Joining forces for pathology diagnostics with AI assistance: The EMPAIA initiative.

Over the past decade, artificial intelligence (AI) methods in pathology have advanced substantially. However, integration into routine clinical practice has been slow due to numerous challenges, including technical and regulatory hurdles in translating research results into clinical diagnostic products and the lack of standardized interfaces. The open and vendor-neutral EMPAIA initiative addresses these challenges. Here, we provide an overview of EMPAIA's achievements and lessons learned. EMPAIA integrates various stakeholders of the pathology AI ecosystem, i.e., pathologists, computer scientists, and industry. In close collaboration, we developed technical interoperability standards, recommendations for AI testing and product development, and explainability methods. We implemented the modular and open-source EMPAIA Platform and successfully integrated 14 AI-based image analysis apps from eight different vendors, demonstrating how different apps can use a single standardized interface. We prioritized requirements and evaluated the use of AI in real clinical settings with 14 different pathology laboratories in Europe and Asia. In addition to technical developments, we created a forum for all stakeholders to share information and experiences on digital pathology and AI. Commercial, clinical, and academic stakeholders can now adopt EMPAIA's common open-source interfaces, providing a unique opportunity for large-scale standardization and streamlining of processes. Further efforts are needed to effectively and broadly establish AI assistance in routine laboratory use. To this end, a sustainable infrastructure, the non-profit association EMPAIA International, has been established to continue standardization and support broad implementation and advocacy for an AI-assisted digital pathology future.

Cadherin Expression Profiles Define Glioblastoma Differentiation and Patient Prognosis.

Cadherins are cell-cell adhesion proteins which have been strongly implicated in cancer invasion, dissemination and metastasis capacity; thus, they are key players in the epithelial-to-mesenchymal transition (EMT) program. However, their role in glioblastoma (GBM), a primary central nervous system aggressive tumor, remains to be clarified. N-, E- and P-cadherin expression was analyzed on a large series of GBMs, characterized with clinical, imaging and neuropathological parameters, as well as with patients' survival data. In addition, cadherins' expression was studied in match-recurrent cases. Using TCGA data, cadherin expression profiles were also evaluated according to GBM transcription subtypes. N-cadherin expression was observed in 81.5% of GBM, followed by E-cadherin in 31% and P-cadherin in 20.8%. Upon tumor recurrence, P-cadherin was the only significantly upregulated cadherin compared with the primary tumor, being positive in 65.8% of the cases. Actually, P-cadherin gain was observed in 51.4% of matched primary-recurrent cases. Cadherins' co-expression was also explored. Interestingly, E- and N-cadherin co-expression identified a GBM subgroup with frequent epithelial differentiation and a significant survival benefit. On the other hand, subgroups with P-cadherin expression carried the worse prognosis. P- and N-cadherin co-expression correlated with the presence of a mesenchymal phenotype. Expressions of isolated P-cadherin or E- and P-cadherin co-expression were associated with imaging characteristics of aggressiveness, to highly heterogeneous tumors, an d to worse patient survival. Classical cadherins co-expression subgroups present consistent clinical, imaging, neuropathological and survival differences, which probably reflect different states of an EMT-like program in GBM.

Geminiviridae and Alphasatellitidae Diversity Revealed by Metagenomic Analysis of Susceptible and Tolerant Tomato Cultivars across Distinct Brazilian Biomes.

The diversity of Geminiviridae and Alphasatellitidae species in tomatoes was assessed via high-throughput sequencing of 154 symptomatic foliar samples collected from 2002 to 2017 across seven Brazilian biomes. The first pool (BP1) comprised 73 samples from the North (13), Northeast (36), and South (24) regions. Sixteen begomoviruses and one Topilevirus were detected in BP1. Four begomovirus-like contigs were identified as putative novel species (NS). NS#1 was reported in the semi-arid (Northeast) region and NS#2 and NS#4 in mild subtropical climates (South region), whereas NS#3 was detected in the warm and humid (North) region. The second pool (BP2) comprised 81 samples from Southeast (39) and Central-West (42) regions. Fourteen viruses and subviral agents were detected in BP2, including two topileviruses, a putative novel begomovirus (NS#5), and two alphasatellites occurring in continental highland areas. The five putative novel begomoviruses displayed strict endemic distributions. Conversely, tomato mottle leaf curl virus (a monopartite species) displayed the most widespread distribution occurring across the seven sampled biomes. The overall diversity and frequency of mixed infections were higher in susceptible (16 viruses + alphasatellites) in comparison to tolerant (carrying the Ty-1 or Ty-3 introgressions) samples, which displayed 9 viruses. This complex panorama reinforces the notion that the tomato-associated Geminiviridae diversity is yet underestimated in Neotropical regions.

Autoimmune Hepatitis Induced by Hepatitis Delta Virus: A Conundrum.

