Improving the extraction of ancient Yersinia pestis genomes from the dental pulp.

Ancient DNA preserved in the dental pulp offers the opportunity to characterize the genome of some of the deadliest pathogens in human history. However, while DNA capture technologies help, focus sequencing efforts, and therefore, reduce experimental costs, the recovery of ancient pathogen DNA remains challenging. Here, we tracked the kinetics of ancient Yersinia pestis DNA release in solution during a pre-digestion of the dental pulp. We found that most of the ancient Y. pestis DNA is released within 60 min at 37°C in our experimental conditions. We recommend a simple pre-digestion as an economical procedure to obtain extracts enriched in ancient pathogen DNA, as longer digestion times release other types of templates, including host DNA. Combining this procedure with DNA capture, we characterized the genome sequences of 12 ancient Y. pestis bacteria from France dating to the second pandemic outbreaks of the 17th and 18th centuries Common Era.

Immunohistologic Features of Cerebral Venous Thrombosis Due to Vaccine-Induced Immune Thrombotic Thrombocytopenia.

OBJECTIVES: Vaccine-induced immune thrombotic thrombocytopenia (VITT), a recently described entity characterized by thrombosis at unusual locations such as cerebral venous sinus and splanchnic vein, has been rarely described after adenoviral-encoded COVID-19 vaccines. In this study, we report the immunohistological correlates in 3 fatal cases of cerebral venous thrombosis related to VITT analyzed at an academic medical center. METHODS: Detailed neuropathologic studies were performed in 3 cases of cerebral venous thrombosis related to VITT after adenoviral COVID-19 vaccination. RESULTS: Autopsy revealed extensive cerebral vein thrombosis in all 3 cases. Polarized thrombi were observed with a high density of neutrophils in the core and a low density in the tail. Endothelial cells adjacent to the thrombus were largely destroyed. Markers of neutrophil extracellular trap and complement activation were present at the border and within the cerebral vein thrombi. SARS-CoV-2 spike protein was detected within the thrombus and in the adjacent vessel wall. DISCUSSION: Data indicate that neutrophils and complement activation associated with antispike immunity triggered by the vaccine is probably involved in the disease process.

Contribution of the use of clavicle bone density in age estimation.

Age estimation is an essential element in the field of forensics and is also of judicial interest in forensic medicine of the living. Despite all the methods, age estimation is often imprecise with many biases, especially in mature individuals. The main objective of our study is to assess the correlation between age and computed tomography bone mineral density of the medial end of the clavicle. A sample of 180 chest multi-slice computed tomography scans without contrast injection performed in living individuals, with suspected respiratory infection, aged 15 to 100 years was used. Bone density measurement was performed on the medial meta-epiphyseal region of the clavicles. A significant negative correlation was found between bone density and age of individuals (p-value < 0.05). The mean absolute error was calculated for men at 13.4 years and 13.1 years for women, which was associated with an absence of bias. Good precision of the estimate for both sexes was also calculated on a subgroup of individuals whose age was greater than 40 years, with average absolute errors of about 12 years, which was associated with an absence of relative error. In view of our preliminary results, the study of bone density of the medial end of the clavicle could be of interest in the estimation of age. Several studies will be necessary to evaluate the reproducibility of these results on independent bone samples and in the estimation of age in the living individual.

Machine Learning Analysis of the Anatomical Parameters of the Upper Airway Morphology: A Retrospective Study from Cone-Beam CT Examinations in a French Population.

The objective of this study is to assess, using cone-beam CT (CBCT) examinations, the correlation between hard and soft anatomical parameters and their impact on the characteristics of the upper airway using symbolic regression as a machine learning strategy. Methods: On each CBCT, the upper airway was segmented, and 24 anatomical landmarks were positioned to obtain six angles and 19 distances. Some anatomical landmarks were related to soft tissues and others were related to hard tissues. To explore which variables were the most influential to explain the morphology of the upper airway, principal component and symbolic regression analyses were conducted. Results: In total, 60 CBCT were analyzed from subjects with a mean age of 39.5 ± 13.5 years. The intra-observer reproducibility for each variable was between good and excellent. The horizontal soft palate measure mostly contributed to the reduction of the airway volume and minimal section area with a variable importance of around 50%. The tongue and the position of the hyoid bone were also linked to the upper airway morphology. For hard anatomical structures, the anteroposterior position of the mandible and the maxilla had some influence. Conclusions: Although the volume of the airway is not accessible on all CBCT scans performed by dental practitioners, this study demonstrates that a small number of anatomical elements may be markers of the reduction of the upper airway with, potentially, an increased risk of obstructive sleep apnea. This could help the dentist refer the patient to a suitable physician.

