Evaluation of genetic demultiplexing of single-cell sequencing data from model species

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Allele-specific expression (ASE) is pivotal in understanding the genetic underpinnings of phenotypic variation within species, differences in disease susceptibility, and responses to environmental factors. We processed 11 different tissue types collected f ...

The stiffness of cells and of their nuclei is a biomarker of several pathological conditions. Current measurement methods rely on invasive physical probes that yield one or two stiffness values for the whole cell. However, the internal distribution of cell ...

In natural habitats, nutrient availability limits bacterial growth. We discovered that bacteria can overcome this limitation by acquiring nutrients by lysing neighboring cells through contact-dependent antagonism. Using single-cell live imaging and isotopi ...

Data augmentation is vital in deep learning for enhancing model robustness by artificially expanding training datasets. However, advanced methods like CutMix blend images and assign labels based on pixel ratios, often introducing label noise by neglecting ...

Motivation Many machine learning (ML) models developed to classify phenotype from gene expression data provide interpretations for their decisions, with the aim of understanding biological processes. For many models, including neural networks, interpretati ...

High-throughput transcriptomics is of increasing fundamental biological and clinical interest. The generation of molecular data from large collections of samples, such as biobanks and drug libraries, is boosting the development of new biomarkers and treatm ...

Viral metagenomics is a useful tool for detecting multiple human viruses in urban sewage. However, more refined protocols are required for its effective use in disease surveillance. In this study, we investigated the performance of three different preampli ...

The worsening of drought events with rising air temperature alters tree water relations causing severe hydraulic impairments and widespread forest mortality. Mixing tree species with contrasting hydraulic traits could reduce forest vulnerability to extreme ...

An image-based methodology is presented for the automatic generation of geometric building models at LOD4, incorporating both interior and exterior geometrical information. Existing approaches often focus on simplified geometries for either exteriors or in ...

Chlorinated compounds are ubiquitous. However, accumulation of chlorine-containing waste has a negative impact on human health and the environment due to the inapplicability of common disposal methods, such as landfill and incineration. Here we report a su ...

Enhancing tree diversity may be important to fostering resilience to drought-related climate extremes. So far, little attention has been given to whether tree diversity can increase the survival of trees and reduce its variability in young forest plantatio ...

A spinal cord injury (SCI) triggers a cascade of molecular and cellular responses involving inflammatory cell infiltration and cytokine release, apoptosis, demyelination, excitotoxicity, ischemia, and the formation of a fibrotic scar surrounded by an astro ...

Cells are the smallest operational units of living systems. Through synthesis of various biomolecules and exchange of signals with the environment, cells tightly regulate their composition to realize a specific functional state. The transformation of a cel ...

Growing evidence indicates that transposable elements (TEs) play important roles in evolution by providing genomes with coding and non-coding sequences. Identification of TE-derived functional elements, however, has relied on TE annotations in individual s ...

In sub-Mediterranean ecosystems, shade-tolerant broadleaf evergreens, especially the invasive Trachycarpus fortunei, are spreading uncontrollably in the forest understorey, impeding the regeneration of the native deciduous woody vegetation. Most invasive s ...

Through site-specific generation of intermediary reactive aldehydes, Horner-Wadsworth-Emmons olefination can now deliver selective functionalization of stable recombinant proteins and monoclonal antibodies, whilst preserving protein integrity. ...

Aquatic ecosystems continue to be threatened by chemical pollution. To what extent organisms are able to cope with chemical exposure depends on their ability to display mechanisms of defense across different organs. Among these mechanisms, biotransformatio ...

Decoding by contrasting layers (DoLa), is designed to improve the generation quality of large language models (LLMs) by contrasting the prediction probabilities between an early exit output (amateur logits) and the final output (expert logits).However, we ...

In the last decade, organoid technology has become a cornerstone in cancer research. Organoids are long-term primary cell cultures, usually of epithelial origin, grown in a three-dimensional (3D) protein matrix and a fully defined medium. Organoids can be ...

Species distribution modeling is a highly versatile tool for understanding the intricate relationship between environmental conditions and species occurrences. However, the available data often lacks information on confirmed species absence and is limited ...

Evaluation of genetic demultiplexing of single-cell sequencing data from model species

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Genome-wide allele-specific expression in multi-tissue samples from healthy male baboons reveals the transcriptional complexity of mammals

Estimation of Stiffness Maps in Deforming Cells Through Optical Flow With Bounded Curvature

Antagonism as a Foraging Strategy in Microbial Communities

SaliencyMix plus : Noise-Minimized Image Mixing Method With Saliency Map in Data Augmentation

A comparative analysis of gene expression profiling by statistical and machine learning approaches

Multi-well plate lid for single-step pooling of 96 samples for high-throughput barcode-based sequencing

Comparison of Three Viral Nucleic Acid Preamplification Pipelines for Sewage Viral Metagenomics

From roots to canopy: Unraveling the influence of species diversity on tree water relations under warmer and drier climates

Generation of LOD4 models for buildings towards the automated 3D modeling of BIMs and digital twins

Tandem catalysis enables chlorine-containing waste as chlorination reagents

Tree diversity reduces variability in sapling survival under drought

Multimodal transcriptomic atlases of mouse spinal cord injury

Deciphering the nature of cell state transitions in single cells using quantitative modeling of temporal dynamics

Ancestral genome reconstruction enhances transposable element annotation by identifying degenerate integrants

Invasive palms have more efficient and prolonged CO2 assimilation compared to native sub-Mediterranean vegetation

Horner-Wadsworth-Emmons olefination for bioconjugation

Organ-specific biotransformation in salmonids: Insight into intrinsic enzyme activity and biotransformation of three micropollutants

Multilingual Contrastive Decoding via Language-Agnostic Layers Skipping

Next-Generation Modeling of Cancer Using Organoids

On the selection and effectiveness of pseudo-absences for species distribution modeling with deep learning