Direct evidence of plant consumption in Neolithic Eastern Sudan from dental calculus analysis

The Neolithic communities of Eastern Sudan combined intensive pastoralism with plant exploitation as their main subsistence strategies. However, to date, it remains unclear which plant species were part of the human diet during the Neolithic. This contribution presents direct data on plant consumption in Eastern Sudan from the Early to Late Neolithic, obtained through the analysis of microdebris inclusions in the dental calculus of 37 individuals, integrated by dentoalveolar pathology analysis of 78 individuals, from the sites UA53 (4th millennium BCE) and Mahal Teglinos (3rd-2nd millennium BCE), located in the Gash Delta/Kassala region. Dental calculus inclusions indicate a diverse intake of cereals, legumes, and tubers during the Middle Neolithic, thus supporting the hypothesis of high reliance on plant resources. Dentoalveolar pathologies, possibly related to the consumption of carbohydrate-rich foods, have also been recorded. For the Late Neolithic, consistent with the shift towards aridity that occurred in the Middle/Late Holocene, dental calculus exclusively indicates the exploitation of sorghum and tubers-species well adapted to arid conditions-showing how the Neolithic communities modified their subsistence in response to environmental changes. Evidence of plant processing techniques, such as cooking/heating, was also revealed from the dental calculus analysis.

Stable population structure in Europe since the Iron Age, despite high mobility

Ancient DNA research in the past decade has revealed that European population structure changed dramatically in the prehistoric period (14,000-3000 years before present, YBP), reflecting the widespread introduction of Neolithic farmer and Bronze Age Steppe ancestries. However, little is known about how population structure changed from the historical period onward (3000 YBP - present). To address this, we collected whole genomes from 204 individuals from Europe and the Mediterranean, many of which are the first historical period genomes from their region (e.g. Armenia and France). We found that most regions show remarkable inter-individual heterogeneity. At least 7% of historical individuals carry ancestry uncommon in the region where they were sampled, some indicating cross-Mediterranean contacts. Despite this high level of mobility, overall population structure across western Eurasia is relatively stable through the historical period up to the present, mirroring geography. We show that, under standard population genetics models with local panmixia, the observed level of dispersal would lead to a collapse of population structure. Persistent population structure thus suggests a lower effective migration rate than indicated by the observed dispersal. We hypothesize that this phenomenon can be explained by extensive transient dispersal arising from drastically improved transportation networks and the Roman Empire's mobilization of people for trade, labor, and military. This work highlights the utility of ancient DNA in elucidating finer scale human population dynamics in recent history.

Intense community dynamics in the pre-Roman frontier site of Fermo (ninth-fifth century BCE, Marche, central Italy) inferred from isotopic data

The Early Iron Age in Italy (end of the tenth to the eighth century BCE) was characterized by profound changes which influenced the subsequent political and cultural scenario in the peninsula. At the end of this period people from the eastern Mediterranean (e.g. Phoenicians and Greek people) settled along the Italian, Sardinian and Sicilian coasts. Among local populations, the so-called Villanovan culture group-mainly located on the Tyrrhenian side of central Italy and in the southern Po plain-stood out since the beginning for the extent of their geographical expansion across the peninsula and their leading position in the interaction with diverse groups. The community of Fermo (ninth-fifth century BCE), related to the Villanovan groups but located in the Picene area (Marche), is a model example of these population dynamics. This study integrates archaeological, osteological, carbon (δ¹³C), nitrogen (δ¹⁵N) (n = 25 human) and strontium (⁸⁷Sr/⁸⁶Sr) isotope data (n = 54 human, n = 11 baseline samples) to explore human mobility through Fermo funerary contexts. The combination of these different sources enabled us to confirm the presence of non-local individuals and gain insight into community connectivity dynamics in Early Iron Age Italian frontier sites. This research contributes to one of the leading historical questions of Italian development in the first millennium BCE.

A case of bilateral humerus varus from the late antiquity Catacomb of Santa Mustiola (Chiusi, Italy)

OBJECTIVE

To report a case of bilateral humerus varus from a late antiquity archeological context in central Italy.

MATERIALS

The individual is a 25-40-year-old female, dated to the 4th cent. CE, from the catacomb of Santa Mustiola in Chiusi, Italy.

METHODS

The bones were examined macroscopically and through CT scan imaging.

RESULTS

Both humeri show evident alterations in shape, including elongated, flattened and distally dislocated humeral heads, shortened anatomical necks, angulated upper diaphyseal shafts, and reduced overall lengths. The scapulae appear to have been mildly affected by this condition and show some bone loss and slight retroversion of the glenoid cavity.

