The Silva pattern-based classification for HPV-associated endocervical adenocarcinoma: A single institution concordance study of trainees and gynecologic pathologists.

The Silva pattern-based classification of HPV-associated endocervical adenocarcinoma has become an integral part of the histologic assessment of these tumors. Unfortunately, the Silva system reproducibility has had mixed results in past studies, and clinical practice still favors the FIGO stage assessment in directing therapeutic interventions for patients. In our study, we aimed to assess our institution's concordance including not only gynecologic pathologists, but also pathology trainees through a series of 69 cases. The grouped total kappa concordance from all participants was 0.439 (Moderate), with an overall trainee kappa of 0.417 (moderate) and an overall pathologist kappa of 0.460 (moderate). Perfect concordance among all 10 study participants was seen in 8/69 cases (11.6 %), corresponding to 5/22 Pattern A cases (22.7 %), 0/16 Pattern B cases (0 %), and 3/31 Pattern C cases (9.7 %), with similar findings between trainees and pathologists when compared within their own cohorts. Recurrence was identified in 2 Pattern A cases, indicating a potential issue with limited excisional specimens which may not fully appreciate the true biologic aggressiveness of the lesions.

Field comparison of broad-spectrum white LED-baited traps with narrow-spectrum green LED-baited traps in the capture of Anopheles mosquitoes (Diptera: Culicidae).

Light-Emitting Diodes (LEDs) have been effective light sources in attracting Anopheles mosquitoes, but the broad-spectrum white light, even with a wide-ranging application in lighting, have not been evaluated yet. In this study, the white light was field evaluated against the green one in the light trapping of anopheline mosquitoes by using two non-suction Silva traps and two CDC-type suction light traps. Anopheline mosquitoes were captured for two 21-night periods of collecting (2022 and 2023). In the first period, two LEDs were used per Silva trap, but three were used in the second one to increase the luminance/illuminance at traps. A CDC-type suction light trap equipped with an incandescent lamp was used in 2022 and a CDC-type suction light trap equipped with a 6 V-white light (higher luminance/illuminance) in 2023. A total of eight species and 3,289 specimens were captured in both periods. The most frequent species were Anopheles triannulatus s.l., An. goeldii, An. evansae and An. argyritarsis. In 2022, white LEDs were less attractive to anopheline mosquitoes than the other light sources, but without statistical difference among treatments (F = 2.703; P = 0.0752; df = 2). In 2023, even with an increased luminance/illuminance at traps, no statistical difference was found between the two LED-baited Silva traps (F = 6.690; P = 0.0024; df = 2), but rather between the 6 V-white-baited CDC-type suction light trap and green-baited Silva traps. Due to some drawbacks and the lower abundance of individuals caught by using white LEDs, the narrow-banded green LEDs is preferable to white ones for attracting anophelines.

Pelvic lymph node involvement and risk of recurrence in HPV-associated endocervical adenocarcinoma stage IA2-IB1 according to Silva's system in two Colombian cancer centers.

OBJECTIVE: To compare the pelvic lymph node involvement and risk of recurrence in patients with human papillomavirus (HPV)-associated endocervical adenocarcinoma stage IA2-IB1 undergoing hysterectomy and/or trachelectomy plus lymphadenectomy, according to Silva's classification system. METHODS: A retrospective cohort study was performed in two Colombian cancer centers. The cases were classified according to the Silva classification system. Clinical, surgical, and histopathological variables were evaluated. Recurrence risk was analyzed by patterns A, B, or C. A logistic regression model was performed for tumor recurrence. The Kaplan-Meier method was used to estimate overall survival and disease-free survival (DFS). A weighted kappa was performed to determine the degree of concordance between pathologists. RESULTS: A total of 100 patients were identified, 33% pattern A, 29% pattern B, and 38% pattern C. The median follow-up time was 42.5 months. No evidence of lymph node involvement was found in patients classified as A and B, while in the C pattern was observed in 15.8% (n = 6) of cases (P < 0.01). There were 7% of cases with recurrent disease, of which 71.5% corresponded to type C pattern. Patients with Silva pattern B and C had 1.22- and 4.46-fold increased risk of relapse, respectively, compared with pattern A. The 5-year DFS values by group were 100%, 96.1%, and 80.3% for patterns A, B, and C, respectively. CONCLUSION: For patients with early-stage HPV-associated endocervical adenocarcinoma, the type C pattern presented more lymph node involvement and risk of recurrence compared to the A and B patterns. The concordance in diagnosis of different Silva's patterns by independents pathologists were good.

