Data-Driven Segmentation of Post-mortem Iris Images

This paper presents a method for segmenting iris images obtained from the deceased subjects, by training a deep convolutional neural network (DCNN) designed for the purpose of semantic segmentation. Post-mortem iris recognition has recently emerged as an alternative, or additional, method useful in forensic analysis. At the same time it poses many new challenges from the technological standpoint, one of them being the image segmentation stage, which has proven difficult to be reliably executed by conventional iris recognition methods. Our approach is based on the SegNet architecture, fine-tuned with 1,300 manually segmented post-mortem iris images taken from the Warsaw-BioBase-Post-Mortem-Iris v1.0 database. The experiments presented in this paper show that this data-driven solution is able to learn specific deformations present in post-mortem samples, which are missing from alive irises, and offers a considerable improvement over the state-of-the-art, conventional segmentation algorithm (OSIRIS): the Intersection over Union (IoU) metric was improved from 73.6% (for OSIRIS) to 83% (for DCNN-based presented in this paper) averaged over subject-disjoint, multiple splits of the data into train and test subsets. This paper offers the first known to us method of automatic processing of post-mortem iris images. We offer source codes with the trained DCNN that perform end-to-end segmentation of post-mortem iris images, as described in this paper. Also, we offer binary masks corresponding to manual segmentation of samples from Warsaw-BioBase-Post-Mortem-Iris v1.0 database to facilitate development of alternative methods for post-mortem iris segmentation

The H1N1 post-mortem

The H1 N1 pandemic started more than a year ago at the end of March in Mexico with Malta having it's first positive cases on the first of July. Since July 2009, we had 913 persons who were positive to Hl Nl with 261 cases hospitalised (207 with H1 N1 and 54 with Influenza A) and from these 8 cases needed intensive care. In all, 5 died as a result of this pandemic locally. Over 91 ,471 residents took the vaccine and 2,700 antiviral courses have been dispensed through the government pharmacies. In retrospect one would easily conclude that a massive amount of money has been spent on a minor threat but judgment using hindsight is not appropriate when dealing with the potential risk of a public health threat. The real question that needs to be asked is what are the aims and objectives for this country if the threat of a novel influenza virus emerged and was spreading all over the world? And where the objectives for the H1 N1 strategy achieved or not?peer-reviewe

Tissue- and Species-Specific Patterns of RNA metabolism in Post-Mortem Mammalian Retina and Retinal Pigment Epithelium.

Accurate analysis of gene expression in human tissues using RNA sequencing is dependent on the quality of source material. One major source of variation in mRNA quality is post-mortem time. While it is known that individual transcripts show differential post-mortem stability, few studies have directly and comprehensively analyzed mRNA stability following death, and in particular the extent to which tissue- and species-specific factors influence post-mortem mRNA stability are poorly understood. This knowledge is particularly important for ocular tissues studies, where tissues obtained post-mortem are frequently used for research or therapeutic applications. To directly investigate this question, we profiled mRNA levels in both neuroretina and retinal pigment epithelium (RPE) from mouse and baboon over a series of post-mortem intervals. We found substantial changes in gene expression as early as 15 minutes in the mouse and as early as three hours in the baboon eye tissues. Importantly, our findings demonstrate both tissue- and species- specific patterns of RNA metabolism, by identifying a set of genes that are either rapidly degraded or very stable in both species and/or tissues. Taken together, the data from this study lay the foundation for understanding RNA regulation post-mortem and provide novel insights into RNA metabolism in the tissues of the mammalian eye

The effects of death and post-mortem cold ischemia on human tissue transcriptomes

Post-mortem tissues samples are a key resource for investigating patterns of gene expression. However, the processes triggered by death and the post-mortem interval (PMI) can significantly alter physiologically normal RNA levels. We investigate the impact of PMI on gene expression using data from multiple tissues of post-mortem donors obtained from the GTEx project. We find that many genes change expression over relatively short PMIs in a tissue-specific manner, but this potentially confounding effect in a biological analysis can be minimized by taking into account appropriate covariates. By comparing ante- and post-mortem blood samples, we identify the cascade of transcriptional events triggered by death of the organism. These events do not appear to simply reflect stochastic variation resulting from mRNA degradation, but active and ongoing regulation of transcription. Finally, we develop a model to predict the time since death from the analysis of the transcriptome of a few readily accessible tissues.Peer ReviewedPostprint (published version

