Using expert-reviewed CSAM to train CNNs and its anthropological analysis

Machine learning methods for the identification of child sexual abuse materials (CSAM) have been previously studied, however, they have serious limitations. Firstly, the training sets used to train the appropriate machine learning algorithms were not previously annotated by a forensic expert in anthropology. Secondly, previously presented solutions have rarely used models trained using real pornographic content involving children. Thirdly, previous studies have not presented a detailed justification for the classification decisions made, which is important due to the recent guidelines of the European Commission (Artificial Intelligence Act). The aim of the study was to train convolution neural networks (CNNs) using expert-labelled CSAM images and thereby identify the elements of the body and/or the environment that are critical for classifications by the neural network. To train and evaluate machine learning models, we used 60,000 images equally divided into four classes (CSAM images, images displaying sexual activity involving adults, images of people without sexual activity, and images not containing people). We used four neural network architectures: MobileNet, ResNet152, xResNet152 and its modification ResNet-s, designed for the purpose of research. The trained models provided high accuracy of classifying CSAM images: xResNet152 (F1 = 0.93, 92,8%), xResNet-s (F1 = 0.93, 93,1%), ResNet152 (F1 = 0.90, 91,39%), MobileNet (F1 ranged from 0.85 to 0.87, accuracy ranged from 86% to 87%). The results of the conducted research suggest that using expert knowledge (in sexology and anthropology) significantly improved the accuracy of the models. In regard to further anthropological analysis, the results indicate that the breasts, face and torso are crucial areas for the classification of pornographic content with children's participation. Results suggests that the ResNet-s neural network may be a reliable tool for clinical work and to support the work of experts witnesses in the field of anthropology. The study design received a positive opinion of the Ethics Committee of the Faculty of Mathematics, Informatics and Mechanics of the University of Warsaw. The clinical material was used for research purposes with the consent of the relevant prosecutor's offices. Authors provided free version of Windows application to classify CSAM for forensic experts, policemen and prosecutors at the OSF repository (DOI: 10.17605/OSF.IO/RU7JX).

Patrilocality and hunter-gatherer-related ancestry of populations in East-Central Europe during the Middle Bronze Age

The demographic history of East-Central Europe after the Neolithic period remains poorly explored, despite this region being on the confluence of various ecological zones and cultural entities. Here, the descendants of societies associated with steppe pastoralists form Early Bronze Age were followed by Middle Bronze Age populations displaying unique characteristics. Particularly, the predominance of collective burials, the scale of which, was previously seen only in the Neolithic. The extent to which this re-emergence of older traditions is a result of genetic shift or social changes in the MBA is a subject of debate. Here by analysing 91 newly generated genomes from Bronze Age individuals from present Poland and Ukraine, we discovered that Middle Bronze Age populations were formed by an additional admixture event involving a population with relatively high proportions of genetic component associated with European hunter-gatherers and that their social structure was based on, primarily patrilocal, multigenerational kin-groups.

MDR carbapenemase-producing Klebsiella pneumoniae of the hypervirulence-associated ST23 clone in Poland, 2009-19

OBJECTIVES

To characterize carbapenemase-producing isolates of the Klebsiella pneumoniae hypervirulent (hvKp) clone ST23 in Poland.

METHODS

Fifteen K. pneumoniae ST23 isolates were identified by the Polish surveillance of carbapenemase-producing Enterobacterales. These comprised a cluster with KPC-2 + NDM-1 (n = 7), KPC-2 (n = 1) or NDM-1 (n = 1) enzymes from one hospital from 2018, and sporadic isolates with KPC-2 (n = 1), NDM-1 (n = 1), VIM-1 (n = 1) or OXA-48 (n = 3), recovered from 2009 to 2019 in different towns. The isolates were sequenced by Illumina MiSeq, followed by MinION for six representatives. Clonality, phylogeny, serotypes, virulomes, resistomes and plasmids of the isolates were analysed and compared with international ST23 strains, using various bioinformatic tools.

RESULTS

Only two diverse isolates with KPC-2 or VIM-1 were of typical hvKp ST23 serotypes K1 and O1v.2, and its predominant phylogenetic clade. These contained multiple chromosomal (ybt, clb) and pK2044/KpVP-1 plasmid (iuc, iro, rmpADC, rmpA2) virulence loci, whereas carbapenemase and other antimicrobial resistance (AMR) genes were on single additional plasmids. All remaining isolates were of K57 and O2v.2 serotypes, and a minor, distant clade of unclear phylogeny, including also ∼10 isolates from other European countries. These had fewer virulence loci (ybt, iuc, rmpADC, rmpA2) but abounded in plasmids, which with several chromosomal AMR mutations conferred more extensive MDR phenotypes than in K1 O1v.2. Lower clonal diversity than in K1, and numerous common characteristics of the isolates supported the hypothesis of the emerging character of the ST23 K57 clade.

