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This paper presents a method for time-lapse 3D cell analysis. Specifically, we consider the problem of accurately localizing and quantitatively analyzing sub-cellular features, and for tracking individual cells from time-lapse 3D confocal cell image stacks. The heterogeneity of cells and the volume of multi-dimensional images presents a major challenge for fully automated analysis of morphogenesis and development of cells. This paper is motivated by the pavement cell growth process, and building a quantitative morphogenesis model. We propose a deep feature based segmentation method to accurately detect and label each cell region. An adjacency graph based method is used to extract sub-cellular features of the segmented cells. Finally, the robust graph based tracking algorithm using multiple cell features is proposed for associating cells at different time instances. We also demonstrate the generality of our tracking method on C. elegans fluorescent nuclei imagery. Extensive experiment results are provided and demonstrate the robustness of the proposed method. The code is available on GitHub and the method is available as a service through the BisQue portal.

This paper discovers new quantum physics, and gives solutions to puzzles of Wheeler's delayed choice and a particle's passing many slits simultaneously by exact quantum physics expressions. We further show new quantum control, new quantum oscillation, new quantum control experiments and new quantum oscillator being able to be installed in quantum communication network etc. We discover that the ability of a photon to hit electrons out in photoelectric effect is complementarily equivalent to the ability of wave of a photon to simultaneously pass through many slits in wave-particle duality. Objective criterion for distinguishing classical and quantum particles is found, and this paper gives applicable realm of quantum theories and new quantum physics expressions of wave-particle duality. All these studies above should be classified as classical and quantum particles, then classical particle and quantum particle wave cannot and can pass many slits, respectively. This paper discovers wave-particle duality's origin of displaying both wave property from plane wave part of the general Fourier expansion and particle property from the general Fourier expansion coefficients with the particle's global property and spins etc. We give the superposition state representation of wave-particle duality, further find the collapse of the duality superposition state to wave or particle state. The collapsed wave or particle state is related to the measure of wave or particle property. Then, we explain why sometimes it's a wave or a particle. Our achieved results are truly tested, and we discover new measured attractive state and quantum wave collapse velocity expression.

VEGF inhibitor drugs are part of standard care in oncology and ophthalmology, but not all patients respond to them. Combinations of drugs are likely to be needed for more effective therapies of angiogenesis-related diseases. In this paper we describe naturally occurring combinations of receptors in endothelial cells that might help to understand how cells communicate and to identify targets for drug combinations. We also develop and share a new software tool called DECNEO to identify them. Single-cell gene expression data are used to identify a set of co-expressed endothelial cell receptors, conserved among species (mice and humans) and enriched, within a network, of connections to up-regulated genes. This set includes several receptors previously shown to play a role in angiogenesis. Multiple statistical tests from large datasets, including an independent validation set, support the reproducibility, evolutionary conservation and role in angiogenesis of these naturally occurring combinations of receptors. We also show tissue-specific combinations and, in the case of choroid endothelial cells, consistency with both well-established and recent experimental findings, presented in a separate paper. The results and methods presented here advance the understanding of signaling to endothelial cells. The methods are generally applicable to the decoding of intercellular combinations of signals.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Do psychedelics affect sexual functioning postacutely? Anecdotal and qualitative evidence suggests they do, but this has never been formally tested. While sexual functioning and satisfaction are generally regarded as an important aspect of human wellbeing, sexual dysfunction is a common symptom of mental health disorders. It is also a common side effect of selective serotonin reuptake inhibitors (SSRIs), a first line treatment for depression. The aim of the present paper was to investigate the post-acute effects of psychedelics on self-reported sexual functioning, combining data from two independent studies, one large and naturalistic and the other a smaller but controlled clinical trial. Naturalistic use of psychedelics was associated with improvements in several facets of sexual functioning and satisfaction, including improved pleasure and communication during sex, satisfaction with ones partner and physical appearance. Convergent results were found in a controlled trial of psilocybin therapy versus an SSRI, escitalopram, for depression. In this trial, patients treated with psilocybin reported positive changes in sexual functioning after treatment, while patients treated with escitalopram did not. Despite focusing on different populations and settings, this is the first research study to quantitively investigate the effects of psychedelics on sexual functioning. Results imply a potential positive effect on post-acute sexual functioning and highlight the need for more research on this.

The emergence of long COVID during the ongoing COVID-19 pandemic has presented considerable challenges for healthcare professionals and researchers. The task of identifying relevant literature is particularly daunting due to the rapidly evolving scientific landscape, inconsistent definitions, and a lack of standardized nomenclature. This paper proposes a novel solution to this challenge by employing machine learning techniques to classify long COVID literature. However, the scarcity of annotated data for machine learning poses a significant obstacle. To overcome this, we introduce a strategy called medical paraphrasing, which diversifies the training data while maintaining the original content. Additionally, we propose a Data-Reweighting-Based Multi-Level Optimization Framework for Domain Adaptive Paraphrasing, supported by a Meta-Weight-Network (MWN). This innovative approach incorporates feedback from the downstream text classification model to influence the training of the paraphrasing model. During the training process, the framework assigns higher weights to the training examples that contribute more effectively to the downstream task of long COVID text classification. Our findings demonstrate that this method substantially improves the accuracy and efficiency of long COVID literature classification, offering a valuable tool for physicians and researchers navigating this complex and ever-evolving field.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

Metagenome sequence datasets can contain terabytes of reads, too many to be coassembled together on a single shared-memory computer; consequently, they have only been assembled sample by sample (multiassembly) and combining the results is challenging. We can now perform coassembly of the largest datasets using MetaHipMer, a metagenome assembler designed to run on supercomputers and large clusters of compute nodes. We have reported on the implementation of MetaHipMer previously; in this paper we focus on analyzing the impact of very large coassembly. In particular, we show that coassembly recovers a larger genome fraction than multiassembly and enables the discovery of more complete genomes, with lower error rates, whereas multiassembly recovers more dominant strain variation. Being able to coassemble a large dataset does not preclude one from multiassembly; rather, having a fast, scalable metagenome assembler enables a user to more easily perform coassembly and multiassembly, and assemble both abundant, high strain variation genomes, and low-abundance, rare genomes. We present several assemblies of terabyte datasets that could never be coassembled before, demonstrating MetaHipMer's scaling power. MetaHipMer is available for public use under an open source license and all datasets used in the paper are available for public download.