Pioneer of Cardiothoracic Surgery - Luiz Tavares da Silva

ABSTRACT Luis Tavares revolutionized cardiac surgery, always bringing the most modern instruments and equipment from his travels to England - surgical forceps, scissors, scalpels, etc. He always insisted that he was not just a thoracic surgeon, for his work extended over a wide field and created three important cardiac surgery centers which promoted a great development of cardiology. He carried out the first open heart surgery (atrial septal defect) employing extracorporeal circulation and closure of a ventricular septal defect with deep surface hypothermia of north and northeast Brazil. He promoted an intense scientific exchange program between Recife and England, resulting in significant advances in medicine, and participated directly in the creation of HEMOPE), leading to radical changes and improvements in blood therapy in the whole country. The PROCAPE, inaugurated in 2006, was the result of the cardiac center created by him in early 1970 at Hospital Oswaldo Cruz and can be considered the second largest public-university cardiology center in Brazil. He is thus widely regarded as an outstanding name in medicine in the 20th century and one of the fathers of modern cardiac surgery in Brazil.

Em benefício dos filhos de amanhã: participação feminina na eugenia brasileira, 1918-1936 / To benefit tomorrow's children: female participation in Brazilian eugenics, 1918-1936

Resumo O texto analisa a participação feminina na eugenia brasileira e os discursos médicos acerca dos papéis e funções sociais dos sexos na primeira metade do século XX. A partir da análise da produção de duas mulheres, Ítala Silva de Oliveira e Eunice Penna Kehl, o objetivo principal é argumentar que determinadas mulheres se engajaram efetivamente no movimento eugênico, trabalhando em prol da aproximação feminina com a eugenia. Tal análise permite explorar uma dimensão pedagógica e de popularização da eugenia por meio da tentativa de formação de uma consciência higiênica e eugênica nas mulheres.

Abstract This text analyzes female participation in Brazilian eugenics and medical discourse on the roles and social functions of the sexes during the first half of the twentieth century. In examining the production of two women, Ítala Silva de Oliveira and Eunice Penna Kehl, we maintain that certain women were effectively engaged in the eugenics movement and worked to bring women closer to eugenics. This analysis makes it possible to explore a pedagogical dimension of eugenics and of the popularization of this movement by attempting to form a hygienist and eugenist consciousness among women.

Field evaluation of a new suction light trap for the capture of phlebotomine sand flies (Diptera: Psychodidae: Phlebotominae), vectors of leishmaniasis.

Phlebotomine sand flies are crepuscular and nocturnal small dipteran insects in the family Psychodidae. Several disease agents, including Leishmania parasites, are transmitted to humans and other vertebrate hosts by the bite of an infected female sand fly. As part of leishmaniasis surveillance programs, light traps have been routinely used in sand fly collections. In this context, new trapping devices are always being required to improve vector monitoring. Here, the efficiency of a new suction light trap, named Silva suction trap or SS trap, was field evaluated in collecting sand flies. Two SS traps, one with green (520 nm, 15,000 mcd) and the other with white (wide spectrum, 18,000 mcd) LEDs, and one CDC-type trap were deployed in a rural forested environment. A total of 4686 phlebotomine sand flies were captured. The most frequent species were females of the Ps. Chagasi series (77.8%) followed by males of Ps. wellcomei (11.6%), Nyssomyia whitmani (3.3%), and Bichromomyia flaviscutellata (2.4%). The CDC-type light trap collected 101.9 ± 20.89 sand flies and 14 species, followed by the white-baited SS trap (87.78 ± 16.36, 14), and the green-baited SS trap (70.61 ± 14.75, 15), but there were no statistically significant differences among traps. A discussion on the considerable advantages of the use of SS traps over CDC traps is included. In this study, the Silva suction trap proved to be efficient and can be an alternative to CDC traps for monitoring adult phlebotomine sand fly populations.