Introduction: The association of hepatitis delta virus (HDV) infection with positive autoantibodies and autoimmune features has been known for decades. However, to date, very few cases of clinical autoimmune hepatitis (AIH) have been reported in association with HDV infection, most of them being in the context of treatment with peginterferon. Case Report: This case refers to a 46-year-old woman born in Guinea-Bissau who moved to Portugal in 2018 to investigate complaints of diffuse abdominal discomfort and nausea. Her initial work-up, including laboratory and liver histology, was consistent with type 1 AIH. She had HBe antigen-negative chronic hepatitis B virus infection with negative DNA and also a positive total anti-HDV antibody, with negative IgM and undetectable RNA. Therefore, after initiating prophylactic tenofovir difumarate, she was started on prednisolone followed by azathioprine, which was later stopped due to presumed hepatotoxicity. Repeated histology showed signs of viral superinfection, and she was treated with acyclovir due to a positive herpes simplex IgM, with HDV RNA remaining negative. A third flare in transaminases prompted the introduction of mycophenolate mofetil (MMF) after a thorough exclusion of additional causes of liver disease. About 6 months later, during another bout of hepatitis, HDV RNA was finally positive and classified as genotype 5. MMF was stopped, and, considering a contraindication to interferon, the patient was offered therapy with bulevirtide, which she refused for personal reasons as she is currently living in her home country. Discussion: This is a challenging case of autoimmune or "autoimmune-like" hepatitis, probably induced by chronic HDV infection. High suspicion of HDV was essential because, had the case been interpreted as refractory AIH, with escalation of immunosuppression, a more severe course of the viral infection might have ensued. Recently, HDV suppression with bulevirtide was shown to reverse autoimmune liver disease. We hypothesize that the same could have happened to our patient, had she accepted this treatment.

Introdução: A associação da infeção pelo vírus da hepatite delta (VHD) com a presença de autoanticorpos e outros aspetos de autoimunidade é conhecida desde há várias décadas. Contudo, até à data, muito poucos casos de hepatite autoimune (HAI) clínica foram reportados em relação com a infeção VHD, sendo a maioria destes no contexto de terapêutica com interferão peguilado. Caso clínico: O caso refere-se a uma mulher de 46 anos natural da Guiné-Bissau, que se mudou para Portugal em 2018 para investigação de queixas de desconforto abdominal difuso e náuseas. A avaliação laboratorial inicial e a histologia hepática foram compatíveis com HAI tipo 1. A doente apresentava também infeção crónica a VHB (vírus da hepatite B) antigénio HBe negativa, com DNA negativo, e anti-VHD (vírus da hepatite delta) total positivo, com IgM negativo e RNA indetetável. Assim, após início de tenofovir difumarato profilático, foi iniciada terapêutica com prednisolona seguida de azatioprina, que posteriormente se interrompeu por presumível hepatotoxicidade. Uma segunda biópsia mostrou aspetos de superinfeção viral e como tal a doente foi tratada com aciclovir, tendo em conta IgM positivo para Herpes Simplex, mantendo-se o RNA VHD negativo. Um terceiro flare de transaminases motivou o início de micofenolato de mofetil, após extensa investigação e exclusão de outras causas de doença hepática. Cerca de 6 meses mais tarde, durante novo episódio de hepatite, o RNA VHD revelou-se finalmente positivo e este foi classificado como genotipo 5. O MMF foi suspenso e, considerando a contra-indicação para interferão, foi proposto à doente tratamento com bulevirtide, que esta recusou, alegando motivos pessoais, visto estar atualmente a residir no seu país de origem. Discussão: Este é um caso desafiante de hepatite autoimune, ou autoimune-like, provavelmente induzida pela infeção crónica pelo VHD. Um elevado índice de suspeição para VHD foi essencial porque, se o caso tivesse sido interpretado como HAI refratária, com incremento de imunossupressão, poderia ter-se verificado um agravamento da hepatite viral. Recentemente, foi reportado que a supressão do VHD pelo bulevirtide pode reverter a doença hepática autoimune. Questionamo-nos se o mesmo poderia ter sucedido com a nossa doente, caso esta tivesse aceite este tratamento.

"There's Still Time to be Happy": The Life Trajectories of Portuguese Transgender Women Who Transitioned at 50+ Years.

The process of transitioning involves making changes to align one's life with their authentic gender identity. This study explores the life trajectories of three Portuguese transgender women who transitioned later in life (50+ years old) by identifying key chapters in their life courses. Through inductive thematic analysis, six chapters were identified from the participants' interviews: (1) awareness of "something different in me," (2) locked into suffering, (3) finding comfort in something that is socially recognized, (4) "it is enough": it is time to recognize and embrace the woman I am, (5) living my life as a woman, and (6) building and leaving a legacy. Aging and the process of self-discovery played pivotal roles in participants' process of transitioning. The perception of finitude and the limitations associated with the time of life led them to realize that there was no time to waste and a sense of urgency to live authentically.