Biochemistry Changes That Occur after Death: Potential Markers for Determining Post-Mortem Interval

Death is likely to result in very extensive biochemical changes in all body tissues due to lack of circulating oxygen, altered enzymatic reactions, cellular degradation, and cessation of anabolic production of metabolites. These biochemical changes may provide chemical markers for helping to more accurately determine the time since death (post-mortem interval), which is challenging to establish with current observation-based methodologies. In this study blood pH and changes in concentration of six metabolites (lactic acid, hypoxanthine, uric acid, ammonia, NADH and formic acid) were examined post-mortem over a 96 hour period in blood taken from animal corpses (rat and pig) and blood from rats and humans stored in vitro. The pH and the concentration of all six metabolites changed post-mortem but the extent and rate of change varied. Blood pH in corpses fell from 7.4 to 5.1. Concentrations of hypoxanthine, ammonia, NADH and formic acid all increased with time and these metabolites may be potential markers for postmortem interval. The concentration of lactate increased and then remained at an elevated level and changes in the concentration were different in the rat compared to the human and pig. This is the first systematic study of multiple metabolic changes post-mortem and demonstrates the nature and extent of the changes that occur, in addition to identifying potential markers for estimating post-mortem interval

The influence of defined ante-mortem stressors on the early post-mortem biochemical processes in the abdominal muscle of the Norway lobster, Nephrops norvegicus (Linnaeus, 1758)

The effects of four different ante-mortem stressors (exercise, emersion, starvation and a patent infection with the parasite Hematodinium sp.) on post-mortem processes have been investigated in the abdominal muscle of Norway lobster Nephrops norvegicus by measuring changes in the pH, the levels of glycogen, l-lactate, arginine phosphate, ATP, ADP, AMP, IMP, HxR, Hx and the adenylate energy charge (AEC) over a time course of 24 h with samples being taken at 0, 3, 6, 12 and 24 h. The acute stresses of intense exercise and 2 h emersion resulted in a premature onset of anaerobic glycolysis, leading both to an enhanced glycogen depletion rate and an early accumulation of l-lactate. The chronic stressors, starvation and parasite infection, resulted in a complete ante-mortem depletion of muscle glycogen and consequently the failure of post-mortem glycolytic fermentation. Post-mortem pH and ATP inter-conversion were significantly altered in chronically stressed animals. Ante-mortem, a rapid, almost complete depletion of arginine phosphate was observed in all stress groups. The AEC was altered significantly by all stresses, indicating a strong energy demand. The findings suggest that ante-mortem stressors strongly influence the post-mortem biochemical processes. The laboratory-based results are compared to 'field' data and effects on post-harvest product quality are discussed

Post mortem

Populationer av saproxyliska organismer, det vill säga arter som är beroende av död ved, är i urbana ekosystem begränsade på grund av att död ved regelbundet tas bort av säkerhetsskäl och estetiska skäl. Beroende på förvaltning och markägande kan dock en mindre mängd död ved ibland lämnas kvar eller flyttas till bristområden i de fall det inte är möjligt att behålla på plats. På så vis kan livsrum skapas i områden som är fragmenterade. Syftet med studien är att utvärdera betydelsen av död ved i urbana områden och staden som potentiell livsmiljö för saproxyliska organismer, samt huruvida förflyttning av avverkade stammar kan skapa eventuella nyttor och utgöra risker på nya platser. Denna studie indikerar att bevarade skogspartier i urbana områden är av stor betydelse för tillgången på död ved och att såväl kommunala stadsparker som privata trädgårdar bidrar med viktiga livsmiljöer för saproxyliska arter.Populations of saproxylic organisms, which means species that depend on dead wood, are limited in urban ecosystems due to the fact that dead wood is regularly removed for safety and aesthetic reasons. Depending on management and land ownership, a small amount of dead wood can sometimes be left behind or moved to deficient areas in cases where it is not possible to keep in place. In this way, living spaces can be created in areas that are fragmented. This study aimed to evaluate the significance of dead wood in urban areas and study urban areas as potential habitat for saproxylic organisms, but also whether relocation of felled trunks can create potential benefits and risks in new locations. This study indicates that preserved forest areas in urban areas are of great importance for access to dead wood and that both municipal city parks and private gardens contribute important habitats for saproxylic species