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Abstract Several studies have emphasised how positive and negative human papillomavirus (HPV+ and HPV−, respectively) oropharyngeal squamous cell carcinoma (OPSCC) has distinct molecular profiles, tumor characteristics, and disease outcomes. Different radiomics-based prediction models have been proposed, by also using innovative techniques such as Convolutional Neural Networks (CNNs). Although some of these models reached encouraging predictive performances, there evidence explaining the role of radiomic features in achieving a specific outcome is scarce. In this paper, we propose some preliminary results related to an explainable CNN-based model to predict HPV status in OPSCC patients. We extracted the Gross Tumor Volume (GTV) of pre-treatment CT images related to 499 patients (356 HPV+ and 143 HPV−) included into the OPC-Radiomics public dataset to train an end-to-end Inception-V3 CNN architecture. We also collected a multicentric dataset consisting of 92 patients (43 HPV+ , 49 HPV−), which was employed as an independent test set. Finally, we applied Gradient-weighted Class Activation Mapping (Grad-CAM) technique to highlight the most informative areas with respect to the predicted outcome. The proposed model reached an AUC value of 73.50% on the independent test. As a result of the Grad-CAM algorithm, the most informative areas related to the correctly classified HPV+ patients were located into the intratumoral area. Conversely, the most important areas referred to the tumor edges. Finally, since the proposed model provided additional information with respect to the accuracy of the classification given by the visualization of the areas of greatest interest for predictive purposes for each case examined, it could contribute to increase confidence in using computer-based predictive models in the actual clinical practice.

Abstract The use of mineral pigments, in particular iron-rich rocks, holds significant importance in understanding the emergence and evolution of human cultures. However, sites that have yielded a number of pieces large enough to precisely identify how the use of this material changed through time are rare. In this study, we examine one of the largest known Middle Stone Age (MSA) ochre collections, from Porc-Epic Cave, Ethiopia, consisting of more than 40 kg of ochre (n = 4213 pieces), 21 ochre processing tools and two ochre-stained artefacts. By combining the analysis of the elemental and mineralogical composition of the archaeological material with that of natural ochre collected in the surroundings of the site, and correlating this information with shifts in ochre modification techniques over time, we unveil how MSA inhabitants of Porc-Epic Cave exploited mineral resources. We show that they could predict the properties of different ochre types accessible in their environment, and gradually adapted their technology to cope with changes in raw material availability. Furthermore, the analysis of ochre residues on a painted pebble, likely used to produce red dots on a surface, identifies an ochre type that was specifically employed for symbolic purposes.

Abstract The earliest European carvings, made of mammoth ivory, depict animals, humans, and anthropomorphs. They are found at Early Aurignacian sites of the Swabian Jura in Germany. Despite the wide geographical spread of the Aurignacian across Europe, these carvings have no contemporaneous counterparts. Here, we document a small, intriguing object, that sheds light on this uniqueness. Found at the Grotte des Gorges (Jura, France), in a layer sandwiched between Aurignacian contexts and dated to c. 36.2 ka, the object bears traces of anthropogenic modifications indicating intentional carving. Microtomographic, microscopic, three-dimensional roughness and residues analyses reveal the carving is a fragment of a large ammonite, which was modified to represent a caniformia head decorated with notches and probably transported for long time in a container stained with ochre. While achieving Swabian Jura-like miniaturization, the Grotte des Gorges specimen displays original features, indicating the craftsman emulated ivory carvings while introducing significant technical, thematic, and stylistic innovations. This finding suggests a low degree of cultural connectivity between Early Aurignacian hunter-gatherer groups in the production of their symbolic material culture. The pattern conforms to the existence of cultural boundaries limiting the transmission of symbolic practices while leaving space for the emergence of original regional expressions.

Abstract Recent advances in machine learning research, combined with the reduced sequencing costs enabled by modern next-generation sequencing, paved the way to the implementation of precision medicine through routine multi-omics molecular profiling of tumours. Thus, there is an emerging need of reliable models exploiting such data to retrieve clinically useful information. Here, we introduce an original consensus clustering approach, overcoming the intrinsic instability of common clustering methods based on molecular data. This approach is applied to the case of non-small cell lung cancer (NSCLC), integrating data of an ongoing clinical study (PROMOLE) with those made available by The Cancer Genome Atlas, to define a molecular-based stratification of the patients beyond, but still preserving, histological subtyping. The resulting subgroups are biologically characterized by well-defined mutational and gene-expression profiles and are significantly related to disease-free survival (DFS). Interestingly, it was observed that (1) cluster B, characterized by a short DFS, is enriched in KEAP1 and SKP2 mutations, that makes it an ideal candidate for further studies with inhibitors, and (2) over- and under-representation of inflammation and immune systems pathways in squamous-cell carcinomas subgroups could be potentially exploited to stratify patients treated with immunotherapy.

