A combined experimental-computational approach uncovers a role for the Golgi matrix protein Giantin in breast cancer progression.

Our understanding of how speed and persistence of cell migration affects the growth rate and size of tumors remains incomplete. To address this, we developed a mathematical model wherein cells migrate in two-dimensional space, divide, die or intravasate into the vasculature. Exploring a wide range of speed and persistence combinations, we find that tumor growth positively correlates with increasing speed and higher persistence.

Whole-genome doubling drives oncogenic loss of chromatin segregation.

Whole-genome doubling (WGD) is a recurrent event in human cancers and it promotes chromosomal instability and acquisition of aneuploidies. However, the three-dimensional organization of chromatin in WGD cells and its contribution to oncogenic phenotypes are currently unknown. Here we show that in p53-deficient cells, WGD induces loss of chromatin segregation (LCS).

Epistasis and evolutionary dependencies in human cancers.

Cancer evolution is driven by the concerted action of multiple molecular alterations, which emerge and are selected during tumor progression. An alteration is selected when it provides an advantage to the tumor cell. However, the advantage provided by a specific alteration depends on the tumor lineage, cell epigenetic state, and presence of additional alterations.

Erratum: Iyer, A., et al. Integrative Analysis and Machine Learning Based Characterization of Single Circulating Tumor Cells. 2020, , 1206.

In the published manuscript [...

Discovering functional evolutionary dependencies in human cancers.

Cancer cells retain genomic alterations that provide a selective advantage. The prediction and validation of advantageous alterations are major challenges in cancer genomics. Moreover, it is crucial to understand how the coexistence of specific alterations alters response to genetic and therapeutic perturbations.

Integrative Analysis and Machine Learning based Characterization of Single Circulating Tumor Cells.

We collated publicly available single-cell expression profiles of circulating tumor cells (CTCs) and showed that CTCs across cancers lie on a near-perfect continuum of epithelial to mesenchymal (EMT) transition. Integrative analysis of CTC transcriptomes also highlighted the inverse gene expression pattern between PD-L1 and MHC, which is implicated in cancer immunotherapy. We used the CTCs expression profiles in tandem with publicly available peripheral blood mononuclear cell (PBMC) transcriptomes to train a classifier that accurately recognizes CTCs of diverse phenotype.

The statistics of how natural images drive the responses of neurons.

To model the responses of neurons in the early visual system, at least three basic components are required: a receptive field, a normalization term, and a specification of encoding noise. Here, we examine how the receptive field, the normalization factor, and the encoding noise affect the drive to model-neuron responses when stimulated with natural images. We show that when these components are modeled appropriately, the response drives elicited by natural stimuli are Gaussian-distributed and scale invariant, and very nearly maximize the sensitivity (d') for natural-image discrimination.

Persistent reduction in global longitudinal strain in the longer term after radiation therapy in patients with breast cancer.

Background: More than 80% of breast cancer patients receive radiotherapy (RT). However, RT can lead to cardiotoxicity, which usually develops insidiously over years, making diagnosis difficult. It is also unknown whether early identification of at-risk patients might improve long-term outcome.

Depth variation and stereo processing tasks in natural scenes.

Local depth variation is a distinctive property of natural scenes, but its effects on perception have only recently begun to be investigated. Depth variation in natural scenes is due to depth edges between objects and surface nonuniformities within objects. Here, we demonstrate how natural depth variation impacts performance in two fundamental tasks related to stereopsis: half-occlusion detection and disparity detection.

CellAtlasSearch: a scalable search engine for single cells.

Owing to the advent of high throughput single cell transcriptomics, past few years have seen exponential growth in production of gene expression data. Recently efforts have been made by various research groups to homogenize and store single cell expression from a large number of studies. The true value of this ever increasing data deluge can be unlocked by making it searchable.

FlavorDB: a database of flavor molecules.

Flavor is an expression of olfactory and gustatory sensations experienced through a multitude of chemical processes triggered by molecules. Beyond their key role in defining taste and smell, flavor molecules also regulate metabolic processes with consequences to health. Such molecules present in natural sources have been an integral part of human history with limited success in attempts to create synthetic alternatives.

Better than the real thing: eliciting fear with moving and static computer-generated stimuli.

As the popularity of virtual reality as an exposure therapy increases, it is important to validate the use of computer-generated stimuli in comparison to standardized images of "real" phobic objects, such as those of the International Affective Picture System (IAPS). The present study examined physiological and subjective measures of negative affect when viewing static IAPS images, static computer-generated images and moving videos of computer-generated images of feared stimuli and other negative stimuli which were not specifically feared. For example, a picture of a spider would be a "feared" stimulus for a spider fearful participant, whereas a picture of a snake would be categorized as a "negative" stimulus for that participant.

A virtual human agent for assessing bias in novice therapists.

Monitoring the psychological and physiological activity of persons interacting with virtual humans poses exacting measurement challenges. Three experiments are reported in this paper. In these experiments we made use of Virtual Human Agent technology to assess persons' psychological and physiological responses to Virtual Standardized Patients.

Neurocognitive and psychophysiological analysis of human performance within virtual reality environments.

Monitoring the neurocognitive and psychophysiological activity of persons operating within a complex environment poses exacting measurement challenges. Three experiments are reported in this paper. In these experiments we made use of VRCPAT to assess persons' neurocognitive and psychophysiological responses to high-fidelity, immersive virtual environments.