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Oral swab analysis (OSA) has been shown to detect Mycobacterium tuberculosis (MTB) DNA in patients with pulmonary tuberculosis (TB). In previous analyses, qPCR testing of swab samples collected from tongue dorsa was up to 93% sensitive relative to sputum GeneXpert, when 2 swabs per patient were tested. The present study modified sample collection methods to increase sample biomass and characterized the viability of bacilli present in tongue swabs. A qPCR targeting conserved bacterial ribosomal rRNA gene (rDNA) sequences was used to quantify bacterial biomass in samples. There was no detectable reduction in total bacterial rDNA signal over the course of 10 rapidly repeated tongue samplings, indicating that swabs collect only a small portion of the biomass available for testing. Copan FLOQSwabs collected ~2-fold more biomass than Puritan PurFlock swabs, the best brand used previously (p = 0.006). FLOQSwabs were therefore evaluated in patients with possible TB in Uganda. A FLOQSwab was collected from each patient upon enrollment (Day 1) and, in a subset of sputum GeneXpert Ultra-positive patients, a second swab was collected on the following day (Day 2). Swabs were tested for MTB DNA by manual IS6110-targeted qPCR. Relative to sputum GeneXpert Ultra, single-swab sensitivity was 88% (44/50) on Day 1 and 94.4% (17/18) on Day 2. Specificity was 79.2% (42/53). Among an expanded sample of Ugandan patients, 62% (87/141) had colony-forming bacilli in their tongue dorsum swab samples. These findings will help guide further development of this promising TB screening method.

Glendonites (from the precursor of ikaite, CaCO3.6H2O) preferentially precipitate within sediments in cold waters (− 2 to 7°C) via either organotrophic or methanogenic sulphate reduction. Here, we report the first occurrence of possible glendonites associated with the end Permian mass extinction in the earliest Triassic (ca. 252 Million years ago, Ma) subtropical marine carbonates on the Arabian Plateau, Oman. The authigenic carbonate crystals are small (< 2 mm) and precipitated either on bedding planes or reworked within micro cross-laminations, erosional scours, or lags at the base of calcisiltite turbidites, supporting a syn-depositional origin. The observed shape and macrostructure bear resemblance to that of glendonites. SEM and cathodoluminescent imaging reveals unzoned internal structures with three mineral phases: irregular, pseudo-hexagonal and spherical low-Mg calcite crystals (Type 1), low-Mg calcite cement (Type 2), and a later void-filling silica cement (Type 3). The pseudomorphs show δ13C values from − 0.14‰ to − 0.85‰ (mean − 0.43‰; n = 5) that are more positive than the associated micritic matrix, where values range from − 0.92‰ to − 2.39‰ (mean − 1.64‰; n = 7), indicating that oceanic dissolved inorganic carbon (DIC) was the primary carbon source rather than either methane or organic matter. These δ13C values significantly differ from typical δ13C signatures of authentic glendonites, except for Ordovician examples. If these are glendonites, we infer that they could have precipitated due to the unusually elevated alkalinity and pH (> 9) oceanic conditions present in the aftermath of the end-Permian extinction associated with highly disrupted carbon cycle dynamics, possibly accompanied with the upwelling of cold, anoxic oceanic water. [ABSTRACT FROM AUTHOR]

It is well known that the sedimentary rock record is both incomplete and biased by spatially highly variable rates of sedimentation. Without absolute age constraints of sufficient resolution, the temporal correlation of spatially disjunct records is therefore problematic and uncertain, but these effects have rarely been analysed quantitatively using signal processing methods. Here we use a computational process model to illustrate and analyse how spatial and temporal geochemical records can be biased by the inherent, heterogenous processes of marine sedimentation and preservation. This confirms that sedimentary hiatuses can span a substantial proportion of geological time, caused by inherent geological processes. Moreover, even in marine geochemical records that are essentially spatially continuous and complete, the signal is irreversibly disguised in time as lower frequency signals by an aliasing effect. We demonstrate that Nyquist's theorem correctly predicts these biased signatures, proving that aliasing can be caused by cyclical and multiscale relative sea-level changes - a natural sampling effect. Our combined results show that deeper marine records are significantly more likely to provide unaliased environmental signatures. Also, some proxy residence times will be sufficiently long that they average over aliased frequencies, cancelling these in the geochemical record. And field observations of changes in sedimentation rate (such as hiatuses, condensation, or lateral expansion) can be used to infer possible aliasing. Where aliasing by natural sampling occurs, this cannot be undone simply by increasing sample resolution (density): aliasing is caused by an absence of sedimentary record, which by definition cannot be sampled at all. To overcome these issues, we propose that spatially separated aliased records may still be correctly correlated in age, and true geochemical cycles inferred, if a paired-sampling strategy informed by local stratigraphy is adopted. In this, two (or more) closely-spaced samples are analysed at each sampling point instead of only one, after which aliased cycles are inferred from geochemical gradients. [ABSTRACT FROM AUTHOR]

Ethnohistoric accounts indicate that the people of Australia's Channel Country engaged in activities rarely recorded elsewhere on the continent, including food storage, aquaculture and possible cultivation, yet there has been little archaeological fieldwork to verily these accounts. Here, the authors report on a collaborative research project initiated by the Mithaka people addressing this lack of archaeological investigation. The results show that Mithaka Country has a substantial and diverse archaeological record, including numerous large stone quarries, multiple ritual structures and substantial dwellings. Our archaeological research revealed unknown aspects, such as the scale of Mithaka quarrying, which could stimulate re-evaluation of Aboriginal socio-economic systems in parts of ancient Australia. Keywords: Australia, Aboriginal, Mithaka, trade networks, cultivation, villages, stone extraction, Introduction In this article, we report the first results of an ongoing archaeological project in the traditional territory of the Mithaka people, in Australia's Channel Country (Figure 1). Located predominantly [...]