CONCLUSIONS

Observations are consistent with a diagnosis of humerus varus deformity likely caused by a traumatic event early in the individual's life.

SIGNIFICANCE

Varus deformity of the proximal humerus is seldom reported in bioarcheological literature. The case presented provides insight into the etiology and effects of this condition and may serve as comparison for future studies.

LIMITATIONS

Even though the absence of other skeletal deformities renders a systemic condition improbable, the traumatic etiology of the condition cannot be confirmed with certainty.

SUGGESTIONS FOR FURTHER RESEARCH

Future publications of new cases may give a broader perspective of the etiology of this condition in the past.

Dataset of oxygen, carbon, and strontium isotope values from the Imperial Roman site of Velia (ca. 1st-2nd c. CE), Italy

The oxygen (δ¹⁸O_carbonate), strontium (⁸⁷Sr/⁸⁶Sr), and previously unpublished carbon (δ¹³C_carbonate) isotope data presented herein from the Imperial Roman site of Velia (ca. 1st to 2nd c. CE) were obtained from the dental enamel of human permanent second molars (M2). In total, the permanent M2s of 20 individuals (10 male and 10 female) were sampled at the Museo delle Civiltà in Rome (formerly the Museo Nazionale Preistorico Etnografico “L. Pigorini”) and were subsequently processed and analysed at McMaster University. A subsample of teeth (n=5) was initially subjected to Fourier transform infrared spectroscopy (FTIR) analysis to assess for diagenetic alteration through calculation of crystallinity index (CI) values. Subsequently, tooth enamel was analysed for δ¹³C_carbonate and δ¹⁸O_carbonate (VPDB) using a VG OPTIMA Isocarb isotope ratio mass spectrometer (IRMS) at McMaster Research for Stable Isotopologues (MRSI), and ⁸⁷Sr/⁸⁶Sr was measured by dynamic multi-collection using a thermal ionization mass spectrometer (TIMS) in the School of Geography and Earth Sciences. The dental enamel isotope data presented represent the first δ¹⁸O, δ¹³C_carbonate, and ⁸⁷Sr/⁸⁶Sr values analysed from Imperial Roman Campania to date, providing data of use for comparative analyses of δ¹⁸O, δ¹³C, and ⁸⁷Sr/⁸⁶Sr values within the region and for assisting in documenting human mobility in archaeological contexts. Full interpretation of the δ¹⁸O and ⁸⁷Sr/⁸⁶Sr data presented here is provided in “Imperial Roman mobility and migration at Velia (1^st to 2^nd c. CE) in southern Italy” [1].

Ten millennia of hepatitis B virus evolution

[Figure: see text].

Who was buried with Nestor's Cup? Macroscopic and microscopic analyses of the cremated remains from Tomb 168 (second half of the 8th century BCE, Pithekoussai, Ischia Island, Italy)

Cremation 168 from the second half of the 8^th century BCE (Pithekoussai’s necropolis, Ischia Island, Italy), better known as the Tomb of Nestor’s Cup, is widely considered as one of the most intriguing discoveries in the Mediterranean Pre-Classic archaeology. A drinking cup, from which the Tomb’s name derives, bears one of the earliest surviving examples of written Greek, representing the oldest Homeric poetry ever recovered. According to previous osteological analyses, the Cup is associated with the cremated remains of a juvenile, aged approximately 10–14 years at death. Since then, a vast body of literature has attempted to explain the unique association between the exceptionality of the grave good complex, the symposiac and erotic evocation of the Nestor’s Cup inscription with the young age of the individual buried with it. This paper reconsiders previous assessments of the remains by combining gross morphology with qualitative histology and histomorphometric analyses of the burnt bone fragments. This work reveals the commingled nature of the bone assemblage, identifying for the first time, more than one human individual mixed with faunal remains. These outcomes dramatically change previous reconstructions of the cremation deposit, rewriting the answer to the question: who was buried with Nestor’s Cup?.

The origin and legacy of the Etruscans through a 2000-year archeogenomic time transect

The origin, development, and legacy of the enigmatic Etruscan civilization from the central region of the Italian peninsula known as Etruria have been debated for centuries. Here we report a genomic time transect of 82 individuals spanning almost two millennia (800 BCE to 1000 CE) across Etruria and southern Italy. During the Iron Age, we detect a component of Indo-European–associated steppe ancestry and the lack of recent Anatolian-related admixture among the putative non–Indo-European–speaking Etruscans. Despite comprising diverse individuals of central European, northern African, and Near Eastern ancestry, the local gene pool is largely maintained across the first millennium BCE. This drastically changes during the Roman Imperial period where we report an abrupt population-wide shift to ~50% admixture with eastern Mediterranean ancestry. Last, we identify northern European components appearing in central Italy during the Early Middle Ages, which thus formed the genetic landscape of present-day Italian populations.

