits of convalescent plasma treatment compared to placebo or no treatment and all-cause mortality in patients with COVID-19, using data from all available randomized clinical trials, including unpublished and ongoing trials (Open Science Framework, https://doi.org/10.17605/OSF.IO/GEHFX ). METHODS: In this collaborative systematic review and meta-analysis, clinical trial registries (ClinicalTrials.gov, WHO International Clinical Trials Registry Platform), the Cochrane COVID-19 register, the LOVE database, and PubMed were searched until April 8, 2021. Investigators of trials registered by March 1, 2021, without published results were contacted via email. Eligible were ongoing, discontinued and completed randomized clinical trials that compared convalescent plasma with placebo or no treatment in COVID-19 patients, regardless of setting or treatment schedule. Aggregated mortality data were extracted from publications or provided by investigators of unpublished trials and combined using the Hartung-Knapp-Sidik-Jonkman random effects model. We investigated the contribution of unpublished trials to the overall evidence. RESULTS: A total of 16,477 patients were included in 33 trials (20 unpublished with 3190 patients, 13 published with 13,287 patients). 32 trials enrolled only hospitalized patients (including 3 with only intensive care unit patients). Risk of bias was low for 29/33 trials. Of 8495 patients who received convalescent plasma, 1997 died (23%), and of 7982 control patients, 1952 died (24%). The combined risk ratio for all-cause mortality was 0.97 (95% confidence interval: 0.92; 1.02) with between-study heterogeneity not beyond chance (I2 = 0%). The RECOVERY trial had 69.8% and the unpublished evidence 25.3% of the weight in the meta-analysis. CONCLUSIONS: Convalescent plasma treatment of patients with COVID-19 did not reduce all-cause mortality. These results provide strong evidence that convalescent plasma treatment for patients with COVID-19 should not be used outside of randomized trials. Evidence synthesis from collaborations among trial investigators can inform both evidence generation and evidence application in patient care

Robust genome-wide ancestry inference for heterogeneous datasets: illustrated using the 1,000 genome project with 3D facial images

Estimates of individual-level genomic ancestry are routinely used in human genetics, and related fields. The analysis of population structure and genomic ancestry can yield insights in terms of modern and ancient populations, allowing us to address questions regarding admixture, and the numbers and identities of the parental source populations. Unrecognized population structure is also an important confounder to correct for in genome-wide association studies. However, it remains challenging to work with heterogeneous datasets from multiple studies collected by different laboratories with diverse genotyping and imputation protocols. This work presents a new approach and an accompanying open-source toolbox that facilitates a robust integrative analysis for population structure and genomic ancestry estimates for heterogeneous datasets. We show robustness against individual outliers and different protocols for the projection of new samples into a reference ancestry space, and the ability to reveal and adjust for population structure in a simulated case-control admixed population. Given that visually evident and easily recognizable patterns of human facial characteristics co-vary with genomic ancestry, and based on the integration of three different sources of genome data, we generate average 3D faces to illustrate genomic ancestry variations within the 1,000 Genome project and for eight ancient-DNA profiles, respectively.status: publishe

Robust genome-wide ancestry inference for heterogeneous datasets : illustrated using the 1,000 genome project with 3D facial images

Estimates of individual-level genomic ancestry are routinely used in human genetics, and related fields. The analysis of population structure and genomic ancestry can yield insights in terms of modern and ancient populations, allowing us to address questions regarding admixture, and the numbers and identities of the parental source populations. Unrecognized population structure is also an important confounder to correct for in genome-wide association studies. However, it remains challenging to work with heterogeneous datasets from multiple studies collected by different laboratories with diverse genotyping and imputation protocols. This work presents a new approach and an accompanying open-source toolbox that facilitates a robust integrative analysis for population structure and genomic ancestry estimates for heterogeneous datasets. We show robustness against individual outliers and different protocols for the projection of new samples into a reference ancestry space, and the ability to reveal and adjust for population structure in a simulated case-control admixed population. Given that visually evident and easily recognizable patterns of human facial characteristics co-vary with genomic ancestry, and based on the integration of three different sources of genome data, we generate average 3D faces to illustrate genomic ancestry variations within the 1,000 Genome project and for eight ancient-DNA profiles, respectively

HIrisPlex-S system for eye, hair, and skin color prediction from DNA : massively parallel sequencing solutions for two common forensically used platforms

