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Automated Fetal Brain Extraction from Clinical Ultrasound Volumes Using 3D Convolutional Neural Networks
© 2020, Springer Nature Switzerland AG. To improve the performance of most neuroimage analysis pipelines, brain extraction is used as a fundamental first step in the image processing. However, in the case of fetal brain development for routing clinical assessment, there is a need for a reliable Ultrasound (US)-specific tool. In this work we propose a fully automated CNN approach to fetal brain extraction from 3D US clinical volumes with minimal preprocessing. Our method accurately and reliably extracts the brain regardless of the large data variations in acquisition (eg. shadows, occlusions) inherent in this imaging modality. It also performs consistently throughout a gestational age range between 14 and 31 weeks, regardless of the pose variation of the subject, the scale, and even partial feature-obstruction in the image, outperforming all current alternatives.
XeMRI to CT Lung Image Registration Enhanced with Personalized 4DCT-Derived Motion Model
© Springer Nature Switzerland AG 2018. This paper presents a novel method for multi-modal lung image registration constrained by a motion model derived from lung 4DCT. The motion model is estimated based on the results of intra-patient image registration using Principal Component Analysis. The approach with a prior motion model is particularly important for regions where there is not enough information to reliably drive the registration process, as in the case of hyperpolarized Xenon MRI and proton density MRI to CT registration. Simultaneously, the method addresses local variations between images in the supervoxel-based motion model parameters optimization step. We compare our results in terms of the plausibility of the estimated deformations and correlation coefficient with 4DCT-based estimated ventilation maps using state-of-the-art multi-modal image registration methods. Our method achieves higher average correlation scores, showing that the application of Principal Component Analysis-based motion model in the deformable registration, helps to drive the registration for the regions of the lungs with insufficient amount of information.
Regional Lung Ventilation Estimation Based on Supervoxel Tracking
© 2018 SPIE. In the case of lung cancer, an assessment of regional lung function has the potential to guide more accurate radiotherapy treatment. This could spare well-functioning parts of the lungs, as well as be used for follow up. In this paper we present a novel approach for regional lung ventilation estimation from dynamic lung CT imaging, which might be used during radiotherapy planning. Our method combines a supervoxel-based image representation with deformable image registration, performed between peak breathing phases, for which we track changes in intensity of previously extracted supervoxels. Such a region-oriented approach is expected to be more physiologically consistent with lung anatomy than previous methods relying on voxel-wise relationships, as it has the potential to mimic the lung anatomy. Our results are compared with static ventilation images acquired from hyperpolarized Xenon129 MRI. In our study we use three patient datasets consisting of 4DCT and XeMRI. We achieve higher correlation (0.487) compared to the commonly used method for estimating ventilation performed in a voxel-wise manner (0.423) on average based on global correlation coefficients. We also achieve higher correlation values for our method when ventilated/non-ventilated regions of lungs are investigated. The increase of the number of layers of supervoxels further improves our results, with one layer achieving 0.393, compared to 0.487 for 15 layers. Overall, we have shown that our method achieves higher correlation values compared to the previously used approach, when correlated with XeMRI.
Mass Transportation for Deformable Image Registration with Application to Lung CT
Computed Tomography (CT) of the lungs play a key role in clinical investigation of thoracic malignancies, as well as having the potential to increase our knowledge about pulmonary diseases including cancer. It enables longitudinal trials to monitor lung disease progression, and to inform assessment of lung damage resulting from radiation therapy. We present a novel deformable image registration method that accommodates changes in the density of lung tissue depending on the amount of air present in the lungs inspiration/expiration state. We investigate the Monge-Kantorovich theory of optimal mass transportation to model the appearance of lung tissue and apply it in a method for registration. To validate the model, we apply our method to an inhale and exhale lung CT data set, and compare it against registration using the sum of squared differences (SSD) as a representative of the most popular similarity measures used in deformable image registration. The results show that the developed registration method has the potential to handle intensity distortions caused by air and tissue compression, and in addition it can provide accurate annotations of the lungs.