O processo de transição envolve mudanças para alinhar a vida com a identidade de género autêntica. Este estudo explora as trajetórias de vida de três mulheres transgénero portuguesas que fizeram a transição mais tardia (depois dos 50 anos), identificando capítulos-chave nos seus percursos de vida. Através da análise temática indutiva, foram identificados seis capítulos a partir das entrevistas dos participantes: (1) consciência de "algo diferente em mim," (2) fechada no sofrimento, (3) encontrar conforto em algo que é socialmente reconhecido, (4) "já chega:" é altura de reconhecer a mulher que sou, (5) viver a minha vida como mulher, e (6) construir e deixar um legado. O envelhecimento e o processo de autodescoberta desempenharam papéis fundamentais no processo de transição das participantes. A perceção da finitude e das limitações associadas ao tempo de vida levou-as a perceber que não havia tempo a perder, dando um sentido de urgência para viver de forma autêntica.

INFLUENCE OF NEOADJUVANT THERAPY ON THE RATIO OF LYMPH NODES.

BACKGROUND: To evaluate the relationship between the ratio of affected lymph nodes (LNR) and clinical and anatomopathological variables in patients with rectal adenocarcinoma submitted or not to neoadjuvant chemoradiotherapy. METHODS: The LNR was determined by dividing the number of compromised LNR by the total number of LNR dissected in the surgical specimen. Patients were divided into two groups: with QRT and without QRT. In each group, the relationship between LNR and the following variables was evaluated: degree of cell differentiation, depth of invasion in the rectal wall, angiolymphatic /perineural invasion, degree of tumor regression and occurrence of metastases. The LNR was evaluated in patients with more than 1, LNR (LNR >12) or less (LNR<12) in the surgical specimen with overall survival (OS) and disease-free survival (DFS). The results were expressed as the mean with the respective standard deviation. Qualitative variables were analyzed using Fisher's exact test, while quantitative variables were analyzed using the Kruskal -Wallis and Mann-Whitney tests. The significance level was 5%. RESULTS: We evaluated 282 patients with QRT and 114 without QRT, between 1995-2011. In the QRT Group, LNR showed a significant association with mucinous tumors (P=0.007) and degree of tumor regression (P=0.003). In both groups, LNR was associated with poorly differentiated tumors (P=0.001, P=0.02), presence of angiolymphatic invasion (P<0.0001 and P=0.01), perineural (P=0.0007, P=0.02), degree of rectal wall invasion (T3>T2; P<0.0001, P=0.02); Compromised LNR (P<0.0001, P<0.01), metastases (P<0.0001, P<0.01). In patients with QRT, LNR<12 was associated with DFS (5.889; 95%CI1.935-19.687; P=0.018) and LNR>12 with DFS and OS (17.984; 95%CI5.931-54.351; P<0.001 and 10.286; 95%CI 2.654-39.854; P=0.007, respectively). CONCLUSION: LNR was associated with histological aspects of poor prognosis, regardless of the use of QRT. In the occurrence of less than 12 evaluated LNR, the LNR was associated only with the DFS. BACKGROUND: • Assessment of the lymph nodes during pathological analysis of the surgical specimen is crucial to determine treatment and prognosis. BACKGROUND: • Neoadjuvance therapy reduces the number of lymph nodes, being lower than recommended, therefore the lymph node ratio can be an alternative analysis for a better prognosis.

Carbon-Induced Changes in the Morphology and Wetting Behavior of Ionic Liquids on the Mesoscale.

Thin films of ionic liquids (ILs) have gained significant attention due to their unique properties and broad applications. Extensive research has focused on studying the influence of ILs' chemical composition and substrate characteristics on the structure and morphology of IL films at the nano- and mesoscopic scales. This study explores the impact of carbon-coated surfaces on the morphology and wetting behavior of a series of alkylimidazolium-based ILs. Specifically, this work investigates the effect of carbon coating on the morphology and wetting behavior of short-chain ([C2C1im][NTf2] and [C2C1im][OTf]) and long-chain ([C8C1im][NTf2] and [C8C1im][OTf]) ILs deposited on indium tin oxide (ITO), silver (Ag), and gold (Au) substrates. A reproducible vapor deposition methodology was utilized for the deposition process. High-resolution scanning electron microscopy, atomic force microscopy, and X-ray photoelectron spectroscopy were used to analyze the morphological and structural characteristics of the substrates and obtained IL films. The experimental data revealed that the IL films deposited on carbon-coated Au substrates showed minor changes in their morphology compared to that of the films deposited on clean Au surfaces. However, the presence of carbon coatings on the ITO and Ag surfaces led to significant morphological alterations in the IL films. Specifically, for short-chain ILs, the carbon film surface induced 2D growth of the IL film, followed by subsequent island growth. In contrast, for long-chain ILs deposited on carbon surfaces, layer-by-layer growth occurred without island formation, resulting in highly uniform and coalesced IL films. The extent of morphological changes observed in the IL films was found to be influenced by two crucial factors: the thickness of the carbon film on the substrate surface and the amount of IL deposition.

