Bayesian Age-Period-Cohort Modeling and Prediction - BAMP

The software package BAMP provides a method of analyzing incidence or mortality data on the Lexis diagram, using a Bayesian version of an age-period-cohort model. A hierarchical model is assumed with a binomial model in the first-stage. As smoothing priors for the age, period and cohort parameters random walks of first and second order, with and without an additional unstructured component are available. Unstructured heterogeneity can also be included in the model. In order to evaluate the model fit, posterior deviance, DIC and predictive deviances are computed. By projecting the random walk prior into the future, future death rates can be predicted.

Bayesian Age-Period-Cohort Modeling and Prediction - BAMP

The software package BAMP provides a method of analyzing incidence or mortality data on the Lexis diagram, using a Bayesian version of an age-period-cohort model. A hierarchical model is assumed with a binomial model in the first-stage. As smoothing priors for the age, period and cohort parameters random walks of first and second order, with and without an additional unstructured component are available. Unstructured heterogeneity can also be included in the model. In order to evaluate the model fit, posterior deviance, DIC and predictive deviances are computed. By projecting the random walk prior into the future, future death rates can be predicted

Bayesian modelling of space-time interactions on the Lexis diagram

We propose a full model-based framework for a statistical analysis of incidence or mortality count data stratified by age, period and space, with specific inclusion of additional cohort effects. The setup will be fully Bayesian based on a series of Gaussian Markov random field priors for each of the components. Additional space-time interactions will be either modelled as space-period or space-cohort effects. Statistical inference is based on efficient algorithms to block update Gaussian Markov random fields, which have recently been proposed in the literature. We illustrate our approach in an analysis of stomach cancer data in West Germany

A Bayesian Model for Spatial Disease Prevalence Data

The analysis of the geographical distribution of disease on the scale of geographic areas such as administrative boundaries plays an important role in veterinary epidemiology. Prevalence estimates of wildlife population surveys are often based on regional count data generated by sampling animals shot by hunters. The observed disease rate per spatial unit is not a useful estimate of the underlying disease prevalence due to different sample sizes and spatial dependencies between neighbouring areas. Therefore, it is necessary to account for extra-sample variation and and spatial correlation in the data to produce more accurate maps of disease incidence. For this purpose a hierarchical Bayesian model in which structured and un-structured overdispersion is modelled explicitly in terms of spatial and non-spatial components was implemented by Markov Chain Monte Carlo methods. The model was empirically compared with the results of the non-spatial beta-binomial model using surveillance data of Pseudorabies virus infections of wildboars in the Federal State of Brandenburg, Germany

An assessment of age determination in fossil fish: the case of the opercula in the Mesozoic actinopterygian Saurichthys

Analyzing and interpreting life history data (e.g., aging and longevity, age at sexual maturity) are fundamental in many paleontological studies. In the case of extant and fossil fishes, otoliths, and to a lesser degree other incrementally growing hard tissue structures such as scales and bones, have been utilized to reveal these data. We investigated the microanatomy and internal microstructure of opercula of Saurichthys, one of the most easily recognized and globally distributed fishes in the Triassic, to elucidate whether these prominent skull bones provide reliable age estimates. Opercula, and where the subopercula is present, of several outgroup taxa were sectioned to provide a phylogenetic framework for the study. The external protrusions and ridges or internal concentric bands or wrinkles are not related to internal age-related bone tissue structures such as annuli and growth zones, but are instead purely ornamental in the case of the former and probably structural/taphonomic in case of the latter. Opercular morphogenesis of Saurichthys opercula differs from that of the extant outgroups examined in that they show rostro-medial to caudo-lateral extending growth increments instead of ones that extend sub-parallel to the opercular bone surfaces. Individual age data could thus not be reliably extracted from those opercula. Furthermore, an odontode-like complex was not encountered in Saurichthys opercula, but a few specimens show a peculiar, weakly birefringent thin tissue layer of unknown origin filling the valleys between the external ornamental ridges. Although all Saurichthys opercula showed growth marks, these could not be counted to produce reliable individual age data, whereas bones with a more concentric cross section, such as the ceratohyal, appear better suited for this purpose

An assessment of age determination in fossil fish: the case of the opercula in the Mesozoic actinopterygian Saurichthys

Analyzing and interpreting life history data (e.g., aging and longevity, age at sexual maturity) are fundamental in many paleontological studies. In the case of extant and fossil fishes, otoliths, and to a lesser degree other incrementally growing hard tissue structures such as scales and bones, have been utilized to reveal these data. We investigated the microanatomy and internal microstructure of opercula of Saurichthys, one of the most easily recognized and globally distributed fishes in the Triassic, to elucidate whether these prominent skull bones provide reliable age estimates. Opercula, and where the subopercula is present, of several outgroup taxa were sectioned to provide a phylogenetic framework for the study. The external protrusions and ridges or internal concentric bands or wrinkles are not related to internal age-related bone tissue structures such as annuli and growth zones, but are instead purely ornamental in the case of the former and probably structural/taphonomic in case of the latter. Opercular morphogenesis of Saurichthys opercula differs from that of the extant outgroups examined in that they show rostro-medial to caudo-lateral extending growth increments instead of ones that extend sub-parallel to the opercular bone surfaces. Individual age data could thus not be reliably extracted from those opercula. Furthermore, an odontode-like complex was not encountered in Saurichthys opercula, but a few specimens show a peculiar, weakly birefringent thin tissue layer of unknown origin filling the valleys between the external ornamental ridges. Although all Saurichthys opercula showed growth marks, these could not be counted to produce reliable individual age data, whereas bones with a more concentric cross section, such as the ceratohyal, appear better suited for this purpose

