Solving the inverse problem of post-mortem interval estimation using Bayesian Belief Networks.

Bayesian Belief Networks (BBNs) can be applied to solve inverse problems such as the post-mortem interval (PMI) by a simple and logical graphical representation of conditional dependencies between multiple taphonomic variables and the observable decomposition effect. This study is the first cross-comparison retrospective study of human decomposition across three different geographical regions. To assess the effect of the most influential taphonomic variables on the decomposition rate (as measured by the Total Decomposition Score (TDS)), decomposition data was examined from the Forensic Anthropology Research Facility at the University of Tennessee (n = 312), the Allegheny County Office of the Medical Examiner in Pittsburgh, US (n = 250), and the Crime Scene Investigation department at Southwest Forensics in the UK (n = 81). Two different BBNs for PMI estimations were created from the US and the UK training data. Sensitivity analysis was performed to identify the most influential parameters of TDS variance, with weaker variables (e.g., age, sex, clothing) being excluded during model refinement. The accuracy of the BBNs was then compared by additional validation cases: US (n = 28) and UK (n = 10). Both models conferred predictive power of the PMI and accounted for the unique combination of taphonomic variables affecting decomposition. Both models had a mean posterior probability of 86% (US) and 81% (UK) in favor of the experimental hypothesis (that the PMI was on, or less than, the prior last known alive date). Neither the US nor the UK datasets represented any cases below 'moderate' support for the value of PMI evidence. By applying coherent probabilistic reasoning to PMI estimations, one logical solution is provided to model the complexities of human decomposition that can quantify the combined effect of several uncertainties surrounding the PMI estimation. This approach communicates the PMI with an associated degree of confidence and provides predictive power on unknown PMI cases.

Individuals lacking ridge detail: A case study in adermatoglyphia.

Adermatoglyphia is a very rare autosomal-dominant condition that is genetically inherited and causes an individual to be born without conventional ridge detail on either their palmar or plantar surfaces (the fingers and palms of the hands and the toes and the soles of the feet). While adermatoglyphia has been the focus of medical and genetic research, no previous research has been conducted with regard to the forensic recovery and identification of marks from an adermatoglyphic individual. By observation of ridge detail donated by an adermatoglyphic subject, the study uses different methods in order to capture fingermarks (methods include: inked capture, livescan (biometric) capture, cyanoacrylate fuming, ninhydrin enhancement, and physical developer). Unusually, the purpose of this paper ends up presenting a number of examples of an absence of evidence; unsuccessful attempts made to capture and enhance fingerprint ridge detail. This is determined over a range of standard means including "live" donations by the adermatoglyphic subject onto the Livescan system, and enhancements of latent donations. The subject shows to leave either insubstantial fingermarks with no detail, or no mark whatsoever.

The effect of seasonality on the application of accumulated degree-days to estimate the early post-mortem interval.

This study investigated the effect of seasonal variables on decomposition in the early post-mortem period using 26 donated human cadavers at the University of Tennessee's Anthropology Research Facility (ARF), USA. The rate and pattern of decomposition in human cadavers (as measured by TBS and the revised TBSsurf methods) did not vary significantly between all seasons. Summer and autumn cadavers had comparable rates of accelerated decomposition despite significant differences in both ADD and temperature (p<0.05). Spring cadavers had the slowest onset of decomposition characteristics, even compared to the few decomposition characteristics expressed in winter. Seasonal variation in humidity, rather than temperature, may be the overarching driving force for decomposition progression in the early post-mortem period. Both TBS and TBSsurf methods were poor predictors of the PMI (R2=0.4) and significantly over-estimated the PMI across all seasons, although to a lesser extent in spring. This study also demonstrated no relationship between known ADD and TBS/TBSsurf (R2=0.025). TBS and TBSsurf are ADD-based PMI estimation models that cannot be validated under experimental conditions. Accounting for seasonal expression of individual decomposition characteristics is needed for improvement of PMI predictability in forensic practice.

Associations between voxel-level accumulated dose and rectal toxicity in prostate radiotherapy.

BACKGROUND AND PURPOSE: Associations between dose and rectal toxicity in prostate radiotherapy are generally poorly understood. Evaluating spatial dose distributions to the rectal wall (RW) may lead to improvements in dose-toxicity modelling by incorporating geometric information, masked by dose-volume histograms. Furthermore, predictive power may be strengthened by incorporating the effects of interfraction motion into delivered dose calculations.Here we interrogate 3D dose distributions for patients with and without toxicity to identify rectal subregions at risk (SRR), and compare the discriminatory ability of planned and delivered dose. MATERIAL AND METHODS: Daily delivered dose to the rectum was calculated using image guidance scans, and accumulated at the voxel level using biomechanical finite element modelling. SRRs were statistically determined for rectal bleeding, proctitis, faecal incontinence and stool frequency from a training set (n = 139), and tested on a validation set (n = 47). RESULTS: SRR patterns differed per endpoint. Analysing dose to SRRs improved discriminative ability with respect to the full RW for three of four endpoints. Training set AUC and OR analysis produced stronger toxicity associations from accumulated dose than planned dose. For rectal bleeding in particular, accumulated dose to the SRR (AUC 0.76) improved upon dose-toxicity associations derived from planned dose to the RW (AUC 0.63). However, validation results could not be considered significant. CONCLUSIONS: Voxel-level analysis of dose to the RW revealed SRRs associated with rectal toxicity, suggesting non-homogeneous intra-organ radiosensitivity. Incorporating spatial features of accumulated delivered dose improved dose-toxicity associations. This may be an important tool for adaptive radiotherapy in the future.

