Ancient human dental calculus metadata collection and sampling strategies: Recommendations for best practices

OBJECTIVES

Ancient human dental calculus is a unique, nonrenewable biological resource encapsulating key information about the diets, lifestyles, and health conditions of past individuals and populations. With compounding calls its destructive analysis, it is imperative to refine the ways in which the scientific community documents, samples, and analyzes dental calculus so as to maximize its utility to the public and scientific community.

MATERIALS AND METHODS

Our research team conducted an IRB-approved survey of dental calculus researchers with diverse academic backgrounds, research foci, and analytical specializations.

RESULTS

This survey reveals variation in how metadata is collected and utilized across different subdisciplines and highlights how these differences have profound implications for dental calculus research. Moreover, the survey suggests the need for more communication between those who excavate, curate, and analyze biomolecular data from dental calculus.

DISCUSSION

Challenges in cross-disciplinary communication limit researchers' ability to effectively utilize samples in rigorous and reproducible ways. Specifically, the lack of standardized skeletal and dental metadata recording and contamination avoidance procedures hinder downstream anthropological applications, as well as the pursuit of broader paleodemographic and paleoepidemiological inquiries that rely on more complete information about the individuals sampled. To provide a path forward toward more ethical and standardized dental calculus sampling and documentation approaches, we review the current methods by which skeletal and dental metadata are recorded. We also describe trends in sampling and contamination-control approaches. Finally, we use that information to suggest new guidelines for ancient dental calculus documentation and sampling strategies that will improve research practices in the future.

Examining the release of synthetic microfibres to the environment via two major pathways: Atmospheric deposition and treated wastewater effluent

Research on the discharge of synthetic microfibres to aquatic environments has typically focused on laundering, where fibres can be discharged via wastewater effluent. However emerging research suggests that microfibres generated during the wear of textiles in normal use could present a major, additional, pathway for microfibre pollution to the environment. This study aimed to quantify and compare the quantities of microfibre entering the marine environment via both these pathways; wastewater discharge and atmospheric deposition. Areas of high and low population density were also evaluated. Samples were collected in and around two British cities (Bristol and Plymouth) both of which are located on tidal waters. Fibres originating from the atmosphere were deposited at an average rate of 81.6 fibres m² d^-1 across urban and rural areas. Treated wastewater effluent contained on an average 0.03 synthetic fibres L^-1. Based on our results we predict ~20,000-500,000 microfibres could be discharged per day from the Wastewater Treatment Plants studied. When the two pathways were compared. Atmospheric deposition of synthetic microfibres appeared the dominant pathway, releasing fibres at a rate several orders of magnitude greater than via treated wastewater effluent. Potential options to reduce the release of microfibres to the environment are discussed and we conclude that intervention at the textile design stage presents the most effective approach. In order to guide policy intervention to inform the Plastics Treaty UNEA 5.2, future work should focus on understanding which permutations of textile design have the greatest influence fibre shedding, during both everyday use and laundering.

Effectiveness of decontamination protocols when analyzing ancient DNA preserved in dental calculus

Ancient DNA analysis of human oral microbial communities within calcified dental plaque (calculus) has revealed key insights into human health, paleodemography, and cultural behaviors. However, contamination imposes a major concern for paleomicrobiological samples due to their low endogenous DNA content and exposure to environmental sources, calling into question some published results. Decontamination protocols (e.g. an ethylenediaminetetraacetic acid (EDTA) pre-digestion or ultraviolet radiation (UV) and 5% sodium hypochlorite immersion treatments) aim to minimize the exogenous content of the outer surface of ancient calculus samples prior to DNA extraction. While these protocols are widely used, no one has systematically compared them in ancient dental calculus. Here, we compare untreated dental calculus samples to samples from the same site treated with four previously published decontamination protocols: a UV only treatment; a 5% sodium hypochlorite immersion treatment; a pre-digestion in EDTA treatment; and a combined UV irradiation and 5% sodium hypochlorite immersion treatment. We examine their efficacy in ancient oral microbiota recovery by applying 16S rRNA gene amplicon and shotgun sequencing, identifying ancient oral microbiota, as well as soil and skin contaminant species. Overall, the EDTA pre-digestion and a combined UV irradiation and 5% sodium hypochlorite immersion treatment were both effective at reducing the proportion of environmental taxa and increasing oral taxa in comparison to untreated samples. This research highlights the importance of using decontamination procedures during ancient DNA analysis of dental calculus to reduce contaminant DNA.

