Luminescence age calculation through Bayesian convolution of equivalent dose and dose-rate distributions:The De_Dr model

In nature, each mineral grain (quartz or feldspar) receives a dose rate (Dr) specific to its environment. The dose-rate distribution, therefore, reflects the micro-dosimetric context of grains of similar size. If all the grains were well bleached at deposition, this distribution is assumed to correspond, within uncertainties, with the distribution of equivalent doses (De). The combination of the De and Dr distributions in the De_Dr model proposed here would then al- low calculation of the true depositional age. If grains whose De values are not representative of this age (hereafter called “outliers”) are present in the De distribution, this model al- lows them to be identified before the age is calculated, en- abling their exclusion. As the De_Dr approach relies only on the Dr distribution to describe the De distribution, the model avoids any assumption about the shape of the De distribu- tion, which can be difficult to justify. Herein, we outline the mathematical concepts of the De_Dr approach (more details are given in Galharret et al., 2021) and the exploitation of this Bayesian modelling based on an R code available in the R package “Luminescence”. We also present a series of tests using simulated Dr and De distributions with and without outliers and show that the De_Dr approach can be an alter- native to available models for interpreting De distributions.Using the world in ancient societies : processes and forms of appropriation of space in Long TimeCREDit - Chronological REference Datasets and Sites (CREDit) towards improved accuracy and precision in luminescence-based chronologie

Prognostic Significance of Estrogen Receptor Alpha in Oral Squamous Cell Carcinoma

Simple Summary: Although the survival rate has improved over the past decades, the prognosis of oral squamous cell carcinoma (OSCC) is still poor, and new treatment strategies are required. The aim of this study was to evaluate estrogen receptor alpha (ERa) expression in OSCC in a large patient cohort as a potential prognostic marker and therapeutic target. The findings indicated a rare expression of ERa that, however, was associated with a dramatic decrease of overall survival in male patients. In ERα-positive OSCC patients, an ER-based therapeutic (adjuvant) approach in the future might be conceivable based on the findings of this study. Abstract: Introduction: Several studies suggest an estrogen receptor alpha (ERα)-mediated influence on the pathogenesis of oral squamous cell carcinoma (OSCC), as described for other malignancies that are not considered to be primarily hormone-dependent. Recently, an association between ERα expression and improved survival in oropharyngeal squamous cell carcinoma (OPSCC) has been found. However, the prognostic relevance of ERα in OSCC has not been proven to date. Therefore, the aim of this study was to evaluate ERα expression in OSCC in a large patient cohort and analyze its influence on survival and recurrence. Material and methods: A total of 316 patients with primary OSCC who received initial surgical therapy were included in this analysis. The expression of ERα was evaluated on tissue microarrays by immunohistochemistry in the primary tumor and/or primary lymph node metastases. The expression level was quantified by light microscopy using the immunoreactive score (IRS) for estrogen receptor detection. An IRS equal to or greater than 2 was considered positive. The 5-year overall survival (OS) and relapse-free survival (RFS) were examined by the Kaplan-Meier method and log-rank test. Results: A total of 316 patients (111 females; 205 males) with a mean age of 61.3 years (range 27-96 years) were included in this study. In 16 patients (5.1%; 6 females and 10 males), positive ERα expression was found in the primary tumor (n = 11; 11/302) or lymph node metastases (n = 5; 5/52). Patients with positive ERα expression in primary tumors/primary lymph node metastases had a significantly lower OS and RFS (p = 0.012; p = 0.0053) compared to ERα-negative patients. Sub-group analysis in relation to gender revealed a highly significant influence of ERα expression on OS and RFS in males but not in females, both for the ERα-positive primary tumor cohort (males: p = 0.0013; p < 0.0001; females: p = 0.56; p = 0.89) and the ERα-positive primary tumor/primary lymph node metastasis cohort (males: p < 0.0001; p < 0.0001; females: p = 0.95; p = 0.96). In multivariate cox regression analysis, the ERα IRS of primary tumors (dichotomized; ERα+ vs. ERα-) was an independent risk factor for OS (HR = 4.230; 95%CI 1.616-11.076; p = 0.003) and RFS (HR = 12.390; 95%CI 4.073-37.693; p < 0.001) in the male cohort. There was a significant difference (p = 0.006) of ERα positivity with regard to the localization of the primary tumor. ERα positivity in the primary tumor was significantly associated (p = 0.026) with UICC stage, with most of the cases being diagnosed in stage IV. Furthermore, there was a significantly (p = 0.049) higher rate of bone infiltration in ERα-positive patients. Conclusion: Expression of ERα is rare in OSCC; however, it is associated with a dramatic decrease in OS in male patients. Further studies are necessary to confirm our results and to evaluate the exact mechanism underlying this observation. Hence, ERα-positive OSCC patients might benefit from an ER-based therapeutic (adjuvant) approach in the future

