The recombination initiation functions DprA and RecFOR suppress microindel mutations in Acinetobacter baylyi ADP1.

Short-Patch Double Illegitimate Recombination (SPDIR) has been recently identified as a rare mutation mechanism. During SPDIR, ectopic DNA single-strands anneal with genomic DNA at microhomologies and get integrated during DNA replication, presumably acting as primers for Okazaki fragments. The resulting microindel mutations are highly variable in size and sequence. In the soil bacterium Acinetobacter baylyi, SPDIR is tightly controlled by genome maintenance functions including RecA. It is thought that RecA scavenges DNA single-strands and renders them unable to anneal. To further elucidate the role of RecA in this process, we investigate the roles of the upstream functions DprA, RecFOR, and RecBCD, all of which load DNA single-strands with RecA. Here we show that all three functions suppress SPDIR mutations in the wildtype to levels below the detection limit. While SPDIR mutations are slightly elevated in the absence of DprA, they are strongly increased in the absence of both DprA and RecA. This SPDIR-avoiding function of DprA is not related to its role in natural transformation. These results suggest a function for DprA in combination with RecA to avoid potentially harmful microindel mutations, and offer an explanation for the ubiquity of dprA in the genomes of naturally non-transformable bacteria.

Practical lessons learned from real-world implementation of the molecular classification for endometrial carcinoma.

OBJECTIVES: This study aimed to explore the practical organisational aspects and difficulties in the implementation of the molecular classification of endometrial carcinoma (EC), and to demonstrate its potential impact in prognostic risk group classification. METHODS: We conducted a multicentre, retrospective cohort study of 230 patients with EC diagnosed between 2019 and 2022. Sample processing, clinicopathological, treatment and follow-up data were collected. Molecular classification was obtained by p53 and mismatch repair proteins immunohistochemistry, and POLE next-generation sequencing. RESULTS: Implementation was achieved through centralization of molecular analysis. In practice, it was possible to optimise turnaround times of complete integrative reports for hysterectomy specimens to a median time of 18 workdays. If genetic study was started in endometrial biopsies before surgery, 82.0% were available at the time of multidisciplinary tumour board, compared to 8.4% if performed in hysterectomy. ECs were classified as follows: 37.8% no specific molecular profile, 31.7% p53 abnormal, 24.3% mismatch repair deficient, and 6.1% POLE mutant. Integration of these results with traditional clinicopathologic factors led to a change in prognostic risk group in 15 (6.5%) patients, most being initially allocated to high-intermediate (n = 8) and low (n = 5) risk groups. Eight patients changed to a higher risk, and 7 to a lower risk group, whereas 2 remained in the same group. CONCLUSIONS: Centralization of EC molecular classification is a feasible option for countries with limited resources. Optimization of workflows may be achieved by earlier analysis in biopsies and prioritisation of patients whose results imply changes in risk group classification.

Hepatic Progenitor Cells in the Form of Ductular Structures within a GIST Liver Metastasis: Supporting a Putative Role in the Hepatic Metastatic Niche.

INTRODUCTION: Recent studies have highlighted the presence of hepatic progenitor cells (HPCs) in metastatic liver carcinomas. We provide further evidence of this phenomenon, presenting a case of a gastrointestinal stromal tumour (GIST) liver metastasis with evidence of intra- and peritumoral HPC. CASE DESCRIPTION: A 64-year-old man presented with a gastric mass diagnosed as a high-risk KIT-mutated GIST. The patient was treated with imatinib, recurring 5 years later with a liver mass. Liver biopsy disclosed a GIST metastasis, hallmarked by a proliferation of ductular structures without cytological atypia intermingled with the tumour cells, with a CK7/CK19/CD56-positive immunophenotype and rare CD44 positivity. The patient underwent liver resection, and the same ductular structures were present in the tumour interior and at its periphery. CONCLUSION: We document for the time the presence of HPC in the form of ductular structures in a GIST liver metastasis, further supporting their role in the liver metastatic niche.

