exploring patterns of morphological integration in the crania of papio hamadryas ursinus and homo sapiens

A Theses submitted to the faculty of science, university of the Witwatersrand, Johannesburg, in fulfilment of the requirements for the degree of doctor of philosophyMorphological integration is the pattern of correlation or covariation among parts due to genetic, developmental and functional processes, and is essential for the viability of an organism. Integration among processes is not uniform but forms distinct modules allowing for their independent evolvability and is thus central to the study of biological evolution. The incongruence between phylogenies estimated using the genotype and the cranial morphology in both the Papionini primates as well as the Hominidae possibly result from the disregard of character integration. Regarding the degree of morphological integration humans display extremely low levels of integration among the primates, while the baboon possesses extremely high levels. This thesis set out to address three broad aims regarding integration of the baboon and human cranium; namely 1) to study the effect of allometry on measures of integration, and when allometry and sexual dimorphism had been accounted for, 2) to assess the patterning of morphological integration into morphological modules; and finally, 3) to assess differences in the pattern of covariation between the cranial base, cranial vault and facial skeleton in humans and baboons. Although allometric growth is divided into neural and somatic, the findings suggest that the effect of allometry conceals more detailed patterns of morphological integration likely resulting from genetic and developmental processes, and should therefore be accounted for in studies of morphological integration. It is unlikely that allometry among cranial regions constrains evolutionary diversity, but rather offers a path of least resistance. The second aim offered up novel methods of exploring the pattern of morphological covariation using clustering and network methods that supported current hypotheses and proposed that the oral and basicranial regions are comprised of additional modules; however, rigorous scientific scrutiny is required for its support. iv The third aim involved the analysis of integration between the cranial base, cranial vault, and facial skeleton. The results supported the proposal that humans and nonhuman primates share a similar pattern of integration likely reflecting shared developmental processes among the primates, but with key differences probably relating to functional demands. Integration between these three cranial regions primarily involve their relative positioning and proportions. The broad pattern of integration likely reflects the role of the cranium as the supporting framework around the organs and functional capsules, the “real” modules, which accommodate one another epigenetically as they develop. The recognition of both independent modules and their pervasive integration are important and depend primarily on the nature of the investigation.GR201

Visualising trends in dentition to lip mouth morphology using geometric morphometrics

Linear measurements taken from bony landmarks are often utilised in facial approximation (FA) to estimate and plan the placement of overlying soft tissue features. This process similarly guides craniofacial superimposition (CFS) practices. Knowledge of how hard and soft tissue features spatially relate around the mouth region is, however, limited. Geometric morphometric techniques have thus been used to investigate size and shape variation in dentition-to-lip mouth morphology in a South African population. Twenty landmarks (twelve dentition, eight lips) were digitised, using cone-beam CT images of the anterior craniofacial complex in a Frankfurt/Frankfort position, for 147 individuals aged between 20 and 75 years. Principal Component Analysis and Canonical Variate Analysis established that much shape variation exists. A two-way ANOVA identified significant (p < 0.0001) population and sex variation with mouth shape. Black individuals presented with thicker lips, with the oral fissure aligning closely to the dental occlusion. Oral fissure position for white individuals corresponded to the inferior one-quarter (females) or one-sixth (males) of the maxillary central incisor crowns. Males presented larger dimensions than females, but females had a greater lip-to-teeth height ratio than their male counterparts. A pooled within-group regression analysis assessed the effect of age on the dentition and lips and found that it had a significant (p < 0.0001) impact on mouth shape. Ageing was associated with a reduced lip and teeth height, increased mouth width, and a lowered oral fissure and cheilion placement. The generated mean shape data, with metric guides, offer a visual and numerical guide that builds on existing FA and CFS standards, enhancing our understanding of hard and soft tissue relationships

Methods for enhancing the reproducibility of biomedical research findings using electronic health records.

BACKGROUND: The ability of external investigators to reproduce published scientific findings is critical for the evaluation and validation of biomedical research by the wider community. However, a substantial proportion of health research using electronic health records (EHR), data collected and generated during clinical care, is potentially not reproducible mainly due to the fact that the implementation details of most data preprocessing, cleaning, phenotyping and analysis approaches are not systematically made available or shared. With the complexity, volume and variety of electronic health record data sources made available for research steadily increasing, it is critical to ensure that scientific findings from EHR data are reproducible and replicable by researchers. Reporting guidelines, such as RECORD and STROBE, have set a solid foundation by recommending a series of items for researchers to include in their research outputs. Researchers however often lack the technical tools and methodological approaches to actuate such recommendations in an efficient and sustainable manner. RESULTS: In this paper, we review and propose a series of methods and tools utilized in adjunct scientific disciplines that can be used to enhance the reproducibility of research using electronic health records and enable researchers to report analytical approaches in a transparent manner. Specifically, we discuss the adoption of scientific software engineering principles and best-practices such as test-driven development, source code revision control systems, literate programming and the standardization and re-use of common data management and analytical approaches. CONCLUSION: The adoption of such approaches will enable scientists to systematically document and share EHR analytical workflows and increase the reproducibility of biomedical research using such complex data sources

