Collapsible tree: interactive web app to present collapsible hierarchies.

Motivation: A crucial component of intuitive data visualization is presenting a hierarchical tree structure with interactive functions. For example, single-cell transcriptomics studies may generate gene expression values with developmental trajectories or cell lineage structures. Two common visualization methods, t-Distributed Stochastic Neighbor Embedding (t-SNE) and Uniform Manifold Approximation and Projection (UMAP), require two separate figures to depict the distribution of cell types and gene expression data, with low-dimension projections that may not capture the hierarchical structures among cells.

Generation of human expandable limb-bud-like progenitors via chemically induced dedifferentiation.

In certain highly regenerative animals, cellular dedifferentiation occurs after injury, allowing specialized cells to become progenitor cells for regeneration. However, this capacity is restricted in human cells due to reduced plasticity. Here, we introduce a chemical-induced dedifferentiation approach that reverts the differentiated cells to a progenitor-like state, conferring the features of human limb bud cells from human adult somatic cells.

Aberrant Mitochondrial tRNA Genes Appear Frequently in Animal Evolution.

Mitochondrial tRNAs have acquired a diverse portfolio of aberrant structures throughout metazoan evolution. With the availability of more than 12,500 mitogenome sequences, it is essential to compile a comprehensive overview of the pattern changes with regard to mitochondrial tRNA repertoire and structural variations. This, of course, requires reanalysis of the sequence data of more than 250,000 mitochondrial tRNAs with a uniform workflow.

Unlocking nature's brilliance: using Antarctic extremophile Shewanella baltica to biosynthesize lanthanide-containing nanoparticles with optical up-conversion.

Both lanthanide-containing and fluorine-containing nanomaterials present challenging targets for microbial biosynthesis because these elements are toxic to most bacteria. Here, we overcome these challenges by using an Antarctic Shewanella baltica strain that tolerates these elements and report the first biosynthesis of lanthanide-doped fluoride nanoparticles (NPs) from them. NaYF NPs doped with Er/Yb are prototypical lanthanide-based upconverting nanoparticles (UCNPs) with upconverted luminescence at visible wavelengths under infrared excitation.

Gene expression prediction from histology images via hypergraph neural networks.

Spatial transcriptomics reveals the spatial distribution of genes in complex tissues, providing crucial insights into biological processes, disease mechanisms, and drug development. The prediction of gene expression based on cost-effective histology images is a promising yet challenging field of research. Existing methods for gene prediction from histology images exhibit two major limitations.

Leveraging the Genetics of Psychiatric Disorders to Prioritize Potential Drug Targets and Compounds.

Background: Genetics has the potential to inform biologically relevant drug treatment and repurposing which may ultimately improve patient care. In this study, we combine methods which leverage the genetics of psychiatric disorders to prioritize potential drug targets and compounds.

Methods: We used the largest available genome-wide association studies, in European ancestry, of four psychiatric disorders [i.

Predicting genome-wide tissue-specific enhancers via combinatorial transcription factor genomic occupancy analysis.

Enhancers are non-coding cis-regulatory elements crucial for transcriptional regulation. Mutations in enhancers can disrupt gene regulation, leading to disease phenotypes. Identifying enhancers and their tissue-specific activity is challenging due to their lack of stereotyped sequences.

sp. nov. and sp. nov., two novel species with the ability to biosynthesize fluorescent nanoparticles, isolated from soil samples at Union Glacier, Antarctica.

Two Gram-stain-positive bacterial strains, EXRC-4A-4 and RC-2-3, were isolated from soil samples collected at Union Glacier, Antarctica. Based on 16S rRNA gene sequence similarity, strain EXRC-4A-4 was identified as belonging to the genus , and strain RC-2-3 to the genus . Further genomic analyses, including average nucleotide identity and digital DNA-DNA hybridization, suggested that these strains represent new species.

Building a multistate model from electronic health records data for modeling long-term diabetes complications.

Objective: The progression of long-term diabetes complications has led to a decreased quality of life. Our objective was to evaluate the adverse outcomes associated with diabetes based on a patient's clinical profile by utilizing a multistate modeling approach.

Methods: This was a retrospective study of diabetes patients seen in primary care practices from 2013 to 2017.

Lossless Approximate Pattern Matching: Automated Design of Efficient Search Schemes.

This study introduces a pioneering approach to automate the creation of search schemes for lossless approximate pattern matching. Search schemes are combinatorial structures that define a series of searches over a partitioned pattern. Each search specifies the processing order of these parts and the cumulative lower and upper bounds on the number of errors in each part of the pattern.

Evolution of the regulatory subunits for the heteromeric acetyl-CoA carboxylase.

The committed step for de novo fatty acid (FA) synthesis is the ATP-dependent carboxylation of acetyl-coenzyme A catalysed by acetyl-CoA carboxylase (ACCase). In most plants, ACCase is a multi-subunit complex orthologous to prokaryotes. However, unlike prokaryotes, the plant and algal orthologues are comprised both catalytic and additional dedicated regulatory subunits.