Identifying Archaeological Bone via Non-Destructive ZooMS and the Materiality of Symbolic Expression: Examples from Iroquoian Bone Points.

Today, practical, functional and symbolic choices inform the selection of raw materials for worked objects. In cases where we can discern the origin of worked bone, tooth, ivory and antler objects in the past, we assume that similar choices are being made. However, morphological species identification of worked objects is often impossible due to the loss of identifying characteristics during manufacture. Here, we describe a novel non-destructive ZooMS (Zooarchaeology by Mass Spectrometry) method which was applied to bone points from Pre-Contact St. Lawrence Iroquoian village sites in southern Quebec, Canada. The traditional ZooMS technique requires destructive analysis of a sample, which can be problematic when dealing with artefacts. Here we instead extracted proteins from the plastic bags in which the points had been stored. ZooMS analysis revealed hitherto unexpected species, notably black bear (Ursus americanus) and human (Homo sapiens sapiens), used in point manufacture. These surprising results (confirmed through genomic sequencing) highlight the importance of advancing biomolecular research in artefact studies. Furthermore, they unexpectedly and exceptionally allow us to identify and explore the tangible, material traces of the symbolic relationship between bears and humans, central to past and present Iroquoian cosmology and mythology

Large expert-curated database for benchmarking document similarity detection in biomedical literature search

Document recommendation systems for locating relevant literature have mostly relied on methods developed a decade ago. This is largely due to the lack of a large offline gold-standard benchmark of relevant documents that cover a variety of research fields such that newly developed literature search techniques can be compared, improved and translated into practice. To overcome this bottleneck, we have established the RElevant LIterature SearcH consortium consisting of more than 1500 scientists from 84 countries, who have collectively annotated the relevance of over 180 000 PubMed-listed articles with regard to their respective seed (input) article/s. The majority of annotations were contributed by highly experienced, original authors of the seed articles. The collected data cover 76% of all unique PubMed Medical Subject Headings descriptors. No systematic biases were observed across different experience levels, research fields or time spent on annotations. More importantly, annotations of the same document pairs contributed by different scientists were highly concordant. We further show that the three representative baseline methods used to generate recommended articles for evaluation (Okapi Best Matching 25, Term Frequency-Inverse Document Frequency and PubMed Related Articles) had similar overall performances. Additionally, we found that these methods each tend to produce distinct collections of recommended articles, suggesting that a hybrid method may be required to completely capture all relevant articles. The established database server located at https://relishdb.ict.griffith.edu.au is freely available for the downloading of annotation data and the blind testing of new methods. We expect that this benchmark will be useful for stimulating the development of new powerful techniques for title and title/abstract-based search engines for relevant articles in biomedical research.Peer reviewe

A blood atlas of COVID-19 defines hallmarks of disease severity and specificity.

Treatment of severe COVID-19 is currently limited by clinical heterogeneity and incomplete description of specific immune biomarkers. We present here a comprehensive multi-omic blood atlas for patients with varying COVID-19 severity in an integrated comparison with influenza and sepsis patients versus healthy volunteers. We identify immune signatures and correlates of host response. Hallmarks of disease severity involved cells, their inflammatory mediators and networks, including progenitor cells and specific myeloid and lymphocyte subsets, features of the immune repertoire, acute phase response, metabolism, and coagulation. Persisting immune activation involving AP-1/p38MAPK was a specific feature of COVID-19. The plasma proteome enabled sub-phenotyping into patient clusters, predictive of severity and outcome. Systems-based integrative analyses including tensor and matrix decomposition of all modalities revealed feature groupings linked with severity and specificity compared to influenza and sepsis. Our approach and blood atlas will support future drug development, clinical trial design, and personalized medicine approaches for COVID-19

From Ahwi to Anikahwi: Deer in Cherokee Subsistence and Social Structure

In the Southeastern United States white-tailed deer remains are recovered in abundance from late prehistoric archaeological sites and have been used to identify numerous social and cultural phenomena including differences in food consumption based on status, feasting, inter-site transport of foodstuffs, and regional variation in subsistence strategies. Meat, marrow, and hide were three important physical contributions of deer to the daily lives of southeastern natives; however, we argue the spiritual and social value of deer were equally important. We combine zooarchaeological analyses of white-tailed deer from Mississippian Period sites with both published and unpublished data from the Native American ethnohistorical, ethnographic and linguistic record. We examine the practices and beliefs that surround the human-animal interaction -- a set of relationships that still exists in communities today. Whereas the contexts for some traditional activities, such as painting deep inside of caves or constructing elaborate architecture, may have changed, native peoples in the southeast still live in environments with animals that are largely the same as their ancestors. Given this persistent context, we use ethnohistorical accounts and ethnographic interviews to provide meaningful insights into the symbolic and social significance of a staple food prior to the arrival of Europeans

