Characterizing the Features of Mitotic Figures Using a Conditional Diffusion Probabilistic Model

Mitotic figure detection in histology images is a hard-to-define, yet clinically significant task, where labels are generated with pathologist interpretations and where there is no ``gold-standard'' independent ground-truth. However, it is well-established that these interpretation based labels are often unreliable, in part, due to differences in expertise levels and human subjectivity. In this paper, our goal is to shed light on the inherent uncertainty of mitosis labels and characterize the mitotic figure classification task in a human interpretable manner. We train a probabilistic diffusion model to synthesize patches of cell nuclei for a given mitosis label condition. Using this model, we can then generate a sequence of synthetic images that correspond to the same nucleus transitioning into the mitotic state. This allows us to identify different image features associated with mitosis, such as cytoplasm granularity, nuclear density, nuclear irregularity and high contrast between the nucleus and the cell body. Our approach offers a new tool for pathologists to interpret and communicate the features driving the decision to recognize a mitotic figure.Comment: Accepted for Deep Generative Models Workshop at Medical Image Computing and Computer Assisted Intervention (MICCAI) 202

Variation in size frequency distribution of coral populations under different fishing pressures in two contrasting locations in the Indian Ocean

This study aimed to assess how the size-frequency distributions of coral genera varied between reefs under different fishing pressures in two contrasting Indian Ocean locations (the Maldives and East Africa). Using generalized linear mixed models, we were able to demonstrate that complex interactions occurred between coral genera, coral size class and fishing pressure. In both locations, we found Acropora coral species to be more abundant in non-fished compared to fished sites (a pattern which was consistent for nearly all the assessed size classes). Coral genera classified as ‘stress tolerant’ showed a contrasting pattern i.e. were higher in abundance in fished compared to non-fished sites. Site specific variations were also observed. For example, Maldivian reefs exhibited a significantly higher abundance in all size classes of ‘competitive’ corals compared to East Africa. This possibly indicates that East African reefs have already been subjected to higher levels of stress and are therefore less suitable environments for ‘competitive’ corals. This study also highlights the potential structure and composition of reefs under future degradation scenarios, for example with a loss of Acropora corals and an increase in dominance of ‘stress tolerant’ and ‘generalist’ coral genera.USAi

MRI-localized biopsies reveal subtype-specific differences in molecular and cellular composition at the margins of glioblastoma

Glioblastomas (GBMs) diffusely infiltrate the brain, making complete removal by surgical resection impossible. The mixture of neoplastic and nonneoplastic cells that remain after surgery form the biological context for adjuvant therapeutic intervention and recurrence. We performed RNA-sequencing (RNA-seq) and histological analysis on radiographically guided biopsies taken from different regions of GBM and showed that the tissue contained within the contrast-enhancing (CE) core of tumors have different cellular and molecular compositions compared with tissue from the nonenhancing (NE) margins of tumors. Comparisons with the The Cancer Genome Atlas dataset showed that the samples from CE regions resembled the proneural, classical, or mesenchymal subtypes of GBM, whereas the samples from the NE regions predominantly resembled the neural subtype. Computational deconvolution of the RNA-seq data revealed that contributions from nonneoplastic brain cells significantly influence the expression pattern in the NE samples. Gene ontology analysis showed that the cell type-specific expression patterns were functionally distinct and highly enriched in genes associated with the corresponding cell phenotypes. Comparing the RNA-seq data from the GBM samples to that of nonneoplastic brain revealed that the differentially expressed genes are distributed across multiple cell types. Notably, the patterns of cell type-specific alterations varied between the different GBM subtypes: the NE regions of proneural tumors were enriched in oligodendrocyte progenitor genes, whereas the NE regions of mesenchymal GBM were enriched in astrocytic and microglial genes. These subtypespecific patterns provide new insights into molecular and cellular composition of the infiltrative margins of GBM

Endoglin, a novel biomarker and therapeutical target to prevent malignant peripheral nerve sheath tumor growth and metastasis.

PURPOSE Malignant peripheral nerve sheath tumors (MPNSTs) are highly aggressive soft-tissue sarcomas that lack effective treatments, underscoring the urgent need to uncover novel mediators of MPNST pathogenesis that may serve as potential therapeutic targets. Tumor angiogenesis is considered a critical event in MPNST transformation and progression. Here, we have investigated whether endoglin (ENG), a TGF-β coreceptor with a crucial role in angiogenesis, could be a novel therapeutic target in MPNSTs. EXPERIMENTAL DESIGN ENG expression was evaluated in human peripheral nerve sheath tumor tissues and plasma samples. Effects of tumor cell-specific ENG expression on gene expression, signaling pathway activation and in vivo MPNST growth and metastasis were investigated. The efficacy of ENG targeting in monotherapy or in combination with MEK inhibition was analyzed in xenograft models. RESULTS ENG expression was found to be upregulated in both human MPNST tumor tissues and plasma circulating small extracellular vesicles. We demonstrated that ENG modulates Smad1/5 and MAPK/ERK pathway activation and pro-angiogenic and pro-metastatic gene expression in MPNST cells and plays an active role in tumor growth and metastasis in vivo. Targeting with ENG-neutralizing antibodies (TRC105/M1043) decreased MPNST growth and metastasis in xenograft models by reducing tumor cell proliferation and angiogenesis. Moreover, combination of anti-ENG therapy with MEK inhibition effectively reduced tumor cell growth and angiogenesis. CONCLUSIONS Our data unveil a tumor-promoting function of ENG in MPNSTs and support the use of this protein as a novel biomarker and a promising therapeutic target for this disease.We apologize to those authors whose work could not be cited due to size limitations. We thank Dr. Eduard Serra, Dr. Conxi Lázaro and Dr. David Lyden for their support in the project. We also thank Héctor Tejero for his help in analyzing RNA-seq data. Dr. Peinado laboratory is funded by US Department of Defense (W81XWH-16-1-0131), Agencia Estatal de Investigación/Ministerio de Ciencia e Innovación (AEI/MCIN) (PID2020-118558RB-I00/AEI/10.13039/501100011033), Fundación Proyecto Neurofibromatosis, European Union’s Horizon 2020 research and innovation programme “proEVLifeCycle” under the Marie Skłodowska-Curie grant agreement No 860303, and Fundación Científica AECC. We are also grateful for the support of the Ministerio de Universidades (Programa de Formación de Profesorado Universitario (FPU)) for the fellowship FPU016/05356 awarded to T. González-Muñoz and to the Translational NeTwork for the CLinical application of Extracellular VesicleS (TeNTaCLES) RED2018-102411-T(AEI/10.13039/501100011033). A. Di Giannatale was supported during this work by a research gran Nuovo-Soldati Foundation. The CNIO, certified as Severo Ochoa Excellence Centre, is supported by the Spanish Government through the Instituto de Salud Carlos III.N

