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In this paper we describe the validation of a focus reduction neutralization test (FRNT) to quantitate human SARS-CoV-2 neutralizing antibodies by using the CTL Immunospot S6 Universal Analyzer. We employed a previously published protocol and compared its performances to a well-established and traditional serum-neutralization assay (SN). To assess diagnostic sensitivity, a total number of 201 human sera positive by SN for SARS-CoV-2 NAbs were processed: 196/201 tested positive by FRNT50 (97.51 %). A diagnostic specificity of 100 % was obtained by evaluating 206 negative serum samples. Repeatability of the test was evaluated by determining the intra and inter-assay coefficient of variation (CV). A standard deviation of 0.83 and a CV of 13 % were evidenced demonstrating an acceptable reproducibility of the assay. Moreover, a Cohen's Kappa of 0.975 was obtained proving an extremely high level of agreement between the FRNT protocol and the SN. Despite an acceptable correlation between methods (p

West Nile virus (WNV) (Flaviviridae, Flavivirus) infection is a mosquito-borne zoonosis able of causing disease and death in humans and animals. Over the past decade, WNV infections have been a significant public health concern in Europe, and Italy has been among the most affected countries since 2008. The 2022 vector season has been characterized by an intense and early circulation of WNV. This report describes cases of co-circulation of WNV L1 and of WNV L2 occurring at the end of the 2022 vector season in Sicily and Tuscany, regions where no strains had ever been sequenced. The phylogenetic analysis of the detected strains confirmed the peculiar WNV scenario that has characterized the Italian West Nile disease (WND) epidemic since its appearance. The circulation observed in Tuscany was in fact a consequence of the spread of endemic strains to new areas while the Sicilian episodes were linked to new introductions of WNV L1 and L2 strains likely from other European countries.

Abstract In the present work, we model the diffusion of scientific knowledge embodied in the textbooks of the Sphaera corpus. This corpus consists of more than 350 different editions of textbooks used for teaching astronomy in European universities during the early modern period. Connections between the editions are based on mutual semantic knowledge and are arranged in a multiplex network of four layers, with each layer representing a different semantic relation. The modeling aims for a better understanding (and possible prediction) of the process of knowledge accumulation in the various editions. We consider semantic text-parts as knowledge units transferred between the editions, and show how these units spread using both an SI model and its modified version, the Bass model. Both models include a parameter representing the rate of transfer, which is interpreted as the mechanism underlying the process of knowledge accumulation; the Bass model has an extra parameter that represents the rate of external influence and stands out as the “resistance to adoption from” and “resistance to be influenced by” other knowledge systems. The modeling has helped us to chart the path and mechanisms of knowledge transformation in the early modern period. Networks are identified by adding further layers whose graphs express socioeconomic relationships and conditional sub-networks. The comparison between the model and these layers enables us to conclude that the accumulation of knowledge was highly dependent on the institutional embedding of scientific production because the diffusion of knowledge was mostly determined by the economic constraints of early modern printers and publishers. It further suggests that geographic proximity played a role—although secondary—in the diffusion of knowledge but only under the condition that the book producers involved were still living. The transformation of early modern scientific knowledge is, therefore, highly dependent on the institutional and economic contexts of the book producers.

This work describes a computational method for reconstructing clusters of social relationships among early modern printers and publishers, the most determinant agents for the process of transformation of scientific knowledge. The method is applied to a dataset retrieved from the Sphaera corpus, a collection of 359 editions of textbooks used at European universities and produced between the years 1472 and 1650. The method makes use of standard bibliographic data and fingerprints; social relationships are defined as “awareness relationships”. The historical background is constituted of the production and economic practices of early modern printers and publishers in the academic book market. The work concludes with empirically validating historical case studies, their historical interpretation, and suggestions for further improvements by utilizing machine learning technologies.

The ultimate objective of this work is to demonstrate that it is possible to reconsider the emergence of modern science as a process of disintegration of the quadrivium, which was considered a stable scheme for the organization of knowledge. The argument considers the quadrivium according to the Boethian systematization that was used to organize the curricula of the late medieval universities. This argument follows the development of each of its disciplines and illustrates the practical turn they underwent. The period between the thirteenth and seventeenth centuries is explored, and shows that during this period, the quadrivium potentially included a fifth autonomous discipline, calendric. The article concludes by describing epistemological considerations to the mechanisms of disintegration of knowledge structures.

