Post-mortem micro-CT for non-invasive autopsies: Experience in > 250 human fetuses

BACKGROUND: Non-invasive 'imaging' autopsy alternatives for fetuses weighing <500g are limited. Micro-CT has been reported as a viable option in small case series with the potential to avoid an invasive autopsy. Implementation of post-mortem micro-CT in a large cohort, as part of routine clinical service has yet been unreported and realistic 'autopsy prevention rates' are unknown. OBJECTIVE: To describe the range of abnormalities detectable on fetal micro-CT in a clinical setting, additional findings identified over the antenatal ultrasound, and to estimate the invasive 'autopsy avoidance rate' (i.e. cases where imaging was sufficient to deem autopsy unnecessary). STUDY DESIGN: A prospective observational case series was conducted over 3 years (2016 - 2019), of all fetuses referred for micro-CT imaging at a single institution. Imaging was reported by two paediatric radiologists prior to autopsy, with "decision to proceed" based on specialist perinatal pathologists' judgement and parental consent. Agreement rates between micro-CT and antenatal ultrasound were evaluated, and where feasible, diagnostic accuracy for micro-CT was calculated using autopsy as reference standard. RESULTS: 268 fetuses were included (2-350g weight; 11 - 24 weeks gestation), with cause for demise in 122/268 (45.5%). Of these, 64/122 (52.5%) demonstrated fetal anomalies. Although 221/268 (82.5%) had consent for invasive autopsy, only 29/221 (13.1%) underwent this procedure giving an 'autopsy avoidance rate' of 192/221 (86.9%). Complete agreement was present for all brain, thoracic and abdominal pathologies, whilst sensitivity and specificity for cardiac anomalies were 66.7% and 91.7% respectively. Micro-CT and antenatal ultrasound agreement was found in 219/266 (81.9%) cases, with partial agreement in 21/266 (7.9%) and disagreement in 26/266 (10.5%), mostly due to additional cardiac, soft tissue or genito-urinary findings by micro-CT, not seen at ultrasound. CONCLUSIONS: Fetal micro-CT imaging is a viable and useful tool for imaging early gestational fetuses, and can avoid the need for invasive autopsy. Confirmation of antenatal diagnoses are achieved in the majority, and additional anomalies may also be detected

Shape Analysis and Computational Fluid Simulations to Assess Feline Left Atrial Function and Thrombogenesis

In humans, there is a well-established relationship between atrial fibrillation (AF), blood flow abnormalities and thrombus formation, even if there is no clear consensus on the role of left atrial appendage (LAA) morphologies. Cats can also suffer heart diseases, often leading to an enlargement of the left atrium that promotes stagnant blood flow, activating the clotting process and promoting feline aortic thromboembolism. The majority of pathological feline hearts have echocardiographic evidence of abnormal left ventricular filling, usually assessed with 2D and Doppler echocardiography and standard imaging tools. Actually, veterinary professionals have limited access to advanced computational techniques that would enable a better understanding of feline heart pathologies with improved morphological and haemodynamic descriptors. In this work, we applied state-of-the-art image processing and computational fluid simulations based on micro-computed tomography images acquired in 24 cases, including normal cats and cats with varying severity of cardiomyopathy. The main goal of the study was to identify differences in the LA/LAA morphologies and blood flow patterns in the analysed cohorts with respect to thrombus formation and cardiac pathology. The obtained results show significant differences between normal and pathological feline hearts, as well as in thrombus vs non-thrombus cases and asymptomatic vs symptomatic cases, while it was not possible to discern in congestive heart failure with thrombus and from non-thrombus cases. Additionally, in-silico fluid simulations demonstrated lower LAA blood flow velocities and higher thrombotic risk in the thrombus cases

Interchain interaction and fractionally charged solitons in a commensurate charge-density-wave system

AbstractA novel MEMS based drug delivery device has been developed, consisting of an array of metallic contacts. The meander structured device created a uniform electric field which stimulates drug releases. An electro-active hydrogel based polymer matrix responds to an electrical stimulus and shrinks or de-swells on application of an electric field from the fabricated device. Different drug candidates can be encapsulated within the polymer matrix. The de-swelling of the polymer enables the encapsulated drug to be released from the matrix. The gel is able to recover its original size once electric stimulation has been stopped. By controlling the voltage and time, the drug release rate and dose can be precisely controlled. Controlled drug delivery devices may be integrated with sensor technology in combined diagnostic / therapeutic point of care devices