Influência da terapia neoadjuvante na razão de linfonodos / Influence of neoadjuvant therapy on the ratio of lymph nodes

ABSTRACT Background: To evaluate the relationship between the ratio of affected lymph nodes (LNR) and clinical and anatomopathological variables in patients with rectal adenocarcinoma submitted or not to neoadjuvant chemoradiotherapy. Methods: The LNR was determined by dividing the number of compromised LNR by the total number of LNR dissected in the surgical specimen. Patients were divided into two groups: with QRT and without QRT. In each group, the relationship between LNR and the following variables was evaluated: degree of cell differentiation, depth of invasion in the rectal wall, angiolymphatic /perineural invasion, degree of tumor regression and occurrence of metastases. The LNR was evaluated in patients with more than 1, LNR (LNR >12) or less (LNR<12) in the surgical specimen with overall survival (OS) and disease-free survival (DFS). The results were expressed as the mean with the respective standard deviation. Qualitative variables were analyzed using Fisher's exact test, while quantitative variables were analyzed using the Kruskal -Wallis and Mann-Whitney tests. The significance level was 5%. Results: We evaluated 282 patients with QRT and 114 without QRT, between 1995-2011. In the QRT Group, LNR showed a significant association with mucinous tumors (P=0.007) and degree of tumor regression (P=0.003). In both groups, LNR was associated with poorly differentiated tumors (P=0.001, P=0.02), presence of angiolymphatic invasion (P<0.0001 and P=0.01), perineural (P=0.0007, P=0.02), degree of rectal wall invasion (T3>T2; P<0.0001, P=0.02); Compromised LNR (P<0.0001, P<0.01), metastases (P<0.0001, P<0.01). In patients with QRT, LNR<12 was associated with DFS (5.889; 95%CI1.935-19.687; P=0.018) and LNR>12 with DFS and OS (17.984; 95%CI5.931-54.351; P<0.001 and 10.286; 95%CI 2.654-39.854; P=0.007, respectively). Conclusion: LNR was associated with histological aspects of poor prognosis, regardless of the use of QRT. In the occurrence of less than 12 evaluated LNR, the LNR was associated only with the DFS.

RESUMO Contexto: Avaliar a relação entre a razão de linfonodos (RLA) acometidos e variáveis clínicas e anatomopatológicas em portadores de adenocarcinoma de reto submetidos ou não à quimiorradioterapia neoadjuvante. Métodos: A RLA foi determinada dividindo-se o número total de linfonodos (LFNs) dissecados no espécime cirúrgico pelo número de comprometidos. Os doentes foram divididos em dois grupos: com QRT e sem QRT. Em cada grupo foi avaliada a relação entre a RLA e as seguintes variáveis: grau de diferenciação celular, profundidade de invasão na parede retal, invasão angiolinfática/perineural, grau de regressão tumoral e ocorrência de metástases. Avaliou-se a RLA em pacientes com mais do que 12 LFNs (RLA>12) ou menos (RLA<12) na peça cirúrgica com a sobrevida global (SG) e sobrevida livre de doença (SLD). Os resultados foram expressos pela média com o respectivo desvio padrão. As variáveis qualitativas foram analisadas utilizando-se o teste exato de Fisher, enquanto as quantitativas pelos testes de Kruskal-Wallis e Mann-Whitney. O nível de significância foi de 5%. Resultados: Foram avaliados 282 pacientes com QRT e 114 sem QRT, entre 1995-2011. No Grupo QRT, RLA mostrou associação significativa com os tumores mucinosos (P=0,007) e grau de regressão tumoral (P=0,003). Nos dois grupos, a RLA associou-se com tumores pouco diferenciados (P=0,001 e P=0,02), presença de invasão angiolinfática (P<0,0001 e P=0,01), perineural (P=0,0007 e P=0,02), grau de invasão da parede retal (T3>T2; P<0,0001 e P=0,02); LFNs comprometidos (P<0,0001 e P<0,01), metástases (P<0,0001 e P<0,01). Nos pacientes com QRT, a RLA <12 associou-se com a SLD (5,889; IC95%1,935-19,687; P=0,018) e a RLA >12 com SLD e SG (17,984; IC95%5,931-54,351; P<0,001 e 10,286; IC95%2,654-39,854; P=0,007, respectivamente). Conclusão: A RLA associou-se a aspectos histológicos de mau prognóstico, independentemente do emprego de QRT. Na ocorrência de menos de 12 LFNs avaliados, a RLA associou-se apenas com a SLD.

Novel plant-associated genomoviruses from the Brazilian Cerrado biome.

The discovery rate of new plant viruses has increased due to studies involving high-throughput sequencing (HTS), particularly for single-stranded DNA viruses of the family Genomoviridae. We carried out an HTS-based survey of genomoviruses in a wide range of native and exotic trees grown in the Brazilian Cerrado biome, and the complete genome sequences of two novel members of the family Genomoviridae from two distinct genera were determined. Specific primers were designed to detect these genomoviruses in individual samples. A new gemykolovirus (Tecoma stans associated gemykolovirus) was detected in Tecoma stans, and a new gemykibivirus (Ouratea duparquetiana associated gemykibivirus) was detected in Ouratea duparquetiana. A gemykrogvirus related to Gila monster associated gemykrogvirus (80% pairwise identity) was also detected in foliar samples of Trembleya parviflora. Our pilot study paves the way for a better characterization of this diverse collection of genomoviruses as well as their interactions with the associated tree species.