Piggybacking on Niche Adaptation Improves the Maintenance of Multidrug-Resistance Plasmids.

The persistence of plasmids in bacterial populations represents a puzzling evolutionary problem with serious clinical implications due to their role in the ongoing antibiotic resistance crisis. Recently, major advancements have been made toward resolving this "plasmid paradox" but mainly in a nonclinical context. Here, we propose an additional explanation for the maintenance of multidrug-resistance plasmids in clinical Escherichia coli strains. After coevolving two multidrug-resistance plasmids encoding resistance to last resort carbapenems with an extraintestinal pathogenic E. coli strain, we observed that chromosomal media adaptive mutations in the global regulatory systems CCR (carbon catabolite repression) and ArcAB (aerobic respiration control) pleiotropically improved the maintenance of both plasmids. Mechanistically, a net downregulation of plasmid gene expression reduced the fitness cost. Our results suggest that global chromosomal transcriptional rewiring during bacterial niche adaptation may facilitate plasmid maintenance.

Post-fire dynamics of tree vegetation in forests with and without a history of selective logging in the Eastern Amazon.

Worldwide, forests are susceptible to fire. Forests with fire and selective logging interactions require monitoring and evaluation. This study evaluated the phytosociology and dynamics of tree vegetation in a disturbed forest (DF) and an undisturbed forest (UF) in selective logging areas affected by fire, in the Brazilian East Amazon. All trees with DBH ≥ 5 cm were measured and identified botanically in 93 plots (5 X 50 m) in the DF area and 58 plots (5 X 50 m) in the UF area, in 2010 (before logging), 2011, 2015 and 2017 (two years after the fire). Analysis of species and tree composition, diversity, similarity, mortality and recruitment were carried out. The fire affected the DF and UF areas in a similar proportion in terms of trees loss and basal area, intensifying the mortality rate. In the short term (2 years), the fire did not cause a significant reduction in species diversity, but there was a tendency towards a similarity loss in species composition in the area disturbed by logging. Subsequent assessments are necessary to understand the forest's recovery mechanisms.

A Survey on Data-Driven Predictive Maintenance for the Railway Industry.

In the last few years, many works have addressed Predictive Maintenance (PdM) by the use of Machine Learning (ML) and Deep Learning (DL) solutions, especially the latter. The monitoring and logging of industrial equipment events, like temporal behavior and fault events-anomaly detection in time-series-can be obtained from records generated by sensors installed in different parts of an industrial plant. However, such progress is incipient because we still have many challenges, and the performance of applications depends on the appropriate choice of the method. This article presents a survey of existing ML and DL techniques for handling PdM in the railway industry. This survey discusses the main approaches for this specific application within a taxonomy defined by the type of task, employed methods, metrics of evaluation, the specific equipment or process, and datasets. Lastly, we conclude and outline some suggestions for future research.

Interactions between plasmids and other mobile genetic elements affect their transmission and persistence.

Plasmids are genetic elements that play a role in bacterial evolution by providing new genes that promote adaptation to diverse conditions. Plasmids are also known to reduce bacterial competitiveness in the absence of selection for plasmid-encoded traits. It is easier to understand plasmid persistence when considering the evidence that plasmid maintenance can improve during co-evolution with the bacterial host, i.e. the chromosome. However, bacteria isolated from nature often harbor diverse mobile elements: phages, transposons, genomic islands and even other plasmids. Recent interest has emerged on the role such elements play on the persistence and evolution of plasmids. Here, we mainly review interactions between different plasmids, but also discuss their interactions with other genetic elements. We focus on interactions that impact fundamental plasmid traits, such as the fitness effect imposed on their hosts and the transfer efficiency into new host cells. We illustrate these phenomena with examples concerning clinically relevant organisms and the spread of plasmids carrying antibiotic resistance genes and virulence factors.