Ballistic research techniques: visualizing gunshot wounding patterns.

There are difficulties associated with mapping gunshot wound (GSW) patterns within opaque models. Depending on the damage measurement parameters required, there are multiple techniques that can provide methods of "seeing" the GSW pattern within an opaque model. The aim of this paper was to test several of these techniques within a cadaveric animal limb model to determine the most effective. The techniques of interest were flash X-ray, ultrasound, physical dissection, and computed-tomography (CT). Fallow deer hind limbs were chosen for the model with four limbs used for each technique tested. Quarantined 7.62 × 39 mm ammunition was used for each shot, and each limb was only shot once, on an outdoor range with shots impacting at muzzle velocity. Flash X-ray provided evidence of yaw within the limb during the projectile's flight; ultrasound though able to visualise the GSW track, was too subjective and was abandoned; dissection proved too unreliable due to the tissue being cadaveric so also too subjective; and lastly, CT with contrast provided excellent imaging in multiple viewing planes and 3D image reconstruction; this allowed versatile measurement of the GSW pattern to collect dimensions of damage as required. Of the different techniques examined in this study, CT with contrast proved the most effective to allow precise GSW pattern analysis within a cadaveric animal limb model. These findings may be beneficial to others wishing to undertake further ballistic study both within clinical and forensic fields.

Forensic reconstruction of two military combat related shooting incidents using an anatomically correct synthetic skull with a surrogate skin/soft tissue layer.

Six synthetic head models wearing ballistic protective helmets were used to recreate two military combat-related shooting incidents (three per incident, designated 'Incident 1' and 'Incident 2'). Data on the events including engagement distances, weapon and ammunition types was collated by the Defence Science and Technology Laboratory. The models were shot with 7.62 × 39 mm ammunition downloaded to mean impact velocities of 581 m/s (SD 3.5 m/s) and 418 m/s (SD 8 m/s), respectively, to simulate the engagement distances. The damage to the models was assessed using CT imaging and dissection by a forensic pathologist experienced in reviewing military gunshot wounds. The helmets were examined by an MoD engineer experienced in ballistic incident analysis. Damage to the helmets was consistent with that seen in real incidents. Fracture patterns and CT imaging on two of the models for Incident 1 (a frontal impact) were congruent with the actual incident being modelled. The results for Incident 2 (a temporoparietal impact) produced realistic simulations of tangential gunshot injury but were less representative of the scenario being modelled. Other aspects of the wounds produced also exhibited differences. Further work is ongoing to develop the models for greater ballistic injury fidelity.

Anatomical change during radiotherapy for head and neck cancer, and its effect on delivered dose to the spinal cord.

BACKGROUND AND PURPOSE: The impact of weight loss and anatomical change during head and neck (H&N) radiotherapy on spinal cord dosimetry is poorly understood, limiting evidence-based adaptive management strategies. MATERIALS AND METHODS: 133 H&N patients treated with daily mega-voltage CT image-guidance (MVCT-IG) on TomoTherapy, were selected. Elastix software was used to deform planning scan SC contours to MVCT-IG scans, and accumulate dose. Planned (DP) and delivered (DA) spinal cord D2% (SCD2%) were compared. Univariate relationships between neck irradiation strategy (unilateral vs bilateral), T-stage, N-stage, weight loss, and changes in lateral separation (LND) and CT slice surface area (SSA) at C1 and the superior thyroid notch (TN), and ΔSCD2% [(DA - DP) D2%] were examined. RESULTS: The mean value for (DA - DP) D2% was -0.07 Gy (95%CI -0.28 to 0.14, range -5.7 Gy to 3.8 Gy), and the mean absolute difference between DP and DA (independent of difference direction) was 0.9 Gy (95%CI 0.76-1.04 Gy). Neck treatment strategy (p = 0.39) and T-stage (p = 0.56) did not affect ΔSCD2%. Borderline significance (p = 0.09) was seen for higher N-stage (N2-3) and higher ΔSCD2%. Mean reductions in anatomical metrics were substantial: weight loss 6.8 kg; C1LND 12.9 mm; C1SSA 12.1 cm2; TNLND 5.3 mm; TNSSA 11.2 cm2, but no relationship between weight loss or anatomical change and ΔSCD2% was observed (all r2 < 0.1). CONCLUSIONS: Differences between delivered and planned spinal cord D2% are small in patients treated with daily IG. Even patients experiencing substantial weight loss or anatomical change during treatment do not require adaptive replanning for spinal cord safety.