At the Origins of Tobacco-Smoking and Tea Consumption in a Virgin Population (Yakutia, 1650-1900 A.D.): Comparison of Pharmacological, Histological, Economic and Cultural Data.

(1) Background: The way tobacco and tea spread among virgin populations is of major interest our understanding of how ancient economic and cultural practices could have influenced current habits. (2) Methods: hair concentrations of theobromine, theophylline, caffeine, nicotine, and cotinine were measured in hair samples from 47 frozen bodies of people from eastern Siberia, dated from the contact with Europeans to the assimilation of people into Russian society. (3) Results: hair concentration of theobromine, theophylline, and caffeine vary with the type of beverage consumed: green, black, or local herbal teas. Shortly after the first contacts, a few heavy consumers of tobacco were found among light or passive consumers. Tobacco-related co-morbidities began to be recorded one century after and heavy tea users were only found from the 19th century (4) Conclusions: Economic factors and social and family contacts seem to have played a decisive role in tobacco consumption very early on. Behavioral evolution governed the process of substance integration into Siberian culture and was a determinant for the continuity of its use across long periods of time. Analyzing the respective contributions of social and economic processes in the use of these substances opens avenues of investigation for today's public health.

Sucrose Is Not the Whole Story: Risk Factors and Oral Health at the Contact (Yakutia, Siberia-16th/19th).

(1) Background: contact between indigenous and European populations has often resulted in changes in oral health attributed to the introduction of sucrose. Most studies are per tooth over considerable periods and with few ethnological references. (2) Aim: dental epidemiology of 96 autochthonous frozen bodies from Yakutia between the early 17th century and the late 19th century; comparisons with historical texts and ethnographic data. (3) Material and methods: we use descriptive statistics and discriminant factorial analyses to identify dominant variables in the dataset and compare periods and subjects, considering all variables. (4) Results: the peculiarities of the population are the rarity of cavities and the relative frequency of dental pathologies leading to death. Assimilation into the Russian Orthodox culture has led to decreased tooth wear and an increase in tooth loss. Dental health evolves only two centuries after the contact. (5) Conclusions: the confrontation with historical data suggests that changes are not related to the growing importance of sucrose but to a combined action: the substitution of dendrophagy by cereal flour; the decrease in immunity linked to the development of chronic infectious diseases; tobacco addiction and the mandibular torus: a risk factor promoting apical cysts.

Age estimation based on computed tomography exploration: a combined method.

Despite an extensive number of existing methods, age estimation of human remains is still an unsolved matter in the field of forensic anthropology, especially when it comes to mature adults. The specific aim of this work was to propose a combined method for age estimation, for forensic purposes, by coupling the Suchey-Brooks method and the measure of the pubic bone density. For this purpose, we used an independent test sample comprising 339 CT scans of living individuals aged 15 to 99 years old. Measurement of bone density and staging according to the Suchey-Brooks phases were performed, followed by estimation of ages based on a combined method and an existing virtual reference sample. Results highlighted a significant negative correlation between bone density and age. Good accuracy was obtained for the measurement of pubic bone density for age estimation of men and women, especially concerning mature adults, with an absolute error ranging from 9 to 16 years for all individuals. The authors propose a practical combined method consisting of, first, allocating phases according to the scannographic approach of the Suchey-Brooks method. For phases I to IV, the age estimation is given using the Suchey-Brooks method. For phases V to VI, the pubic bone density measurement is used. Further study will be needed to assess the reproducibility of these results on cadavers and dry bones, as the post-mortem process could interfere with the measurement of mineral bone density.

Sexual dimorphism of the mandibular conformational changes in aging human adults: A multislice computed tomographic study by geometric morphometrics.