CpG-creating mutations are costly in many human viruses.
Mutations can occur throughout the virus genome and may be beneficial, neutral or deleterious. We are interested in mutations that yield a C next to a G, producing CpG sites. CpG sites are rare in eukaryotic and viral genomes. For the eukaryotes, it is thought that CpG sites are rare because they are prone to mutation when methylated. In viruses, we know less about why CpG sites are rare. A previous study in HIV suggested that CpG-creating transition mutations are more costly than similar non-CpG-creating mutations. To determine if this is the case in other viruses, we analyzed the allele frequencies of CpG-creating and non-CpG-creating mutations across various strains, subtypes, and genes of viruses using existing data obtained from Genbank, HIV Databases, and Virus Pathogen Resource. Our results suggest that CpG sites are indeed costly for most viruses. By understanding the cost of CpG sites, we can obtain further insights into the evolution and adaptation of viruses.
Correction to: CpG‑creating mutations are costly in many human viruses (Evolutionary Ecology, (2020), 34, 3, (339-359), 10.1007/s10682-020-10039-z)
© 2020, Springer Nature Switzerland AG. In the original article, the co-author name "Jennifer Kim" has been inadvertently missed during the publication process. The complete author group is given in this correction.
Evaluation of phylogenetic methods for inferring the direction of HIV transmission: HPTN 052.
BACKGROUND:Phylogenetic analysis can be used to assess HIV transmission in populations. We inferred the direction of HIV transmission using whole-genome HIV sequences from couples with known linked infection and known transmission direction. METHODS:Complete next generation sequencing (NGS) data were obtained for 105 unique index-partner sample pairs from 32 couples enrolled in the HIV Prevention Trials Network (HPTN) 052 trial (up to two samples/person). Index samples were obtained up to 5.5 years before partner infection; partner samples were obtained near the time of seroconversion. The bioinformatics method, phyloscanner, was used to infer transmission direction. Analyses were performed using samples from individual sample pairs, samples from all couples (one sample/person; group analysis) and all available samples (multi-sample group analysis). Analysis was also performed using NGS data from defined regions of the HIV genome (gag, pol, env). RESULTS:Using whole-genome NGS data, transmission direction was inferred correctly (index to partner) for 98/105 (93.3%) of the individual sample pairs, 99/105 (94.3%) sample pairs using group analysis, and 31 (96.9%) of the 32 couples using multi-sample group analysis. There were no cases where the incorrect transmission direction (partner to index) was inferred. The accuracy of the method was higher with greater time between index and partner sample collection. Pol region sequences performed better than env or gag sequences for inferring transmission direction. CONCLUSIONS:We demonstrate the potential of a phylogenetic method to infer the direction of HIV transmission between two individuals using whole-genome and pol NGS data.
Third human challenge trial conference, Oxford, United Kingdom, February 6-7, 2020, a meeting report.
The third Human Challenge Trial Meeting brought together a broad range of international stakeholders, including academia, regulators, funders and industry, with a considerable delegation from Low- and Middle-Income Countries. Controlled human infection models (CHIMs) can be helpful to study pathogenesis and for the development of vaccines. As challenge agents are used to infect healthy volunteers, ethical considerations include that the challenge studies need to be safe and results should be meaningful. The meeting provided a state-of-the-art overview on a wide range of CHIMs, including viral, bacterial and parasitic challenge agents. Recommendations included globally aligned guidance documents for CHIM studies; further definition of a CHIM, based on the challenge agent used; standardization of methodology and study endpoints; capacity building in Low- and Middle-Income Countries, in performance as well as regulation of CHIM studies; guidance on compensation for participation in CHIM studies; and preparation of CHIM studies, with strong engagement with stakeholders.
A de novo approach to inferring within-host fitness effects during untreated HIV-1 infection.