Proteins that bind methylated DNA and human cancer: reading the wrong words

DNA methylation and the machinery involved in epigenetic regulation are key elements in the maintenance of cellular homeostasis. Epigenetic mechanisms are involved in embryonic development and the establishment of tissue-specific expression, X-chromosome inactivation and imprinting patterns, and maintenance of chromosome stability. The balance between all the enzymes and factors involved in DNA methylation and its interpretation by different groups of nuclear factors is crucial for normal cell behaviour. In cancer and other diseases, misregulation of epigenetic marks is a common feature, also including DNA methylation and histone post-translational modifications. In this scenario, it is worth mentioning a family of proteins characterized by the presence of a methyl-CpG-binding domain (MBDs) that are involved in interpreting the information encoded by DNA methylation and the recruitment of the enzymes responsible for establishing a silenced state of the chromatin. The generation of novel aberrantly hypermethylated regions during cancer development and progression makes MBD proteins interesting targets for their biological and clinical implications

Mutagenesis Objective Search and Selection Tool (MOSST): an algorithm to predict structure-function related mutations in proteins

<p>Abstract</p> <p>Background</p> <p>Functionally relevant artificial or natural mutations are difficult to assess or predict if no structure-function information is available for a protein. This is especially important to correctly identify functionally significant non-synonymous single nucleotide polymorphisms (nsSNPs) or to design a site-directed mutagenesis strategy for a target protein. A new and powerful methodology is proposed to guide these two decision strategies, based only on conservation rules of physicochemical properties of amino acids extracted from a multiple alignment of a protein family where the target protein belongs, with no need of explicit structure-function relationships.</p> <p>Results</p> <p>A statistical analysis is performed over each amino acid position in the multiple protein alignment, based on different amino acid physical or chemical characteristics, including hydrophobicity, side-chain volume, charge and protein conformational parameters. The variances of each of these properties at each position are combined to obtain a global statistical indicator of the conservation degree of each property. Different types of physicochemical conservation are defined to characterize relevant and irrelevant positions. The differences between statistical variances are taken together as the basis of hypothesis tests at each position to search for functionally significant mutable sites and to identify specific mutagenesis targets. The outcome is used to statistically predict physicochemical consensus sequences based on different properties and to calculate the amino acid propensities at each position in a given protein. Hence, amino acid positions are identified that are putatively responsible for function, specificity, stability or binding interactions in a family of proteins. Once these key functional positions are identified, position-specific statistical distributions are applied to divide the 20 common protein amino acids in each position of the protein's primary sequence into a group of functionally non-disruptive amino acids and a second group of functionally deleterious amino acids.</p> <p>Conclusions</p> <p>With this approach, not only conserved amino acid positions in a protein family can be labeled as functionally relevant, but also non-conserved amino acid positions can be identified to have a physicochemically meaningful functional effect. These results become a discriminative tool in the selection and elaboration of rational mutagenesis strategies for the protein. They can also be used to predict if a given nsSNP, identified, for instance, in a genomic-scale analysis, can have a functional implication for a particular protein and which nsSNPs are most likely to be functionally silent for a protein. This analytical tool could be used to rapidly and automatically discard any irrelevant nsSNP and guide the research focus toward functionally significant mutations. Based on preliminary results and applications, this technique shows promising performance as a valuable bioinformatics tool to aid in the development of new protein variants and in the understanding of function-structure relationships in proteins.</p

The Methyl-CpG Binding Proteins Mecp2, Mbd2 and Kaiso Are Dispensable for Mouse Embryogenesis, but Play a Redundant Function in Neural Differentiation

The precise molecular changes that occur when a neural stem (NS) cell switches from a programme of self-renewal to commit towards a specific lineage are not currently well understood. However it is clear that control of gene expression plays an important role in this process. DNA methylation, a mark of transcriptionally silent chromatin, has similarly been shown to play important roles in neural cell fate commitment in vivo. While DNA methylation is known to play important roles in neural specification during embryonic development, no such role has been shown for any of the methyl-CpG binding proteins (Mecps) in mice.. No evidence for functional redundancy between these genes in embryonic development or in the derivation or maintenance of neural stem cells in culture was detectable. However evidence for a defect in neuronal commitment of triple knockout NS cells was found.Although DNA methylation is indispensable for mammalian embryonic development, we show that simultaneous deficiency of three methyl-CpG binding proteins genes is compatible with apparently normal mouse embryogenesis. Nevertheless, we provide genetic evidence for redundancy of function between methyl-CpG binding proteins in postnatal mice