The aging process has an impact on mandibular bone morphology and can therefore affect shape sexual dimorphism. Understanding the effect of senescence on mandibular shape changes is particularly important to correctly estimate the sex of an individual and predict age-related conformational modifications. The purpose of this study was to assess age-related changes in mandibular shape and sexual dimorphism. The study sample comprised 160 Multi Slice Computed Tomography examinations of individuals aged 40 to 79 years. Geometric morphometric analysis of fourteen osteometric landmarks was used to examine sexual dimorphism and patterns of mandibular shape variation with age. Results showed that mandibular sexual dimorphism of shape remained significant with aging. Conformational changes occurred between 50 and 70 years and were different for male and female individuals. Females presented earlier and more marked age-related shape changes than males. These observations suggest that mandibular senescence is a sexually dimorphic process since its onset, rate, and the areas subjected to conformational changes differ from male to female individuals. Senescence-related changes present substantial variability, and further investigation is required to determine precisely the age that marks their onset.

Gunshot residue detection in stagnant water: SEM-EDX or ICP-MS? A preliminary study.

The identification of gunshot residue (GSR) on wounds enables the differentiation of entry and exit wounds. Unfortunately, studies analyzing GSR on degraded bodies have been poorly documented, and no data exist regarding GSR detection after stagnant water immersion. The aim of this preliminary experimental study was to detect GSR on wounds altered in stagnant water, using scanning electron microscopy coupled with energy-dispersive X (SEM-EDX) and inductively coupled plasma mass spectrometry (ICP-MS). Shots were performed on sheep limbs with a 22LR at a distance of 20 cm. The limbs were then submerged in stagnant water and analyzed on days 0, 6, and 14. SEM-EDX was performed on previously dehydrated wounds. For ICP-MS analysis, the wounds were rubbed with a cotton swab that was then analyzed. In the SEM studies, a higher number of particles were detected in entry wounds compared to exit wounds under every set of experimental conditions. Unfortunately, SEM-EDX failed to detect GSR particles, even on day 0. ICP-MS enabled the detection of Pb, Sb, and Ba at every stage with higher quantities on entry than in exit. These elements remained detectable following limb immersion. ICP-MS enabled differentiate entry from exit wounds, even after immersion in stagnant water. Nevertheless, when manually swabbing the wounds, quantities of matter collected is highly variable. ICP-MS is a more suitable technique than SEM-EDX for GSR identification of wounds after decomposition in stagnant water; however, standardization is needed.

No particular genomic features underpin the dramatic economic consequences of 17th century plague epidemics in Italy.

The 17th century plague epidemic had a particularly strong demographic toll in Southern Europe, especially Italy, where it caused long-lasting economical damage. Whether this resulted from ineffective sanitation measures or more pathogenic Yersinia pestis strains remains unknown. DNA screening of 26 skeletons from the 1629-1630 plague cemetery of Lariey (French Alps) identified two teeth rich in plague genetic material. Further sequencing revealed two Y. pestis genomes phylogenetically closest to those from the 1636 outbreak of San Procolo a Naturno, Italy. They both belonged to a cluster extending from the Alps to Northern Germany that probably propagated during the Thirty Years war. Sequence variation did not support faster evolutionary rates in the Italian genomes and revealed only rare private non-synonymous mutations not affecting virulence genes. This, and the more heterogeneous spatial diffusion of the epidemic outside Italy, suggests environmental or social rather than biological causes for the severe Italian epidemic trajectory.

The last battle of Anne of Brittany: Solving mass grave through an interdisciplinary approach (paleopathology, biological anthropology, history, multiple isotopes and radiocarbon dating).

Mass graves are usually key historical markers with strong incentive for archeological investigations. The identification of individuals buried in mass graves has long benefitted from traditional historical, archaeological, anthropological and paleopathological techniques. The addition of novel methods including genetic, genomic and isotopic geochemistry have renewed interest in solving unidentified mass graves. In this study, we demonstrate that the combined use of these techniques allows the identification of the individuals found in two Breton historical mass graves, where one method alone would not have revealed the importance of this discovery. The skeletons likely belong to soldiers from the two enemy armies who fought during a major event of Breton history: the siege of Rennes in 1491, which ended by the wedding of the Duchess of Brittany with the King of France and signaled the end of the independence of the region. Our study highlights the value of interdisciplinary approaches with a particular emphasis on increasingly accurate isotopic markers. The development of the sulfur isoscape and testing of the triple isotope geographic assignment are detailed in a companion paper [13].