Automated customized retrieval of radiotherapy data for clinical trials, audit and research.

OBJECTIVE: To enable fast and customizable automated collection of radiotherapy (RT) data from tomotherapy storage. METHODS: Human-readable data maps (TagMaps) were created to generate DICOM-RT (Digital Imaging and Communications in Medicine standard for Radiation Therapy) data from tomotherapy archives, and provided access to "hidden" information comprising delivery sinograms, positional corrections and adaptive-RT doses. RESULTS: 797 data sets totalling 25,000 scans were batch-exported in 31.5 h. All archived information was restored, including the data not available via commercial software. The exported data were DICOM-compliant and compatible with major commercial tools including RayStation, Pinnacle and ProSoma. The export ran without operator interventions. CONCLUSION: The TagMap method for DICOM-RT data modelling produced software that was many times faster than the vendor's solution, required minimal operator input and delivered high volumes of vendor-identical DICOM data. The approach is applicable to many clinical and research data processing scenarios and can be adapted to recover DICOM-RT data from other proprietary storage types such as Elekta, Pinnacle or ProSoma. Advances in knowledge: A novel method to translate data from proprietary storage to DICOM-RT is presented. It provides access to the data hidden in electronic archives, offers a working solution to the issues of data migration and vendor lock-in and paves the way for large-scale imaging and radiomics studies.

Applying physical science techniques and CERN technology to an unsolved problem in radiation treatment for cancer: the multidisciplinary 'VoxTox' research programme.

The VoxTox research programme has applied expertise from the physical sciences to the problem of radiotherapy toxicity, bringing together expertise from engineering, mathematics, high energy physics (including the Large Hadron Collider), medical physics and radiation oncology. In our initial cohort of 109 men treated with curative radiotherapy for prostate cancer, daily image guidance computed tomography (CT) scans have been used to calculate delivered dose to the rectum, as distinct from planned dose, using an automated approach. Clinical toxicity data have been collected, allowing us to address the hypothesis that delivered dose provides a better predictor of toxicity than planned dose.

The 'Molecule of the Month' Website-An Extraordinary Chemistry Educational Resource Online for over 20 Years.

The Molecule of the Month website (http://www.chm.bris.ac.uk/motm/motm.htm) is an educational resource that is celebrating its 20th anniversary. Here we reflect on its pioneering role in promoting new technology for visualizing and presenting chemical information on the web, as well as its achievements, as a free educational resource, both as a teaching aid and as a multi-user, multi-author learning platform. We discuss the legal aspects of such sites, as well as issues around how to make the content permanent. Finally, we look forward to how such sites may evolve in the future.

Recalculation of dose for each fraction of treatment on TomoTherapy.

OBJECTIVE: The VoxTox study, linking delivered dose to toxicity requires recalculation of typically 20-37 fractions per patient, for nearly 2000 patients. This requires a non-interactive interface permitting batch calculation with multiple computers. METHODS: Data are extracted from the TomoTherapy(®) archive and processed using the computational task-management system GANGA. Doses are calculated for each fraction of radiotherapy using the daily megavoltage (MV) CT images. The calculated dose cube is saved as a digital imaging and communications in medicine RTDOSE object, which can then be read by utilities that calculate dose-volume histograms or dose surface maps. The rectum is delineated on daily MV images using an implementation of the Chan-Vese algorithm. RESULTS: On a cluster of up to 117 central processing units, dose cubes for all fractions of 151 patients took 12 days to calculate. Outlining the rectum on all slices and fractions on 151 patients took 7 h. We also present results of the Hounsfield unit (HU) calibration of TomoTherapy MV images, measured over an 8-year period, showing that the HU calibration has become less variable over time, with no large changes observed after 2011. CONCLUSION: We have developed a system for automatic dose recalculation of TomoTherapy dose distributions. This does not tie up the clinically needed planning system but can be run on a cluster of independent machines, enabling recalculation of delivered dose without user intervention. ADVANCES IN KNOWLEDGE: The use of a task management system for automation of dose calculation and outlining enables work to be scaled up to the level required for large studies.

A new computer-tomography-based method of sex estimation: Development of Turkish population-specific standards.

