Towards Responsible Destructive Analysis: A guide to the recording of archaeological tooth samples with laboratory process visualisation

Objectives: The aim of this study is to evaluate the internal consistency of sex estimation using metric (long bone length) and morphological (os coxae) methodologies from different bones and across different archaeological populations from different regions. Materials and Methods: Sex was estimated using characteristics of the pelvis and compared with sex estimations using long bone length. Portuguese (659 females; 906 males) and English (141 females; 277 males) archaeological collections were analysed in this study. A set of long bone length functions were developed using one of the archaeological collections (531 females; 600 males) and its coincidence with sex estimated from the pelvis was compared to the coincidence between the pelvis and long bone length sex estimations using functions developed from contemporary collections. Intra- and inter-observer errors were calculated, as well as the sexual dimorphism index for each bone and osteological collection. Results: The accuracy of the developed functions and the other methods tested is highly variable, ranging between 25 and 100%. The accuracy of the standard forensic methods varied between collections and analysed bones. Discussion: This study reinforces that long bone length is highly population-specific, even between samples of close chronology and geography. Metric methods are good options to strengthen the sex estimations, but they need to be carefully chosen and always report the estimated probability of being male or female in either forensic or archaeological analysis.

Forensic anthropologists are often tasked with determining skeletal age‐at‐death to assist law enforcement in identifying skeletal remains. If the remains are skeletally mature, degenerative changes in articular surfaces are typically assessed to determine age. If the skeleton is immature tooth eruption, dental development, and/or epiphyseal union are used to estimate age. Forensic anthropologists derive an age‐at‐death estimate by comparing our assessment of skeletal age indicator(s) to standards derived from skeletal collections of known age‐at‐death. Prior to the establishment of modern skeletal collections such at the William M. Bass Donated Collection at the University of Tennessee, anthropologists developed age estimation techniques using late 19th and early 20th century anatomical collections (e.g. the Hamann‐Todd Osteology Collection at the Cleveland Museum of Natural History and Terry Anatomical Collection at the Smithsonian Institution). However, research on Bass Collection skeletons has demonstrated remarkable changes in skeletal morphology in modern Americans compared to early 19th century birth cohorts, illustrating that standards derived from modern populations are imperative for forensic casework; anatomical collections and archaeological samples are not appropriate reference samples. Age estimation in forensic casework is further complicated by the age distribution of the forensic case population. Forensic cases often involve accidental deaths, homicides, and suicides of individuals from a younger age demographic than natural deaths which comprise many of the reference samples used to derive age estimates. This difference between the age distribution of the reference sample and that of the “target” population leads to ‘age mimicry’, whereby skeletal age‐at‐death may be under‐estimated. This presentation will highlight research that illustrates the impact of secular change and reference sample composition on the accuracy and precision of forensic skeletal age‐at‐death estimation. The documentation of significant changes in skeletal morphology illustrates what evolutionary biologists already know—phenotype is dynamic, not static. These short‐term evolutionary changes in skeletal form have implications for anatomical research beyond the hard tissues.Support or Funding InformationNational Institute of JusticeThis abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal.

In the grave environment, microorganisms are major ecological participants in the successional decomposition of vertebrates and could infiltrate the skeleton/skeletal material during taphonomic processes. The diversity of archaeological skeleton‐associated microbial assemblages and the impact of various factors are poorly understood. This study aimed to evaluate the taxonomic microbial composition of archaeological human bone and teeth samples from the 7th to 11th centuries AD from two burial sites in Latvia. Samples were analysed by a shotgun metagenomics‐based approach. The results showed a strong presence of the environmental DNA in the samples, and variability in microbial community structure between individual samples. Differences in microbial composition were observed between bone and tooth samples, as well as between different burial sites. Furthermore, the presence of endogenous ancient DNA (aDNA) in tooth samples was detected. Overall, compositions of microbial communities associated with archaeological human remains in Latvia dated 7–11th century AD were influenced by the sample type and burial location. These findings indicate that, while the content of historical DNA in archaeological samples is low, the comparison of archaeological skeleton‐associated microbial assemblages across time and space, along with aDNA damage profile analysis, is important and could help to reveal putative ancient microorganisms.

