cytoviewer: an R/Bioconductor package for interactive visualization and exploration of highly multiplexed imaging data

BACKGROUND: Highly multiplexed imaging enables single-cell-resolved detection of numerous biological molecules in their spatial tissue context. Interactive visualization of multiplexed imaging data is crucial at any step of data analysis to facilitate quality control and the spatial exploration of single cell features. However, tools for interactive visualization of multiplexed imaging data are not available in the statistical programming language R. RESULTS: Here, we describe cytoviewer, an R/Bioconductor package for interactive visualization and exploration of multi-channel images and segmentation masks. The cytoviewer package supports flexible generation of image composites, allows side-by-side visualization of single channels, and facilitates the spatial visualization of single-cell data in the form of segmentation masks. As such, cytoviewer improves image and segmentation quality control, the visualization of cell phenotyping results and qualitative validation of hypothesis at any step of data analysis. The package operates on standard data classes of the Bioconductor project and therefore integrates with an extensive framework for single-cell and image analysis. The graphical user interface allows intuitive navigation and little coding experience is required to use the package. We showcase the functionality and biological application of cytoviewer by analysis of an imaging mass cytometry dataset acquired from cancer samples. CONCLUSIONS: The cytoviewer package offers a rich set of features for highly multiplexed imaging data visualization in R that seamlessly integrates with the workflow for image and single-cell data analysis. It can be installed from Bioconductor via https://www.bioconductor.org/packages/release/bioc/html/cytoviewer.html . The development version and further instructions can be found on GitHub at https://github.com/BodenmillerGroup/cytoviewer

Musiikkia, politiikkaa, kannanottoja

Venäjän Ukrainaan kohdistaman hyökkäyssodan aiheuttama kärsimys ja sen kirvoittamat erilaiset eettiset ja moraalifilosofiset kysymykset ovat myös meille musiikintutkijoille näkyvissä lähes päivittäin. Opetus- ja kulttuuriministeriön korkeakouluille maaliskuussa antaman suosituksen mukaisesti yliopistot ovat pidättäytyneet korkeakoulu- ja tiedeyhteistyöstä venäläisten organisaatioiden kanssa. Suosituksen mukaisesti jo olemassa oleva organisaatioiden välinen yhteistyö on keskeytetty toistaiseksi eikä uusia hankkeita käynnistetä. Tutkijoiden liikkuvuutta on jäädytetty, vierailuja ei suositeta eikä asiantuntijalausuntoja sovi pyytää eikä antaa. Tämä on vaikuttanut monen tutkijan arkeen, verkostoihin ja hankesuunnitteluihin yllättävin tavoin, eivätkä ratkaisut tilanteisiin aina ole olleet yksiselitteisiä. Suomessa toimivien venäläisten ja ukrainalaisten tutkijoiden sekä jatko- ja perusopiskelijoiden on pitänyt harkita monta ammattiyhteisöllistä kysymystä uudessa valossa. Nähtäväksi jää, millaista tuhoa Venäjän hyökkäyssota saa vielä aikaan esimerkiksi karjalaisen musiikkiperinteen tutkimuksessa. </p

Faecal haemoglobin concentrations are associated with all-cause mortality and cause of death in colorectal cancer screening