Digitization of Pathology Labs: A Review of Lessons Learned.

Pathology laboratories are increasingly using digital workflows. This has the potential of increasing laboratory efficiency, but the digitization process also involves major challenges. Several reports have been published describing the individual experiences of specific laboratories with the digitization process. However, a comprehensive overview of the lessons learned is still lacking. We provide an overview of the lessons learned for different aspects of the digitization process, including digital case management, digital slide reading, and computer-aided slide reading. We also cover metrics used for monitoring performance and pitfalls and corresponding values observed in practice. The overview is intended to help pathologists, information technology decision makers, and administrators to benefit from the experiences of others and to implement the digitization process in an optimal way to make their own laboratory future-proof.

Tomato golden net virus and tomato yellow net virus: two novel New World begomoviruses with monopartite genomes.

Two novel tomato-infecting begomoviruses were discovered via high-throughput sequencing in Brazil. Both viruses were also Sanger-sequenced and displayed DNA-A components phylogenetically related to New World bipartite begomoviruses. The names tomato golden net virus (ToGNV) and tomato yellow net virus (ToYNV) were proposed. The majority of the New World begomoviruses has bipartite genomes. However, extensive analyses revealed that ToGNV and ToYNV have monopartite genomes, because no cognate DNA-B components were detected. Hence, they may comprise a unique group of monopartite New World begomoviruses, which have enormous biological, molecular, and plant breeding interest.

Antiplasmodial, Trypanocidal, and Genotoxicity In Vitro Assessment of New Hybrid α,α-Difluorophenylacetamide-statin Derivatives.

BACKGROUND: Statins present a plethora of pleiotropic effects including anti-inflammatory and antimicrobial responses. A,α-difluorophenylacetamides, analogs of diclofenac, are potent pre-clinical anti-inflammatory non-steroidal drugs. Molecular hybridization based on the combination of pharmacophoric moieties has emerged as a strategy for the development of new candidates aiming to obtain multitarget ligands. METHODS: Considering the anti-inflammatory activity of phenylacetamides and the potential microbicidal action of statins against obligate intracellular parasites, the objective of this work was to synthesize eight new hybrid compounds of α,α-difluorophenylacetamides with the moiety of statins and assess their phenotypic activity against in vitro models of Plasmodium falciparum and Trypanosoma cruzi infection besides exploring their genotoxicity safety profile. RESULTS: None of the sodium salt compounds presented antiparasitic activity and two acetated compounds displayed mild anti-P. falciparum effect. Against T. cruzi, the acetate halogenated hybrids showed moderate effect against both parasite forms relevant for human infection. Despite the considerable trypanosomicidal activity, the brominated compound revealed a genotoxic profile impairing future in vivo testing. CONCLUSIONS: However, the chlorinated derivative was the most promising compound with chemical and biological profitable characteristics, without presenting genotoxicity in vitro, being eligible for further in vivo experiments.

Diploid Nuclei Occur throughout the Life Cycles of Pucciniales Fungi.

Within Eukaryotes, fungi are the typical representatives of haplontic life cycles. Basidiomycota fungi are dikaryotic in extensive parts of their life cycle, but diploid nuclei are known to form only in basidia. Among Basidiomycota, the Pucciniales are notorious for presenting the most complex life cycles, with high host specialization, and for their expanded genomes. Using cytogenomic (flow cytometry and cell sorting on propidium iodide-stained nuclei) and cytogenetic (FISH with rDNA probe) approaches, we report the widespread occurrence of replicating haploid and diploid nuclei (i.e., 1C, 2C and a small proportion of 4C nuclei) in diverse life cycle stages (pycnial, aecial, uredinial, and telial) of all 35 Pucciniales species analyzed, but not in sister taxa. These results suggest that the Pucciniales life cycle is distinct from any cycle known, i.e., neither haplontic, diplontic nor haplodiplontic, corroborating patchy and disregarded previous evidence. However, the biological basis and significance of this phenomenon remain undisclosed. IMPORTANCE Within Eukaryotes, fungi are the typical representatives of haplontic life cycles, contrasting with plants and animals. As such, fungi thus contain haploid nuclei throughout their life cycles, with sexual reproduction generating a single diploid cell upon karyogamy that immediately undergoes meiosis, thus resuming the haploid cycle. In this work, using cytogenetic and cytogenomic tools, we demonstrate that a vast group of fungi presents diploid nuclei throughout their life cycles, along with haploid nuclei, and that both types of nuclei replicate. Moreover, haploid nuclei are absent from urediniospores. The phenomenon appears to be transversal to the organisms in the order Pucciniales (rust fungi) and it does not occur in neighboring taxa, but a biological explanation or function for it remains elusive.