Towards an improvement of optically stimulated luminescence (OSL) age uncertainties:Modelling OSL ages with systematic errors, stratigraphic constraints and radiocarbon ages using the R package BayLum

International audienceAbstract. Statistical analysis has become increasingly important in optically stimulated luminescence (OSL) dating since it has become possible to measure signals at the single-grain scale. The accuracy of large chronological datasets can benefit from the inclusion, in chronological modelling, of stratigraphic constraints and shared systematic errors. Recently, a number of Bayesian models have been developed for OSL age calculation; the R package “BayLum” presented herein allows different models of this type to be implemented, particularly for samples in stratigraphic order which share systematic errors. We first show how to introduce stratigraphic constraints in BayLum; then, we focus on the construction, based on measurement uncertainties, of dose covariance matrices to account for systematic errors specific to OSL dating. The nature (systematic versus random) of errors affecting OSL ages is discussed, based – as an example – on the dose rate determination procedure at the IRAMAT-CRP2A laboratory (Bordeaux). The effects of the stratigraphic constraints and dose covariance matrices are illustrated on example datasets. In particular, the benefit of combining the modelling of systematic errors with independent ages, unaffected by these errors, is demonstrated. Finally, we discuss other common ways of estimating dose rates and how they may be taken into account in the covariance matrix by other potential users and laboratories. Test datasets are provided as a Supplement to the reader, together with an R markdown tutorial allowing the reproduction of all calculations and figures presented in this study

Cerebral near-infrared spectroscopy monitoring versus treatment as usual for extremely preterm infants:A protocol for the SafeBoosC randomised clinical phase III trial

Cerebral oxygenation monitoring may reduce the risk of death and neurologic complications in extremely preterm infants, but no such effects have yet been demonstrated in preterm infants in sufficiently powered randomised clinical trials. The objective of the SafeBoosC III trial is to investigate the benefits and harms of treatment based on near-infrared spectroscopy (NIRS) monitoring compared with treatment as usual for extremely preterm infants

A One Base Pair Deletion in the Canine ATP13A2 Gene Causes Exon Skipping and Late-Onset Neuronal Ceroid Lipofuscinosis in the Tibetan Terrier