SARS-CoV-2 was a worldwide threat during the COVID-19 pandemic, and the state of Mato Grosso had the second highest mortality rate in Brazil, with 427. 4 deaths/100,000 inhabitants. However, no large-scale study among dogs and cats in such highly infected areas of Brazil has so far been conducted. Accordingly, the present study reports on a serosurvey among dogs and cats in Cuiabá, capital of Mato Grosso from November 2020 to July 2021, where the human mortality rate was 605/100,000 at that time. Overall, 33/762 dogs (4.3%) and 4/182 cats (2.2%) were found to be seropositive for SARS-CoV-2 through ELISA, and 3/762 dogs (0.4%) and 3/182 cats (1.6%) were seropositive through the serum neutralization test. Cats presented higher seroprevalence with higher titers of neutralizing antibodies. Although N-protein based ELISA may be a good screening test, cross-reactivity with other canine coronaviruses may impair its diagnostic use among dogs.

We propose a 3D stochastic cellular automaton model, governed by evolutionary game theory, to simulate bone remodeling dynamics. The model includes four voxel states: Formation, Quiescence, Resorption, and Environment. We simulate the Resorption and Formation processes on separate time scales to explore the parameter space and derive a phase diagram that illustrates the sensitivity of these processes to parameter changes. Combining these results, we simulate a full bone remodeling cycle. Furthermore, we show the importance of modeling small neighborhoods for studying local bone microenvironment controls. This model can guide experimental design and, in combination with other models, it could assist to further explore external impacts on bone remodeling. Consequently, this model contributes to an improved understanding of complex dynamics in bone remodeling dynamics and exploring alterations due to disease or drug treatment. [ABSTRACT FROM AUTHOR]

Abstract Background As research on HIV vaccines continues to advance, studies exploring the feasibility of this intervention are necessary to inform uptake and dissemination strategies with key populations, including people who use drugs (PWUD). Methods We conducted 25 in-depth qualitative interviews examining HIV vaccine acceptability among PWUD in Vancouver, Canada. Participants were recruited from an ongoing prospective cohort of HIV-negative PWUD. Data were coded using NVivo, and analyzed thematically. Results Acceptability was framed by practical considerations such as cost and side effects, and was influenced by broader trust of government bodies and health care professionals. While an HIV vaccine was perceived as an important prevention tool, willingness to be vaccinated was low. Results suggest that future vaccine implementation must consider how to minimize the burden an HIV vaccine may place on PWUD. Centering the role of health care providers in information dissemination and delivery may assist with uptake. Conclusions Our findings suggest improvements in care and improved patient-provider relationships would increase the acceptability of a potential HIV vaccine among this population.

This paper presents a novel approach for fragmented solid object classification exploiting neural networks based on point clouds. This work is the initial step of a project in collaboration with the Institution of ‘Ente Parco Archeologico del Colosseo’ in Rome, which aims to reconstruct ancient artifacts from their fragments. We built from scratch a synthetic dataset (DS) of fragments of different 3D objects including aging effects. We used this DS to train deep learning models for the task of classifying internal and external fragments. As model architectures, we adopted PointNet and dynamical graph convolutional neural network, which take as input a point cloud representing the spatial geometry of a fragment, and we optimized model performance by adding additional features sensitive to local geometry characteristics. We tested the approach by performing several experiments to check the robustness and generalization capabilities of the models. Finally, we test the models on a real case using a 3D scan of artifacts preserved in different museums, artificially fragmented, obtaining good performance.

Recent advances in object detection facilitated by deep learning have led to numerous solutions in a myriad of fields ranging from medical diagnosis to autonomous driving. However, historical research is yet to reap the benefits of such advances. This is generally due to the low number of large, coherent, and annotated datasets of historical documents, as well as the overwhelming focus on Optical Character Recognition to support the analysis of historical documents. In this paper, we highlight the importance of visual elements, in particular illustrations in historical documents, and offer a public multi-class historical visual element dataset based on the Sphaera corpus. Additionally, we train an image extraction model based on YOLO architecture and publish it through a publicly available web-service to detect and extract multi-class images from historical documents in an effort to bridge the gap between traditional and computational approaches in historical studies.