Human mobility in a Bronze Age Vatya 'urnfield' and the life history of a high-status woman

In this study, we present osteological and strontium isotope data of 29 individuals (26 cremations and 3 inhumations) from Szigetszentmiklós-Ürgehegy, one of the largest Middle Bronze Age cemeteries in Hungary. The site is located in the northern part of the Csepel Island (a few kilometres south of Budapest) and was in use between c. 2150 and 1500 BC, a period that saw the rise, the apogee, and, ultimately, the collapse of the Vatya culture in the plains of Central Hungary. The main aim of our study was to identify variation in mobility patterns among individuals of different sex/age/social status and among individuals treated with different burial rites using strontium isotope analysis. Changes in funerary rituals in Hungary have traditionally been associated with the crises of the tell cultures and the introgression of newcomers from the area of the Tumulus Culture in Central Europe around 1500 BC. Our results show only slight discrepancies between inhumations and cremations, as well as differences between adult males and females. The case of the richly furnished grave n. 241 is of particular interest. The urn contains the cremated bones of an adult woman and two 7 to 8-month-old foetuses, as well as remarkably prestigious goods. Using 87Sr/86Sr analysis of different dental and skeletal remains, which form in different life stages, we were able to reconstruct the potential movements of this high-status woman over almost her entire lifetime, from birth to her final days. Our study confirms the informative potential of strontium isotopes analyses performed on different cremated tissues. From a more general, historical perspective, our results reinforce the idea that exogamic practices were common in Bronze Age Central Europe and that kinship ties among high-rank individuals were probably functional in establishing or strengthening interconnections, alliances, and economic partnerships.

Ancient Rome: A genetic crossroads of Europe and the Mediterranean

Ancient Rome was the capital of an empire of ~70 million inhabitants, but little is known about the genetics of ancient Romans. Here we present 127 genomes from 29 archaeological sites in and around Rome, spanning the past 12,000 years. We observe two major prehistoric ancestry transitions: one with the introduction of farming and another prior to the Iron Age. By the founding of Rome, the genetic composition of the region approximated that of modern Mediterranean populations. During the Imperial period, Rome's population received net immigration from the Near East, followed by an increase in genetic contributions from Europe. These ancestry shifts mirrored the geopolitical affiliations of Rome and were accompanied by marked interindividual diversity, reflecting gene flow from across the Mediterranean, Europe, and North Africa.

Towards a new osteometric method for sexing ancient cremated human remains. Analysis of Late Bronze Age and Iron Age samples from Italy with gendered grave goods

Sex estimation of human remains is one of the most important research steps for physical anthropologists and archaeologists dealing with funerary contexts and trying to reconstruct the demographic structure of ancient societies. However, it is well known that in the case of cremations sex assessment might be complicated by the destructive/transformative effect of the fire on bones. Osteometric standards built on unburned human remains and contemporary cremated series are often inadequate for the analysis of ancient cremations, and frequently result in a significant number of misclassifications. This work is an attempt to overcome the scarcity of methods that could be applied to pre-proto-historic Italy and serve as methodological comparison for other European contexts. A set of 24 anatomical traits were measured on 124 Bronze Age and Iron Age cremated individuals with clearly engendered grave goods. Assuming gender largely correlated to sex, male and female distributions of each individual trait measured were compared to evaluate sexual dimorphism through inferential statistics and Chaktaborty and Majumder's index. The discriminatory power of each variable was evaluated by cross-validation tests. Eight variables yielded an accuracy equal to or greater than 80%. Four of these variables also show a similar degree of precision for both sexes. The most diagnostic measurements are from radius, patella, mandible, talus, femur, first metatarsal, lunate and humerus. Overall, the degree of sexual dimorphism and the reliability of estimates obtained from our series are similar to those of a modern cremated sample recorded by Gonçalves and collaborators. Nevertheless, mean values of the male and female distributions in our case study are lower, and the application of the cut-off point calculated from the modern sample to our ancient individuals produces a considerable number of misclassifications. This result confirms the need to build population-specific methods for sexing the cremated remains of ancient individuals.

