A deep hybrid learning pipeline for accurate diagnosis of ovarian cancer based on nuclear morphology

Nuclear morphological features are potent determining factors for clinical diagnostic approaches adopted by pathologists to analyze the malignant potential of cancer cells. Considering the structural alteration of the nucleus in cancer cells, various groups have developed machine learning techniques based on variation in nuclear morphometric information like nuclear shape, size, nucleus-cytoplasm ratio and various non-parametric methods like deep learning have also been tested for analyzing immunohistochemistry images of tissue samples for diagnosing various cancers. We aim to correlate the morphometric features of the nucleus along with the distribution of nuclear lamin proteins with classical machine learning to differentiate between normal and ovarian cancer tissues. It has already been elucidated that in ovarian cancer, the extent of alteration in nuclear shape and morphology can modulate genetic changes and thus can be utilized to predict the outcome of low to a high form of serous carcinoma. In this work, we have performed exhaustive imaging of ovarian cancer versus normal tissue and developed a dual pipeline architecture that combines the matrices of morphometric parameters with deep learning techniques of auto feature extraction from pre-processed images. This novel Deep Hybrid Learning model, though derived from classical machine learning algorithms and standard CNN, showed a training and validation AUC score of 0.99 whereas the test AUC score turned out to be 1.00. The improved feature engineering enabled us to differentiate between cancerous and non-cancerous samples successfully from this pilot study.

Centripetal nuclear shape fluctuations associate with chromatin condensation towards mitosis

The cell nucleus plays a central role in several key cellular processes, including chromosome organisation, replication and transcription. Recent work intriguingly suggests an association between nuclear mechanics and cell-cycle progression, but many aspects of this connection remain unexplored. Here, by monitoring nuclear shape fluctuations at different cell cycle stages, we uncover increasing inward fluctuations in late G2 and early mitosis, which are initially transient, but develop into instabilities that culminate into nuclear-envelope breakdown in mitosis. Perturbation experiments and correlation analysis reveal an association of these processes with chromatin condensation. We propose that the contrasting forces between an extensile stress and centripetal pulling from chromatin condensation could link mechanically chromosome condensation and nuclear-envelope breakdown, the two main nuclear processes during mitosis.

New measurement of the β-spectrum of 210Bi with a silicon 4πβ-spectrometer

The shape of 210Bi β-spectrum was measured using a spectrometer based on Si(Li) detectors with a 4π geometry. Full absorption spectrometer allows for a direct measurement of the β-spectra without using the electron backscattering corrections for the response function. The measured value of nuclear shape factor C(W)=1+(-0.4378±0.0072)W+ (0.0526±0.0021) W2 is in agreement with the results of previous studies.

PSXII-17 Fertility prediction model for Nilli-Ravi buffalo bulls through Fourier harmonic analysis of sperm

A model to predict Nili-ravi buffalo bull fertility was developed based on Fourier harmonic analysis of sperm. Seventeen bulls with 3032 AI records were categorizes based on fertility rate (FR) as low (36.5±0.2, n = 6: SD< ˗1 from mean FR), medium (39.9±0.2, n = 3; SD +1 to -1 from mean FR) and high fertility (41.4±0.1, n = 8; SD > +1 from mean FR). Cryopreserved semen samples from these bulls were investigated for Fourier harmonic analysis of sperm nuclear shape. Hoechst-33342 and YOYO-1 fluorescent stains were used to identify live and dead sperm. Digital images were analyzed to get sperm nuclear perimeter points at different phase angles to generate Fourier functions. Mean harmonic amplitude (HA) 0 was different (P < 0.05) for 1700 live vs. 1294 dead sperm from the 17 bulls, thus live sperm were used for remaining analyses. The mean, variance, skewness and kurtosis values of 100 live sperm nuclei/bull were compared for HA0-5 between high (n = 6) and low (n = 6) fertility groups, considering equal number of bulls in each category. The mean HA2 (0.739±0.01 vs 0.686±0.00) and 4 (0.105±0.001 vs 0.007±0.001) were higher in high vs low fertility group respectively (P < 0.05). Sperm nuclear perimeter among high fertility group sperm was more elongated. There was also an increased skewness of HA0 as fertility increased (P < 0.05). Discriminant analysis defined a fertility model by using mean HA4, skewness HA0 and variance HA2, that resulted in 91.7% bulls into their correct fertility group upon cross-validation (canonical correlation=0.928; P < 0.05). Higher values of mean HA4, skewness HA0 and variance HA2 increase the chance of bulls being placed in the high fertility group. In conclusion, sperm nuclear shape in Nili-ravi buffalo bull is related to in vivo fertility. A fertility model using reported discriminant measures could be used to objectively identify Nili-ravi buffalo bulls of varying fertility.

