In forensic entomology, determining species identity is a crucial step towards estimating post mortem interval. DNA barcoding can aid in the identification of unknown forensically relevant species, and this requires the comparison of DNA barcodes to reference data from known species. However, there is a lack of DNA barcode reference data of forensically relevant Calliphoridae species in the Western Cape (South Africa). DNA barcodes were generated for the COI and ITS2 markers for 41 forensically relevant Calliphoridae specimens, representing seven species from six localities in the Western Cape: Chrysomya albiceps (n = 3), Chrysomya chloropyga (n = 8), Chrysomya marginalis (n = 5), Chrysomya megacephala (n = 7), Hemipyrellia fernandica (n = 1), Lucilia cuprina (n = 8) and Lucilia sericata (n = 9). This data was combined with that from Cooke et al. (2018) (n = 40), and subjected to rigorous statistical and phylogenetic analyses. Phylogenetic analysis which combined data for both COI and ITS2 barcodes returned monophyletic clades for each species with increased support when compared to using each barcode individually. This combined dataset was able to discriminate between L. cuprina and L. sericata with full support (100% pP), which was not achieved previously. DNA barcodes were evaluated for intra- and inter-specific variance as well as haplotype patterning. No haplotype patterning was observed for either barcodes across sampled localities. Lastly, a single-blinded approach was used to assess the dataset, whereby DNA barcodes from ‘unknown’ specimens were correctly identified using this reference data. These identifications were more accurate than those using GenBank® or BOLD, highlighting the importance of using locally relevant reference data. This study has contributed new data pertaining to DNA barcodes for seven Calliphoridae species, which was previously scarce for the Western Cape, and this has directly contributed to an improvement in the accuracy of local species identification.

Death due to cranial blunt force trauma is a major issue not just in South Africa but worldwide. The vast majority of studies conducted on cranial blunt force trauma have analysed trauma to the frontal portion of the head. This is due to the involvement of the frontal portion of the head in automotive accidents. The lateral portion of the head is however no less important and is often impacted during homicidal assault. In cases involving cranial blunt force trauma, a common question asked of experts relates to the amount of force involved with a particular trauma. The goal of forensic science in general is to provide objective, repeatable results. At present, however, answering this question relies on a subjective rating scale of mild, moderate or severe force. Determining the severity of the force is also subjective, in that it relies heavily on the experience of the expert. Forensic anthropology by its nature is often subjective; however there is a need to move away from conducting analyses based predominantly on the experience of the investigator. With this in mind, this dissertation offers background information on fracture mechanics and impact biomechanics and provides a current review of the literature surrounding lateral impact to the skull. The research conducted as part of this dissertation attempts to quantify the force and energy involved with lateral impact to the skull due to a blow by a hammer, as well as describes the wound morphology associated with such impacts. Human tissue for experimentation is becoming increasingly difficult to acquire. There is therefore a need to determine suitable models for use in such testing. In the current study whole porcine heads were impacted on the fronto-parietal portion of the cranium. Half of the specimens were impacted with an implement resembling the shape and weight of a hammer. These hammer tests were conducted primarily to determine the type of trauma associated with such impacts and determine if a correlation exists between velocity or energy of impact and the level of trauma sustained. The remaining specimens were impacted with a Hopkinson pressure bar of the same diameter as the striker in the hammer tests. The Hopkinson pressure bar apparatus allows for the determination of the force of impact. The use of the Hopkinson pressure bar to determine fracture forces in whole specimens is novel. The fracture forces obtained in the current study agree considerably with the literature previously published on lateral, cranial blunt force trauma to both human and porcine specimens. The fractures produced, however, are atypical and may indicate a need to conduct further tests on other animal models.