Post-fire recovery of a dense ombrophylous forest in Amazon.

The fires that occur in the Amazon are as damaging as the deforestation is. There is a need for further long-term studies on dynamics of tree communities in forests affected by fires. In the present study we evaluated the dynamics of tree species, before and after an accidental fire that occurred in 1997 in an experimental area of terra firme forest in the Floresta Nacional do Tapajós, in western Pará State, Brazil. Approximately 3500 trees with diameter measured at 1.30 m above ground (DBH) ≥ 5 cm were botanically identified and measured in 12 permanent plots of 0.25 ha (50 m x 50 m), in 1983, 1987, 1989, 1995, 2008 and 2012. Analyses of survival, mortality and recruitment of trees were performed. The results showed that although the fire has increased the mortality and recruitment rates after 15 years, the highest mortality occurred on trees with smaller diameters (DBH < 30 cm), so the fire did not affect the survival of large trees in the long term, explaining why the reduction in density of living trees has not greatly influenced the decrease in basal area in the burned forest.

Human Activity Recognition Using Inertial Sensors in a Smartphone: An Overview.

The ubiquity of smartphones and the growth of computing resources, such as connectivity, processing, portability, and power of sensing, have greatly changed people's lives. Today, many smartphones contain a variety of powerful sensors, including motion, location, network, and direction sensors. Motion or inertial sensors (e.g., accelerometer), specifically, have been widely used to recognize users' physical activities. This has opened doors for many different and interesting applications in several areas, such as health and transportation. In this perspective, this work provides a comprehensive, state of the art review of the current situation of human activity recognition (HAR) solutions in the context of inertial sensors in smartphones. This article begins by discussing the concepts of human activities along with the complete historical events, focused on smartphones, which shows the evolution of the area in the last two decades. Next, we present a detailed description of the HAR methodology, focusing on the presentation of the steps of HAR solutions in the context of inertial sensors. For each step, we cite the main references that use the best implementation practices suggested by the scientific community. Finally, we present the main results about HAR solutions from the perspective of the inertial sensors embedded in smartphones.

Impact of plasmid interactions with the chromosome and other plasmids on the spread of antibiotic resistance.

Naturally occurring plasmids have medical importance given that they frequently code for virulence or antibiotic resistance. In many cases, plasmids impose a fitness cost to their hosts, meaning that the growth rate of plasmid-bearing cells is lower than that of plasmid-free cells. However, this does not fit with the fact that plasmids are ubiquitous in nature nor that plasmids and their hosts adapt to each other very fast - as has been shown in laboratory evolutionary assays. Even when plasmids are costly, they seem to largely interact in such a way that the cost of two plasmids is lower than the cost of one of them alone. Moreover, it has been argued that transfer rates are too low to compensate for plasmid costs and segregation. Several mechanisms involving interactions between plasmids and other replicons could overcome this limitation, hence contributing to the maintenance of plasmids in bacterial populations. We examine the importance of these mechanisms from a clinical point of view, particularly the spread of antibiotic resistance genes.

Co-resident plasmids travel together.

Conjugative plasmids encode genes that enable them to transfer, by conjugation, from a given host cell to another cell. Conjugative transfer, despite being an important feature of conjugative plasmids, is not constitutive for most plasmids, the reason being that genes involved in horizontal transfer are mostly repressed. Only upon their transient de-repression are plasmids able to transfer horizontally. If host cells harbour multiple plasmids, their simultaneous transfer depends on simultaneous transient de-repression of all plasmids. If de-repression of different plasmids was random and independent events, simultaneous de-repression should be a rare event because the probability of simultaneous de-repression would be the product of the probabilities of de-repression of each plasmid. Some previous observations support this hypothesis, while others show that co-transfer of plasmids is more frequent than this reasoning indicates. Here, we show that co-transfer of multiple plasmids mainly results from non-independent events: the probability that all plasmids within a cell become de-repressed is much higher than if de-repression of plasmids genes were independent. We found a simple model for the probability of co-transfer: the plasmid having the lowest conjugation rates is the one who limits co-transfer. In this sense, cells receiving the plasmid with the lower transfer rate also receive the other plasmid. If de-repression happens simultaneously on co-resident plasmids, common cues may stimulate de-repression of distinct plasmids.