In the absence of effective antiviral therapy, HIV-1 evolves in response to the within-host environment, of which the immune system is an important aspect. During the earliest stages of infection, this process of evolution is very rapid, driven by a small number of CTL escape mutations. As the infection progresses, immune escape variants evolve under reduced magnitudes of selection, while competition between an increasing number of polymorphic alleles (i.e., clonal interference) makes it difficult to quantify the magnitude of selection acting upon specific variant alleles. To tackle this complex problem, we developed a novel multi-locus inference method to evaluate the role of selection during the chronic stage of within-host infection. We applied this method to targeted sequence data from the p24 and gp41 regions of HIV-1 collected from 34 patients with long-term untreated HIV-1 infection. We identify a broad distribution of beneficial fitness effects during infection, with a small number of variants evolving under strong selection and very many variants evolving under weaker selection. The uniquely large number of infections analysed granted a previously unparalleled statistical power to identify loci at which selection could be inferred to act with statistical confidence. Our model makes no prior assumptions about the nature of alleles under selection, such that any synonymous or non-synonymous variant may be inferred to evolve under selection. However, the majority of variants inferred with confidence to be under selection were non-synonymous in nature, and in most cases were have previously been associated with either CTL escape in p24 or neutralising antibody escape in gp41. We also identified a putative new CTL escape site (residue 286 in gag), and a region of gp41 (including residues 644, 648, 655 in env) likely to be associated with immune escape. Sites inferred to be under selection in multiple hosts have high within-host and between-host diversity although not all sites with high between-host diversity were inferred to be under selection at the within-host level. Our identification of selection at sites associated with resistance to broadly neutralising antibodies (bNAbs) highlights the need to fully understand the role of selection in untreated individuals when designing bNAb based therapies.
Evidence of initial success for China exiting COVID-19 social distancing policy after achieving containment.
Background: The COVID-19 epidemic was declared a Global Pandemic by WHO on 11 March 2020. By 24 March 2020, over 440,000 cases and almost 20,000 deaths had been reported worldwide. In response to the fast-growing epidemic, which began in the Chinese city of Wuhan, Hubei, China imposed strict social distancing in Wuhan on 23 January 2020 followed closely by similar measures in other provinces. These interventions have impacted economic productivity in China, and the ability of the Chinese economy to resume without restarting the epidemic was not clear. Methods: Using daily reported cases from mainland China and Hong Kong SAR, we estimated transmissibility over time and compared it to daily within-city movement, as a proxy for economic activity. Results: Initially, within-city movement and transmission were very strongly correlated in the five mainland provinces most affected by the epidemic and Beijing. However, that correlation decreased rapidly after the initial sharp fall in transmissibility. In general, towards the end of the study period, the correlation was no longer apparent, despite substantial increases in within-city movement. A similar analysis for Hong Kong shows that intermediate levels of local activity were maintained while avoiding a large outbreak. At the very end of the study period, when China began to experience the re-introduction of a small number of cases from Europe and the United States, there is an apparent up-tick in transmission. Conclusions: Although these results do not preclude future substantial increases in incidence, they suggest that after very intense social distancing (which resulted in containment), China successfully exited its lockdown to some degree. Elsewhere, movement data are being used as proxies for economic activity to assess the impact of interventions. The results presented here illustrate how the eventual decorrelation between transmission and movement is likely a key feature of successful COVID-19 exit strategies.
Genome-wide association study identifies 74 loci associated with educational attainment.
Educational attainment is strongly influenced by social and other environmental factors, but genetic factors are estimated to account for at least 20% of the variation across individuals. Here we report the results of a genome-wide association study (GWAS) for educational attainment that extends our earlier discovery sample of 101,069 individuals to 293,723 individuals, and a replication study in an independent sample of 111,349 individuals from the UK Biobank. We identify 74 genome-wide significant loci associated with the number of years of schooling completed. Single-nucleotide polymorphisms associated with educational attainment are disproportionately found in genomic regions regulating gene expression in the fetal brain. Candidate genes are preferentially expressed in neural tissue, especially during the prenatal period, and enriched for biological pathways involved in neural development. Our findings demonstrate that, even for a behavioural phenotype that is mostly environmentally determined, a well-powered GWAS identifies replicable associated genetic variants that suggest biologically relevant pathways. Because educational attainment is measured in large numbers of individuals, it will continue to be useful as a proxy phenotype in efforts to characterize the genetic influences of related phenotypes, including cognition and neuropsychiatric diseases.