Abstract Intrahepatic cholangiocarcinoma (iCCA) is a rare malignancy, recently classified in small duct and large duct morphological subtypes. Growing evidence suggests asbestos as a putative risk factor for iCCA, albeit no correlation between asbestos and iCCA morphology has been investigated so far. The aim of the present study was to assess the relationship between asbestos exposure and iCCA morphological subtype. Forty patients with surgically removed iCCA were prospectively enrolled: asbestos exposure was assessed according to the Italian National Mesothelioma Register questionnaire. From the surgical iCCA specimens the main histopathological variables were collected, including the small duct (sd-iCCA, 32 patients) and large duct subtypes (ld-iCCA, 8 patients). Five sd-iCCA cases had a definite/probable occupational exposure to asbestos, while no cases of ld-iCCA were classified as being occupationally exposed (definite/probable). Other kind of asbestos exposure (i.e. possible occupational, familial, environmental) were recorded in 16 sd-iCCA and 3 ld-iCCA. Cases with unlikely exposure to asbestos were 11 sd-iCCA (35.5%) and 5 ld-iCCA (62.5%). In conclusion, these findings seem to indicate that sd-iCCA might be more frequently associated to asbestos exposure rather than ld-iCCA, suggesting that asbestos fibres might represent a parenchymal, rather than a ductal risk factor for iCCA. This pilot study must be confirmed by further case–control studies or large independent cohorts.

Abstract Microplastics of fibrous shape are esteemed to be the most abundant micro-debris form present in the environment. Despite the occurrence of microfibers in fish may pose a risk to human health, the literature is scarce regarding studies on the contamination in commercial marine fish mostly due to methodological issues. In this study, a versatile approach, able to discriminate among natural and synthetic microfibers according to the evaluation of specific morphological features, is proposed in farmed mussels (Mytilus galloprovincialis). The approach was useful to determine that microfibers were present in 74% of mussel samples, with a mean number of 14.57 microfibers/individual, corresponding to 3.13 microfibers/g w.w. A negative correlation between the size of analysed mussels and the amount of microfibers/g w.w. was detected, showing that smaller specimens contained more microfibers than the larger ones. This work paves the way to further studies aimed to adequately assess the risk that microfibers may pose to marine biota, also considering the commercial value as seafood items of many species of the Mytilus genus and the potential implication for human exposure.

Abstract Fully shaped, morphologically standardized bone tools are generally considered reliable indicators of the emergence of modern behavior. We report the discovery of 23 double-beveled bone tools from ~ 80,000–60,000-year-old archaeological layers at Sibudu Cave in KwaZulu-Natal, South Africa. We analyzed the texture of use-wear on the archaeological bone tools, and on bone tool replicas experimentally used in debarking trees, processing rabbit pelts with and without an ochre compound, digging in sediment in and outside a cave, and on ethnographic artefacts. Debarking trees and digging in humus-rich soil produce use-wear patterns closely matching those observed on most Sibudu tools. This tool type is associated with three different Middle Stone Age cultural traditions at Sibudu that span 20,000 years, yet they are absent at contemporaneous sites. Our results support a scenario in which some southern African early modern human groups developed and locally maintained specific, highly standardized cultural traits while sharing others at a sub-continental scale. We demonstrate that technological and texture analyses are effective means by which to infer past behaviors and assess the significance of prehistoric cultural innovations.

Abstract Chemosensory impairments have been established as a specific indicator of COVID-19. They affect most patients and may persist long past the resolution of respiratory symptoms, representing an unprecedented medical challenge. Since the SARS-CoV-2 pandemic started, we now know much more about smell, taste, and chemesthesis loss associated with COVID-19. However, the temporal dynamics and characteristics of recovery are still unknown. Here, capitalizing on data from the Global Consortium for Chemosensory Research (GCCR) crowdsourced survey, we assessed chemosensory abilities after the resolution of respiratory symptoms in participants diagnosed with COVID-19 during the first wave of the pandemic in Italy. This analysis led to the identification of two patterns of chemosensory recovery, partial and substantial, which were found to be associated with differential age, degrees of chemosensory loss, and regional patterns. Uncovering the self-reported phenomenology of recovery from smell, taste, and chemesthetic disorders is the first, yet essential step, to provide healthcare professionals with the tools to take purposeful and targeted action to address chemosensory disorders and their severe discomfort.

Abstract Microplastics released from textiles during the washing process represent the most prevalent type of microparticles found in different environmental compartments and ecosystems around the world. Release of microfibres during the washing process of synthetic textiles is due to the mechanical and chemical stresses that clothes undergo in washing machines. Several washing process parameters, conditions, formulations of laundering additives have been correlated to microfibre release and some of them have been identified to affect microfibre release during washing process, while no correlation has been evaluated between microfibre release and washing load. In the present study, microfibre release was evaluated as function of the washing load in a real washing process, indicating a progressive decrease of microfibre release with increasing washing load. The quantity of released microfibres increased by around 5 times by decreasing the washing load due to a synergistic effect between water-volume to fabric ratio and mechanical stress during washing. Moreover, the higher mechanical stress to which the fabric is subjected in the case of a low washing load, hinders the discrimination of the effect on the release of other washing parameters like the type of detergent and laundry additives used.