BackgroundDespite the potential population-level impact of a health-promoting schools approach, schools face challenges in implementation, indicating a gap between school health research and practice. Knowledge exchange provides an opportunity to reduce this gap; however, there has been limited evaluation of these initiatives. This research explored researchers’ and knowledge users’ perceptions of outcomes associated with a knowledge exchange initiative within COMPASS, a longitudinal study of Canadian secondary students and schools. Schools received annual tailored summaries of their students’ health behaviours and suggestions for action and were linked with knowledge brokers to support them in taking action to improve student health.MethodsQualitative semi-structured interviews were conducted with COMPASS researchers (n = 13), school staff (n = 13), and public health stakeholders (n = 4) to explore their experiences with COMPASS knowledge exchange. Key issues included how knowledge users used school-specific findings, perceived outcomes of knowledge exchange, and suggestions for change.ResultsOutcomes for both knowledge users and researchers were identified; interestingly, knowledge users attributed more outcomes to using school-specific findings than knowledge brokering. School and public health participants indicated school-specific findings informed their programming and planning. Importantly, knowledge exchange provided a platform for partnerships between researchers, schools, and public health units. Knowledge brokering allowed researchers to gain feedback from knowledge users to enhance the study and a better understanding of the school environment. Interestingly, COMPASS knowledge exchange outcomes aligned with Samdal and Rowling’s eight theory-driven implementation components for health-promoting schools. Hence, knowledge exchange may provide a mechanism to help schools implement a health-promoting schools approach.ConclusionsThis research contributes to the limited literature regarding outcomes of knowledge brokering in public health and knowledge exchange in school health research. However, since not all schools engaged in knowledge brokering, and not all schools that engaged discussed these outcomes, further research is needed to determine the amount of engagement required for change and examine the process of COMPASS knowledge brokering to consider how to increase school engagement.

Identification of preserved fatty acids in archaeological floor sediments from prehistoric sites at Ban Non Wat and Nong Hua Raet in northeast Thailand using gas chromatography

Public health practice and efforts to improve the social determinants of health operate within a climate characterised by multiple and intersecting crises. This includes the Covid-19 pandemic as well as more protracted crises such as climate change and persistent social inequalities that impact health. We sought to understand and compare how knowledge exchange (KE) processes occur across different crises, and how knowledge on improving social determinants of health can be utilised at times of crisis to reduce health inequalities and strengthen public systems. We conducted a scoping review to understand how KE on improving social determinants of health can occur across different types of crises (e.g. environmental, pandemics, humanitarian). Relevant studies were identified through electronic searching of Medline, EMBASE, Global Health, Scopus and Web of Science databases. We identified 86 studies for inclusion in the review. Most studies concerned pandemic or environmental crises. Fewer studies explored KE during technical (e.g. nuclear), terror-related or humanitarian crises. This may reflect a limitation of the searches. Few studies assessed KE as part of longer-term responses to social and economic impacts of crises, with studies more likely to focus on immediate response or early recovery stages. Exchange of research evidence or data with policy or practice contextual knowledge was common but there was variation in the extent that lay (public) knowledge was included as part of KE processes. As ongoing crises continue with significant public health implications, KE processes should appropriately reflect the complexity inherent in crises and foreground health inequalities. Doing so could include the utilisation of systems or complexity-informed methods to support planning and evaluation of KE, a greater focus on KE to support action to address social determinants of health, and the inclusion of a plurality of knowledge-including lived experience-in planning and responding to crises.

BackgroundPublic research organizations and their interactions with industry partners play a crucial role for public health and access to medicines. The development and commercialization of the Human Papillomavirus (HPV) vaccines illustrate how licensing practices of public research organizations can contribute to high prices of the resulting product and affect accessibility to vulnerable populations. Efforts by the international community to improve access to medicines have recognised this issue and promote the public health-sensitive management of research conducted by public research organizations. This paper explores: how medical knowledge is exchanged between public and private actors; what role inventor scientists play in this process; and how they view the implementation of public health-sensitive knowledge exchange strategies.MethodsWe conducted a systematic qualitative literature review on medical knowledge exchange and qualitative interviews with a purposive sample of public sector scientists working on HPV vaccines. We explored the strategies by which knowledge is exchanged across institutional boundaries, how these strategies are negotiated, and the views of scientists regarding public health-sensitive knowledge exchange.ResultsWe included 13 studies in the systematic review and conducted seven semi-structured interviews with high-ranking scientists. The main avenues of public-private medical knowledge exchange were publications, formal transfer of patented knowledge, problem-specific exchanges such as service agreements, informal exchanges and collaborative research. Scientists played a crucial role in these processes but appeared to be sceptical of public health-sensitive knowledge exchange strategies, as these were believed to deter corporate interest in the development of new medicines and thus risk the translation of the scientists’ research.ConclusionMedical scientists at public research institutions play a key role in the exchange of knowledge they generate and are concerned about the accessibility of medicines resulting from their research. Their scepticism towards implementing public health-sensitive knowledge management strategies appears to be based on a biased understanding of the costs and risks involved in drug development and a perceived lack of alternatives to private engagement. Scientists could be encouraged to exchange knowledge in a public health-sensitive manner through not-for-profit drug development mechanisms, education on industry engagement, and stronger institutional and legal backing.