Introduction: In South Africa (SA), the forensic sector faces significant challenges including how to meet increasing public expectations for high quality, reliable and valid scientific and medico legal results, whilst dealing with increasing caseloads and restricted resources in a developing country. Internationally, lean six-sigma and/or business-based frameworks have been developed to define, measure and analyse the efficiency, effectiveness and output of forensic laboratories, so as to assess performance to meet such challenges. Aim: This pilot project aimed to investigate the effectiveness and efficiency of forensic pathology practice at Salt River Mortuary (SRM) by applying lean six sigma principles (define, measure, analyse and improve) and FORESIGHT metric analyses to retrospective case and staffing data, as well as prospective observational analyses. Methods: A retrospective analysis of cases admitted to Salt River Mortuary in 2015 was conducted to define and measure a snapshot of forensic pathology practice in Cape Town. In addition, observations of autopsy processes were conducted to identify bottlenecks in the system and provide suggestions for improvement. Results: An analysis of post-mortem report turn-around for 3567 cases admitted to SRM in 2015 showed that approximately 10% of cases were closed (cause of death was determined) on the day of the post-mortem, 65% within 14 days and 80% closed within a 30 day period. Certain requested ancillary investigations delayed the finalisation of cause of death; for example, only 8.33% of carbon monoxide testing and 30.31% of histological examinations were completed within the year. A process map outlining autopsy practices at SRM was generated through observational data, which also identified key bottlenecks in the process (e.g.: equipment issues). Preliminary financial data suggested that it cost on average R16 155.03 per case. Staff data demonstrated a lack of pathologists compared to other staff categories and high case load requirements. Discussion: This pilot study investigates the utilization of metrics and strategic frameworks to assess forensic pathology processes in Cape Town. This study offers a cross-sectional insight into financial performance, efficiency and effectiveness of post-mortem investigations at SRM, highlighting bottlenecks and inefficiencies, and providing suggestions for improvement. The findings will assist in forming a basis for future work into the development of a framework for monitoring performance and progress, and developing benchmark standards for the death investigation system in South Africa

Introduction: Pesticides offer great benefits in the agricultural sector, but exposure may pose both acute and chronic health risks to humans. In developing countries, morbidity and mortality rates related to pesticide exposure are high and in certain areas (such as in rural, lower socioeconomic and/or agricultural-dependent communities), pesticides may be stored in and around homes, which may increase the risk of accidental exposure as well as intentional poisoning. In Cape Town, South Africa, this public health issue is exacerbated by the informal selling of street pesticides. These are pesticides that usually comprise of a mixture of these chemicals, sold unregistered as liquids or granules in bottles or packages without clear identification labels, for domestic use. While cheap and widely available in informal settlements; these pesticide formulations are not regulated and extremely toxic. Data illustrating the extent and nature of fatalities related to acute and chronic pesticide exposure in Cape Town, particularly as related to street pesticides, is limited. This dissertation provides an overview of the literature associated with pesticide toxicity and related mortality, paying particular attention to available South African research. This is followed by a study investigating pesticide deaths at Salt-River Mortuary over a period of five years. Aim: The aim of this study was to determine the prevalence and characteristics of deaths associated with suspected acute pesticide toxicity, to broaden the spectrum of knowledge concerning pesticide-related deaths in Cape Town, South Africa. Methods: A retrospective analysis of cases admitted to Salt River Mortuary (SRM) from 2011 to 2015 (inclusive) was conducted. Demographic, autopsy, investigative and toxicological data (where available) were collected from post-mortem and other investigative reports. Results: Of the total of 16,453 cases admitted to SRM over a five-year period from January 2011 until December 2015, 104 (0.63%) were deemed to be acutely pesticide-related based on available autopsy data. There was an equal number of male (n=52; 50%) and female (n=52; 50%) victims. Most deaths (n=74; 71%) occurred at medical centres following exposure, and Terbufos was found to be the common pesticide detected analytically (n=42, 61%) in toxicology reports available (76%). Results revealed that (60%) of acute pesticide toxicity cases were suspected suicides, while (6%) of cases were suspected accidents and (3%) cases were suspected homicides, while the remainder were still undetermined pending toxicological investigations. Conclusion: A history of ingestion, autopsy findings and toxicological results (if available) assisted in identification of these cases, most of which came from lower socio-economic communities. While the number of overall cases is low, it is evident that these deaths are a public health burden, and may be preventable through improved notification and policy development. Challenges with this study involved the inability to distinguish mortality associated with chronic pesticide exposure, the lack of toxicological results available, limited scene investigation information to identify street pesticide contributions, and that the study was limited to one mortuary in Western Cape. An extension of this research to other mortuaries in Western Cape as well as collaborative work with community and public health sectors on availability and toxicity of street pesticides will assist in strategic intervention methods and policy reform to reduce accidental and suicidal mortality associated with acute pesticide exposure.