Daksi: The Ethnozooarchaeology of the Eastern Box Turtle Terrepene Carolina

The development of connections between archaeologically known populations and contemporary peoples is a crucial missing piece in understanding the story of southeastern native peoples. Ethnoecological models demonstrate the persistence of practices in durable environmental contexts as opposed to the interpretation of signs, symbols and structures left behind. We developed a protocol for extending the anthropological interpretation of late precontact archaeological sites by combining zooarchaeological analysis of Eastern box turtles from Mississippian sites with the Native American ethnohistorical, ethnographic and linguistic record. This protocol allows for greater insights into subsistence, medicinal, technological, and ecological practices prior to the arrival of Europeans

Identifying Turtle Shell Rattles in the Archaeological Record of the Southeastern United States

The construction of rattles from turtle (Testudines) shells is an important consideration when distinguishing between food and non-food uses of archaeological turtle remains. However, the identification of turtle shell rattles in prehistoric contexts can be quite challenging. Equifinality is a major problem for being able to distinguish rattles from food refuse, particularly when a carapace is not burnt or modified. In addition, diversity, abundance, and distribution of Chelonian taxa varies throughout the southeastern United States, creating differential access for indigenous groups. Thus, multiple lines of evidence are needed from archaeological, ethnographic, and ethnohistoric records to successfully argue for the production and use of turtle shell rattles in the prehistoric southeastern United States. In this article, we present examples of turtle shell rattles in the southeastern United States to highlight their function and use by indigenous groups, the construction process, and several common characteristics, or an object trait list, that can aid in the identification of fragmentary turtle shell rattle remains. Proper identification of turtle remains is important for interpreting faunal remains and may be of interest to indigenous groups claiming cultural items under the Native American Graves Protection and Repatriation Act (NAGPRA)

An experimental study of turtle shell rattle production and the implications for archaeofaunal assemblages

<div><p>Turtle shell rattles are percussion instruments used by Indigenous peoples of the Americas in ceremonial contexts to keep rhythm. Archaeological investigations in the southeastern United States produced several complete and partial Eastern box turtle (<i>Terrapene carolina</i>) shell rattles from mortuary contexts dating from the Archaic (ca. 8000–1000 BC) through Mississippian periods (ca. AD 800–1500). Fragmentary turtle remains, some identified as Eastern box turtle, are frequently recovered from non-mortuary contexts. Traditionally, these fragmentary remains are attributed to food waste. Given the archaeological and ethnographic evidence for turtle shell rattles, we need to consider how fragmentary remains might fit into the chaîne opératoire of rattle production. This paper presents the results of an experimental study designed to identify one such chaîne opératoire of rattle production. During this experiment, the data on taphonomic processes such as manufacturing marks, use-wear, and breakage patterns, were recorded. We then tested the taphonomic findings from the experimental study and an object trait list we compiled from known rattle specimens and documentary sources with archaeological turtle remains recovered from non-mortuary contexts at two Mississippian period (ca. AD 1000–1450) sites in Middle Tennessee. Historic indigenous groups are known to have, and still do into the present-day, make and use turtle shell rattles in the region. Ultimately, we determined that “food refuse” should not be the default interpretation of fragmentary box turtle remains, and instead the taphonomic history and contextual associations must be considered in full. The experimental process of crafting turtle shell rattles enhances our understanding of an ancient musical instrument and the success rate of identifying musical artifacts and distinguishing between other modified turtle remains in the archaeological record. This study expands our knowledge of ancient music in North America and prompts re-analysis of curated turtle remains in museums for rattle-related modifications.</p></div

Tools and samples used in experimental study.

<p>Items include bow and chert drill, the drilled carapace (Drill Holes 5 and 6), river pebbles, and river cane.</p