Biology subjects

Uno, K.

Publications and source records attributed to Uno, K..

5 recordsLinked to original sources

bioRxiv2026

The Pan-European Impact of the Balkan Hunter-Gatherers

During the Last Glacial Maximum (LGM) 26-19 thousand years ago (kya), Europe had three principal refugia not covered by ice: the Iberian, Italian, and Balkan peninsulas1,2. While the Iberian and Italian refugia have been studied with ancient DNA3-7, the legacy of the Balkan refugium has remained a mystery due to a lack of genetic data 30-12 kya. We present genome-wide data from nine newly reported individuals: three Epipaleolithic from Romania, one Epipaleolithic from Bosnia and Herzegovina, three Mesolithic from Greece, one Epipaleolithic from Southern Italy, and one Mesolithic from Sardinia. We find that the Epipaleolithic individuals from Romania and the Mesolithic individual from mainland Greece were from a previously unsampled population that was the primary source for later European hunter-gatherers. Westward expansion of Balkan Epipaleolithic people into the Italian Peninsula and mixture with a minority contribution from pre-LGM Italians, produced a population that then spread further west to become the primary ancestry of west-ern European Mesolithic people. Northeastward expansion, bypassing Italy, contributed the European ancestry source of Scandinavian and Eastern European hunter-gatherers. Southeastward expansion to the Aegean led to Anatolian-European mixtures before the spread of farming.

genetics↗

bioRxiv2024

A Computational Approach to Interpreting the Embedding Space of Dimension Reduction

Nonlinear dimension reduction methods are widely applied in studies analyzing gene and protein expression, by revealing patterns of discrete groups and continuous orders in high-dimensional data. However, the tools are limited to understanding the obtained embedding structures of biological mechanisms, hindering the full exploitation of data. Here, we propose a novel framework to interpret embedding systematically by identifying and mapping associated biological functions. The method performs statistical tests and visualizes significantly enriched functions essential for the organization of the embedding structure, by applying it to the embedding results of two datasets: the Genotype Tissue Expression dataset and a Caenorhabditis elegans embryogenesis dataset, one capturing distinct cluster structures and the other capturing continuous developmental trajectories. We identified the associated functions for interpreting the two embeddings and confirmed it as a useful explainable AI tool in exploratory data analysis by providing annotations to the embedding space.

bioinformatics↗

bioRxiv2022

Types of anomalies in two-dimensional video-based gait analysis in uncontrolled environments

Two-dimensional video-based pose estimation is a technique that can estimate human skeletal coordinates from video data alone. It is also being applied to gait analysis and, particularly, due to its simplicity of measurement, it has the potential to be applied to the gait analysis of large populations. In contrast, it is considered difficult to completely homogenize the environment and settings during the measurement of large populations. Therefore, it is necessary to appropriately deal with technical errors that are not related to the biological factors of interest. In this study, by analyzing a large cohort database, we have identified four major types of anomalies that occur during gait analysis using OpenPose in uncontrolled environments: anatomical, biomechanical, and physical anomalies and errors due to estimation. We have also developed a workflow for identifying and correcting those anomalies and confirmed that the workflow is reproducible through simulation experiments. Our results will help obtain a comprehensive understanding of the anomalies to be addressed in a pre-processing for 2D video-based gait analysis of large populations. Author summaryGait is one of the important biomarkers of health conditions. With developing mobile health technologies, it is becoming easier to measure our health. However, to realize preventive medicine, establishing evidence is a critical issue, and we need to collect data from a large population. Two-dimensional video-based pose estimation can be a solution for the gait analysis of such a population. However, the technical accuracy and limitations of this analysis have not yet been sufficiently discussed. In this study, by analyzing the largest database currently available, we systematically identified four types of technical anomalies that occur during gait measurement: anatomical, biomechanical, and physical anomalies and errors dues to estimation. We have also shown how to deal with these issues and made solutions available as software so that researchers can reproduce them. In the future, increasing number of studies will use 2D video-based pose estimation to research health-related gait among large populations. We believe that our work will provide a guideline for researchers and clinicians involved in these studies to discuss design and algorithms.

physiology↗

bioRxiv2020

RoDiCE: Robust differential protein co-expression analysis for cancer complexome

MotivationThe full spectrum of abnormalities in cancer-associated protein complexes remains largely unknown. Comparing the co-expression structure of each protein complex between tumor and healthy cells may provide insights regarding cancer-specific protein dysfunction. However, the technical limitations of mass spectrometry-based proteomics, including contamination with biological protein variants, causes noise that leads to non-negligible over- (or under-) estimating co-expression. ResultsWe propose a robust algorithm for identifying protein complex aberrations in cancer based on differential protein co-expression testing. Our method based on a copula is sufficient for improving identification accuracy with noisy data compared to conventional linear correlation-based approaches. As an application, we use large-scale proteomic data from renal cancer to show that important protein complexes, regulatory signaling pathways, and drug targets can be identified. The proposed approach surpasses traditional linear correlations to provide insights into higher order differential co-expression structures. Availability and Implementationhttps://github.com/ymatts/RoDiCE.

bioinformatics↗

bioRxiv2020

N-Aryl Pyrido Cyanine derivatives: nuclear and organelle DNA markers for two-photon and super-resolution imaging

Live cell imaging using DNA-binding fluorescent probes is an essential molecular tool in various biological and biomedical fields. The major challenges in currently used DNA probes are to avoid UV light photo-excitation with high DNA selectivity and cell-permeability and are the availability of the cutting-edge imaging techniques such as a super-resolution microscopy. Herein we report new orange to red fluorogenic DNA probes having N-aryl pyrido cyanine (PC) moiety as a basic skeleton. Their DNA selectivity and cell-permeabilities are so high that organelle DNA as well as nuclear DNA can be clearly stained in various cell types and plant tissues with wash-free manner. PC dyes are also compatible with a stimulated emission depletion fluorescent lifetime imaging microscopy (STED-FLIM) for super-resolution imaging as well as two-photon microscopy for deep tissue imaging, should release the utilization limitation of synthetic DNA probes.

cell biology↗