Confirmation of Groundnut ringspot orthotospovirus (GRSV) Infection in Eggplant Cultivars in Brazil.

Eggplant (Solanum melongena L.) is an economically important vegetable crop in Brazil, especially in family-based farming. Eggplant hybrids 'Ciça' and 'Napoli' (≈ 400 plants) were detected exhibiting virus-like symptoms (5-20% incidence) in field surveys (2015-2018) in Brasília-DF (Figure 1). Symptoms included chlorosis, mosaic and apical leaf deformation. Six symptomatic leaf samples were collected from fruit-bearing plants (around 100 days after planting) aiming at verifying the potential orthotospovirus infection. Double antibody sandwich enzyme-linked immunosorbent assay (DAS-ELISA) was carried out with polyclonal antibodies (produced at Centro Nacional de Pesquisa de Hortaliças - CNPH) against the N gene coat protein of the three major orthotospoviruses: tomato spotted wilt orthotospovirus (TSWV), groundnut ringspot orthotospovirus (GRSV) and, tomato chlorotic spot orthotospovirus (TCSV). Strong serological reactions were observed only against GRSV antibodies in the extracts from symptomatic samples, but not in the controls. To confirm the causal agent of those symptoms, total RNA was extracted from infected leaf samples via the standard Trizol® (Sigma) protocol and subsequently used in a two-step reverse transcriptase polymerase chain reaction (RT-PCR) approach. Synthesis of the cDNA was carried out with the J13 primer (5'-CCC GGA TCC AGA GCA AT-3') (Cortez et al., 2001) followed by PCR assays with the primer pair BR60 (5'-AGA GCA ATC GTG TCA-3`) and BR65 (5`-ATC AAG CCT TCT GAA AGT CAT-3') (Eiras et al., 2002). This primer set amplifies a fragment of 453 bp including the 3' untranslated region at the 3' terminus of the S RNA and the protein N-coding gene of at least five species: TSWV, GRSV, TCSV, chrysanthemum stem necrosis orthotospovirus (CSNV) and zucchini lethal chlorosis orthotospovirus (ZLCV). In addition, GRSV-specific primers (LNA Reis, unpublished) were used for amplification of all three segments: L segment: LF/LR (5'-AAC AGG ATT CAG CAA TAT GG-3'/ 5'-AAT TCC TTG AAG ACA ATT GTG T -3'); M segment: MF/MR (5'-TTT GTC CAA CCA TAC CAG ACC C- 3' / 5'-GGC TTC AAT AAA GGC TTG GG-3') and, S segment: SF/SR (5'-TTC AAA CTC AGT TGT ACT CTG A-3'/5'-TTA CTT TCG ATC TGG TTG AA- 3'). Amplicons with 509 bp (MT043204), 289 bp (MT043205), and 901 bp (MT043203) were obtained for L, M and S segments of the eggplant isolate DF-687. PCR amplicons corresponding to a segment of the N-coding gene (396 bp) of a second eggplant isolate (BJL02; MK176337) were obtained with the primer pair BR60/BR65 and subjected to Sanger dideoxy sequencing at CNPH. Alignments of nucleotide sequences of both isolates revealed identity levels varying around 99% to the corresponding genomic regions of a large set of GRSV isolates from GenBank database. PCR assays using total RNA as template yielded 494 bp amplicons solely with GRSV-specific primers (Webster et al., 2011), but no products were obtained with TSWV-specific primers (Adkins and Rosskopf, 2002), confirming the former as the sole causal agent of the field symptoms. Leaves of eggplant cv. 'Ciça' and indicator hosts, including Nicotiana rustica, Capsicum chinense 'PI 159236' (with the Tsw gene), and S. lycopersicum cv. Santa Clara were rub inoculated with extracts prepared from eggplant samples naturally infected with GRSV. Mosaic, necrotic ringspots and systemic leaf deformation symptoms were observed around ten days after inoculation on newly emerged leaves of all inoculated plants. GRSV infection was confirmed by DAS-ELISA and RT-PCR ten days after inoculation. Eggplant was erroneously listed as a host of GRSV in Brazil (Kitajima, 2020). Hence, this is the first report of eggplant infection by this virus in South America. No significant yield losses have been observed in eggplant due to GRSV infection since the overall symptoms are often mild. However, this natural host of GRSV might impact disease management strategies since eggplant is quite often cultivated under family-based farming conditions as a companion crop of highly susceptible tomato, sweet-pepper, and lettuce cultivars. References: Adkins, S., and Rosskopf, E. N. 2002. Plant Dis. 86: 1310. Cortez, I., et al. 2001. Arch. Virol. 146:265. Eiras, M. et al., 2002. Fitopatol. Bras. 27:285. Kitajima, E.W. 2020. Biota Neotrop. 20: e2019932. Webster, C. G., et al. 2011. Virology 413: 216.

Explainability and causability in digital pathology.