Chemical pre-treatment is a common methodological step aimed to remove exogenous materials introduced to archaeological tooth enamel in the burial environment through diagenetic processes. However, some of these methods, involving the use of oxidising reagents such as NaClO, H2O2, as well as weak acids like CH3COOH, have been shown to alter the chemical composition and stable isotope values of enamel. Here, we aim to re-examine the effects of commonly used pre-treatment protocols on bioapatite δ13C and δ18O values, and investigate the relationship between diagenetic alteration and measured isotope values, as indicated by pre-screening using attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy. Modern and archaeological samples were subjected to 10 commonly used pre-treatment protocols that apply NaClO, H2O2 and/or CH3COOH to tooth enamel powders at treatment lengths. Preservation status and diagenetic alteration prior to and after treatment were investigated using ATR-FTIR. δ13C and δ18O values were measured before and after treatment to determine if different wet chemistry protocols induced isotopic shifts. The results show that all pre-treatment protocols imparted shifts in δ13C and δ18O values of up to ± 1.5‰ in both archaeological and modern samples. Most treated samples display increased crystallinity, likely indicating sample recrystallisation. We suggest that these changes indicate the removal of contamination and diagenetic alteration, and also the dissolution and restructuring of enamel carbonate leading to changes in the invivo isotope signal. We discourage the use of H2O2 and NaClO to remove organic matter from samples as it incurs unwanted changes to the enamel structure and carbon and oxygen isotope ratios. We also recommend the use of only short-duration acetic acid treatment protocols to avoid recrystallisation caused by prolonged acid exposure and concomitant unwanted change to invivo isotope values.

The small glass bead technique was developed to assay precious silicic samples for geochemical and archeological analyses. Undersized (12.5 mm diameter) glass beads were prepared for wavelength dispersive X‐ray fluorescence determination of major oxides (Na2O, MgO, Al2O3, SiO2, P2O5, K2O, CaO, TiO2, MnO, and total Fe2O3). Synthetic calibration standards were prepared by compounding chemical reagents (oxides, carbonates, and diphosphate). For reliable calibration, recipe compositions of standard specimens were constructed on the basis of the evenness of plot intervals on a calibration curve. Calibration curves showed good linearity (correlation coefficient: r > 0.998). Analytical results of major oxides in granitic and basaltic rocks, obsidian, and ancient pottery were obtained with good precision (relative standard deviations were the following: <3% for more than 10.0 mass% of analyte, <5% for 1.0–10.0 mass% of analyte, and <15% for 0.1–1.0 mass% of analyte). Lower limits of detection were roughly a sub‐percentage of analyte in an unprepared sample: 0.3 mass% for Na2O, 1.0 mass% for SiO2, 0.01 mass% for MnO, and so on. The present preparation reduced the following analytical scales: (1) amount of sample from 400 mg to 11 mg (97% cutting out), (2) amount of Li2B4O7 as an alkali flux from 4000 mg to 396 mg (90% cutting out), and (3) weight of platinum crucible from 80 g to 12.5 g (84% cutting out). This small‐scale preparation might enable us to conduct destructive pretreatment of valuable and limited silicic samples such as archeological ceramics and stone tools, geochemical minerals in rock, and sediments and sand. Copyright © 2012 John Wiley & Sons, Ltd.