Pioneer of Cardiothoracic Surgery - Luiz Tavares da Silva.

Luis Tavares revolutionized cardiac surgery, always bringing the most modern instruments and equipment from his travels to England - surgical forceps, scissors, scalpels, etc. He always insisted that he was not just a thoracic surgeon, for his work extended over a wide field and created three important cardiac surgery centers which promoted a great development of cardiology. He carried out the first open heart surgery (atrial septal defect) employing extracorporeal circulation and closure of a ventricular septal defect with deep surface hypothermia of north and northeast Brazil. He promoted an intense scientific exchange program between Recife and England, resulting in significant advances in medicine, and participated directly in the creation of HEMOPE), leading to radical changes and improvements in blood therapy in the whole country. The PROCAPE, inaugurated in 2006, was the result of the cardiac center created by him in early 1970 at Hospital Oswaldo Cruz and can be considered the second largest public-university cardiology center in Brazil. He is thus widely regarded as an outstanding name in medicine in the 20th century and one of the fathers of modern cardiac surgery in Brazil.

Development and validation of a deep learning algorithm for pattern-based classification system of cervical cancer from pathological sections.

Background: Multi-center research has demonstrated that adopting Silva's pattern-based classification system (SPBC) enhances the clinical prognosis and facilitates hierarchical management of patients with endocervical adenocarcinomas (EAC). However, inconsistencies in SPBC can arise due to variations in pathologists' experience levels. Thus, the implementation of standardized decision-making tools becomes crucial to enhance the practicality of SPBC in clinical diagnosis and treatment. Methods: We enrolled a total of 90 patients with EAC in this study, of which 63 were assigned to the training group, and the remaining 27 were allocated to the validation group. To create and validate the prediction models for SPBC, we utilized a deep learning system (DLS) and calculated the area under the receiver operating characteristic curve (AUC). Results: In Silva pattern classification, ResNet50 achieved an average accuracy of 74.36% (63.64% for pattern A, 55.56% for pattern B, and 89.47% for pattern C respectively). Moreover, in test set, ResNet50 achieved an AUC of 0.69 for pattern A, 0.58 for pattern B, and 0.91 for pattern C. Conclusions: We successfully established a DLS for SPBC, which holds the potential to aid pathologists in accurately classifying patients with EAC.

Metagenomics Databases for Bacteria.

The booming sequencing technologies have turned metagenomics into a widely used tool for microbe-related studies, especially in the areas of clinical medicine and ecology. Accordingly, the toolkit of metagenomics data analysis is growing stronger to provide multiple approaches for solving various biological questions and understanding the component and function of microbiome. As part of the toolkit, metagenomics databases play a central role in the creation and maintenance of processed data such as definition of taxonomic classifications, annotation of gene functions, sequence alignment, and phylogenetic tree inference. The availability of a large quantity of high-quality bacterial genomic sequences contributes significantly to the construction and update of metagenomics databases, which constitute the core resource for metagenomics data analysis at various scales. This chapter presents the key concepts, technical options, and challenges for metagenomics projects as well as the curation processes and versatile functions for the four representative bacterial metagenomics databases, including Greengenes, SILVA, Ribosomal Database Project (RDP), and Genome Taxonomy Database (GTDB).

In sickness and in health: the dynamics of the fruit bat gut microbiota under a bacterial antigen challenge and its association with the immune response.

