Artificial intelligence-based image analysis can predict outcome in high-grade serous carcinoma via histology alone

High-grade extrauterine serous carcinoma (HGSC) is an aggressive tumor with high rates of recurrence, frequent chemotherapy resistance, and overall 5-year survival of less than 50%. Beyond determining and confirming the diagnosis itself, pathologist review of histologic slides provides no prognostic or predictive information, which is in sharp contrast to almost all other carcinoma types. Deep-learning based image analysis has recently been able to predict outcome and/or identify morphology-based representations of underlying molecular alterations in other tumor types, such as colorectal carcinoma, lung carcinoma, breast carcinoma, and melanoma. Using a carefully stratified HGSC patient cohort consisting of women (n = 30) with similar presentations who experienced very different treatment responses (platinum free intervals of either = 18 months), we used whole slide images (WSI, n = 205) to train a convolutional neural network. The neural network was trained, in three steps, to identify morphologic regions (digital biomarkers) that are highly associating with one or the other treatment response group. We tested the classifier using a separate 22 slide test set, and 18/22 slides were correctly classified. We show that a neural network based approach can discriminate extremes in patient response to primary platinum-based chemotherapy with high sensitivity (73%) and specificity (91%). These proof-of-concept results are novel, because for the first time, prospective prognostic information is identified specifically within HGSC tumor morphology.Peer reviewe

Increased MIB-1 expression in salivary gland pleomorphic adenoma that recurs and undergoes malignant transformation

Correction: Volume12, Issue1 Article Number10828 DOI: 10.1038/s41598-022-15267-7The objective of this retrospective study was to explore possible changes in histopathological features and expression of cyclin D1 and MIB-1 in salivary gland pleomorphic adenoma (PA) that recur or undergo malignant transformation. Knowledge of these characteristics might help to guide the management of these rare tumors. The histopathology and immunohistochemical staining characteristics of such tumors were analyzed in a cohort of 65 patients constituting three different groups of tumors: PA, recurrent pleomorphic adenoma (RPA) and carcinoma ex PA (CxPA). The RPAs were divided into two subgroups: primary PA that were known to recur later (PA-prim) and recurrent tumors appearing after a primary tumor (PA-rec). RPAs and CxPAs were compared with PAs without recurrence, which served as a control group. In our study, CxPA and PA-rec, but not PA-prim, showed increased MIB-1 expression compared with the control group. Neither cyclin D1 expression nor any histopathological features showed any association in statistical analyses. CxPA showed increased mitotic activity, squamous metaplasia, and nuclear atypia. Tumor multifocality was more frequent in PA-rec and CxPA. The different MIB-1 expression in CxPA and PA-rec in comparison to PA-prim suggests that the changes in expression could develop after the primary tumor.Peer reviewe

QuantISH : RNA in situ hybridization image analysis framework for quantifying cell type-specific target RNA expression and variability

RNA in situ hybridization (RNA-ISH) is a powerful spatial transcriptomics technology to characterize target RNA abundance and localization in individual cells. This allows analysis of tumor heterogeneity and expression localization, which are not readily obtainable through transcriptomic data analysis. RNA-ISH experiments produce large amounts of data and there is a need for automated analysis methods. Here we present QuantISH, a comprehensive open-source RNA-ISH image analysis pipeline that quantifies marker expressions in individual carcinoma, immune, and stromal cells on chromogenic or fluorescent in situ hybridization images. QuantISH is designed to be modular and can be adapted to various image and sample types and staining protocols. We show that in chromogenic RNA in situ hybridization images of high-grade serous carcinoma (HGSC) QuantISH cancer cell classification has high precision, and signal expression quantification is in line with visual assessment. We further demonstrate the power of QuantISH by showing that CCNE1 average expression and DDIT3 expression variability, as captured by the variability factor developed herein, act as candidate biomarkers in HGSC. Altogether, our results demonstrate that QuantISH can quantify RNA expression levels and their variability in carcinoma cells, and thus paves the way to utilize RNA-ISH technology.Peer reviewe