Neuronal ceroid lipofuscinosis (NCL) is a progressive neurodegenerative disease characterized by brain and retinal atrophy and the intracellular accumulation of autofluorescent lysosomal storage bodies resembling lipofuscin in neurons and other cells. Tibetan terriers show a late-onset lethal form of NCL manifesting first visible signs at 5–7 years of age. Genome-wide association analyses for 12 Tibetan-terrier-NCL-cases and 7 Tibetan-terrier controls using the 127K canine Affymetrix SNP chip and mixed model analysis mapped NCL to dog chromosome (CFA) 2 at 83.71–84.72 Mb. Multipoint linkage and association analyses in 376 Tibetan terriers confirmed this genomic region on CFA2. A mutation analysis for 14 positional candidate genes in two NCL-cases and one control revealed a strongly associated single nucleotide polymorphism (SNP) in the MAPK PM20/PM21 gene and a perfectly with NCL associated single base pair deletion (c.1620delG) within exon 16 of the ATP13A2 gene. The c.1620delG mutation in ATP13A2 causes skipping of exon 16 presumably due to a broken exonic splicing enhancer motif. As a result of this mutation, ATP13A2 lacks 69 amino acids. All known 24 NCL cases were homozygous for this deletion and all obligate 35 NCL-carriers were heterozygous. In a sample of 144 dogs from eleven other breeds, the c.1620delG mutation could not be found. Knowledge of the causative mutation for late-onset NCL in Tibetan terrier allows genetic testing of these dogs to avoid matings of carrier animals. ATP13A2 mutations have been described in familial Parkinson syndrome (PARK9). Tibetan terriers with these mutations provide a valuable model for a PARK9-linked disease and possibly for manganese toxicity in synucleinopathies

Algorithm for predicting valvular heart disease from heart sounds in an unselected cohort

ObjectiveThis study aims to assess the ability of state-of-the-art machine learning algorithms to detect valvular heart disease (VHD) from digital heart sound recordings in a general population that includes asymptomatic cases and intermediate stages of disease progression.MethodsWe trained a recurrent neural network to predict murmurs from heart sound audio using annotated recordings collected with digital stethoscopes from four auscultation positions in 2,124 participants from the Tromsø7 study. The predicted murmurs were used to predict VHD as determined by echocardiography.ResultsThe presence of aortic stenosis (AS) was detected with a sensitivity of 90.9%, a specificity of 94.5%, and an area under the curve (AUC) of 0.979 (CI: 0.963–0.995). At least moderate AS was detected with an AUC of 0.993 (CI: 0.989–0.997). Moderate or greater aortic and mitral regurgitation (AR and MR) were predicted with AUC values of 0.634 (CI: 0.565–703) and 0.549 (CI: 0.506–0.593), respectively, which increased to 0.766 and 0.677 when clinical variables were added as predictors. The AUC for predicting symptomatic cases was higher for AR and MR, 0.756 and 0.711, respectively. Screening jointly for symptomatic regurgitation or presence of stenosis resulted in an AUC of 0.86, with 97.7% of AS cases (n = 44) and all 12 MS cases detected.ConclusionsThe algorithm demonstrated excellent performance in detecting AS in a general cohort, surpassing observations from similar studies on selected cohorts. The detection of AR and MR based on HS audio was poor, but accuracy was considerably higher for symptomatic cases, and the inclusion of clinical variables improved the performance of the model significantly

Cerebral near-infrared spectroscopy monitoring versus treatment as usual for extremely preterm infants: a protocol for the SafeBoosC randomised clinical phase III trial.

BACKGROUND: Cerebral oxygenation monitoring may reduce the risk of death and neurologic complications in extremely preterm infants, but no such effects have yet been demonstrated in preterm infants in sufficiently powered randomised clinical trials. The objective of the SafeBoosC III trial is to investigate the benefits and harms of treatment based on near-infrared spectroscopy (NIRS) monitoring compared with treatment as usual for extremely preterm infants. METHODS/DESIGN: SafeBoosC III is an investigator-initiated, multinational, randomised, pragmatic phase III clinical trial. Inclusion criteria will be infants born below 28 weeks postmenstrual age and parental informed consent (unless the site is using 'opt-out' or deferred consent). Exclusion criteria will be no parental informed consent (or if 'opt-out' is used, lack of a record that clinical staff have explained the trial and the 'opt-out' consent process to parents and/or a record of the parents' decision to opt-out in the infant's clinical file); decision not to provide full life support; and no possibility to initiate cerebral NIRS oximetry within 6 h after birth. Participants will be randomised 1:1 into either the experimental or control group. Participants in the experimental group will be monitored during the first 72 h of life with a cerebral NIRS oximeter. Cerebral hypoxia will be treated according to an evidence-based treatment guideline. Participants in the control group will not undergo cerebral oxygenation monitoring and will receive treatment as usual. Each participant will be followed up at 36 weeks postmenstrual age. The primary outcome will be a composite of either death or severe brain injury detected on any of the serial cranial ultrasound scans that are routinely performed in these infants up to 36 weeks postmenstrual age. Severe brain injury will be assessed by a person blinded to group allocation. To detect a 22% relative risk difference between the experimental and control group, we intend to randomise a cohort of 1600 infants. DISCUSSION: Treatment guided by cerebral NIRS oximetry has the potential to decrease the risk of death or survival with severe brain injury in preterm infants. There is an urgent need to assess the clinical effects of NIRS monitoring among preterm neonates. TRIAL REGISTRATION: ClinicalTrial.gov, NCT03770741. Registered 10 December 2018