The neutron camera upgrade for MAST Upgrade

The Neutron Camera Upgrade (NCU) is a neutron flux monitor consisting of six lines of sight (LoSs) under installation on Mega Ampere Spherical Tokamak (MAST) Upgrade. The NCU is expected to contribute to the study of the confinement of fast ions and on the efficiency of non-inductive current drive in the presence of on-axis and off-axis neutral beam injection by measuring the neutron emissivity profile along the equatorial plane. This paper discusses the NCU main design criteria, the engineering and interfacing issues, and the solutions adopted. In addition, the results from the characterization and performance studies of the neutron detectors using standard γ-rays sources and a ²⁵²Cf source are discussed. The proposed design has a time resolution of 1 ms with a statistical uncertainty of less than 10% for all MAST Upgrade scenarios with a spatial resolution of 10 cm: higher spatial resolution is possible by moving the LoSs in-between plasma discharges. The energy resolution of the neutron detector is better than 10% for a light output of 0.8 MeVee, and the measured pulse shape discrimination is satisfactory.

Preservation of the metaproteome: variability of protein preservation in ancient dental calculus

Proteomic analysis of dental calculus is emerging as a powerful tool for disease and dietary characterisation of archaeological populations. To better understand the variability in protein results from dental calculus, we analysed 21 samples from three Roman-period populations to compare: 1) the quantity of extracted protein; 2) the number of mass spectral queries; and 3) the number of peptide spectral matches and protein identifications. We found little correlation between the quantity of calculus analysed and total protein identifications, as well as no systematic trends between site location and protein preservation. We identified a wide range of individual variability, which may be associated with the mechanisms of calculus formation and/or post-depositional contamination, in addition to taphonomic factors. Our results suggest dental calculus is indeed a stable, long-term reservoir of proteins as previously reported, but further systematic studies are needed to identify mechanisms associated with protein entrapment and survival in dental calculus.

Diet and health in Central-Southern Italy during the Roman Imperial time

<p align="left">The reconstruction of ancient diets by means of stable isotopes analyses acquires a deeper meaning when their results are compared with other odonto-skeletal indicators which are strongly contextualized in the light of historical and archaeological evidence. Nevertheless, the outcomes can be contradictory or, more realistically, they may not completely satisfy our hypotheses on how complex and diverse conditions - such as health status, life style, diet and nutrition - can actually interrelate in the life course of an individual.</p><p align="left">In this study we present and discuss evidences from Isola Sacra and Velia, two Roman Imperial Age coastal towns. The õ¹⁵N and õ¹³C values are compared with demographic and health status parameters, such as age, sex, stature, auricular exostoses, DISH, <em>cribra orbitalia</em>, enamel defects.</p><p> </p>

Compositional generative mapping for tree-structured data--part II: topographic projection model

We introduce GTM-SD (Generative Topographic Mapping for Structured Data), which is the first compositional generative model for topographic mapping of tree-structured data. GTM-SD exploits a scalable bottom-up hidden-tree Markov model that was introduced in Part I of this paper to achieve a recursive topographic mapping of hierarchical information. The proposed model allows efficient exploitation of contextual information from shared substructures by a recursive upward propagation on the tree structure which distributes substructure information across the topographic map. Compared to its noncompositional generative counterpart, GTM-SD is shown to allow the topographic mapping of the full sample tree, which includes a projection onto the lattice of all the distinct subtrees rooted in each of its nodes. Experimental results show that the continuous projection space generated by the smooth topographic mapping of GTM-SD yields a finer grained discrimination of the sample structures with respect to the state-of-the-art recursive neural network approach.

Water-related occupations and diet in two Roman coastal communities (Italy, first to third century AD): correlation between stable carbon and nitrogen isotope values and auricular exostosis prevalence

The reconstruction of dietary patterns in the two Roman imperial age coastal communities of Portus and Velia (I-III AD) by means of stable isotope analysis of bone remains has exposed a certain degree of heterogeneity between and within the two samples. Results do not correlate with any discernible mortuary practices at either site, which might have pointed to differential social status. The present study tests the hypothesis of a possible connection between dietary habits and occupational activities in the two communities. Among skeletal markers of occupation, external auricular exostosis (EAE) has proved to be very informative. Clinical and retrospective epidemiological surveys have revealed a strong positive correlation between EAE development and habitual exposure to cold water. In this study, we show that there is a high rate of occurrence of EAE among adult males in both skeletal samples (21.1% in Portus and 35.3% in Velia). Further, there is a statistically significant higher prevalence of EAE among those individuals at Velia with very high nitrogen isotopic values. This points to fishing (coastal, low-water fishing) as the sea-related occupation most responsible for the onset of the ear pathology. For Portus, where the consumption of foods from sea and river seems to be more widespread through the population, and where the scenario of seaport and fluvial activities was much more complex than in Velia, a close correlation between EAE and fish consumption by fishermen is less easy to establish.