Introduction: Interactions between the gut microbiome (GM) and the immune system influence host health and fitness. However, few studies have investigated this link and GM dynamics during disease in wild species. Bats (Mammalia: Chiroptera) have an exceptional ability to cope with intracellular pathogens and a unique GM adapted to powered flight. Yet, the contribution of the GM to bat health, especially immunity, or how it is affected by disease, remains unknown. Methods: Here, we examined the dynamics of the Egyptian fruit bats' (Rousettus aegyptiacus) GM during health and disease. We provoked an inflammatory response in bats using lipopolysaccharides (LPS), an endotoxin of Gram-negative bacteria. We then measured the inflammatory marker haptoglobin, a major acute phase protein in bats, and analyzed the GM (anal swabs) of control and challenged bats using high-throughput 16S rRNA sequencing, before the challenge, 24h and 48h post challenge. Results: We revealed that the antigen challenge causes a shift in the composition of the bat GM (e.g., Weissella, Escherichia, Streptococcus). This shift was significantly correlated with haptoglobin concentration, but more strongly with sampling time. Eleven bacterial sequences were correlated with haptoglobin concentration and nine were found to be potential predictors of the strength of the immune response, and implicit of infection severity, notably Weissella and Escherichia. The bat GM showed high resilience, regaining the colony's group GM composition rapidly, as bats resumed foraging and social activities. Conclusion: Our results demonstrate a tight link between bat immune response and changes in their GM, and emphasize the importance of integrating microbial ecology in ecoimmunological studies of wild species. The resilience of the GM may provide this species with an adaptive advantage to cope with infections and maintain colony health.

Clinicopathological features and immunophenotype of Silva pattern system in endocervical adenocarcinoma.

The aim of this study was to investigate the correlation between Silva pattern system and clinicopathological features of endocervical adenocarcinoma. Moreover, it was to find molecular markers helpful for Silva classification, and thus we also explored the expression levels of invasion, adhesion and proliferation biomarkers in cases of Silva non-invasive and invasive types. The survival based on Silva pattern system was analysed by Kaplan-Meier survival analysis, Log-rank test and  a COX risk proportionality model. Sixty samples were chosen to detect the MMP-2, MMP-9, u-PA, E-cadherin, ß-catenin, EGF, TGF-α, HDGF, c-Met and RGN expression by immunohistochemistry. Multivariate analysis showed that pattern A/pattern B/pattern C Silva pattern system provided independent risk factors for prognosis. Our results found the levels of MMP-2, MMP-9 and u-PA were significantly higher in endocervical adenocarcinoma with destructive growth than in the  nondestructive group. The levels of E-cadherin and ß-catenin were significantly lower in endocervical adenocarcinoma with destructive growth than in the nondestructive group. The levels of EGF, TGF-α and HDGF were significantly higher in endocervical adenocarcinoma with destructive growth than in the nondestructive group. Compared with 'non-invasive/invasive Silva pattern', this study suggests 'pattern A/pattern B/pattern C Silva pattern' could be a better criteria for predicting the prognosis. Furthermore, the dual-marker combination of 'MMP-2 and u-PA' and 'E-cadherin and ß-catenin' is very important in the diagnosis of Silva pattern classification.

Molecular correlates of invasion pattern in HPV-associated endocervical adenocarcinoma: emergence of two distinct risk-stratified tiers.

BACKGROUND: The pattern-based (Silva) classification of invasive human papilloma virus (HPV)-associated endocervical adenocarcinomas (HPVA) is an established and reproducible method to predict outcomes for this otherwise stage-dependent group of tumours. Previous studies utilising targeted sequencing have shown a correlation between mutational profiles and an invasive pattern. However, such correlation has not been explored using comprehensive molecular testing. DESIGN: Clinicopathologic data including invasive pattern (Silva groups A, B, and C) was collected for a cohort of invasive HPVA, which previously underwent massive parallel sequencing using a panel covering 447 genes. Pathogenic alterations, molecular signatures, tumour mutational burden (TMB), and copy number alterations (CNA) were correlated with pattern of invasion. RESULTS: Forty five HPVA (11 pattern A, 17 pattern B, and 17 pattern C tumours) were included. Patients with pattern A presented at stage I with no involved lymph nodes or evidence of recurrence (in those with >2 months of follow-up). Patterns B and C patients also mostly presented at stage I with negative lymph nodes, but had a greater frequency of recurrence; 3/17 pattern B and 1/17 pattern C HPVAs harboured lymphovascular space invasion (LVI). An APOBEC mutational signature was detected only in Silva pattern C tumours (5/17), and pathogenic PIK3CA changes were detected only in destructively invasive HPVA (patterns B and C). When cases were grouped as low-risk (pattern A and pattern B without LVI) and high-risk (pattern B with LVI and pattern C), high-risk tumours were enriched in mutations in PIK3CA, ATRX, and ERBB2. There was a statistically significant difference in TMB between low-risk and high-risk pattern tumours (P = 0.006), as well as between Pattern C tumours with and without an APOBEC signature (P = 0.002). CNA burden increased from pattern A to C. CONCLUSION: Our findings further indicate that key molecular events in HPVA correlate with the morphologic invasive properties of the tumour and their aggressiveness. Pattern B tumours with LVI clustered with pattern C tumours, whereas pattern B tumours without LVI approached pattern A genotypically. Our study provides a biologic foundation for consolidating the Silva system into low-risk (pattern A + B without LVI) and high-risk (pattern B with LVI and pattern C) categories.