SARS-CoV-2 has been shown to lose the furin polybasic cleavage site (FCS) following adaptation on cell culture. Deletion occurring in this region, which may include also the FCS flanking regions, seem not to affect virus replication in vitro; however, a chimeric SARS-CoV-2 virus without the sole FCS motif has been associated with lower virulence in mice and lower neutralization values. Moreover, SARS-CoV-2 virus lacking the FCS was shed to lower titers from experimentally infected ferrets and was not transmitted to cohoused sentinel animals, unlike wild-type virus. In this study, we investigated the replication kinetics and cellular tropism of a SARS-CoV-2 isolate carrying a 10-amino acid deletion in the spike protein spanning the FCS in lung ex vivo organ cultures of mink. Furthermore, we tested the neutralization capabilities of human convalescent SARS-CoV-2 positive serum samples against this virus. We showed that this deletion did not significantly hamper neither ex vivo replication nor neutralization activity by convalescent serum samples. This study highlights the importance of the preliminary phenotypic characterization of emerging viruses in ex vivo models and demonstrates that mink lung tissues are permissive to the replication of a mutant form of SARS-CoV-2 showing a deletion spanning the FCS. Notably, we also highlight the need for sequencing viral stocks before any infection study as large deletions may occur leading to the misinterpretation of results.

Simple Summary: West Nile virus (WNV) infection is a significant public health concern in Europe and Italy is one of the most affected countries since 2008. This brief report describes circulation cases of West Nile virus lineage 1 and lineage 2 strains occurring at the end of the 2022 vector season in Sicily and Tuscany, regions where no strains had ever been sequenced. The genetic characterization of the WNV strains responsible for these cases confirmed the peculiar WNV Italian scenario, marked by endemic Italian circulation spreading to new areas of the country (Tuscany case) and novel introductions from different European and Italian areas (Sicilian episode). It highlights the importance of continuous molecular surveillance for the early detection of viral circulation throughout the country and the monitoring of the arrival of new strains and the evolution of novel variants, in order to trigger adequate measures and limit its spread and human infections. West Nile virus (WNV) (Flaviviridae, Flavivirus) infection is a mosquito-borne zoonosis able of causing disease and death in humans and animals. Over the past decade, WNV infections have been a significant public health concern in Europe, and Italy has been among the most affected countries since 2008. The 2022 vector season has been characterized by an intense and early circulation of WNV. This report describes cases of co-circulation of WNV L1 and of WNV L2 occurring at the end of the 2022 vector season in Sicily and Tuscany, regions where no strains had ever been sequenced. The phylogenetic analysis of the detected strains confirmed the peculiar WNV scenario that has characterized the Italian West Nile disease (WND) epidemic since its appearance. The circulation observed in Tuscany was in fact a consequence of the spread of endemic strains to new areas while the Sicilian episodes were linked to new introductions of WNV L1 and L2 strains likely from other European countries. [ABSTRACT FROM AUTHOR]

In recent years, the Ribosome profiling technique (Ribo–seq) has emerged as a powerful method for globally monitoring the translation process in vivo at single nucleotide resolution. Based on deep sequencing of mRNA fragments, Ribo–seq allows to obtain profiles that reflect the time spent by ribosomes in translating each part of an open reading frame. Unfortunately, the profiles produced by this method can vary significantly in different experimental setups, being characterized by a poor reproducibility. To address this problem, we have employed a statistical method for the identification of highly reproducible Ribo–seq profiles, which was tested on a set of E. coli genes. State-of-the-art artificial neural network models have been used to validate the quality of the produced sequences. Moreover, new insights into the dynamics of ribosome translation have been provided through a statistical analysis on the obtained sequences.