The current move towards digital pathology enables pathologists to use artificial intelligence (AI)-based computer programmes for the advanced analysis of whole slide images. However, currently, the best-performing AI algorithms for image analysis are deemed black boxes since it remains - even to their developers - often unclear why the algorithm delivered a particular result. Especially in medicine, a better understanding of algorithmic decisions is essential to avoid mistakes and adverse effects on patients. This review article aims to provide medical experts with insights on the issue of explainability in digital pathology. A short introduction to the relevant underlying core concepts of machine learning shall nurture the reader's understanding of why explainability is a specific issue in this field. Addressing this issue of explainability, the rapidly evolving research field of explainable AI (XAI) has developed many techniques and methods to make black-box machine-learning systems more transparent. These XAI methods are a first step towards making black-box AI systems understandable by humans. However, we argue that an explanation interface must complement these explainable models to make their results useful to human stakeholders and achieve a high level of causability, i.e. a high level of causal understanding by the user. This is especially relevant in the medical field since explainability and causability play a crucial role also for compliance with regulatory requirements. We conclude by promoting the need for novel user interfaces for AI applications in pathology, which enable contextual understanding and allow the medical expert to ask interactive 'what-if'-questions. In pathology, such user interfaces will not only be important to achieve a high level of causability. They will also be crucial for keeping the human-in-the-loop and bringing medical experts' experience and conceptual knowledge to AI processes.

In silico and in vitro assessment of anti-Trypanosoma cruzi efficacy, genotoxicity and pharmacokinetics of pentasubstituted pyrrolic Atorvastatin-aminoquinoline hybrid compounds.

Atorvastatin (AVA) is a third-generation statin with several pleiotropic effects, considered the last synthetic pharmaceutical blockbuster. Recently, our group described the effects of AVA on DNA damage prevention and against Trypanosoma cruzi infection. In this study, our aim was to evaluate the efficacy, safety, and in silico pharmacokinetic profile of four hybrids of aminoquinolines with AVA 4a-d against T. cruzi using in vitro and in silico models. These synthetic compounds were designed by hybridization of the pentapyrrolic moiety of AVA with the aminoquinolinic unit of chloroquine or primaquine. Pharmacokinetics (ADME) and toxicity parameters were predicted by SwissADME, admetSAR and LAZAR in silico algorithms. The trypanocidal activity of AVA-quinoline hybrids were evaluated in vitro against amastigotes and trypomastigotes of T. cruzi, from Y (Tc II) and Tulahuen (Tc VI) strains. In vitro cardiocytotoxicity was assessed using primary cultures of mouse embryonic cardiac cells and in vitro hepatocytotoxicity on bidimensional and 3D-cultured HepG2 cells. Genotoxicity was evaluated by Ames test and micronucleus assay. Despite the overall good in silico ADMET profile, all tested compounds were predicted to be hepatotoxic. All hybrid derivatives presented high trypanocidal activity, against both trypomastigote and intracellular forms of T. cruzi, presenting EC50's lower than 1 µM besides superior selectivity than the reference drug, without evidences of cardiotoxicity in vitro. The compounds 4a and 4b presented a time-dependent toxicity in monolayer culture of HepG2 but no detectable toxic effects in their spheroids, opposing to the in silico prediction. We can conclude that the AVA-aminoquinoline hybrids presented a hit profile as antiparasitic agents in synthetic pharmaceutical innovation platforms.

A Case Report on Metamizole-Induced Agranulocytosis: Is the Benefit Worth the Risk?

Metamizole is a drug with analgesic and antipyretic properties widely available in Portugal. Its use is highly controversial because of the risk of agranulocytosis, a rare but serious adverse event. A 70-year-old female patient with a recent history of treatment with metamizole for post-surgery fever and pain presented to the ED with sustained fever, diarrhea, and painful mouth ulcers. Laboratory tests revealed agranulocytosis. The patient was placed under protective isolation and started treatment with granulocyte-colony stimulating factor (G-CSF) and empiric antibiotic therapy with piperacillin/tazobactam and vancomycin for neutropenic fever. After an extensive workup, no source of infection was identified. During hospitalization, infectious and neoplastic causes of agranulocytosis were investigated, but the results were negative. Metamizole-induced agranulocytosis was suspected. The patient completed a total of three days of G-CSF and eight days of empiric antibiotic therapy with sustained clinical improvement. She was discharged completely asymptomatic and remained clinically stable during follow-up without a resurgence of agranulocytosis. This case report is intended to increase awareness of metamizole-induced agranulocytosis. While this is a well-known side effect, it is also often overlooked. It is paramount that both physicians and patients know how to correctly manage metamizole to prevent and promptly treat agranulocytosis.

Salmonellosis in Children at a Portuguese Hospital: A Retrospective Study.