The analysis of colors is omnipresent in forensics. While their use for macroscopic evidence such as soil sees a large amount of research, their correct handling is more challenging when observed under a microscope. Either for hairs or textile fibers, their color (from melanin, dyes or for birefringence analysis) is crucial in being able to compare between fibers found at a crime scene. Typically, color is quantified using a color space, such as RGB, XYZ, L*a*b*, and L*u*v*. Unfortunately, color is very subjective and often difficult to quantify accurately, even using digital detectors. Finding true matches of colors has been limited by factors including illumination, optics transmission function, and in many cases the human eye. The colors produced by the birefringence of fibers under analysis using polarized light microscopy (PLM) are known to provide quick information on the fiber identification. Nonetheless, the exact determination of the accurate colors is still either subjective to the operator or the correct calibration of the software. In this thesis, calibration of the color response of a polarizing light microscope was performed using a UV-Vis broadband spectrometer to characterize its illuminant and camera. All the color images obtained with the camera were then transformed from the common RGB encoding to L*a*b* color space using MATLAB. An empirical Michel-Lévy chart was also designed using a quartz wedge in order to calibrate retardation with empirical L*a*b* color values, also as a teaching tool for the UCF undergraduate class "Forensic Microscopy", and with a qualitative comparison with common textile fibers. The discriminatory power and uncertainty of color perception of the microscope camera and of human vision were measured and will be discussed.

Latent print evidence collected from crime scenes are analyzed and compared by examiners using the ACE-V protocol (Analysis, Comparison, Evaluation-Verification) to identify potential suspects. However, smudged and poor-quality prints, usually deemed inconclusive, could be utilized for source association or discrimination based on the chemistry of the oils and sweat that comprises the latent print residue (LPR). For this research, LPRs were collected from various places on the face and analyzed via two-dimensional gas chromatography-mass spectrometry (2D GC-MS), one-dimensional (1D) GC-MS, and direct analysis in real time-high resolution mass spectrometry (DART-HRMS). LPR recovery with two common sample preparation methods, derivatization and non-derivatization, was examined when collected on a porous and non-porous substrate. The method that provided high correlation and low relative standard deviation for each substrate was used for subsequent studies. Then, the LPRs were investigated to observe if association to a source can be achieved in either 1D or 2D GC. Comparison methods of Pearson correlation coefficient (PCC), principal component analysis (PCA), hierarchical cluster analysis (HCA), and receiving operating characteristic (ROC) curves were used to test source association. An aging study was performed to analyze the change in latent print chemistry when simulating evidence storage for up to three months via 1D GC and DART-HRMS. During this time, a longevity study was conducted by collecting LPRs every two weeks to test the intra- and inter-variability of the recovered chemistry. Correlation and similarity metrics such as PCC, Spearman's rank correlation, and Euclidean distance were used to compare the monthly and weekly changes of the LPRs.

The ability to associate a smokeless powder, smokeless powder residue, or organic gunshot residue (OGSR) to one another may be helpful in determining the origin of a suspected sample and aid in linking a suspect to a crime scene. In this study, smokeless powders were extracted and analyzed via gas chromatography – mass spectrometry (GC-MS) and direct analysis in real time – high resolution mass spectrometry (DART-HRMS). Subsequently, group definition was performed using hierarchical cluster analysis and principal component analysis followed by internally validated classification models. Then, smokeless powder residues were generated in-lab and extracted. Resulting residue data from each instrument was classified within the respective smokeless powder model using linear discriminant analysis (LDA) with external test sets. Residue groupings and classification models were also generated. Ammunition was loaded with known smokeless powder, then fired to collect OGSR from cloth targets. The OGSR was extracted and analyzed via DART-HRMS and GC-MS, then tested against the smokeless powder and residue models to determine the association of OGSR to its intact smokeless powder as well as to lab generated residues. Reference classes for the OGSR samples in the LDA prediction were determined via flow charts for informed analyst determination of class in smokeless powder and residue models. Standards of common smokeless powder components were pyrolyzed and an expected pyrolysis products profile was created for each sample based on the intact composition. Similarity and correlation metrics including Pearson's correlation, Sørensen-Dice similarity coefficient, and Concordance correlation were evaluated in the comparison of smokeless powder to residue and residue to expected pyrolysis products. Pearson's correlation was used in the comparison of smokeless powder to OGSR and smokeless powder residue to OGSR.