This article discusses cross-sensitization between sesame and other seeds in children with food allergies. Sesame allergy is becoming more prevalent due to its increased presence in our diets. The study found a high rate of cross-sensitization among sesame and other seeds, such as flax, sunflower, and pumpkin seeds. The severity of sesame allergy in children was confirmed, and the role of sesame 11S and 7S globulins in cross-sensitization was highlighted. Further studies are needed to explore the clinical relevance of cross-reactivity among seeds. [Extracted from the article]

The egress and fertilization of Plasmodium gametes and development of a motile ookinete are the first crucial steps that mediate the successful transmission of the malaria parasites from humans to the Anopheles vector. However, limited information exists about the cell biology and regulation of this process. Technical impediments in the establishment of in vitro conditions for ookinete maturation in Plasmodium falciparum and other human malaria parasites further constrain a detailed characterization of ookinete maturation. Here, using fluorescence microscopy and immunolabeling, we compared P. falciparum ookinete maturation in Anopheles coluzzii mosquitoes in vivo and in cell culture in vitro. Our results identified two critical steps in ookinete maturation that are regulated by distinct mosquito factors, thereby highlighting the role of the mosquito environment in the transmission efficiency of malaria parasites.

The development of the field of digital humanities in recent years has led to the increased use of knowledge graphs within the community. Many digital humanities projects tend to model their data based on CIDOC-CRM ontology, which offers a wide array of classes appropriate for storing humanities and cultural heritage data. The CIDOC-CRM ontology model leads to a knowledge graph structure in which many entities are often linked to each other through chains of relations, which means that relevant information often lies many hops away from their entities. In this paper, we present a method based on graph walks and text processing to extract entity information and provide semantically relevant embeddings. In the process, we were able to generate similarity recommendations as well as explore their underlying data structure. This approach was then demonstrated on the Sphaera Dataset which was modeled according to the CIDOC-CRM data structure.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved rapidly, leading to viral lineages characterized by multiple mutations in the spike protein, which could potentially confer to the virus the ability to avoid the vaccine-induced immune response, making the vaccines less effective or ineffective. Here, we initially evaluated the neutralization capabilities in vitro by serum neutralization (SN) of six serum samples collected from recipients of the BNT162b2 vaccine against 11 SARS-CoV-2 isolates belonging to the major SARS-CoV-2 lineages that had been circulating in Italy. Then, we considered 30 additional serum samples by SN assay against the dominant B.1.617.2 (Delta) variant. A B.1 lineage isolate was used as a reference. In the first analysis, significant differences when compared with the reference strain (p > 0.05) were not evidenced; instead, when the panel of 30 sera was tested against the B.1.617.2 (Delta) variant, a significant (p = 0.0015) 2.38-fold reduction in neutralizing titres compared with the reference after the first vaccine dose was demonstrated. After the second vaccine dose, the reduction was not significant (p = 0.1835). This study highlights that the BNT162b2 vaccine stimulates a humoral response able to neutralize all tested SARS-CoV-2 variants, thus suggesting a prominent role in mitigating the impact of the SARS-CoV-2 pandemic in real-world conditions. Long-term follow-up is currently ongoing.

Abstract Background The basophil activation test (BAT), has been proposed as a possible assay for the diagnosis of immediate-type allergy to beta-lactams (BLs). The aim of this study was to assess the utility of BAT in the diagnosis of amoxicillin (AMX) or AMX-clavulanate (AMX-C) IgE-mediated hypersensitivity in children and adults. Material and methods Eighteen children and 21 adults, with clinical history of immediate reactions to AMX or AMX-C, were referred to Anna Meyer Children’s Hospital and San Giovanni di Dio Hospital, respectively. They underwent in vivo tests (skin prick test and intradermal test). Moreover, BAT with AMX or AMX-C was performed within 6 months from the reaction. Results In the pediatric group, the concordance between the skin tests (ST) and BAT results was 83.3%. Upon comparing the symptom grades and ST results to the BAT results, we found that the reaction severity and ST positivity did not correlate with BAT results in children. In the adult group, the concordance between the ST and BAT results was 61.9%. Upon comparing patients with severe reactions and patients with mild reactions in terms of BAT results, we found a BAT sensitivity of 38.5% and a specificity of 100%. When comparing the symptom grades to the BAT results, we found that no patients with mild symptoms had a positive BAT result, whereas 38.5% of patients with severe symptoms had a positive BAT result. Conclusions BAT does not seem to be a useful tool to increase the sensitivity of an allergy work-up to diagnose immediate hypersensitivity to AMX or AMX-C.