Conjugation efficiency depends on intra and intercellular interactions between distinct plasmids: Plasmids promote the immigration of other plasmids but repress co-colonizing plasmids.

Conjugative plasmids encode the genes responsible for the synthesis of conjugative pili and plasmid transfer. Expression of the conjugative machinery (including conjugative pili) may be costly to bacteria, not only due to the energetic/metabolic cost associated with their expression but also because they serve as receptors for certain viruses. Consequently, the presence of two plasmids in the same cell may be disadvantageous to each plasmid, because they may impose a higher fitness cost on the host. Therefore, plasmids may encode mechanisms to cope with co-resident plasmids. Moreover, it is possible that the transfer rate of a plasmid is affected by the presence of a distinct plasmid in the recipient cell. In this work, we measured transfer rates of twelve natural plasmids belonging to seven incompatibility groups in three situations, namely when: (i) donor cells contain a plasmid and recipient cells are plasmid-free; (ii) donor cells contain two unrelated plasmids and recipient cells are plasmid-free; and (iii) half of the cells contain a given plasmid and the other half contain another, unrelated, plasmid. In the third situation, recipient cells of a plasmid are the donor cells of the other plasmid. We show that there are more negative interactions (reduction of a plasmid's conjugative efficiency) between plasmids if they reside in the same cell than if they reside in different cells. However, if plasmids interacted intercellularly, the transfer rate of one of the plasmids was often higher (when the unrelated conjugative plasmid was present in the recipient cell) than if the recipient cell was plasmid-free - a positive effect. Experimental data retrieved from the study of mutant plasmids not expressing conjugative pili on the cell surface suggest that positive effects result from a higher efficiency of mating pair formation. Overall, our results suggest that negative interactions are significantly more frequent when plasmids occupy the same cell. Such interactions may determine how antibiotic resistance disseminates in bacterial populations.

Multiple plasmid interference - Pledging allegiance to my enemy's enemy.

As shown in the previous article, two distinct conjugative plasmids sometimes interact within bacterial cells, implicating changes of transfer rates. In most cases of interactions within bacteria, the transfer of one of the plasmids decreases. Less frequently, the transfer rate of one of the plasmids increases. Here we analyse what happens if three distinct conjugative plasmids colonize the same bacterial cell. Our aim is to understand how interactions between two plasmids affect the transfer rate of the third plasmid. After showing that plasmids interact in 59 out of 84 possible interactions we show that, with some exceptions, if the transfer rate of a plasmid decreases in the presence of a second plasmid, a decrease is also observed in the presence of a third plasmid. Moreover, if the conjugation rate of a plasmid increases in the presence of another, an increase is also observed if there is a third plasmid in the cell. Both types of interactions are mostly independent of the third plasmid's identity, even if sometimes the third plasmid quantitatively distorts the interaction of the other two plasmids. There is a bias towards negative intensifying interactions, which provide good news concerning the spread conjugative plasmids encoding antibiotic-resistance genes and virulence factors.

Immune subversion and quorum-sensing shape the variation in infectious dose among bacterial pathogens.