BACKGROUND: Colorectal cancer (CRC) screening reduces all-cause and CRC-related mortality. New research demonstrates that the faecal haemoglobin concentration (f-Hb) may indicate the presence of other serious diseases not related to CRC. We investigated the association between f-Hb, measured by a faecal immunochemical test (FIT), and both all-cause mortality and cause of death in a population-wide cohort of screening participants. METHODS: Between 2014 and 2018, 1,262,165 participants submitted a FIT for the Danish CRC screening programme. We followed these participants, using the Danish CRC Screening Database and several other national registers on health and population, until December 31, 2018. We stratified participants by f-Hb and compared them using a Cox proportional hazards regression on all-cause mortality and cause of death reported as adjusted hazard ratios (aHRs). We adjusted for several covariates, including comorbidity, socioeconomic factors, demography and prescription medication. RESULTS: We observed 21,847 deaths in the study period. Our multivariate analyses indicated an association relationship between increasing f-Hb and the risk of dying in the study period. This risk increased steadily from aHR 1.38 (95% CI: 1.32, 1.44) in those with a f-Hb of 7.1–11.9 μg Hb/g faeces to 2.20 (95% CI: 2.10, 2.30) in those with a f-Hb ≥60.0 μg Hb/g faeces, when compared to those with a f-Hb ≤7.0 μg Hb/g faeces. The pattern remained when excluding CRC from the analysis. Similar patterns were observed between incrementally increasing f-Hb and the risk of dying from respiratory disease, cardiovascular disease and cancers other than CRC. Furthermore, we observed an increased risk of dying from CRC with increasing f-Hb. CONCLUSIONS: Our findings support the hypothesis that f-Hb may indicate an elevated risk of having chronic conditions if causes for the bleeding have not been identified. The mechanisms still need to be established, but f-Hb may be a potential biomarker for several non-CRC diseases. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1186/s12916-022-02724-3

The seeding of ice algal blooms in Arctic pack ice: The multiyear ice seed repository hypothesis

Source at http://dx.doi.org/10.1002/2016JG003668 During the Norwegian young sea ICE expedition (N-ICE2015) from January to June 2015 the pack ice in the Arctic Ocean north of Svalbard was studied during four drifts between 83° and 80°N. This pack ice consisted of a mix of second year, fi rst year, and young ice. The physical properties and ice algal community composition was investigated in the three different ice types during the winter-spring-summer transition. Our results indicate that algae remaining in sea ice that survived the summer melt season are subsequently trapped in the upper layers of the ice column during winter and may function as an algal seed repository. Once the connectivity in the entire ice column is established, as a result of temperature-driven increase in ice porosity during spring, algae in the upper parts of the ice are able to migrate toward the bottom and initiate the ice algal spring bloom. Furthermore, this algal repository might seed the bloom in younger ice formed in adjacent leads. This mechanism was studied in detail for the dominant ice diatom Nitzschia frigida . The proposed seeding mechanism may be compromised due to the disappearance of older ice in the anticipated regime shift toward a seasonally ice-free Arctic Ocean

Biomimetic Oxygen Reduction by Cofacial Porphyrins at a Liquid-Liquid Interface

Oxygen reduction catalyzed by cofacial metalloporphyrins at the 1,2-dichlorobenzene-water interface was studied with two lipophilic electron donors of similar driving force, 1,1'-dimethylferrocene (DMFc) and tetrathiafulvalene (TTF). The reaction produces mainly water and some hydrogen peroxide, but the mediator has a significant effect on the selectivity, as DMFc and the porphyrins themselves catalyze the decomposition and the further reduction of hydrogen peroxide. Density functional theory calculations indicate that the biscobaltporphyrin, 4,5-bis[5-(2,8,13,17-tetraethyl-3,7,12,18-tetramethylporphyrinyl)]-9,9-dimethylxanthene, Co-2(DPX), actually catalyzes oxygen reduction to hydrogen peroxide when oxygen is bound on the "exo" side ("dock-on") of the catalyst, while four-electron reduction takes place with oxygen bound on the "endo" side ("dock-in") of the molecule. These results can be explained by a "dock-on/dock-in" mechanism. The next step for improving bioinspired oxygen reduction catalysts would be blocking the "dock-on" path to achieve selective four-electron reduction of molecular oxygen

Bi-framelet systems with few vanishing moments characterize Besov spaces

International audienceWe study the approximation properties of wavelet bi-frame systems in Lp(R^d). For wavelet bi-frame systems the approximation spaces associated with best m-term approximation are completely characterized for a certain range of smoothness parameters limited by the number of vanishing moments of the generators of the dual frame. The approximation spaces turn out to be essentially Besov spaces, just as in the classical orthonormal wavelet case. We also prove that for smooth functions, the canonical expansion in the wavelet bi-frame system is sparse and one can reach the optimal rate of approximation by simply thresholding the canonical expansion. For twice oversampled MRA based wavelet frames, a characterization of the associated approximation space is obtained without any restrictions given by the number of vanishing moments, but at a price of replacing the canonical expansion by another linear expansion