Titan's cold case files - Outstanding questions after Cassini-Huygens

Abstract The entry of the Cassini-Huygens spacecraft into orbit around Saturn in July 2004 marked the start of a golden era in the exploration of Titan, Saturn's giant moon. During the Prime Mission (2004–2008), ground-breaking discoveries were made by the Cassini orbiter including the equatorial dune fields (flyby T3, 2005), northern lakes and seas (T16, 2006), and the large positive and negative ions (T16 & T18, 2006), to name a few. In 2005 the Huygens probe descended through Titan's atmosphere, taking the first close-up pictures of the surface, including large networks of dendritic channels leading to a dried-up seabed, and also obtaining detailed profiles of temperature and gas composition during the atmospheric descent. The discoveries continued through the Equinox Mission (2008–2010) and Solstice Mission (2010–2017) totaling 127 targeted flybys of Titan in all. Now at the end of the mission, we are able to look back on the high-level scientific questions from the start of the mission, and assess the progress that has been made towards answering these. At the same time, new scientific questions regarding Titan have emerged from the discoveries that have been made. In this paper we review a cross-section of important scientific questions that remain partially or completely unanswered, ranging from Titan's deep interior to the exosphere. Our intention is to help formulate the science goals for the next generation of planetary missions to Titan, and to stimulate new experimental, observational and theoretical investigations in the interim

Immune boosting by B.1.1.529 (Omicron) depends on previous SARS-CoV-2 exposure

The Omicron, or Pango lineage B.1.1.529, variant of SARS-CoV-2 carries multiple spike mutations with high transmissibility and partial neutralizing antibody (nAb) escape. Vaccinated individuals show protection from severe disease, often attributed to primed cellular immunity. We investigated T and B cell immunity against B.1.1.529 in triple mRNA vaccinated healthcare workers (HCW) with different SARS-CoV-2 infection histories. B and T cell immunity against previous variants of concern was enhanced in triple vaccinated individuals, but magnitude of T and B cell responses against B.1.1.529 spike protein was reduced. Immune imprinting by infection with the earlier B.1.1.7 (Alpha) variant resulted in less durable binding antibody against B.1.1.529. Previously infection-naïve HCW who became infected during the B.1.1.529 wave showed enhanced immunity against earlier variants, but reduced nAb potency and T cell responses against B.1.1.529 itself. Previous Wuhan Hu-1 infection abrogated T cell recognition and any enhanced cross-reactive neutralizing immunity on infection with B.1.1.529

Quantitative, multiplexed, targeted proteomics for ascertaining variant specific SARS-CoV-2 antibody response

Determining the protection an individual has to severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants of concern (VoCs) is crucial for future immune surveillance, vaccine development, and understanding of the changing immune response. We devised an informative assay to current ELISA-based serology using multiplexed, baited, targeted proteomics for direct detection of multiple proteins in the SARS-CoV-2 anti-spike antibody immunocomplex. Serum from individuals collected after infection or first- and second-dose vaccination demonstrates this approach and shows concordance with existing serology and neutralization. Our assays show altered responses of both immunoglobulins and complement to the Alpha (B.1.1.7), Beta (B.1.351), and Delta (B.1.617.1) VoCs and a reduced response to Omicron (B1.1.1529). We were able to identify individuals who had prior infection, and observed that C1q is closely associated with IgG1 (r > 0.82) and may better reflect neutralization to VoCs. Analyzing additional immunoproteins beyond immunoglobulin (Ig) G, provides important information about our understanding of the response to infection and vaccination

Visualising trends in dentition to lip mouth morphology using geometric morphometrics.

Linear measurements taken from bony landmarks are often utilised in facial approximation (FA) to estimate and plan the placement of overlying soft tissue features. This process similarly guides craniofacial superimposition (CFS) practices. Knowledge of how hard and soft tissue features spatially relate around the mouth region is, however, limited. Geometric morphometric techniques have thus been used to investigate size and shape variation in dentition-to-lip mouth morphology in a South African population. Twenty landmarks (twelve dentition, eight lips) were digitised, using cone-beam CT images of the anterior craniofacial complex in a Frankfurt/Frankfort position, for 147 individuals aged between 20 and 75 years. Principal Component Analysis and Canonical Variate Analysis established that much shape variation exists. A two-way ANOVA identified significant (p < 0.0001) population and sex variation with mouth shape. Black individuals presented with thicker lips, with the oral fissure aligning closely to the dental occlusion. Oral fissure position for white individuals corresponded to the inferior one-quarter (females) or one-sixth (males) of the maxillary central incisor crowns. Males presented larger dimensions than females, but females had a greater lip-to-teeth height ratio than their male counterparts. A pooled within-group regression analysis assessed the effect of age on the dentition and lips and found that it had a significant (p < 0.0001) impact on mouth shape. Ageing was associated with a reduced lip and teeth height, increased mouth width, and a lowered oral fissure and cheilion placement. The generated mean shape data, with metric guides, offer a visual and numerical guide that builds on existing FA and CFS standards, enhancing our understanding of hard and soft tissue relationships

Pharmaceutical Waste Disposal: Current Practices in Tirana, Albania

Managing pharmaceutical waste effectively can reduce risks to the environment and public health. - In collaboration with the EDEN Center, an Albanian environmental NGO, our study assessed and analyzed the current pharmaceutical waste management system in Tirana. We interviewed ten percent of the over 730 pharmacies in Tirana as well as other stakeholders to identify the current practices, challenges, and opportunities for improvement. Our study concluded that pharmacists would benefit from more information regarding laws, treatment companies, and their environmental impact. We also recommend additional incentives and regulations be implemented by the government, and a further study be conducted to expand upon our finding