Tooth cementum annulation: Confounding difficulties remain when inferring life history parameters from archeological tooth samples

Characterization of building materials by means of spectral remote sensing: The example of Carcassonne's defensive wall (Aude, France)

Recent advances in high-throughput molecular analyses of collagen peptides, especially ZooMS (Zooarchaeology by Mass Spectrometry), have permitted breakthroughs in the analysis of archaeological material that is highly fragmented, a factor that hinders morphological identification. Despite these advances, the challenge of successfully analysing archaeological samples with poorer collagen preservation persists. This paper examines the potential of two mass analysers, TOF (Time of Flight) and FTICR (Fourier-transform ion cyclotron resonance), and addresses how they can be used to optimise the ZooMS workflow. Type 1 collagen (COL1) was extracted from 89 archaeological bones from the French Palaeolithic site of Le Piage (37-34 ka cal BP). Three ZooMS extraction protocols were applied, an acid-free buffer method (AmBic), offering rapid and less destructive analysis, and two methods of acid demineralisation (HCl and TFA) that provide higher peptide resolution. After analysing the specimens with MALDI-TOF and MALDI-FTICR, we used bottom-up and PRM (Parallel Reaction Monitoring) LC-MS/MS, and MALDI-CASI-FTICR (Continuous Accumulation of Selected Ions) to verify 26 ambiguous identifications. Overall, 99% of the samples could be identified to at least family level, with the rate of identification and precision varying by method. Despite challenges in detecting specific biomarkers with MALDI-FTICR-especially peptide A (COL1ɑ2 978-990), which tends to be unstable and poorly ionised-the high resolution of this method allowed the successful identification of more degraded specimens, including burnt bones. Our work highlights the robustness of traditional MALDI-TOF ZooMS for retrieving collagen and for providing taxonomic identifications with low failure rates, features that are critical when processing large numbers of samples. MALDI-FTICR shows better potential when working with precious samples or degraded collagen. This study advances the analytical detection of peptides by optimising the ZooMS workflow and by tailoring it to specific archaeological contexts showing variation in degree of preservation.

EMBO Reports (2018) e47143 Basic and translational biomedical research explores biological and pathophysiological mechanisms with the aim of developing novel therapies, preventive measures, and diagnostics to improve human health. Disappointingly, however, most new therapies fail when they are tested in clinical trials. Although the causes of this “translational attrition” are diverse and often rooted in the complexity of the underlying biology, it has also become clear that methodology is a major issue. The “translational roadblock”, along with what has been dubbed a “reproducibility crisis” [1], has fueled discussions about the reliability and reproducibility of biomedical research in general. There is strong evidence that weaknesses in planning, conducting, analyzing, and (non)reporting of research [2], as well as misidentification or contamination of reagents, biologicals, and cell lines [3], are prevalent factors. Meta‐research has shown that these problems can lead to an inflation of effect size and false positives and consequently decrease the reproducibility and predictiveness of research results. At the same time, the increasing methodological complexity combined with the immense proliferation in research outputs greatly complicates the production and evaluation of reliable evidence. Pressure to publish and hypercompetition for resources further compromise the robustness and rigor of research. Arguably, basic and translational biomedical research has a quality problem. In the 1970s, US cars had major quality problems. By comparison, Japanese cars were much more reliable. The introduction of rigorous quality management in the production process was largely credited for this competitive advantage, which helped the Japanese car industry to dominate the market for decades to come. By now, most industries, including US car manufacturers, the health and pharmaceutical industries as well as clinical medicine, have established sophisticated quality management systems (QMS) on which they spend several percent of their budget. Clearly, these investments pay off as companies …

Exploring DNA preservation and taxonomic diversity in postmedieval human tooth samples in Latvia

Access to public knowledge is a prerequisite for the good functioning of developed economies. Universities strive and are also requested to contribute to this knowledge both locally and internationally. Traditional studies on the geography of knowledge flows have identified a localisation effect; however, these studies do not use the country as the unit of observation and hence do not explore national patterns. In this paper, we hypothesise that the localisation of university knowledge flows is directly related to share of firm expenditure on research and development. To test this hypothesis, we use references to universities in patent documents as indicators based on a data set of around 20,000 university references, for 37 countries in the period 1990–2007, resulting in panels of around 300–500 observations. We build indicators for the university knowledge flows both inside and outside the applicant country, which we explain as a function of some proxies for national size and research structure based on econometric estimations. We draw some conclusions as to the importance of national business scientific strength for fostering increased domestic university knowledge flows.