Sudden unexpected death in the young (SUDY) is the unanticipated demise of individuals aged between 1 and 40 years. In South Africa, these deaths are referred for forensic investigation. The primary aim of this study was to retrospectively investigate the frequency of known risk factors in SUDY cases admitted to Salt River Mortuary in Cape Town and explore differences between males and females. There were 1 088 SUDY cases identified with 0.9% (10/1 088) missing files. Reviewed cases were n=1 078, 62.6% (675/1 078) males, and 37.4% (403/1 078) females; 83.5% (901/1 078) adults and 16.4% (177/1 078) children, accounting for 5.6% of total admissions between 1 January 2010 and 31 December 2015. Despite the predominance of males, significantly more females (61.8%) were obese (p < 0.05). At least one primary medical condition was present in 53.7% of cases, with the leading conditions being tuberculosis (11.9 % of adult males), epilepsy (11.7% of adult males; 10.3% of female children), HIV (10.7% of adult females) and asthma (11.1% of male children). In the subset of the study population where information was available, before death, 74% of individuals were reported to have experienced prodromal symptoms; 37.6% of males and 32.4% of females did not seek medical intervention following symptoms. Information regarding a family history of sudden death was known in 237/1078 cases. In 3.2% of these cases, a family history of sudden death was reported. Significantly more males than females reported the use of tobacco, alcohol, and other illicit drugs (p < 0.05). More females were unemployed (p < 0.05). Interventions based on lifestyle modification, social support, pharmacologic needs, and awareness should be targeted at individuals with the above profiles, especially those with a family history of sudden death, as they may be high-risk groups. Findings from this study contribute new and relevant local reference data for SUDY risk profiles of males and females admitted to Salt River Mortuary.

Carbon monoxide (CO) is a gas that exerts its toxicity on humans, when inhaled, by bonding with haemoglobin (Hb) to produce carboxyhaemoglobin (COHb). This results in tissue hypoxia which can be fatal at high blood saturation levels. Carboxyhaemoglobin may be measured using a Radiometer ABL825 FLEX analyser, a spectrophotometric instrument that applies a technique called CO-oximetry to measure Hb derivatives such as COHb and methaemoglobin (MetHb). The latter is an oxidised form of Hb that can cause or contribute to mortality at high concentrations. Methaemoglobin is notorious for its instability in vitro. This study, therefore, sought to determine handling conditions best suited for the stability of MetHb in post-mortem blood such that the ABL825 FLEX analyser may be used for the simultaneous measurement of COHb and MetHb. To this end, blood samples collected from 15 cases of potential CO poisoning at Salt River Mortuary were aliquoted into red (no additive)-, green (containing lithium heparin)-, and purple (containing ethylenediaminetetraacetic acid)-top tubes. The samples were stored at 4°C or –80°C and retrieved from storage on days 0, 1, 4, 7, 14, and 30, for analysis. While COHb remained stable in all storage conditions over a 30-day period, this was not true for MetHb. When samples were stored at 4°C, a rapid increase followed by a gradual decline was observed for MetHb in all the tube types investigated. The MetHb content was at its lowest after two weeks of storage, which was consistent with COHb levels at the same time period and temperature. At –80°C, continuous increase of MetHb was observed, with the samples stored in green-top tubes showing the least amount of overall change from the reference (day zero) values. The study provided useful data regarding the stability of MetHb under the considered storage conditions, the investigators concluded that refrigerating blood samples in either red-, purple-, or green-top tube was suitable for the accurate simultaneous determination of both COHb and MetHb, if the analytes are measured immediately after collection or after two weeks of storage. Given that the nature of post-mortem forensic casework is such that suitable blood specimens are not always available for toxicological analyses, for the second aim of the study, the researchers sought to investigate the suitability of thoracic cavity fluid as an alternative specimen for the measurement of COHb. For this aim, thoracic cavity fluid collected into green-top tubes from the aforementioned cases was analysed immediately after collection. The results were compared to those obtained from the analysis of blood collected into green-top tubes and analysed on day zero (before storage). The statistical analyses used for this assessment indicated that thoracic cavity fluid would be a suitable alternative to blood for the measurement of COHb using the ABL825 FLEX analyser.