The identification of victims involved in mass fatality incidents has become an increasingly important issue nowadays, and identification of unknown individuals is an important aspect in criminal cases and Disaster Victim Identification scenarios. Therefore, the sex estimation is one of the most important biological attributes towards establishing personal identity. In addition, several studies have demonstrated that metric sex determination methods of the skeleton are population-specific due to variation in size and patterns of sexual dimorphism. Unfortunately, the modern Turkish population still lacks wide and representative population standards for identification. Previous research has shown that modern technologies, such as CT scanning appear to offer promising means for the establishment of new standards for contemporary populations. The main aim of this project is to examine the application of measurements taken from the femur in order to assess sex, as well as to contribute to the establishment of discriminant function equations for the Turkish population for forensic applications. The sample population was composed of CT images taken from 200 adult hospital patients. The images of the femora were segmented from the surrounding bones to ensure correct usage of landmarks as accurately as possible. The 3D reconstructions were then created using the volume-rendering function in OsiriX (v.5.6.). Thirteen measurements were acquired using a 3D viewer and were located and marked on each of the CT reconstructed femora. Thirteen anthropometric parameters were measured and analysed by basic descriptive statistics and discriminant analysis methods using the SPSS 21.0 software package. The intra-observer variation was assessed by obtaining the inter-cross correlation coefficient in order to evaluate the accuracy of the linear measurements taken. The accuracy of sex prediction ranged from 63.5 to 88% with single variables. In stepwise analysis, Epicondylar Breadth, Femur Vertical Diameter of Neck and Medial Lateral Subtrochanteric Diameter were found to be the most discriminating variables providing an accuracy of 91%. Ultimately, it is envisaged that this research study will produce data and interpretations that will inform on and improve standards of sex estimation from postcranial osteometric landmarks. Additionally, this research will consider how this data provides value for a developing discipline of forensic anthropology and how it integrates within the existing systems of criminal investigation and Disaster Victim Identification practices in Turkey.

Accumulated dose to the rectum, measured using dose-volume histograms and dose-surface maps, is different from planned dose in all patients treated with radiotherapy for prostate cancer.

OBJECTIVE: We sought to calculate accumulated dose (DA) to the rectum in patients treated with radiotherapy for prostate cancer. We were particularly interested in whether dose-surface maps (DSMs) provide additional information to dose-volume histograms (DVHs). METHODS: Manual rectal contours were obtained for kilovoltage and daily megavoltage CT scans for 10 participants from the VoxTox study (380 scans). Daily delivered dose recalculation was performed using a ray-tracing algorithm. Delivered DVHs were summated to create accumulated DVHs. The rectum was considered as a cylinder, cut and unfolded to produce daily delivered DSMs; these were summated to produce accumulated DSMs. RESULTS: Accumulated dose-volumes were different from planned in all participants. For one participant, all DA levels were higher and all volumes were larger than planned. For four participants, all DA levels were lower and all volumes were smaller than planned. For each of these four participants, ≥1% of pixels on the accumulated DSM received ≥5 Gy more than had been planned. CONCLUSION: Differences between accumulated and planned dose-volumes were seen in all participants. DSMs were able to identify differences between DA and planned dose that could not be appreciated from the DVHs. Further work is needed to extract the dose data embedded in the DSMs. These will be correlated with toxicity as part of the VoxTox Programme. ADVANCES IN KNOWLEDGE: DSMs are able to identify differences between DA and planned dose that cannot be appreciated from DVHs alone and should be incorporated into future studies investigating links between DA and toxicity.

The spatial distribution of postblast RDX residue: forensic implications.

Locating exactly where trace explosive residue samples should be sought during sample collection at bomb scenes is not specified in the published literature or guidelines; in this area, it is generally acknowledged that forensic practices are based on tradition rather than evidence. This study investigated patterns in the spatial distribution of postblast 1,3,5-trinitro-1,3,5-triazocyclohexane residue from a series of unconfined detonations, over a range of sampling sites, and at two different detonation heights. The amount of residue recovered from the sites decreased as a function of distance from the center of the explosion. [Correction added after online publication 27 December 2012: In the preceding sentence, "increased" was corrected to "decreased" to agree with the conclusion of the article.] As the height of the detonations increased, more residues were found from all sampling sites. The findings of this empirical study have a number of important practical implications including determining where residue samples are best sought at crime scenes.

Combating bioterrorism with personal computers.

Using personal computers in a grid is permitting the in silico screening of millions of molecules to seek out potential inhibitors of agents that pose bioterror threats. Current projects are targeting anthrax and smallpox, but the approach has many attractions for investigating any known protein target and its inhibition.

Pattern recognition and massively distributed computing.

A feature of Peter Kollman's research was his exploitation of the latest computational techniques to devise novel applications of the free energy perturbation method. He would certainly have seized upon the opportunities offered by massively distributed computing. Here we describe the use of over a million personal computers to perform virtual screening of 3.5 billion druglike molecules against protein targets by pharmacophore pattern matching, together with other applications of pattern recognition such as docking ligands without any a priori knowledge about the binding site location.