Secret societies, involving restricted and hierarchically organised initiation rituals, are conspicuous in the chronicles of many past and present societies. These rarely leave a substantial written record and yet archaeology can provide vivid insight into past performances, for example in relation to Roman 'mystery cults'. Far less research, however, has focused on Australia and the Pacific Islands. This article presents archaeological evidence for ceremonies practised on Woeydhul Island in the Western Torres Strait, exploring initiation rituals at the cusp of contemporary memory. By doing so, it provides a detailed and long-term history for Torres Strait Islander secret societies and ritual activities involving dugong bone mounds, stone arrangements and worked stingray spines. Keywords: Australia, Torres Strait, Woeydhul, Waiat, culture hero, secret societies, Introduction For millennia, people across the globe have sought to understand the mysteries of life and death through connection with their ancestors. Secret societies, defined here as 'an association with [...]

Radiocarbon dates on charred plant remains are often used to define the chronology of archives such as lake cores and fluvial sequences. However, charcoal is often older than its depositional context because old-wood can be burnt and a range of transport and storage stages exist between the woodland and stream or lake bed ("inherited age"). In 1978, Blong and Gillespie dated four size fractions of charcoal found floating or saltating in the Macdonald River, Australia. They found larger fragments gave younger age estimates, raising the possibility that taphonomic modifications could help identify the youngest fragments. In 1978 each date required 1000s charcoal fragments. This study returns to a sample from the Macdonald River to date individual charcoal fragments and finds the inherited age may be more than 1700 years (mode 250 years) older than the collection date. Taphonomic factors, e.g., size, shape or fungal infestation cannot identify the youngest fragments. Only two fragments on short-lived materials correctly estimated the date of collection. In SE Australia, this study suggests that wood charcoal will overestimate the age of deposition, taphonomic modifications cannot be used to identify which are youngest, and multiple short-lived materials are required to accurately estimate the deposition age. [ABSTRACT FROM AUTHOR]

Cremated bones are a commonly preserved material and often found in burial environments where unburned bone may not be preserved. As such direct radiocarbon dating of cremated bone could be essential in determining the chronology of an event. Pretreatment of cremated bone exploits the structural carbonate component of the bone which survives cremation. However, due to the low abundance (ca. 0.1%) of this component, the extraction of an amount of endogenous carbon sufficient for radiocarbon dating may represent a challenge. Here we investigate two modifications to the phosphoric acid digestion protocol used during the preparation of cremated bones at the Oxford Radiocarbon Accelerator Unit (ORAU). The first of these was to use ultrasonication to release evolved CO2 from the viscous phosphoric acid and cremated bone mixture that is formed during digestion. The second was to double the amount of time during which evolved CO2 was removed from the reaction vessel by transfer into a cryogenically cooled ampoule. Ultrasonication of the digestion mixture failed to produce a significantly higher carbon yield, while double-time collection resulted in an average 21.5±13.8% increase of C yield without affecting the measured age. Extending the collection time can better enable reliable dating of small (less than 1 g) samples. [ABSTRACT FROM AUTHOR]

Accelerator mass spectrometry (AMS) radiocarbon (14C) dating is central to the development of robust chronologies in archaeological and paleoenvironmental contexts spanning the last 50,000 years. For dates to be accurate, samples must be free of exogenous carbon contamination. At the Oxford Radiocarbon Accelerator Unit (ORAU), considerable advancements in the dating of bone collagen have been made through the development of a high performance liquid chromatography (HPLC) method for the dating of the amino acid hydroxyproline, which can mitigate the effects of carbon contamination. However, recent changes in ligand manufacturing methods for the mixed-mode column used in the ORAU protocol (Primesep A, SIELC Technologies; IL, USA) have resulted in unacceptably high analytical backgrounds. Prior to the manufacturing change, backgrounds of > 50k BP were achievable. Since the manufacturing change, a mean background of 32.5k BP has been measured. Due to column bleed, the Primesep A is therefore no longer suitable for 14C measurement of hydroxyproline from older material. Here, we present background data and the chromatography conditions used to isolate hydroxyproline using an alternative column, a preparative-scale Newcrom AH, which shows promising potential as an alternative for the routine isolation and AMS dating of hydroxyproline—especially approaching the age and mass limits of the method. [ABSTRACT FROM AUTHOR]

The drivers of Ediacaran-Cambrian metazoan radiations remain unclear, as does the fidelity of the record. We use a global age framework [580-510 million years (Ma) ago] to estimate changes in marine sedimentary rock volume and area, reconstructed biodiversity (mean genus richness), and sampling intensity, integrated with carbonate carbon isotopes (δ13Ccarb) and global redox data [carbonate Uranium isotopes (δ238Ucarb)]. Sampling intensity correlates with overall mean reconstructed biodiversity >535 Ma ago, while second-order (~10-80 Ma) global transgressive-regressive cycles controlled the distribution of different marine sedimentary rocks. The temporal distribution of the Avalon assemblage is partly controlled by the temporally and spatially limited record of deep-marine siliciclastic rocks. Each successive rise of metazoan morphogroups that define the Avalon, White Sea, and Cambrian assemblages appears to coincide with global shallow marine oxygenation events at δ13Ccarb maxima, which precede major sea level transgressions. While the record of biodiversity is biased, early metazoan radiations and oxygenation events are linked to major sea level cycles. [ABSTRACT FROM AUTHOR]