Increased MIB-1 expression in salivary gland pleomorphic adenoma that recurs and undergoes malignant transformation

The objective of this retrospective study was to explore possible changes in histopathological features and expression of cyclin D1 and MIB-1 in salivary gland pleomorphic adenoma (PA) that recur or undergo malignant transformation. Knowledge of these characteristics might help to guide the management of these rare tumors. The histopathology and immunohistochemical staining characteristics of such tumors were analyzed in a cohort of 65 patients constituting three different groups of tumors: PA, recurrent pleomorphic adenoma (RPA) and carcinoma ex PA (CxPA). The RPAs were divided into two subgroups: primary PA that were known to recur later (PA-prim) and recurrent tumors appearing after a primary tumor (PA-rec). RPAs and CxPAs were compared with PAs without recurrence, which served as a control group. In our study, CxPA and PA-rec, but not PA-prim, showed increased MIB-1 expression compared with the control group. Neither cyclin D1 expression nor any histopathological features showed any association in statistical analyses. CxPA showed increased mitotic activity, squamous metaplasia, and nuclear atypia. Tumor multifocality was more frequent in PA-rec and CxPA. The different MIB-1 expression in CxPA and PA-rec in comparison to PA-prim suggests that the changes in expression could develop after the primary tumor

QuantISH: RNA in situ hybridization image analysis framework for quantifying cell type-specific target RNA expression and variability

RNA in situ hybridization (RNA-ISH) is a powerful spatial transcriptomics technology to characterize target RNA abundance and localization in individual cells. This allows analysis of tumor heterogeneity and expression localization, which are not readily obtainable through transcriptomic data analysis. RNA-ISH experiments produce large amounts of data and there is a need for automated analysis methods. Here we present QuantISH, a comprehensive open-source RNA-ISH image analysis pipeline that quantifies marker expressions in individual carcinoma, immune, and stromal cells on chromogenic or fluorescent in situ hybridization images. QuantISH is designed to be modular and can be adapted to various image and sample types and staining protocols. We show that in chromogenic RNA in situ hybridization images of high-grade serous carcinoma (HGSC) QuantISH cancer cell classification has high precision, and signal expression quantification is in line with visual assessment. We further demonstrate the power of QuantISH by showing that CCNE1 average expression and DDIT3 expression variability, as captured by the variability factor developed herein, act as candidate biomarkers in HGSC. Altogether, our results demonstrate that QuantISH can quantify RNA expression levels and their variability in carcinoma cells, and thus paves the way to utilize RNA-ISH technology

Basin scale variability of Ostreopsis spp. blooms provides evidence of effectiveness of an integrated sampling approach

Special issue Marine Benthic Harmful Algal Blooms.-- 12 pages, 8 figures, 5 tables.-- Data availability: Data will be made available on requestOstreopsis spp. blooms have been occurring in the last two decades in the Mediterranean Sea in association with a variety of biotic and abiotic substrata (macroalgae, seagrasses, benthic invertebrates, sand, pebbles and rocks). Cells proliferate attached to the surfaces through mucilaginous trichocysts, which lump together microalgal cells, and can also be found in the plankton and on floating aggregates: such tychoplanktonic behavior makes the quantitative assessment of blooms more difficult than planktonic or benthic ones. Different techniques have been so far applied for quantifying cell abundances of benthic microalgae for research, monitoring and risk assessment purposes. In this context, the Benthic Dinoflagellates Integrator (BEDI), a non-destructive quantification method for benthic dinoflagellate abundances, was developed and tested within the EU ENPI-CBCMED project M3-HABs. This device allows mechanical detachment of cells without collecting the benthic substrate, providing an integrated assessment of both epiphytic and planktonic cells, i.e. of the number of cells potentially made available in the water volume from “resuspension” which could have harmful effects on other organisms (including humans). The present study confirms the effectiveness of the BEDI sampling device across different environments across the Mediterranean Sea and constitutes the first large-scale study of Ostreopsis spp. blooms magnitude in function of different macro- and meso‑habitat features across the basinThis publication has been produced with the financial assistance of the European Union under the ENPI CBC Mediterranean Sea Basin Programme, within the project M3-HABs, and the project OstreoRisk (CTM2014–53818-R) of the Spanish Government (MINECO) and the “Severo Ochoa Centre of Excellence” Accreditation under Grant CEX2019–000928-SPeer reviewe