How to define fish pathogen relatives from a 16S rRNA sequence library and Pearson correlation analysis between defined OTUs from the library: Supplementary data to the research article "Presence and habitats of bacterial fish pathogen relatives in a marine salmon post-smolt RAS".

This paper provides supplementary data to the research paper ''Presence and habitats of bacterial fish pathogen relatives in a marine salmon post-smolt RAS" [1]. Here, environmental samples from a marine recirculating aquaculture system (RAS) were subjected to microbiome studies. This data article adds value to the research article by providing open access to data files that increased information retrieval from the 16S rRNA sequence library. A fasta file of full-length 16S rRNA sequences from fish pathogenic microbes was deposited in the Mendeley data repository, a collection named "Fish Pathogen Database". Alignment of this database against the short sequences in the 16S rRNA library revealed the fish pathogen-relatives. Furthermore, a link to a CSV file containing Pearson correlation data was provided, an analysis based on the relative abundance information of all operational taxonomic units defined in the microbiome dataset. Included also, the methodological description of the Pearson correlation analysis, as well as a table where correlation data for the defined fish pathogen-relatives was retrieved from the large data file (Table 1).

Short-Finned Pilot Whale Strandings Associated with Pilot Whale Morbillivirus, Brazil.

Cetacean morbillivirus (CeMV) causes illness and death in cetaceans worldwide; the CeMV strains circulating in the Southern Hemisphere are poorly known. We detected a pilot whale CeMV strain in 3 short-finned pilot whales (Globicephala macrorhynchus) stranded in Brazil during July-October 2020. Our results confirm this virus circulates in this species.

Silva cumulative score and its relationship with prognosis in Endocervical adenocarcinoma.

BACKGROUND: The Silva system has been demonstrated to have a good predictive value of lymph node metastasis (LNM) in endocervical adenocarcinoma (EAC). Tumours were classified based on the highest identified pattern of invasion in this system, this may not exactly reflect the true situation when it presents with a "mixed pattern" in some cases. Recent study has shown that patients with lymphovascular invasion (LVI) have worse prognosis in EAC. Here we design a Silva cumulative score (SCS) system which also combined the LVI status to explore its prognostic role in EAC patients. METHODS: A total of 120 patients with EAC were included in this study. Clinicopathological characteristics were retrospectively retrieved from the medical records and follow-up data were obtained. The clinicopathological information included age at diagnosis, depth of invasion (DOI), LNM, LVI, Silva classification, and SCS. SCS is a classification system based on the sum score of different Silva pattern which is founded on morphological phenomena. The relationships between the pathological characteristics and prognoses were analyzed. RESULTS: According to the Silva system, 11 (9.2%), 22 (18.3%) and 87 (72.5%) patients had patterns A, B, and C, respectively. Patients with pattern C had the highest incidence of LVI and LNM (p < 0.05). Although the Kaplan-Meier curves demonstrated that survival decreased with increasing Silva classification for A-C cancers, there was no statistically significant difference [disease-free survival (DFS): p = 0.181; overall survival (OS): p = 0.205]. There were 45 cases presented as mixed-type of Silva patterns. According to the SCS, 23 cases (19.2%) were rated as grade I, 31 cases (25.8%) as grade II and 66 (55.0%) cases as grade III. Patients with SCS grade III had the highest incidence of LVI and LNM (p < 0.05). Kaplan-Meier analysis revealed that patients with higher SCS had significantly shorter DFS and OS than those with lower SCS (p < 0.05). High SCS was an independent predictor of poorer OS and DFS (p < 0.05) in patients with EAC. CONCLUSIONS: The application of the Silva system could effectively predict the LNM of patients and may be helpful in selecting an appropriate surgical procedure. The SCS system we designed showed a good predictive value for DFS and OS in EAC.