Recruitment of lateral rostral prefrontal cortex in spontaneous and task-related thoughts

Behavioural and neuroimaging studies suggest that spontaneous and task-related thought processes share common cognitive mechanisms and neural bases. Lateral rostral prefrontal cortex (RPFC) is a brain region that has been implicated both in spontaneous thought and in high-level cognitive control processes, such as goal/subgoal integration and the manipulation of self-generated thoughts. We therefore propose that the recruitment of lateral RPFC may follow a U-shaped function of cognitive demand: relatively high in low-demand situations conducive to the emergence of spontaneous thought, and in high-demand situations depending on processes supported by this brain region. We used functional magnetic resonance imaging to investigate brain activity while healthy participants performed two tasks, each with three levels of cognitive demands, in a block design. The frequency of task-unrelated thoughts, measured by questionnaire, was highest in the low cognitive demand condition. Low and high cognitive demand conditions were each compared to the intermediate level. Lateral RPFC and superior parietal cortex were recruited in both comparisons, with additional activations specific to each contrast. These results suggest that RPFC is involved both when (a) task demands are low, and the mind wanders, and (b) the task requires goal/subgoal integration and manipulation of self-generated thoughts

Neural Mechanisms of Interference Control in Working Memory: Effects of Interference Expectancy and Fluid Intelligence

A critical aspect of executive control is the ability to limit the adverse effects of interference. Previous studies have shown activation of left ventrolateral prefrontal cortex after the onset of interference, suggesting that interference may be resolved in a reactive manner. However, we suggest that interference control may also operate in a proactive manner to prevent effects of interference. The current study investigated the temporal dynamics of interference control by varying two factors - interference expectancy and fluid intelligence (gF) - that could influence whether interference control operates proactively versus reactively.A modified version of the recent negatives task was utilized. Interference expectancy was manipulated across task blocks by changing the proportion of recent negative (interference) trials versus recent positive (facilitation) trials. Furthermore, we explored whether gF affected the tendency to utilize specific interference control mechanisms. When interference expectancy was low, activity in lateral prefrontal cortex replicated prior results showing a reactive control pattern (i.e., interference-sensitivity during probe period). In contrast, when interference expectancy was high, bilateral prefrontal cortex activation was more indicative of proactive control mechanisms (interference-related effects prior to the probe period). Additional results suggested that the proactive control pattern was more evident in high gF individuals, whereas the reactive control pattern was more evident in low gF individuals.The results suggest the presence of two neural mechanisms of interference control, with the differential expression of these mechanisms modulated by both experimental (e.g., expectancy effects) and individual difference (e.g., gF) factors

The projected degradation of subtropical coral assemblages by recurrent thermal stress

1. Subtropical coral assemblages are threatened by similar extreme thermal stress events to their tropical counterparts. Yet, the mid‐ and long‐term thermal stress responses of corals in subtropical environments remain largely unquantified, limiting our capacity to predict their future viability. 2. The annual survival, growth and recruitment of 311 individual corals within the Solitary Islands Marine Park (Australia) was recorded over a 3‐year period (2016–2018), including the 2015/2016 thermal stress event. These data were used to parameterise integral projection models quantifying the effect of thermal stress within a subtropical coral assemblage. Stochastic simulations were also applied to evaluate the implications of recurrent thermal stress scenarios predicted by four different Representative Concentration Pathways. 3. We report differential shifts in population growth rates (λ) among coral populations during both stress and non‐stress periods, confirming contrasting bleaching responses among taxa. However, even during non‐stress periods, the observed dynamics for all taxa were unable to maintain current community composition, highlighting the need for external recruitment sources to support the community structure. 4. Across all coral taxa, projected stochastic growth rates (λs) were found to be lowest under higher emissions scenarios. Correspondingly, predicted increases in recurrent thermal stress regimes may accelerate the loss of coral coverage, species diversity and structural complexity within subtropical regions. 5. We suggest that these trends are primarily due to the susceptibility of subtropical specialists and endemic species, such as Pocillopora aliciae, to thermal stress. Similarly, the viability of many tropical coral populations at higher latitudes is highly dependent on the persistence of up‐current tropical systems. As such, the inherent dynamics of subtropical coral populations appear unable to support their future persistence under unprecedented thermal disturbance scenarios