[Compensation of damage in cancerology]. / Réparation du dommage en cancérologie.

In a few situations, the consequences secondary to a carcinological pathology require an assessment of damages for compensatory purposes. This is particularly the case when liable parties have been found to be at cause of the disease: occupational pathologies in the case of inexcusable employer's fault, exposure to a radioactive risk, for example in the context of full compensation for damages suffered by the victims of nuclear experiments performed by France, or lastly, in the after-effects of late diagnosis. This article does not discuss the imputability of cancer pathologies to an event, but it proposes an adaptation of methods for assessing damages, in an attempt to provide full compensation for damages.

Comparison of different machine learning approaches to predict dental age using Demirjian's staging approach.

CONTEXT: Dental age, one of the indicators of biological age, is inferred by radiological methods. Two of the most commonly used methods are using Demirjian's radiographic stages of permanent teeth excluding the third molar (Demirjian's and Willems' method). The major drawbacks of these methods are that they are based on population-specific conversion tables and may tend to over- or underestimate dental age in other populations. Machine learning (ML) methods make it possible to create complex data schemas more simply while keeping the same annotation system. The objectives of this study are to compare (1) the capacity of ten machine learning algorithms to predict dental age in children using the seven left permanent mandibular teeth compared to reference methods and (2) the capacity of ten machine learning algorithms to predict dental age from childhood to young adulthood using the seven left permanent mandibular teeth and the four third molars. METHODS: Using a large radiological database of 3605 orthopantomograms (1734 females and 1871 males) of healthy French patients aged between 2 and 24 years, seven left permanent mandibular teeth and the 4 third molars were assessed using Demirjian's stages. Dental age estimation was then performed using Demirjian's reference method and various ML regression methods. Two analyses were performed: with the 7 left mandibular teeth without third molars for the under 16 age group and with the third molars for the entire study population. The different methods were compared using mean error, mean absolute error, root mean square error as metrics, and the Bland-Altman graph. RESULTS: All ML methods had a mean absolute error (MAE) under 0.811 years. With Demirjian's and Willems' methods, the MAE was 1.107 and 0.927 years, respectively. Except for the Bayesian ridge regression that gives poorer accuracy, there was no statistical difference between all ML tested. CONCLUSION: Compared to the two reference methods, all the ML methods based on the maturation stages defined by Demirjian were more accurate in estimating dental age. These results support the use of ML algorithms instead of using standard population tables.

Homicide by unusual-edged weapons: Forensic considerations of two cases.

Homicide by stab wound is common worldwide. However, the use of unusual edged weapons is rarely reported in the forensic literature. Here, we report two cases of homicide involving a Japanese sword, or katana, and a sickle. Both of these weapons can create either stab or incised wounds with some particularities. In our cases, characteristics of the external wounds, internal injuries, and the depth of penetration raised the possibility of an unusual weapon. Meticulous forensic examination of these injuries (morphological characteristics, depth of penetration, trajectories, and cut marks in the bone) may allow the forensic expert to determine the type of weapon used.

The cardiovascular health of prisoners who use cannabis: An exploratory study among hospitalised prisoners.