Abstract Muon radiography is a methodology which enables measuring the mass distribution within large objects. It exploits the abundant flux of cosmic muons and uses detectors with different technologies depending on the application. As the sensitive surface and geometric acceptance are two fundamental parameters for increasing the collection of muons, the optimization of the detectors is very significant. Here we show a potentially innovative detector of size and shape suitable to be inserted inside a borehole, that optimizes the sensitive area and maximizes the angular acceptance thanks to its cylindrical geometry obtained using plastic arc-shaped scintillators. Good spatial resolution is obtained with a reasonable number of channels. The dimensions of the detector make it ideal for use in 25 cm diameter wells. Detailed simulations based on Monte Carlo methods show great cavity detection capability. The detector has been tested in the laboratory, achieving overall excellent performance.

Abstract Middle Paleolithic Neanderthal populations occupied Eurasia for at least 250,000 years prior to the arrival of anatomically modern humans. While a considerable body of archaeological research has focused on Neanderthal material culture and subsistence strategies, little attention has been paid to the relationship between regionally specific cultural trajectories and their associated existing fundamental ecological niches, nor to how the latter varied across periods of climatic variability. We examine the Middle Paleolithic archaeological record of a naturally constrained region of Western Europe between 82,000 and 60,000 years ago using ecological niche modeling methods. Evaluations of ecological niche estimations, in both geographic and environmental dimensions, indicate that 70,000 years ago the range of suitable habitats exploited by these Neanderthal populations contracted and shifted. These ecological niche dynamics are the result of groups continuing to occupy habitual territories that were characterized by new environmental conditions during Marine Isotope Stage 4. The development of original cultural adaptations permitted this territorial stability.

Abstract Cystic fibrosis (CF) is characterized by an airway obstruction caused by a thick mucus due to a malfunctioning Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) protein. The sticky mucus restricts drugs in reaching target cells limiting the efficiency of treatments. The development of new approaches to enhance drug delivery to the lungs represents CF treatment's main challenge. In this work, we report the production and characterization of hybrid core–shell nanoparticles (hNPs) comprising a PLGA core and a dipalmitoylphosphatidylcholine (DPPC) shell engineered for inhalation. We loaded hNPs with a 7-mer peptide nucleic acid (PNA) previously considered for its ability to modulate the post-transcriptional regulation of the CFTR gene. We also investigated the in vitro release kinetics of hNPs and their efficacy in PNA delivery across the human epithelial airway barrier using an ex vivo model based on human primary nasal epithelial cells (HNEC) from CF patients. Confocal analyses and hNPs transport assay demonstrated the ability of hNPs to overcome the mucus barrier and release their PNA cargo within the cytoplasm, where it can exert its biological function.

The earliest European carvings, made of mammoth ivory, depict animals, humans, and anthropomorphs. They are found at Early Aurignacian sites of the Swabian Jura in Germany. Despite the wide geographical spread of the Aurignacian across Europe, these carvings have no contemporaneous counterparts. Here, we document a small, intriguing object, that sheds light on this uniqueness. Found at the Grotte des Gorges (Jura, France), in a layer sandwiched between Aurignacian contexts and dated to c. 36.2 ka, the object bears traces of anthropogenic modifications indicating intentional carving. Microtomographic, microscopic, three-dimensional roughness and residues analyses reveal the carving is a fragment of a large ammonite, which was modified to represent a caniformia head decorated with notches and probably transported for long time in a container stained with ochre. While achieving Swabian Jura-like miniaturization, the Grotte des Gorges specimen displays original features, indicating the craftsman emulated ivory carvings while introducing significant technical, thematic, and stylistic innovations. This finding suggests a low degree of cultural connectivity between Early Aurignacian hunter-gatherer groups in the production of their symbolic material culture. The pattern conforms to the existence of cultural boundaries limiting the transmission of symbolic practices while leaving space for the emergence of original regional expressions. [ABSTRACT FROM AUTHOR]

Fully shaped, morphologically standardized bone tools are generally considered reliable indicators of the emergence of modern behavior. We report the discovery of 23 double-beveled bone tools from ~ 80,000–60,000-year-old archaeological layers at Sibudu Cave in KwaZulu-Natal, South Africa. We analyzed the texture of use-wear on the archaeological bone tools, and on bone tool replicas experimentally used in debarking trees, processing rabbit pelts with and without an ochre compound, digging in sediment in and outside a cave, and on ethnographic artefacts. Debarking trees and digging in humus-rich soil produce use-wear patterns closely matching those observed on most Sibudu tools. This tool type is associated with three different Middle Stone Age cultural traditions at Sibudu that span 20,000 years, yet they are absent at contemporaneous sites. Our results support a scenario in which some southern African early modern human groups developed and locally maintained specific, highly standardized cultural traits while sharing others at a sub-continental scale. We demonstrate that technological and texture analyses are effective means by which to infer past behaviors and assess the significance of prehistoric cultural innovations. [ABSTRACT FROM AUTHOR]