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

ATLANTIC-CAMTRAPS: a dataset of medium and large terrestrial mammal communities in the Atlantic Forest of South America

Our understanding of mammal ecology has always been hindered by the difficulties of observing species in closed tropical forests. Camera trapping has become a major advance for monitoring terrestrial mammals in biodiversity rich ecosystems. Here we compiled one of the largest datasets of inventories of terrestrial mammal communities for the Neotropical region based on camera trapping studies. The dataset comprises 170 surveys of medium to large terrestrial mammals using camera traps conducted in 144 areas by 74 studies, covering six vegetation types of tropical and subtropical Atlantic Forest of South America (Brazil and Argentina), and present data on species composition and richness. The complete dataset comprises 53,438 independent records of 83 species of mammals, includes 10 species of marsupials, 15 rodents, 20 carnivores, eight ungulates and six armadillos. Species richness averaged 13 species (±6.07 SD) per site. Only six species occurred in more than 50% of the sites: the domestic dog Canis familiaris, crab-eating fox Cerdocyon thous, tayra Eira barbara, south American coati Nasua nasua, crab-eating raccoon Procyon cancrivorus and the nine-banded armadillo Dasypus novemcinctus. The information contained in this dataset can be used to understand macroecological patterns of biodiversity, community, and population structure, but also to evaluate the ecological consequences of fragmentation, defaunation, and trophic interactions. © 2017 by the Ecological Society of Americ

The 1000 Mitoses Project : A Consensus-Based International Collaborative Study on Mitotic Figures Classification

Introduction. The identification of mitotic figures is essential for the diagnosis, grading, and classification of various different tumors. Despite its importance, there is a paucity of literature reporting the consistency in interpreting mitotic figures among pathologists. This study leverages publicly accessible datasets and social media to recruit an international group of pathologists to score an image database of more than 1000 mitotic figures collectively. Materials and Methods. Pathologists were instructed to randomly select a digital slide from The Cancer Genome Atlas (TCGA) datasets and annotate 10-20 mitotic figures within a 2 mm2 area. The first 1010 submitted mitotic figures were used to create an image dataset, with each figure transformed into an individual tile at 40x magnification. The dataset was redistributed to all pathologists to review and determine whether each tile constituted a mitotic figure. Results. Overall pathologists had a median agreement rate of 80.2% (range 42.0%-95.7%). Individual mitotic figure tiles had a median agreement rate of 87.1% and a fair inter-rater agreement across all tiles (kappa = 0.284). Mitotic figures in prometaphase had lower percentage agreement rates compared to other phases of mitosis. Conclusion. This dataset stands as the largest international consensus study for mitotic figures to date and can be utilized as a training set for future studies. The agreement range reflects a spectrum of criteria that pathologists use to decide what constitutes a mitotic figure, which may have potential implications in tumor diagnostics and clinical management.Peer reviewe