Sexual lubricants are used to enable sexual encounters. There are different types of sexual lubricants such as water-based, oil-based, and silicone-based. They come pre-applied to condoms and separately in bottles as personal lubricants. Although sexual lubricants are intended for consensual use, they are also unfortunately used during the commission of sexual assaults. The analysis of sexual lubricants facilitates sexual assault investigations. With the increased usage of condoms in sexual assault cases, the potential of collected DNA evidence in each case is reduced. In the absence of biological evidence, the presence of sexual lubricants after a sexual assault can provide an additional link between a suspect and the crime scene and/or victim. Having the ability to compare known and unknown sexual lubricants may be the only actionable information available for investigators. Current lubricant analysis only classifies samples into lubricant types based on the major component such as glycerol, petrolatum, and polydimethylsiloxane for water-based, oil-based, and silicone-based lubricants respectively. Differentiation within major types has not been explored. Previously, protocols have been developed to detect and categorize personal lubricants using Fourier transform infrared (FTIR) spectroscopy, gas chromatography-mass spectrometry (GC-MS), liquid chromatography mass spectrometry (LC-MS), and pyrolysis GC-MS. FTIR is routinely used as a screening tool to detect peaks of the major lubricant components and the mass spectrometry (MS) techniques are commonly used to confirm the presence of some of the major components, excluding PDMS. This thesis focused on the differentiation of silicone-based personal and condom lubricants because it is a common type of lubricant due to its ability to reduce friction for a longer period of time. Fifty-six (56) silicone personal and condom lubricants were analyzed to identify unique characteristics that can be used to determine individual sub-classes and test those sub-classes. Direct analysis in real time-time of flight mass spectrometry (DART-TOFMS) was utilized because minor and unique molecular ions that could be attributed to different sub-groups can easily be distinguished from the major sample peaks. This is primarily based on the direct mass spectrometry design of the instrumentation that can differentiate minor components from major components that might not be observed using traditional chromatographic separation. The DART source creates molecular ions for individual components in mixed samples under atmospheric conditions in either positive or negative mode. The TOF-MS, which is capable of high resolution and accurate mass analysis, allows more accurate and precise detection of molecular component ions. Additionally, no sample preparation is required to analyze neat samples, which minimizes potential contamination issues. Attenuated total reflectance-FTIR (ATR-FIR) was used to analyze the training set personal lubricants to compare previous methods of analysis to the newly developed DART-TOFMS method of analysis. Principle component analysis (PCA) and cluster analysis were used to identify potential sub-groups and subsequently a classification scheme. Linear discriminant analysis was utilized to conduct leave one out cross validation and to categorize test samples. Eight sub-groups were developed based on the presence and/or absence of PDMS and minor component peaks observed. A classification scheme was developed using the eight sub-groups identified through PCA and cluster analysis. This classification scheme was tested using LDA to classify blind samples. One group includes a scented personal lubricant. Another group includes flavored condom lubricants. The other groups were developed based on the relative intensity of PDMS peaks and minor component peaks. Variation of the intensity of PDMS peaks between and within samples of different lot numbers causes some misclassification of samples. This classification scheme also doesn't take into account real-world factors such as dilution and biodegradation. Although further research is required to create a more stable classification scheme, the identified sub-groups are a good foundation for the creation of a lubricant database and finalized classification scheme.