A strawberry accession with elevated methyl anthranilate fruit concentration is naturally resistant to the pest fly Drosophila suzukii

During the past decade, Drosophila suzukii has established itself as a global invasive fruit pest, enabled by its ability to lay eggs into fresh, ripening fruit. In a previous study, we investigated the impact of different strawberry accessions on the development of D. suzukii eggs, in the search of natural resistance. We identified several accessions that significantly reduced adult fly emergence from infested fruit. In the present study, we aimed at understanding the chemical basis of this effect. We first noted that one of the more resistant accessions showed an unusual enrichment of methyl anthranilate within its fruit, prompting us to investigate this fruit compound as a possible cause limiting fly development. We found that methyl anthranilate alone triggers embryo lethality in a concentration-dependent manner, unlike another comparable organic fruit compound. We also showed that a chemical fraction of the resistant strawberry accession that contains methyl anthranilate carries some activity toward the egg hatching rate. Surprisingly, in spite of the lethal effect of this compound to their eggs, adult females are not only attracted to methyl anthranilate at certain concentrations, but they also display a concentration-dependent preference to lay on substrates enriched in methyl anthranilate. This study demonstrates that methyl anthranilate is a potent agonist molecule against D. suzukii egg development. Its elevated concentration in a specific strawberry accession proven to reduce the fly development may explain, at least in part the fruit resistance. It further illustrates how a single, natural compound, non-toxic to humans could be exploited for biological control of a pest species

Towards an MLOps Architecture for XAI in Industrial Applications

Machine learning (ML) has become a popular tool in the industrial sector as it helps to improve operations, increase efficiency, and reduce costs. However, deploying and managing ML models in production environments can be complex. This is where Machine Learning Operations (MLOps) comes in. MLOps aims to streamline this deployment and management process. One of the remaining MLOps challenges is the need for explanations. These explanations are essential for understanding how ML models reason, which is key to trust and acceptance. Better identification of errors and improved model accuracy are only two resulting advantages. An often neglected fact is that deployed models are bypassed in practice when accuracy and especially explainability do not meet user expectations. We developed a novel MLOps software architecture to address the challenge of integrating explanations and feedback capabilities into the ML development and deployment processes. In the project EXPLAIN, our architecture is implemented in a series of industrial use cases. The proposed MLOps software architecture has several advantages. It provides an efficient way to manage ML models in production environments. Further, it allows for integrating explanations into the development and deployment processes

Semiconductor Bloch-equations formalism: Derivation and application to high-harmonic generation from Dirac fermions

We rederive the semiconductor Bloch equations emphasizing the close link to the Berry connection. Our rigorous derivation reveals the existence of two further contributions to the current, in addition to the frequently considered intraband and polarization-related interband terms. The extra contributions become sizable in situations with strong dephasing or when the dipole-matrix elements are strongly wave-number dependent. We apply the formalism to high-harmonic generation for a Dirac metal. The extra terms add to the frequency-dependent emission intensity (high-harmonic spectrum) significantly at certain frequencies changing the total signal up to a factor of 10

Post-mortem magnetic resonance imaging with computed tomography-guided biopsy for foetuses and infants: a prospective, multicentre, cross-sectional study

BACKGROUND: Post-mortem imaging has been suggested as an alternative to conventional autopsy in the prenatal and postnatal periods. Noninvasive autopsies do not provide tissue for histological examination, which may limit their clinical value, especially when infection-related morbidity and mortality are suspected. METHODS: We performed a prospective, multicentre, cross-sectional study to compare the diagnostic performance of post-mortem magnetic resonance imaging with computed tomography-guided biopsy (Virtopsy®) with that of conventional autopsy in foetuses and infants. Cases referred for conventional autopsy were eligible for enrolment. After post-mortem imaging using a computed tomography scanner and a magnetic resonance imaging unit, computed tomography-guided tissue sampling was performed. Virtopsy results were compared with conventional autopsy in determining the likely final cause of death and major pathologies. The primary outcome was the proportion of cases for which the same cause of death was determined by both methods. Secondary outcomes included the proportion of false positive and false negative major pathological lesions detected by virtopsy and the proportion of computed tomography-guided biopsies that were adequate for histological examination. RESULTS: Overall, 101 cases (84 fetuses, 17 infants) were included. Virtopsy and autopsy identified the same cause of death in 91 cases (90.1%, 95% CI 82.7 to 94.5). The sensitivity and specificity of virtopsy for determining the cause of death were 96.6% (95% CI 90.6 to 98.8) and 41.7% (95% CI 19.3 to 68.0), respectively. In 32 cases (31.7%, 95% CI 23.4 to 41.3), major pathological findings remained undetected by virtopsy, and in 45 cases (44.6%, 95% CI 35.2 to 54.3), abnormalities were diagnosed by virtopsy but not confirmed by autopsy. Computed tomography-guided tissue sampling was adequate for pathological comments in 506 of 956 biopsies (52.7%) and added important diagnostic value in five of 30 cases (16.1%) with an unclear cause of death before autopsy compared with postmortem imaging alone. In 19 of 20 infective deaths (95%), biopsies revealed infection-related tissue changes. Infection was confirmed by placental examination in all fetal cases. CONCLUSIONS: Virtopsy demonstrated a high concordance with conventional autopsy for the detection of cause of death but was less accurate for the evaluation of major pathologies. Computed tomography-guided biopsy had limited additional diagnostic value. TRIAL REGISTRATION: ClinicalTrials.gov (NCT01888380)