OBJECTIVE: It is essential that health professionals who practice medicine in prison rely on accurate knowledge about their patients to provide them with adapted care. The use of cannabis can influence the health status of prisoners, but data are lacking regarding the potentially related adverse health consequences. The objective of this descriptive study was to describe the cardiovascular outcomes related to cannabis use in prisoners from several detention centres hospitalised in a French hospital. METHODS: In France, prisoners who require a longer than 48-hour hospitalisation are admitted in specific secured polyvalent units called inter-regional secured hospital units (ISHU). Hospitalisations in the ISHU of Toulouse University Hospital between 2012 and 2016 for cardiovascular disorders potentially related to the use of cannabis were extracted from the French hospital database and analysed using a previously validated methodology. Included patients were those hospitalised for an inaugural cardiovascular event or deterioration of a preexisting cardiovascular illness who declared having used cannabis while imprisoned. RESULTS: Overall, 31 cardiovascular outcomes were identified in cannabis-using hospitalised prisoners among 411 hospitalisations for cardiovascular disorders (all men, mean age 43±SD years old). All used cannabis (daily: 56%) and tobacco (more than 15 PY: 83.3%), 5 used cocaine, and none used alcohol. The most frequent were coronaropathy (n=13), followed by obliterating arteriopathy of the lower limb (OALL, n=7), arrhythmic cardiomyopathy (n=4), venous thrombosis (n=3), infectious cardiopathy (n=2), and ischemic stroke (n=2). CONCLUSION: This description of serious cardiovascular outcomes in prisoners who use cannabis provides insights into the clinical features possibly observed in this vulnerable population The findings indicate that 7.5% of hospitalizations of prisoners for cardiovascular disorders are potentially linked to cannabis used in prison.

Technical note: age estimation by using pubic bone densitometry according to a twofold mode of CT measurement.

In forensic anthropology, age estimation is a major element in the determination of a biological profile and the identification of individuals. Thus, many anatomical structures have been studied, such as the pubic symphysis, which is a source of major interest due to its late maturation. One of the most well-known methods of assessment is the Suchey-Brooks (SB) system based on the morphological characteristics of the pubic symphysis. The aim of this study was to propose linear regression formulae in order to deduce chronological age from bone density, using both Hounsfield unit (HU), and mean bone density (mBD) values of the pubic symphysis. Moreover, we intended to test the reliability and then to explore the feasibility of using HU instead of mBD values for age estimation. We built retrospectively a reference sample of 400 pubic symphyses using computed tomography at a French hospital and a test sample of 120 pubic symphyses. Equations were created to establish linear regression models for age estimation. Inaccuracy and bias were calculated for individuals aged more or less than 40 years. We highlighted homogeneous mean absolute errors for both HU and mBD values, most of them being less than 10 years. Moreover, we reported a moderate overestimation for younger individuals and a very small underestimation for older individuals. This study proposes a correlation between the bone density and age of individuals with a valuable level of reliability. Finally, HU measurements seem to be suitable for linking bone density with the age of individuals in forensic practice.

Sexual and ethnic polymorphism result in considerable mismatch between native trochlear geometry and off-the-shelf TKA prostheses.

PURPOSE: To determine if trochlear morphology in healthy knees depends on sex and ethnicity, and to compare it to off-the-shelf TKA prostheses. METHODS: Three retrospective series of CT angiograms from France (female, 124; male, 135), China (female, 122; male, 137) and South Africa (female, 21; male, 62) were used to digitize osseous landmarks at the level of the femoral epicondyles. Sulcus angle, trochlear rotation, lateral trochlear inclination, trochlear asymmetry ratio, and trochlear depth index were quantified for each knee and for 10 total knee arthroplasty (TKA) models. Univariable regression analyses were performed to determine associations of the five trochlear parameters with sex and ethnicity. Interquartile ranges (IQR) of native trochlear parameters were compared to the trochlear parameters of 10 off-the-shelf TKA prostheses. RESULTS: Compared to French knees, Chinese knees had greater sulcus angle (ß = 6.3°, p < 0.001), trochlear rotation (ß = 0.8°, p = 0.004) and trochlear depth index (ß = 1.60, p < 0.001). Conversely, South African knees had greater trochlear rotation (ß = 1.9°, p < 0.001) and lateral trochlear inclination (ß = 3.7°, p < 0.001). Female knees had smaller trochlear asymmetry ratios (ß = - 0.03, p = 0.05) but greater trochlear rotation angles (ß = 0.7, p = 0.005). Considerable mismatches in trochlear morphology were revealed between native knees and off-the-shelf TKA prostheses. CONCLUSIONS: The findings suggest that thresholds used in the diagnosis of patellofemoral instability should be adapted to patient sex and ethnicity, and that standard off-the-shelf TKA may not restore native trochlear parameters in all patients. LEVEL OF EVIDENCE: III, retrospective comparative.