CONCLUSIONS

A new MDR ST23 lineage has emerged in Europe, causing a potential threat to public health.

Mitochondrial genomes from Bronze Age Poland reveal genetic continuity from the Late Neolithic and additional genetic affinities with the steppe populations

OBJECTIVE

In this work we aim to investigate the origins and genetic affinities of Bronze Age populations (2,400-1,100 BC) from the region of southern Poland and to trace maternal kinship patterns present in the burials of those populations by the use of complete mitochondrial genomes.

MATERIALS AND METHODS

We performed ancient DNA analyses for Bronze Age individuals from present-day Poland associated with the Strzyżow culture, the Mierzanowice culture, and the Trzciniec Cultural circle. To obtain complete mitochondrial genomes, we sequenced genomic libraries using Illumina platform. Additionally, hybridization capture was used to enrich some of the samples for mitochondrial DNA. AMS ¹⁴ C-dating was conducted for 51 individuals to verify chronological and cultural attribution of the analyzed samples.

RESULTS

Complete ancient mitochondrial genomes were generated for 80 of the Bronze Age individuals from present-day Poland. The results of the population genetic analyses indicate close maternal genetic affinity between Mierzanowice, Trzciniec, and Corded Ware culture-associated populations. This is in contrast to the genetically more distant Strzyżów people that displayed closer maternal genetic relation to steppe populations associated with the preceding Yamnaya culture and Catacomb culture, and with later Scythians. Potential maternal kinship relations were identified in burials of Mierzanowice and Trzciniec populations analyzed in this study.

DISCUSSION

Results revealed genetic continuity from the Late Neolithic Corded Ware groups to Bronze Age Mierzanowice and Trzciniec-associated populations, and possible additional genetic contribution from the steppe to the formation of the Strzyżów-associated group at the end of 3rd millennium BC. Mitochondrial patterns indicated several pairs of potentially maternally related individuals mostly in Trzciniec-associated group.

[Replication of HCV in bone marrow of patients with haematological disorders]

The aim of the study was to evaluate the presence of HCV replication in bone marrow cells derived from patients displaying hematological disorders. We analysed serum, peripheral blood mononuclear cells (PBMC) and bone marrow samples obtained from 27 patients displaying the following dysfunctions: lymphoma, trombocytopenia, haemophilia, pancytopenia and acute myeloid leukemia (AML). The presence of HCV-RNA in samples was detected by RT-PCR. All the serum samples were HCV-RNA positive as well as 9 out of 27 (33%) PBMC and 17 out of 27 (63%) of bone marrow samples. Independently to the disorder type, the co-presence of HCV-RNA in serum and bone marrow with the simultaneous absence of the viral genetic material in PBMC was detected in 5 (18.5%) of patients. This result suggests that bone marrow is a site of active viral replication. To check whether a viral replication generates any mutations, an SSCP analysis of the 5'UTR viral region was performed. The difference in the viral sequence derived from serum, PBMC and bone marrow was detected in one case. This result may indicate the occurrence of mutation process during the viral replication in bone marrow. An immunohistochemical analysis of bone marrow smears showed the presence of HCV antigens.

CONCLUSION

bone marrow cells of patients displaying hematological disorders represent a putative site of extrahepatic HCV replication.

[Bone marrow cellularity in acute lymphoblastic leukemia of children]

The early response to therapy in childhood acute lymphoblastic leukemia (ALL) is typically assessed by bone marrow status. The clearance of blast cells in peripheral blood and bone marrow during induction therapy was analysed in 38 children (27 precursor-B-ALL and 11 precursor T-ALL) treated according to BFM90 or New York 93 protocols. Leukocyte count and peripheral blood smear taken at diagnosis, day 8, day 14 and day 33 as well as bone marrow cellularity and percentage of blasts on days: 0, 14, 33 were analysed. The number of blasts in bone marrow was correlated to bone marrow cellularity (Spearman's rho = 0.72, p = 0.001). Patients with T-ALL were more frequently resistant to steroids in vivo and reached remission later in comparison to precursor-B-ALL children (p = 0.019), however blasts reduction ratio was comparable in both lineages. Bone marrow cellularity on days 14 and 33 of induction therapy was similar.