A novel Silva pattern-based model for precisely predicting recurrence in intermediate-risk cervical adenocarcinoma patients.

BACKGROUND: Considering the unique biological behavior of cervical adenocarcinoma (AC) compared to squamous cell carcinoma, we now lack a distinct method to assess prognosis for AC patients, especially for intermediate-risk patients. Thus, we sought to establish a Silva-based model to predict recurrence specific for the intermediate-risk AC patients and guide adjuvant therapy. METHODS: 345 AC patients were classified according to Silva pattern, their clinicopathological data and survival outcomes were assessed. Among them, 254 patients with only intermediate-risk factors were identified. The significant cutoff values of four factors (tumor size, lymphovascular space invasion (LVSI), depth of stromal invasion (DSI) and Silva pattern) were determined by univariate and multivariate Cox analyses. Subsequently, a series of four-, three- and two-factor Silva-based models were developed via various combinations of the above factors. RESULTS: (1) We confirmed the prognostic value of Silva pattern using a cohort of 345 AC patients. (2) We established Silva-based models with potential recurrence prediction value in 254 intermediate-risk AC patients, including 12 four-factor models, 30 three-factor models and 16 two-factor models. (3) Notably, the four-factor model, which includes any three of four intermediate-risk factors (Silva C, ≥ 3 cm, DSI > 2/3, and > mild LVSI), exhibited the best recurrence prediction performance and surpassed the Sedlis criteria. CONCLUSIONS: Our study established a Silva-based four-factor model specific for intermediate-risk AC patients, which has superior recurrence prediction performance than Sedlis criteria and may better guide postoperative adjuvant therapy.

Aureanin: a new iridoid from the leaves of Tabebuia aurea (Silva Manso) Benth. & Hook.f. ex S.Moore.

One new iridoid named aureanin (1) was isolated from the leaves of Tabebuia aurea (Silva Manso) Benth. & Hook.f. ex S.Moore, together with eight known compounds, isoquercetin (2), astragalin (3), callicoside B (4), amphipaniculoside E (5), rehmaglutin D (6), quercetin-3-sambubioside (7), rutin (8), kaempferol-3-O-rutinoside (9). The structures of the isolated compounds were elucidated and confirmed by spectroscopic methods, including 1 D and 2 D NMR experiments, as well as HR-ESI-MS. Compounds 1-9 were evaluated for their in vitro cytotoxic activity against three human cancer cell lines (A549, HepG2, and MCF-7) and Leishmania major. Compound 4 showed activity against A549 (IC50: 36.8 ± 1.5 µg/mL, etoposide (positive control): 28.1 ± 4.2 µg/mL), however, none of the compounds were active against L. major.

Research Note: Choice of microbiota database affects data analysis and interpretation in chicken cecal microbiota.