Forensic DNA Phenotyping (FDP) provides the ability to predict externally visible characteristics from minute amounts of crime scene DNA, which can help find unknown perpetrators who are typically unidentifiable via conventional forensic DNA profiling. Fundamental human genetics research has led to a better understanding of the specific DNA variants responsible for physical appearance characteristics, particularly eye, hair, and skin color. Recently, we introduced the HIrisPlex-S system for the simultaneous prediction of eye, hair, and skin color based on 41 DNA variants generated from two forensically validated SNaPshot multiplex assays using capillary electrophoresis (CE). Here we introduce massively parallel sequencing (MPS) solutions for the HIrisPlex-S (HPS) system on two MPS platforms commonly used in forensics, Ion Torrent and MiSeq, that cover all 41 DNA variants in a single assay, respectively. Additionally, we present the forensic developmental validation of the two HPS-MPS assays. The Ion Torrent MPS assay, based on Ion AmpliSeq technology, illustrated the successful generation of full HIrisPlex-S genotypic profiles from 100 pg of input control DNA, while the MiSeq MPS assay based on an in-house design yielded complete profiles from 250 pg of input DNA. Assessing simulated forensic casework samples such as saliva, hair (bulb), blood, semen, and low quantity touch DNA, as well as artificially damaged DNA samples, concordance testing, and samples from numerous species, all illustrated the ability of both versions of the HIrisPlex-S MPS assay to produce results that motivate forensic applications. By also providing an integrated bioinformatics analysis pipeline, MPS data can now be analyzed and a file generated for upload to the publically accessible HIrisPlex online webtool (https://hirisplex.erasmusmc.nl). In addition, we updated the website to accept VCF input data for those with genome sequence data. We thus provide a user-friendly and semi-automated MPS workflow from DNA sample to individual eye, hair, and skin color prediction probabilities. Furthermore, we present a 2-person mixture separation tool that not only assesses genotype reliability with regards genotyping confidence but also provides the most fitting mixture scenario for both minor and major contributors, including profile separation. We envision this MPS implementation of the HIrisPlex-S system for eye, hair, and skin color prediction from DNA as a starting point for further expanding MPS-based forensic DNA phenotyping. This may include the future addition of SNPs predictive for more externally visible characteristics, as well as SNPs for bio-geographic ancestry inference, provided the statistical framework for DNA prediction of these traits is in place

1327. The Diagnosis of Subarachnoid Neurocysticercosis Is Often Delayed And Other Findings of a Multicenter Retrospective in the USA

Abstract Background Subarachnoid (racemose) neurocysticercosis (SANCC) is an uncommon but severe form of Taenia solium infection. There is limited evidence to guide clinical management of these patients. Methods We performed a multicenter retrospective chart review of 15 U.S. sites. A total of 69 subjects with racemose disease were entered. Results The most common region of exposure was Mexico (67%) followed by Central America (24%). Median age was 43 years (range 15-76) and 71% were male. Common symptoms at the time of index admission were headache (80%), nausea/vomiting (46%), dizziness (44%), and blurry vision (33%). Cysts were intracranial in 64 (93%) subjects and exclusively intraspinal in 4. One patient had meningitis without visible cystic lesions. Incident admission magnetic resonance imaging (MRI) demonstrated ventriculomegaly in 41 (59%) and focal findings in 9 (13%) including ischemic infarct, subarachnoid hemorrhage, and/or arterial aneurysm. For 55 (80%), SANCC was first diagnosed during the index admission. Of these, 23 (42%) had prior medical visits and substantial delay in diagnosis (i.e. previously seen with hydrocephalus [27%], stroke [5.5%], and/or meningitis [11%], missed diagnostic radiologic features [4%], or inadequate imaging [5.5%]). Of the 69 subjects, 54% underwent a neurosurgical procedure during index admission (cyst removal n=16, EVD/shunt/ventriculostomy n=24). At the time of discharge, 6 (8.6%) patients were not given albendazole and/or praziquantel due to cost or availability. Six months following discharge, 4 weeks was associated with increased risk for new cyst development on follow up imaging at a median of 3.8 years following discharge (range 2.6 months-8 years). Those with a delayed diagnosis received a significantly longer duration of corticosteroids (median 8 weeks) than those without a delay (median 5 weeks, p=0.047). Conclusion The diagnosis of SANCC is often missed, and most patients require neurosurgical intervention. Antiparasitic therapy is suboptimal, especially with regimens developed for parenchymal NCC. Disclosures Jeffrey D. Jenks, MD, MPH, Astellas: Grant/Research Support|F2G: Grant/Research Support|Pfizer: Grant/Research Suppor

Additional file 7 of Association between convalescent plasma treatment and mortality in COVID-19: a collaborative systematic review and meta-analysis of randomized clinical trials

Additional file 7. Sensitivity analyses: various meta-analytic approaches

Additional file 2 of Association between convalescent plasma treatment and mortality in COVID-19: a collaborative systematic review and meta-analysis of randomized clinical trials

Additional file 2. Email invitation

Additional file 1 of Association between convalescent plasma treatment and mortality in COVID-19: a collaborative systematic review and meta-analysis of randomized clinical trials

Additional file 1. Search strategy