Atmospheric microplastic deposition in an urban environment and an evaluation of transport

Microplastics are a global environmental issue contaminating aquatic and terrestrial environments. They have been reported in atmospheric deposition, and indoor and outdoor air, raising concern for public health due to the potential for exposure. Moreover, the atmosphere presents a new vehicle for microplastics to enter the wider environment, yet our knowledge of the quantities, characteristics and pathways of airborne microplastics is sparse. Here we show microplastics in atmospheric deposition in a major population centre, central London. Microplastics were found in all samples, with deposition rates ranging from 575 to 1008 microplastics/m²/d. They were found in various shapes, of which fibrous microplastics accounted for the great majority (92%). Across all samples, 15 different petrochemical-based polymers were identified. Bivariate polar plots indicated dependency on wind, with different source areas for fibrous and non-fibrous airborne microplastics. This is the first evidence of airborne microplastics in London and confirms the need to include airborne pathways when consolidating microplastic impacts on the wider environment and human health.

Luminance and Contrast Performance of Liquid Crystal Displays for Mammographic Applications

Liquid crystal displays (LCDs) are gradually replacing cathode-ray tubes (CRTs) as the primary means of electronic display of digital radiographs. The transition from CRT to LCD is fueled by advantages of the LCD technology such as enhanced maximum luminance and smaller form factor. This transition is expected to extend to digital mammography as well. The purpose of this study was to report the on-axis luminance and contrast performance of five medical-grade LCDs in terms of compliance with the DICOM grayscale display function (GSDF) and AAPM TG18 guidelines. The display devices included two 3 Mpx monochrome LCDs (Planar Dome C3, and NDS 20.8 “Nova), two 5 Mpx monochrome LCDs (NDS 21.3” Nova, and Totoku ME511L), and one 9 Mpx color LCD (IBM T221). The on-axis luminance values were measured at all 8-bit driving levels using the TG18-LN test patterns and a baffled luminance meter and the results averaged. The luminance data were analyzed according to the AAPM TG18 methodology. The measured Lmin, Lmax, mean ΔJND/Δ p, and maximum local deviation in ΔJND/Δ p from GSDF, κ256, ranged within 0.43–0.87 cd/m2, 263–715 cd/m2, 2.15–2.72, and 0.79–1.46 intervals, respectively. While the values varied notably between different devices, all devices conformed to the TG18 criteria for primary class displays in terms of on-axis luminance response, and thus judged suitable for mammographic applications from on-axis luminance standpoint. Notwithstanding the findings, other factors such as matrix size, angular response, and color functionality should further be taken into consideration.

Longitudinal study of prevalence of Campylobacter jejuni and Campylobacter coli from turkeys and swine grown in close proximity

Eastern North Carolina is a major contributor to both turkey and swine production in the United States. In this region, turkeys and swine are frequently grown in close proximity and by common growers. To further characterize colonization of turkeys and swine with Campylobacter in such a setting, we investigated the prevalence of thermophilic campylobacters in eight paired operations involving turkey farms in close proximity to finishing swine farms. All 15 surveyed flocks and 15 herds were Campylobacter positive at one or more sampling times. Campylobacter was isolated from 1,310 (87%) of the 1,512 turkey samples and 1,116 (77%) of the 1,448 swine samples. Most (> 99%) campylobacters from swine samples were Campylobacter coli, found in 59 to 97% of the samples from the different herds. Both Campylobacterjejuni and C. coli were recovered from the turkey flocks (overall prevalences of 52 and 35%, respectively). Prevalence among flocks ranged from 31 to 86% for C. jejuni and 0 to 67% for C. coli, and both species were recovered from most flocks. Relative prevalence of C. coli was higher in young birds (brooders), whereas C. jejuni predominated in grow-out birds (P < 0.0001). The prevalence of C. coli in a swine herd was generally not a good predictor for prevalence of this species in the corresponding turkey flock. These findings indicate that even though turkeys and swine grown in proximity to each other were commonly colonized with thermophilic campylobacters, the relative prevalences of C. jejuni and C. coli appear to be host associated.