The chicken microbiota is often analyzed to address questions about the effects of diet or disease on poultry health. To analyze the microbiota, bioinformatic platforms such as QIIME 2 and mothur are used, which incorporate public taxonomic databases such as Greengenes, the ribosomal database project (RDP), and SILVA to assign taxonomies to bacterial sequences. Many chicken microbiota studies continue to incorporate the Greengenes database, which has not been updated since 2013. To determine whether a choice of database could affect results, this study compared the results of bioinformatic analyses obtained using the Greengenes, RDP, and SILVA databases on a cecal luminal microbiome dataset. The QIIME 2 platform was used to process 16S bacterial sequences and assign taxonomies with Greengenes, RDP, and SILVA. Linear discriminant analysis effect size (LEfSe) was performed, allowing for the comparison of taxonomies considered significantly differentially abundant between the three databases. Some notable differences between databases were observed in results, in particular the ability of SILVA database to classify members of the family Lachnospiraceae into separate genera, while these members remained in one group of unclassified Lachnospiraceae through Greengenes and RDP. LEfSe analyses showed that the SILVA database produced more differentially abundant genera, in large part due to the classification of these separate Lachnospiraceae genera. Additionally, the relative abundance of unclassified Lachnospiraceae in SILVA results was significantly lower than in RDP results. Our results show the choice of taxonomic database can influence the results of a microbiota study at the genus level, potentially affecting the interpretation of the results. The use of the SILVA database is recommended over Greengenes in chicken microbiota studies, as more specific classifications at the genus level may provide more accurate interpretations of changes in the microbiota.

Clinical correlation of lymphovascular invasion and Silva pattern of invasion in early-stage endocervical adenocarcinoma: proposed binary Silva classification system.

Silva invasion pattern can help predict lymph node metastasis risk in endocervical adenocarcinoma. We analysed Silva pattern of invasion and lymphovascular invasion to determine associations with clinical outcomes in stage IA and IB1 endocervical adenocarcinomas. International Federation of Gynecology and Obstetrics (FIGO; 2019 classification) stage IA-IB1 endocervical adenocarcinomas from 15 international institutions were examined for Silva pattern, presence of lymphovascular invasion, and other prognostic parameters. Lymph node metastasis status, local/distant recurrences, and survival data were compared using appropriate statistical tests. Of 399 tumours, 152 (38.1%) were stage IA [IA1, 77 (19.3%); IA2, 75 (18.8%)] and 247 (61.9%) were stage IB1. On multivariate analysis, lymphovascular invasion (p=0.008) and Silva pattern (p<0.001) were significant factors when comparing stage IA versus IB1 endocervical adenocarcinomas. Overall survival was significantly associated with lymph node metastasis (p=0.028); recurrence-free survival was significantly associated with lymphovascular invasion (p=0.002) and stage (1B1 versus 1A) (p=0.002). Five and 10 year overall survival and recurrence-free survival rates were similar among Silva pattern A cases and Silva pattern B cases without lymphovascular invasion (p=0.165 and p=0.171, respectively). Silva pattern and lymphovascular invasion are important prognostic factors in stage IA1-IB1 endocervical adenocarcinomas and can supplement 2019 International Federation of Gynecology and Obstetrics staging. Our binary Silva classification system groups patients into low risk (patterns A and B without lymphovascular invasion) and high risk (pattern B with lymphovascular invasion and pattern C) categories.

Simple Matching Using QIIME 2 and RDP Reveals Misidentified Sequences and an Underrepresentation of Fungi in Reference Datasets.

Simple nucleotide matching identification methods are not as accurate as once thought at identifying environmental fungal sequences. This is largely because of incorrect naming and the underrepresentation of various fungal groups in reference datasets. Here, we explore these issues by examining an environmental metabarcoding dataset of partial large subunit rRNA sequences of Basidiomycota and basal fungi. We employed the simple matching method using the QIIME 2 classifier and the RDP Classifier in conjunction with the latest releases of the SILVA (138.1, 2020) and RDP (11, 2014) reference datasets and then compared the results with a manual phylogenetic binning approach. Of the 71 query sequences tested, 21 and 42% were misidentified using QIIME 2 and the RDP Classifier, respectively. Of these simple matching misidentifications, more than half resulted from the underrepresentation of various groups of fungi in the SILVA and RDP reference datasets. More comprehensive reference datasets with fewer misidentified sequences will increase the accuracy of simple matching identifications. However, we argue that the phylogenetic binning approach is a better alternative to simple matching since, in addition to better accuracy, it provides evolutionary information about query sequences.