Integrating whole-genome sequencing within the National Antimicrobial Resistance Surveillance Program in the Philippines.
National networks of laboratory-based surveillance of antimicrobial resistance (AMR) monitor resistance trends and disseminate these data to AMR stakeholders. Whole-genome sequencing (WGS) can support surveillance by pinpointing resistance mechanisms and uncovering transmission patterns. However, genomic surveillance is rare in low- and middle-income countries. Here, we implement WGS within the established Antimicrobial Resistance Surveillance Program of the Philippines via a binational collaboration. In parallel, we characterize bacterial populations of key bug-drug combinations via a retrospective sequencing survey. By linking the resistance phenotypes to genomic data, we reveal the interplay of genetic lineages (strains), AMR mechanisms, and AMR vehicles underlying the expansion of specific resistance phenotypes that coincide with the growing carbapenem resistance rates observed since 2010. Our results enhance our understanding of the drivers of carbapenem resistance in the Philippines, while also serving as the genetic background to contextualize ongoing local prospective surveillance.
Whole genome characterization of sequence diversity of 15,220 Icelanders.
Understanding of sequence diversity is the cornerstone of analysis of genetic disorders, population genetics, and evolutionary biology. Here, we present an update of our sequencing set to 15,220 Icelanders who we sequenced to an average genome-wide coverage of 34X. We identified 39,020,168 autosomal variants passing GATK filters: 31,079,378 SNPs and 7,940,790 indels. Calling de novo mutations (DNMs) is a formidable challenge given the high false positive rate in sequencing datasets relative to the mutation rate. Here we addressed this issue by using segregation of alleles in three-generation families. Using this transmission assay, we controlled the false positive rate and identified 108,778 high quality DNMs. Furthermore, we used our extended family structure and read pair tracing of DNMs to a panel of phased SNPs, to determine the parent of origin of 42,961 DNMs.
Parental influence on human germline de novo mutations in 1,548 trios from Iceland.
The characterization of mutational processes that generate sequence diversity in the human genome is of paramount importance both to medical genetics and to evolutionary studies. To understand how the age and sex of transmitting parents affect de novo mutations, here we sequence 1,548 Icelanders, their parents, and, for a subset of 225, at least one child, to 35× genome-wide coverage. We find 108,778 de novo mutations, both single nucleotide polymorphisms and indels, and determine the parent of origin of 42,961. The number of de novo mutations from mothers increases by 0.37 per year of age (95% CI 0.32-0.43), a quarter of the 1.51 per year from fathers (95% CI 1.45-1.57). The number of clustered mutations increases faster with the mother's age than with the father's, and the genomic span of maternal de novo mutation clusters is greater than that of paternal ones. The types of de novo mutation from mothers change substantially with age, with a 0.26% (95% CI 0.19-0.33%) decrease in cytosine-phosphate-guanine to thymine-phosphate-guanine (CpG>TpG) de novo mutations and a 0.33% (95% CI 0.28-0.38%) increase in C>G de novo mutations per year, respectively. Remarkably, these age-related changes are not distributed uniformly across the genome. A striking example is a 20 megabase region on chromosome 8p, with a maternal C>G mutation rate that is up to 50-fold greater than the rest of the genome. The age-related accumulation of maternal non-crossover gene conversions also mostly occurs within these regions. Increased sequence diversity and linkage disequilibrium of C>G variants within regions affected by excess maternal mutations indicate that the underlying mutational process has persisted in humans for thousands of years. Moreover, the regional excess of C>G variation in humans is largely shared by chimpanzees, less by gorillas, and is almost absent from orangutans. This demonstrates that sequence diversity in humans results from evolving interactions between age, sex, mutation type, and genomic location.