Many studies have been devoted to understand the mechanisms used by pathogenic bacteria to exploit human hosts. These mechanisms are very diverse in the detail, but share commonalities whose quantification should enlighten the evolution of virulence from both a molecular and an ecological perspective. We mined the literature for experimental data on infectious dose of bacterial pathogens in humans (ID50) and also for traits with which ID50 might be associated. These compilations were checked and complemented with genome analyses. We observed that ID50 varies in a continuous way by over 10 orders of magnitude. Low ID50 values are very strongly associated with the capacity of the bacteria to kill professional phagocytes or to survive in the intracellular milieu of these cells. Inversely, high ID50 values are associated with motile and fast-growing bacteria that use quorum-sensing based regulation of virulence factors expression. Infectious dose is not associated with genome size and shows insignificant phylogenetic inertia, in line with frequent virulence shifts associated with the horizontal gene transfer of a small number of virulence factors. Contrary to previous proposals, infectious dose shows little dependence on contact-dependent secretion systems and on the natural route of exposure. When all variables are combined, immune subversion and quorum-sensing are sufficient to explain two thirds of the variance in infectious dose. Our results show the key role of immune subversion in effective human infection by small bacterial populations. They also suggest that cooperative processes might be important for successful infection by bacteria with high ID50. Our results suggest that trade-offs between selection for population growth-related traits and selection for the ability to subvert the immune system shape bacterial infectiousness. Understanding these trade-offs provides guidelines to study the evolution of virulence and in particular the micro-evolutionary paths of emerging pathogens.

Classification of Pulmonary Nodules in 2-[18F]FDG PET/CT Images with a 3D Convolutional Neural Network.

Purpose: 2-[18F]FDG PET/CT plays an important role in the management of pulmonary nodules. Convolutional neural networks (CNNs) automatically learn features from images and have the potential to improve the discrimination between malignant and benign pulmonary nodules. The purpose of this study was to develop and validate a CNN model for classification of pulmonary nodules from 2-[18F]FDG PET images. Methods: One hundred thirteen participants were retrospectively selected. One nodule per participant. The 2-[18F]FDG PET images were preprocessed and annotated with the reference standard. The deep learning experiment entailed random data splitting in five sets. A test set was held out for evaluation of the final model. Four-fold cross-validation was performed from the remaining sets for training and evaluating a set of candidate models and for selecting the final model. Models of three types of 3D CNNs architectures were trained from random weight initialization (Stacked 3D CNN, VGG-like and Inception-v2-like models) both in original and augmented datasets. Transfer learning, from ImageNet with ResNet-50, was also used. Results: The final model (Stacked 3D CNN model) obtained an area under the ROC curve of 0.8385 (95% CI: 0.6455-1.0000) in the test set. The model had a sensibility of 80.00%, a specificity of 69.23% and an accuracy of 73.91%, in the test set, for an optimised decision threshold that assigns a higher cost to false negatives. Conclusion: A 3D CNN model was effective at distinguishing benign from malignant pulmonary nodules in 2-[18F]FDG PET images. Supplementary Information: The online version contains supplementary material available at 10.1007/s13139-023-00821-6.

Embryonal Sarcoma of the Liver in the Adult: Challenges in the Diagnosis of a Rare Entity.

Introduction: Embryonal sarcoma of the liver (ESL) is a rare neoplasm of the liver occurring mainly in paediatric ages. Making the correct diagnosis can be challenging as the laboratory and radiological findings that are often nonspecific, and the tumour immunophenotype is poorly defined and even somewhat variable. Case Presentation: A large epigastric mass was detected in a computerized tomography scan of a 43-year-old woman presenting with abdominal pain and bloating. The mass was biopsied and submitted to histopathological study. Microscopically the tumour had sarcomatoid features and showed multinucleated cells with periodic acid-Schiff (PAS)-positive globules. Immunostaining revealed positivity for vimentin, CD10, glypican-3, and α1-antitrypsin and negativity for keratins, muscle, adipocytic, and melanocytic differentiation markers. The patient was then submitted to a left hepatectomy with similar histological findings. Discussion: ESL in adults is a rarity and its diagnosis requires the exclusion of other entities. While some microscopic features are very common, they remain nonspecific. The main feature is the presence of multinucleated cells with PAS-positive hyaline globules. While ancillary testing is key, the immunophenotype also lacks specificity and ESL may have variable staining for glypican-3 and epithelial or muscle differentiation markers. Although it has been described for more than 3 decades, the prognosis and optimal treatment are still not well defined, but surgery has yielded favourable results.