Analysis of the internal representations developed by neural networks for structures applied to quantitative structure--activity relationship studies of benzodiazepines

An application of recursive cascade correlation (CC) neural networks to quantitative structure-activity relationship (QSAR) studies is presented, with emphasis on the study of the internal representations developed by the neural networks. Recursive CC is a neural network model recently proposed for the processing of structured data. It allows the direct handling of chemical compounds as labeled ordered directed graphs, and constitutes a novel approach to QSAR. The adopted representation of molecular structure captures, in a quite general and flexible way, significant topological aspects and chemical functionalities for each specific class of molecules showing a particular chemical reactivity or biological activity. A class of 1,4-benzodiazepin-2-ones is analyzed by the proposed approach. It compares favorably versus the traditional QSAR treatment based on equations. To show the ability of the model in capturing most of the structural features that account for the biological activity, the internal representations developed by the networks are analyzed by principal component analysis. This analysis shows that the networks are able to discover relevant structural features just on the basis of the association between the molecular morphology and the target property (affinity).

Discriminant pattern recognition using transformation-invariant neurons

To overcome the problem of invariant pattern recognition, Simard, LeCun, and Denker (1993) proposed a successful nearest-neighbor approach based on tangent distance, attaining state-of-the-art accuracy. Since this approach needs great computational and memory effort, Hastie, Simard, and Säckinger (1995) proposed an algorithm (HSS) based on singular value decomposition (SVD), for the generation of nondiscriminant tangent models. In this article we propose a different approach, based on a gradient-descent constructive algorithm, called TD-Neuron, that develops discriminant models. We present as well comparative results of our constructive algorithm versus HSS and learning vector quantization (LVQ) algorithms. Specifically, we tested the HSS algorithm using both the original version based on the two-sided tangent distance and a new version based on the one-sided tangent distance. Empirical results over the NIST-3 database show that the TD-Neuron is superior to both SVD- and LVQ-based algorithms, since it reaches a better trade-off between error and rejection.

Intra- and interobserver concordance in scoring Harris lines: a test on bone sections and radiographs

Little attention has been devoted to assessing the reproducibility of (paleo) pathological observations. Harris lines (HL) are among the markers most used to determine chronology of stresses suffered during growth. Nevertheless, their scoring entails remarkable methodological difficulty. Bone sections (S) and radiographs (R) of 29 adult tibiae of archeological provenance (medieval) were scored for HL by five observers. At regular intervals of time, each observer gave two independent counts on both series. Results show a) a substantial interobserver disagreement of HL estimates for both sectional and radiographic records, and b) a high level of intraobserver error.

Behavior-induced auditory exostoses in imperial Roman society: evidence from coeval urban and rural communities near Rome

Presence and features of auditory exostoses were investigated in two cranial samples of Roman imperial age (1st-3rd century A.D.). The skeletal material comes from the necropolises of Portus (Isola Sacra) and Lucus Feroniae (Via Capenate), two towns along the Tevere River, in close relation with the social and economic life of Rome. Deep-rooted differences between the human communities represented by the skeletal samples (83 and 71 individuals, respectively, in this study) are documented both historically and archaeologically. The results show lack of exostoses in the female sex, a negligible incidence among the males of Lucus Feroniae, but a high frequency in the male sample from Isola Sacra (31.3%). Auditory exostoses are commonly recognised as localized hyperplastic growths of predominantly acquired origin. Features of the exostoses found in the male crania from Isola Sacra (particularly in relation to the age at death of the affected individuals) support this view. Furthermore, several clinical and anthropological studies have pointed out close links between the occurrence of auditory exostoses and prolonged cold water exposure, generally due to the practice of aquatic sports, or to working activities involving water contact or diving. In this perspective, the differences observed between the two Roman populations and between the sexes (in Isola Sacra) appear to result from different social habits: the middle class population of Portus habitually used thermal baths, whereas it is probable that thermae were seldom frequented (if at all) by the Lucus Feroniae population represented in the necropolis (mostly composed by slaves or freedmen farm laborers).(ABSTRACT TRUNCATED AT 250 WORDS)