Zonula occludens 2 and Cell-Cell Contacts Are Required for Normal Nuclear Shape in Epithelia

MAGUK protein ZO-2 is present at tight junctions (TJs) and nuclei. In MDCK ZO-2 knockdown (KD) cells, nuclei exhibit an irregular shape with lobules and indentations. This condition correlates with an increase in DNA double strand breaks, however cells are not senescent and instead become resistant to UV-induced senescence. The irregular nuclear shape is also observed in isolated cells and in those without TJs, due to the lack of extracellular calcium. The aberrant nuclear shape of ZO-2 KD cells is not accompanied by a reduced expression of lamins A/C and B and lamin B receptors. Instead, it involves a decrease in constitutive and facultative heterochromatin, and microtubule instability that is restored with docetaxel. ZO-2 KD cells over-express SUN-1 that crosses the inner nuclear membrane and connects the nucleoskeleton of lamin A to nesprins, which traverse the outer nuclear membrane. Nesprins-3 and -4 that indirectly bind on their cytoplasmic face to vimentin and microtubules, respectively, are also over-expressed in ZO-2 KD cells, whereas vimentin is depleted. SUN-1 and lamin B1 co-immunoprecipitate with ZO-2, and SUN-1 associates to ZO-2 in a pull-down assay. Our results suggest that ZO-2 forms a complex with SUN-1 and lamin B1 at the inner nuclear membrane, and that ZO-2 and cell–cell contacts are required for a normal nuclear shape.

Tissue scale properties of the extracellular matrix regulates nuclear shape, organisation and fate in the embryonic midline sutures

Balancing self-renewal and differentiation is a key feature of every stem cell niche and one that is tuned by mechanical interactions of cells with their neighbors and surrounding extracellular matrix. The fibrous stem cell niches that develop as sutures between skull bones must balance the complex extracellular environment that emerges to define them with self-renewal and bone production. Here, we address the role for physical stimuli in suture development by probing the relationship between nuclear shape, organization and gene expression in response to a developing collagen network in embryonic midline sutures. This work complements genetic approaches used to study sutures and provides the first quantitative analyses of physical structure in these sutures. By combining multiple imaging modalities with novel shape description, in addition to network analysis methods, we find the early emergence of a complex extracellular collagen network to have an important role in regulating morphogenesis and cell fate. We show that disrupted collagen crosslinking can alter ECM organization of midline sutures as well as stimulate expression of bone differentiation markers. Further, our findings suggest that in vivo, skeletal tissues can uncouple the response of the nuclear lamina from collagen mediated tissue stiffening seen in vitro. Our findings highlight a crucial relationship between the cellular microenvironment, tissue stiffness and geometry with gene expression in normal development and maintenance of progenitor fate in embryonic sutures.

An RNAi screen for genes that affect nuclear morphology in Caenorhabditis elegans reveals the involvement of unexpected processes

Aberration in nuclear morphology is one of the hallmarks of cellular transformation. However, the processes that, when mis-regulated, result aberrant nuclear morphology are poorly understood. In this study we carried out a systematic, high-throughput RNAi screen for genes that affect nuclear morphology in Caenorhabditis elegans embryos. The screen employed over 1700 RNAi constructs against genes required for embryonic viability. Nuclei of early embryos are typically spherical, and their NPCs are evenly distributed. The screen was performed on early embryos expressing a fluorescently tagged component of the nuclear pore complex (NPC), allowing visualization of nuclear shape as well as the distribution of NPCs around the nuclear envelope. Our screen uncovered 182 genes whose down-regulation resulted in one or more abnormal nuclear phenotypes, including multiple nuclei, micronuclei, abnormal nuclear shape, anaphase bridges and abnormal NPC distribution. Many of these genes fall into common functional groups, including some that were not previously known to affect nuclear morphology, such as genes involved in mitochondrial function, the vacuolar ATPase and the CCT chaperonin complex. The results of this screen add to our growing knowledge of processes that affect nuclear morphology and that may be altered in cancer cells that exhibit abnormal nuclear shape.

Study of signature inversion in 123,125I using Particle Rotor Model calculations

The phenomenon of signature inversion in positive parity yrast states of [Formula: see text]I nuclei has been studied using the Particle Rotor Model (PRM) calculations. The experimentally observed signature inversion is well reproduced from the PRM calculations. The change in the value of a triaxial parameter [Formula: see text] was observed after the inversion. The PRM calculations were also used to describe the reduced transition probabilities. The derived change in the value of “[Formula: see text]” (in Lund convention) after inversion is interpreted as the change in nuclear shape from near triaxial to tending towards noncollective oblate.