Introdução: O sarcoma embrionario do figado (SEF) e uma neoplasia rara do figado que ocorre principalmente em idades pediatricas. Fazer o diagnostico correto pode ser um desafio, uma vez que os achados laboratoriais e radiologicos sao muitas vezes inespecificos e o imunofenotipo desta entidade e mal definido e algo variavel. Apresentação do caso: Foi detetada em tomografia computorizada (CT) abdominal uma massa epigastrica volu-mosa numa mulher de 43 anos apresentando dor abdominal e distensao abdominal. A massa foi biopsada e submetida a estudo histopatologico. Microscopicamente, o tumor tinha caracteristicas sarcomatoides e apresentava celulas multinucleadas com globulos hialinos com positividade para acido periodico Schiff (APS). O estudo imunohistoquimico revelou positividade para vimentina, CD10, glipicano-3 e α1-antitripsina e negatividade para queratinas e marcadores de diferenciacao muscular, adipocitica e melanocitica. Discussão/Conclusão: O SEF no adulto e uma raridade e o seu diagnostico requer a exclusao de outras entidades. Embora algumas caracteristicas microscopicas sejam muito comuns, estas permanecem inespecificas. A principal caracteristica e a presenca de celulas multinucleadas com globulos hialinos positivos para APS. Ainda que o estudo imunohistoquimico seja fundamental, o imunofenotipo tambem carece de especificidade e o SEF pode ter marcacao variavel para glipicano− 3 e marcadores de diferenciacao epitelial ou muscular. Apesar de ter sido descrito ha mais de tres decadas, o prognostico e o tratamento ideal ainda nao estao bem definidos, mas a cirurgia tem apresentado resultados favoraveis.

Extraskeletal myxoid chondrosarcoma metastasis to a Meckel's diverticulum adenocarcinoma.

Extraskeletal myxoid chondrosarcoma is a rare soft tissue tumour with a high local and distant metastasis rate and limited response to chemotherapy. Meckel's diverticulum is the most frequent congenital anomaly, and it is associated with a considerable risk of malignant transformation. In this case report, we describe a 50-year-old female patient with a history of extraskeletal myxoid chondrosarcoma of the lower limb and metastasis to the forearm who went to the emergency department with abdominal pain. The investigations revealed a caecal volvulus. A lesion in the middle third of the ileum was incidentally discovered and removed during surgery. Pathology examination revealed a Meckel's diverticulum adenocarcinoma, with metastasis of extraskeletal myxoid chondrosarcoma. Resection was complete; however, the patient had diffuse metastatic pulmonary disease and died eight months later due to disease progression. This mechanism of tumour-to-tumour metastasis is described in other locations, but, regarding the Meckel's diverticulum, this is a unique situation, previously unreported in the literature.

B-cell lymphoma 2 family members and sarcomas: a promising target in a heterogeneous disease.

Targeting the B-cell lymphoma 2 (Bcl-2) family proteins has been the backbone for hematological malignancies with overall survival improvements. The Bcl-2 family is a major player in apoptosis regulation and, has captured the researcher's interest in the treatment of solid tumors. Sarcomas are a heterogeneous group of diseases, comprising several entities, with high morbidity and mortality and with few specific therapies available. The treatment for sarcomas is based on platinum regimens, with variable results and poor outcomes, especially in advanced lesions. The high number of different sarcoma entities makes treatment standardization as well as the performance of clinical trials difficult. The use of Bcl-2 family members modifiers has revealed promising results in in vitro and in vivo models and may be a valid option, especially when used in combination with chemotherapy. In this article, a revision of these results and possibilities for the use of Bcl-2 family members inhibitors in sarcomas was performed.