The EU Horizon 2020 project GRACE : integrated oil spill response actions and environmental effects

This article introduces the EU Horizon 2020 research project GRACE (Integrated oil spill response actions and environmental effects), which focuses on a holistic approach towards investigating and understanding the hazardous impact of oil spills and the environmental impacts and benefits of a suite of marine oil spill response technologies in the cold climate and ice-infested areas of the North Atlantic and the Baltic Sea. The response methods considered include mechanical collection in water and below ice, in situ burning, use of chemical dispersants, natural biodegradation, and combinations of these. The impacts of naturally and chemically dispersed oil, residues resulting from in situ burning, and non-collected oil on fish, invertebrates (e.g. mussels, crustaceans) and macro-algae are assessed by using highly sensitive biomarker methods, and specific methods for the rapid detection of the effects of oil pollution on biota are developed. By observing, monitoring and predicting oil movements in the sea through the use of novel online sensors on vessels, fixed platforms including gliders and the so-called SmartBuoys together with real-time data transfer into operational systems that help to improve the information on the location of the oil spill, situational awareness of oil spill response can be improved. Methods and findings of the project are integrated into a strategic net environmental benefit analysis tool (environment and oil spill response, EOS) for oil spill response strategy decision making in cold climates and ice-infested areas

A historical overview of the classification, evolution, and dispersion of Leishmania parasites and sandflies

Background The aim of this study is to describe the major evolutionary historical events among Leishmania, sandflies, and the associated animal reservoirs in detail, in accordance with the geographical evolution of the Earth, which has not been previously discussed on a large scale. Methodology and Principal Findings Leishmania and sandfly classification has always been a controversial matter, and the increasing number of species currently described further complicates this issue. Despite several hypotheses on the origin, evolution, and distribution of Leishmania and sandflies in the Old and New World, no consistent agreement exists regarding dissemination of the actors that play roles in leishmaniasis. For this purpose, we present here three centuries of research on sandflies and Leishmania descriptions, as well as a complete description of Leishmania and sandfly fossils and the emergence date of each Leishmania and sandfly group during different geographical periods, from 550 million years ago until now. We discuss critically the different approaches that were used for Leishmana and sandfly classification and their synonymies, proposing an updated classification for each species of Leishmania and sandfly. We update information on the current distribution and dispersion of different species of Leishmania (53), sandflies (more than 800 at genus or subgenus level), and animal reservoirs in each of the following geographical ecozones: Palearctic, Nearctic, Neotropic, Afrotropical, Oriental, Malagasy, and Australian. We propose an updated list of the potential and proven sandfly vectors for each Leishmania species in the Old and New World. Finally, we address a classical question about digenetic Leishmania evolution: which was the first host, a vertebrate or an invertebrate? Conclusions and Significance We propose an updated view of events that have played important roles in the geographical dispersion of sandflies, in relation to both the Leishmania species they transmit and the animal reservoirs of the parasites