A sequence variant associating with educational attainment also affects childhood cognition.
Only a few common variants in the sequence of the genome have been shown to impact cognitive traits. Here we demonstrate that polygenic scores of educational attainment predict specific aspects of childhood cognition, as measured with IQ. Recently, three sequence variants were shown to associate with educational attainment, a confluence phenotype of genetic and environmental factors contributing to academic success. We show that one of these variants associating with educational attainment, rs4851266-T, also associates with Verbal IQ in dyslexic children (P = 4.3 × 10-4, β = 0.16 s.d.). The effect of 0.16 s.d. corresponds to 1.4 IQ points for heterozygotes and 2.8 IQ points for homozygotes. We verified this association in independent samples consisting of adults (P = 8.3 × 10-5, β = 0.12 s.d., combined P = 2.2 x 10-7, β = 0.14 s.d.). Childhood cognition is unlikely to be affected by education attained later in life, and the variant explains a greater fraction of the variance in verbal IQ than in educational attainment (0.7% vs 0.12%,. P = 1.0 × 10-5).
Genome-wide analysis identifies 12 loci influencing human reproductive behavior.
The genetic architecture of human reproductive behavior-age at first birth (AFB) and number of children ever born (NEB)-has a strong relationship with fitness, human development, infertility and risk of neuropsychiatric disorders. However, very few genetic loci have been identified, and the underlying mechanisms of AFB and NEB are poorly understood. We report a large genome-wide association study of both sexes including 251,151 individuals for AFB and 343,072 individuals for NEB. We identified 12 independent loci that are significantly associated with AFB and/or NEB in a SNP-based genome-wide association study and 4 additional loci associated in a gene-based effort. These loci harbor genes that are likely to have a role, either directly or by affecting non-local gene expression, in human reproduction and infertility, thereby increasing understanding of these complex traits.
The effects of an aerobic training intervention on cognition, grey matter volumes and white matter microstructure.
While there is strong evidence from observational studies that physical activity is associated with reduced risk of cognitive decline and dementia, the extent to which aerobic training interventions impact on cognitive health and brain structure remains subject to debate. In a pilot study of 46 healthy older adults (66.6 years ± 5.2 years, 63% female), we compared the effects of a twelve-week aerobic training programme to a waitlist control condition on cardiorespiratory fitness, cognition and magnetic resonance imaging (MRI) outcomes. Cardiorespiratory fitness was assessed by VO2 max testing. Cognitive assessments spanned executive function, memory and processing speed. Structural MRI analysis included examination of hippocampal volume, and voxel-wise assessment of grey matter volumes using voxel-based morphometry. Diffusion tensor imaging analysis of fractional anisotropy, axial diffusivity and radial diffusivity was performed using tract-based spatial statistics. While the intervention successfully increased cardiorespiratory fitness, there was no evidence that the aerobic training programme led to changes in cognitive functioning or measures of brain structure in older adults. Interventions that are longer lasting, multi-factorial, or targeted at specific high-risk populations, may yield more encouraging results.
Strengthening ethical community engagement in contemporary Malawi
Although community engagement is increasingly promoted in global health research to improve ethical research practice, there is sometimes a disconnect between the broader moral ambitions for community engagement in the literature and guidelines on the one hand and its rather narrower practical application in health research on the other. In practice, less attention is paid to engaging communities for the ‘intrinsic’ value of showing respect and ensuring inclusive participation of community partners in research design. Rather, more attention is paid to the use of community engagement for ‘instrumental’ purposes to improve community understanding of research and ensure successful study implementation. Against this backdrop, we reviewed the literature and engaged various research stakeholders at a workshop to discuss ways of strengthening ethical engagement of communities and to develop context-relevant guidelines for community engagement in health research in Malawi.