Disruption of ETV6 in intron 2 results in upregulatory and insertional events in childhood acute lymphoblastic leukaemia

We describe four cases of childhood B-cell progenitor acute lymphoblastic leukaemia (BCP-ALL) and one of T-cell (T-ALL) with unexpected numbers of interphase signals for ETV6 with an ETV6-RUNX1 fusion probe. Three fusion negative cases each had a telomeric part of 12p terminating within intron 2 of ETV6, attached to sequences from 5q, 7p and 7q, respectively. Two fusion positive cases, with partial insertions of ETV6 into chromosome 21, also had a breakpoint in intron 2. Fluorescence in situ hybridisation (FISH), array comparative genomic hybridization (aCGH) and Molecular Copy-Number Counting (MCC) results were concordant for the T-cell case. Sequences downstream of TLX3 on chromosome 5 were deleted, leaving the intact gene closely apposed to the first two exons of ETV6 and its upstream promoter. qRT-PCR showed a significant upregulation of TLX3. In this study we provide the first incontrovertible evidence that the upstream promoter of ETV6 attached to the first two exons of the gene was responsible for the ectopic expression of a proto-oncogene that became abnormally close as the result of deletion and translocation. We have also shown breakpoints in intron 2 of ETV6 in two cases of insertion with ETV6-RUNX1 fusion.

Clonal population structure and specific genotypes of multidrug-resistant Campylobacter coli from Turkeys

Commercial turkey flocks in North Carolina have been found to be colonized frequently with Campylobacter coli strains that are resistant to several antimicrobials (tetracycline, streptomycin, erythromycin, kanamycin, and ciprofloxacin/nalidixic acid). Such strains have been designated multidrug resistant (MDR). However, the population structure of MDR C. coli from turkeys remains poorly characterized. In this study, an analysis of multilocus sequence typing (MLST)-based sequence types (STs) of 59 MDR strains from turkeys revealed that the majority of these strains corresponded to one of 14 different STs, with three STs accounting for 41 (69%) of the strains. The major STs were turkey specific, and most (87%) of the strains with these STs were resistant to the entire panel of antibiotics mentioned above. Some (13%) of the strains with these STs were susceptible to just one or two of the antibiotics in this panel. Further subtyping using fla typing and pulsed-field gel electrophoresis with SmaI and KpnI revealed that the major MDR STs corresponded to strains of related but distinct subtypes, providing evidence for genomic diversification within these STs. These findings suggest that MDR strains of C. coli from turkeys have a clonal population structure characterized by the presence of a relatively small number of clonal groups that appear to be disseminated in the turkey production system. In addition, the observed correlation between STs and the MDR profiles of the microbes indicates that MLST-based typing holds potential for source-tracking applications specific to the animal source (turkeys) and the antimicrobial resistance profile (MDR status) of C. coli.