INTRODUCTION: Salmonellosis represents a considerable health, social and economic burden in both high- and low-income countries. Recently, in Portugal, most cases of Salmonella infections have been reported in children under 15 years of age. The main aim of this study was to characterize, from an epidemiological, microbiological, and clinical perspective, cases of Salmonella isolation among children. MATERIAL AND METHODS: The authors performed a descriptive study using retrospective analysis of cases of salmonellosis, in pediatric age, at a Portuguese Level II Hospital, between January 2015 and July 2020. RESULTS: The population included a total of 63 children, of which 81% were Portuguese. Ethnicity was identified in 13 children, most of whom were African. The median age at diagnosis was four years old (3.5 - 9 years old). Despite the small number of cases per year in our study (11), one-third were severe enough to require hospitalization. Overall, 13% of patients were treated with antibiotics. In 63% of the isolates, serotype was identified: Salmonella Enteriditis (38%), Salmonella Typhimurium (22%), and Salmonella Typhi (3%). Antibiotic resistance rates were 19% for ampicillin and 6.4% for amoxicillinclavulanic acid and cotrimoxazole. No resistance to third-generation cephalosporins was found. CONCLUSION: Given the obtained results, we intend to improve knowledge on salmonellosis in Portugal and, consequently improve prevention strategies, treatment and its notification. Although the incidence of salmonellosis has been decreasing in recent years it is the second most frequent gastrointestinal infection in the European Union, contributing to significant rates of hospitalizations and use of antibiotics in Portugal.

MULTIPLE NEUROENDOCRINE NEOPLASIA IN A PATIENT WITH TYPE I NEUROFIBROMATOSIS (NF1): REPORT OF A NEW MUTATION (NF1, EXONS 2-30 DELETION) AND LITERATURE REVIEW.

BACKGROUND: Plexiform neurofibromas represent a common neoplasia of type 1 neurofibromatosis in which neurofibromas arise from multiple nerves involving connective tissue and skin and rarely affect the colon and rectum. Co-occurrence of plexiform neurofibromas, neuroendocrine tumors with primary involvement of the rectum, and medullary thyroid carcinoma in patients with neurofibromatosis type 1 is a previously undescribed condition. The aim of this manuscript was to present a case of primary plexiform neurofibroma and neuroendocrine tumors of the upper rectum in a patient with neurofibromatosis type 1 whose genetic sequencing found a novel mutation in the neurofibromatosis type 1 gene and to review the literature. CASE REPORT: A 49-year-old woman with a familial history of neurofibromatosis type 1 complained of abdominal cramps for 6 months. She had previously been submitted for a total thyroidectomy due to medullary thyroid carcinoma. She was submitted to a colonoscopy, which identified a submucosa lesion located in the upper rectum. The patient was referred for a laparoscopic rectosigmoidectomy, and the histopathological study of the surgical specimen identified two different tumors. An immunohistochemical panel was done for histopathological confirmation of the etiology of both lesions. The results of the panel showed intense immunoexpression of S100 protein in the largest and superficial lesion, as well as positivity for chromogranin and synaptophysin in the minor and deep lesion confirming the diagnosis of rectal plexiform neurofibromas concomitant with neuroendocrine tumors. The proliferative activity rate using Ki-67 antibodies showed that both tumors had a low rate of mitotic activity (<1%). Genetic sequence panel identified an undescribed mutation in the neurofibromatosis type 1 gene (deletion, exons 2-30). The patient's postoperative evolution was uneventful, and she remains well, without recurrence, 3 years after surgery. CONCLUSION: The co-occurrence of medullary thyroid carcinoma, plexiform neurofibromas, and neuroendocrine tumors of the rectum in patients with neurofibromatosis type 1 is an exceptional and undescribed possibility, whose diagnosis can be confirmed by the immunohistochemical staining and genetic panel.

Synthetic hydrazones: In silico studies and in vitro evaluation of the antileishmania potential.

Bioprospecting and synthesis of strategically designed molecules have been used in the search for drugs that can be in leishmaniasis. Hydrazones (HDZ) are promising compounds with extensive biological activities. The objective of this work was to perform in silico studies of hydrazones 1-5 and to evaluate their antileishmanial, cytotoxic and macrophage immunomodulatory potential in vitro. Hydrazones were subjected to prediction and molecular docking studies. Antileishmanial protocols on promastigotes and amastigotes of Leishmania amazonensis, cytotoxicity and macrophage immunomodulatory activity were performed. Hydrazones showed a good pharmacokinetic profile and hydrazone 3 and hydrazone 5 were classified as non-carcinogenic. Hydrazone 5 obtained the best conformation with trypanothione reductase. Hydrazone 1 and hydrazone 3 obtained the best mean inhibitory concentration (IC50) values for promastigotes, 4.4-61.96 µM and 8.0-58.75 µM, respectively. It also showed good activity on intramacrophagic amastigotes, with hydrazone 1 being the most active (IC50 = 6.79 µM) with selectivity index of 56. In cytotoxicity to macrophages hydrazone 3 was the most cytotoxic (CC50 = 256.3 ± 0,04 µM), while hydrazone 4 the least (CC50 = 1055.9 ± 0.03 µM). It can be concluded that the hydrazones revealed important pharmacokinetic and toxicological properties, in addition to antileishmania potential in reducing infection and infectivity in parasitized macrophages.