Kiteytynyt se että keskustelupuheessa: Rakenne ja vuorovaikutustehtävät

Artikkelissa käsitellään suomen kiteytynyttä se että -yhtymää puhutussa kielessä. Tutkimuksen kohteena ovat sellaiset keskusteluvuorot, joissa sanat se ja että ja niitä seuraava puhunnos eivät ole syntaktisesti osa mitään laajempaa lausekokonaisuutta vaan muodostavat oman rakenteellisen ja toiminnallisen kokonaisuutensa. Tutkimus kytkeytyy funktionaaliseen ja käyttöpohjaiseen kieliopin kuvaukseen, ja sen näkökulma on vuorovaikutuslingvistinen ja keskustelunanalyyttinen. Tutkimuksen pääasiallinen aineisto koostuu suomenkielisten arkikeskustelujen morfosyntaktisesta tietokannasta Arkisynistä, joka sisältää 30 tuntia vuosina 1996–2015 kerättyjä kasvokkais- ja puhelinkeskusteluja. Lisäksi tutkimuksessa hyödynnetään Lauseopin arkiston murrekorpusta, joka koostuu 142 haastattelumuotoisesta, eri puolilla Suomea vuosina 1960–1970 käydystä keskustelusta. Se että -kiteymä esiintyy aineistossa yhtäältä pitkien, monipolvisten vuorojen loppu­puolella ja toisaalta vuoronalkuisena elementtinä lyhyemmissä väite- ja kannanotto­vuoroissa, jotka ovat jonkinlaisia reaktioita tai responsseja juuri edeltävään vuoroon. Kiteymä sijoittuu vuoron rakenneyksikön alkupuolelle projisoiden jatkoa ja osoittaen, että sitä seuraava puhe on kontekstissaan keskeistä. Kiteymä on tyypillisesti prosodisesti kulunut, ja sitä edeltää usein jokin partikkeli. Sitä seuraava puhunnos rakennetaan vastaanottajalle tunnistettavaksi, mutta vuoroon tulevat responssit eivät kuitenkaan aina vahvista vuoron sisältämää tietoa tutuksi. Artikkelissa osoitetaan, että se että -kiteymän käytössä ja käytön variaatiossa on tiettyjä kieliopillistuneille kielenaineksille tyypillisiä piirteitä, mutta eri ikäisissä, tutkimuksessa käytössä olleissa keskustelupuheen aineistoissa se että -yhtymää käytetään kuitenkin samalla tavoin ja samantapaisissa konteksteissa. Aineisto ei siten anna aihetta olettaa, että nykypuheen se että olisi kieliopillistumisprosessin lopputulos, vaan pikemminkin se on käyttökonteksteistaan emergoituva ilmaisu, jolla on omat, tietynlaiset tehtävänsä vuorovaikutuksessa. The fixed expression se että in conversation: structure and interactional functions Our article concerns the fixed expression se että in spoken Finnish. We focus on turns at talk where the words se and että and the utterance that follows are not syntactically integrated in any other clausal construct but rather form their own structural and ­actional unit. Our research is based on the functional and usage-based grammatical tradition and is conducted from the perspective of Interactional Linguistics and Conversation Analysis. Our main data are Finnish everyday conversations from the morpho­syntactically coded Arkisyn database containing 30 hours of face-to-face and telephone conversations recorded between the years 1996–2015. We also utilize the D­ialect Corpus of the Syntax Archives of the University of Turku, which contains 142 interviews of elderly speakers conducted in different areas of Finland in 1960–1970. The fixed expression se että occurs in our data toward the end of lengthy, complex turns and on the other hand as a turn-initial element in shorter assertion and assessment turns which function as reactions or responses to a just preceding turn. The fixed expression comes early in the turn-constructional unit, projecting continuation and indexing what follows as central in its context. The expression is typically prosodically reduced and is often preceded by a particle. The utterance that follows se että is constructed as identifiable to the addressee but the responses do not always confirm that the content of the turn is previously familiar. The article shows that the use and patterns of variation of the se että expression contain features typical of grammaticization, but in the conversational data from the different periods of time used in the study, the se että expression is used in similar ways and in similar contexts. Therefore, the data we use does not lead us to conclude that the present-day se että expression would be a result of a recent process of grammaticization. Rather, it is a projective expression, emergent from its contexts of use with its particular functions in interaction