The present work investigates the process of emergence of new epistemic communities. The research is based on semantic, content-related data extracted from a corpus of 359 printed editions, mainly of textbooks used to teach cosmology at European universities between 1472 and 1650. Epistemic communities are identified as families of editions, grouped according to their content, that eventually came to shape knowledge within and by way of the European educational framework. First, a method of classifying the textual content of the books is introduced. Second, a directed, multiplex network is constructed in five layers whose tructures are defined specifically for the research question at hand. Then the network is analyzed, first by making use of the aggregated graph—which accounts for the connectivity between books when any of the potential semantic relations are indistinctly considered—and second by showing the contribution of each layer to the emergence of new families of editions. Finally, we interpret the results within a historical framework and identify an epistemic community that represents continuity with the medieval tradition, plus two new scientific and diverging communities that originated in the cultural context of the Reformed countries, which appear in the 1530s. The characteristics of the identified epistemic communities are further analyzed in order to draw general inferences concerning mechanisms of emergence of epistemic communities and their identification in corpora of historical sources. The work concludes by describing future research endeavors related to the corpus, also based on new series of data.

Outbreaks of Rift Valley fever (RVF) occurred in Namibia in 2010 and 2011. Complete genome characterization was obtained from virus isolates collected during disease outbreaks in southern Namibia in 2010 and from wildlife in Etosha National Park in 2011, close to the area where RVF outbreaks occurred in domestic livestock. The virus strains were sequenced using Sanger sequencing (Namibia_2010) or next generation sequencing (Namibia_2011). A sequence-independent, single-primer amplification (SISPA) protocol was used in combination with the Illumina Next 500 sequencer. Phylogenetic analysis of the sequences of the small (S), medium (M), and large (L) genome segments of RVF virus (RVFV) provided evidence that two distinct RVFV strains circulated in the country. The strain collected in Namibia in 2010 is genetically similar to RVFV strains circulating in South Africa in 2009 and 2010, confirming that the outbreaks reported in the southern part of Namibia in 2010 were caused by possible dissemination of the infection from South Africa. Isolates collected in 2011 were close to RVFV isolates from 2010 collected in humans in Sudan and which belong to the large lineage containing RVFV strains that caused an outbreak in 2006–2008 in eastern Africa. This investigation showed that the RVFV strains circulating in Namibia in 2010 and 2011 were from two different introductions and that RVFV has the ability to move across regions. This supports the need for risk-based surveillance and monitoring.

Camelpox is a viral contagious disease of Old-World camelids sustained by Camelpox virus (CMLV). The disease is characterized by mild, local skin or severe systemic infections and may have a major economic impact due to significant losses in terms of morbidity and mortality, weight loss, and low milk yield. Prevention of camelpox is performed by vaccination. In this study, we investigated the composition of a CMLV-based, live-attenuated commercial vaccine using next-generation sequencing (NGS) technology. The results of this analysis revealed genomic sequences of Modified Vaccinia virus Ankara (MVA).

Atopic dermatitis (AD) is a common chronic inflammatory skin disorder in childhood. Skin barrier impairment exposes infants to food allergens, potentially causing sensitization followed by IgE-mediated food allergy. We describe the case of an infant with severe AD in whom several sensitizations to foods are detected, with consequently difficult weaning, and a history of anaphylaxis to cashew nut. Foods for which skin tests were negative were introduced into the infant's diet. Then, when AD control was managed, oral food challenges (OFCs) for foods to which the patient was sensitized, with the exception of cashew nut, were performed. The simultaneous presence of sensitization toward multiple foods made it difficult to introduce them using classic OFC. Therefore, it was decided to perform the low-dose, gradual controlled OFC. This led to an introduction of sensitized foods into the infant's diet, with the exception of cashew nut, avoiding allergic reactions. Absolute recommendations on how, when, and where to perform OFCs with allergenic food to which the child with AD is sensitized are lacking so far. In our opinion, OFCs and the subsequent ntroduction of allergenic foods should be individualized, evaluating some factors such as their social and nutritional importance, the patient's age and clinical phenotype (including the history of anaphylaxis), and the sensitization profile. There is agreement on the fact that the dietary approach in children with moderate-severe AD should no longer include a strict elimination diet. We believe that an early, gradual controlled introduction of all allergenics to identify the amount of food tolerated in the absence of reactions, even if low dose, may improve patients' and families' quality of life. However, even if discussing a vast relevant literature, the limitation of our work is that we describe the management of a single patient. Extensive and high-quality research is needed in this field to improve the available evidence in the area. [ABSTRACT FROM AUTHOR]