Sexual diergism in rat hypothalamic-pituitary-adrenal axis responses to cholinergic stimulation and antagonism

The hypothalamic-pituitary-adrenal (HPA) axis has differential physiological activity in male and female animals (sexual diergism). Central cholinergic systems stimulate this endocrine axis. In the present study we investigated muscarinic and nicotinic cholinergic influences on HPA axis activity in male and female rats by pretreatment with selective cholinergic receptor antagonists followed by stimulation with physostigmine (PHYSO), an acetylcholinesterase inhibitor. Hormonal measures were plasma arginine vasopressin (AVP), adrenocorticotropic hormone (ACTH), and corticosterone (CORT). Male rats had significantly greater AVP and ACTH responses to PHYSO alone than did females. Scopolamine (SCOP) enhanced the AVP response to PHYSO to a greater extent in males than in females. In contrast, mecamylamine (MEC) enhanced the AVP response in females but decreased it in males. SCOP potentiated, and MEC inhibited, the stimulatory effect of PHYSO on ACTH in both sexes, but SCOP potentiation was greater in males, and MEC inhibition was greater in females. Absolute CORT increases following PHYSO were greater in females, but percent increases over baseline were greater in males. Similar to their effects on ACTH responses, MEC attenuated, and SCOP enhanced, CORT responses to PHYSO. These results suggest that cholinergic receptor subtypes may influence HPA axis activity differentially in male and female rats.

New adjunctive therapy for ischemic syndromes

Because anticoagulant and GP IIb/IIIa inhibitors reduce mortality, myocardial ischemia, AMI, and reintervention, these agents are now becoming the standard of care for patients with USA and NQWMI. Unanswered questions remain about the best treatment regimen, appropriate dosing, long-term benefit, and cost-effectiveness of these agents, however, and many additional trials are ongoing or planned. As nurses administer these drugs, assess the patients' responses to therapy, and educate patients and families about these agents, they contribute to recent advances in preventing ischemic heart disease.

The primary care practice in transition: strategies for managing the evolution from fee for service to prepaid care

Changing old thought patterns, habits and preconceived notions is not always easy in today's ever-changing world of health care practice and administration. This paper offers advice on solutions pertaining to implementation of prepaid care programs.

Drug diffusion and binding in ionizable interpenetrating networks from poly(vinyl alcohol) and poly(acrylic acid)

Hydrogels of poly(vinyl alcohol) (PVA), poly(acrylic acid) (PAA), and their interpenetrating networks (IPNs) were prepared using glutaraldehyde and ethylene glycol dimethacrylate as crosslinking agents. The hydrogels were characterized by measuring their equilibrium polymer volume fraction, equilibrium swelling ratio, and mesh size. Drug and protein diffusion through these hydrogels were studied. Solutes studied included theophylline, vitamin B12 and myoglobin. The ratio of PVA and PAA in the IPNs was varied to study the effect of ionic polymer content on the polymer/drug interactions and on the drug diffusion rate. Attenuated total reflectance-Fourier transform infrared (ATR-FTIR) spectroscopy was used to analyze the polymer/drug binding interactions. It was concluded that drug diffusion may be impeded by associated drug binding, especially in IPN hydrogels containing high amounts of PAA.

Collective coping with stress: group reactions to fear, anxiety, and ambiguity

A review of studies examining the fear-affiliation relationship revealed that none had ever observed groups in interaction while awaiting a fearful event. It was predicted that such groups would, consistent with individual member's previously studied affiliative preferences, spend more time interacting in the service of social comparison needs than would groups facing anxiety or ambiguity. This prediction was strongly supported, and in addition, it was found, as expected, that groups in the fear condition developed a relatively high degree of cohesiveness as measured by intragroup attraction ratings. The implication of these results for the interpretation of the functional relationship between stress and cohesiveness was discussed.

Collective coping with stress: Group reactions to fear, anxiety, and ambiguity

A review of studies examining the fear-affiliation relationship revealed that none had ever observed groups in interaction while awaiting a fearful event. It was predicted that such groups would, consistent with individual member's previously studied affiliative preferences, spend more time interacting in the service of social comparison needs than would groups facing anxiety or ambiguity. This prediction was strongly supported, and in addition, it was found, as expected, that groups in the fear condition developed a relatively high degree of cohesiveness as measured by intragroup attraction ratings. The implication of these results for the interpretation of the functional relationship between stress and cohesiveness was discussed.