Research works

Typology of transit-oriented development to promote sustainable urban structure

<title>Abstract</title> Transit-Oriented Development (TOD) has emerged as a transformative strategy in sustainable urban planning, aiming to integrate land use and public transportation to foster compact, walkable, and mixed-use communities centered around high-capacity transit s...

Measuring Ocean Surface Waves

Abstract Propagating waves on the ocean surface can be represented as a stochastic process whose statistics are characterized by a spectrum. This paper reviews methods for measuring the wave spectrum and related quantities. Observations begin by sensing fluid dynamical properties...

The choice-wide behavioral association study: data-driven identification of interpretable behavioral components

Behavior contains rich structure across many timescales, but there is a dearth of methods to identify relevant components, especially over the longer periods required for learning and decision-making. Inspired by the goals and techniques of genome-wide association studies, we pre...

A Clifford algebra approach to bosonic strings with fermionic boundaries

Abstract The Brauer–Weyl theorem (Brauer, Weyl. 1935 Am. J. Maths. 57, 425–449. (doi:10.2307/2371218)) states that the algebra of tensor products of spinors is isomorphic to the Clifford (geometric) algebra, in any number of space–time dimensions. The algebraic relation between f...

Water, pipes and the cholera pathogen: The colonial politics of germs and water infrastructures in the Philippines

This paper examines how the politics of water governance intersected with germ suppression during US colonial rule in the Philippines. Drawing on historical materials and policy documents, we critically trace two interrelated processes of hydroterritorialization through which cho...

Forest canopy decline under elevated CO 2 during the Paleocene-Eocene Thermal Maximum

Uncertainty remains regarding the impact of rapid anthropogenic warming on forest ecosystem structure, biodiversity, and function. As an analog, we reconstruct forest canopy density and compositional change in Wyoming, USA, through the Paleocene-Eocene Thermal Maximum (PETM), an...

Cryo-EM structure of pro-aggregant P301L/S320F double-mutant tau filaments formed in mouse brains following peripheral AAV delivery

Abstract Tauopathies are characterized by the accumulation of abnormally phosphorylated tau filaments, with disease-specific folds revealed by cryo-electron microscopy (cryo-EM). Here, we delivered a recombinant human tau carrying the P301L/S320F double mutation into App NL-G-F /...

Photoproximity labeling of c-Myc reveals SLK as a cancer-specific co-regulator

Transcription factors (TFs) have long been aspirational therapeutic targets for the treatment of diseases, as their dysregulation is a common mechanism for altered cell states. Despite this, many TFs implicated in disease have disordered structures and lack canonical binding pock...

Characterization of microbial dark matter at scale with MetaSBT and taxonomy-aware Sequence Bloom Trees

ABSTRACT Metagenomics has become a powerful tool for studying microbial communities, allowing researchers to investigate microbial diversity within complex environmental samples. Recent advances in sequencing technology have enabled the recovery of near-complete microbial genomes...

3D chemotaxis chip for investigating natural killer cell migration mechanisms

Abstract Introduction Natural killer (NK) cells are a promising tool for cancer immunotherapy, as they can rapidly recognize and kill cancer cells without prior knowledge of tumor-specific antigens while leaving healthy cells unharmed. However, a major challenge in NK cell-based...

plsMD: a plasmid reconstruction tool from short-read assemblies

Abstract Background While whole genome sequencing has become a cornerstone of antimicrobial resistance surveillance, the reconstruction of plasmid sequences from short-read data remains a challenge due to repetitive sequences and assembly fragmentation. Current computational tool...

Clustered coloring of graphs excluding a subgraph and a minor

A graph coloring has bounded clustering if each monochromatic component has bounded size. Equivalently, it is a partition of the vertices into induced subgraphs with bounded size components. This paper studies clustered colorings of graphs, where the number of colors depends on a...

Catalogue of strong nonlinear surprises in ocean, sea-ice, and atmospheric variables in CMIP6

Abstract. The Coupled Model Intercomparison Project Phase 6 (CMIP6) archive was analysed for the occurrence of Strong Nonlinear Surprises (SNS) in future climate-change projections. To this end, we built an automated detection algorithm to identify SNS in a reproducible manner. T...

Adherence to the Eatwell Guide and associations with markers of adiposity: a prospective analysis within the UK Biobank cohort

Abstract Background Obesity remains a major public health concern in the UK, contributing towards increased disease risk and premature mortality. The Eatwell Guide - the UK’s health eating model - is widely applied in policy and practice, yet evidence linking adherence to this di...

Inhibition of RhoA-mediated secretory autophagy in megakaryocytes mitigates myelofibrosis in mice

Abstract Megakaryocytes (MKs) are large, polyploid cells that contribute to bone marrow homeostasis through the secretion of cytokines such as transforming growth factor β1 (TGFβ1). During neoplastic transformation, immature MKs accumulate in the bone marrow where they induce fib...

LncPNdeep: A long non-coding RNA classifier based on large language model with peptide and nucleotide embedding

Abstract Long non-coding RNA plays an important role in various gene transcription and peptide interactions. Classifying lncRNAs from coding RNA is a crucial step in bioinformatics analysis which seriously affects the post-analysis for transcriptome annotation. Although several m...

MuSpAn: a toolbox for multiscale spatial analysis

Abstract Advances in multiplex imaging and spatial omics have revolutionised spatial data generation in biology, revealing complex tissue organisation across multiple scales. However, methods for analysing these data have lagged behind, with fragmented, study-specific pipelines a...

BioTwin-PE: An Uncertainty-Aware Multimodal State-Space Framework and Validation Protocol for Longitudinal Placental Monitoring

Placental assessment is necessarily intermittent, while ma- ternal and fetal physiology evolve continuously. This mis- match limits the ability of conventional visit-level prediction models to represent changes occurring between examinations. We present BioTwin-PE, a methods fram...

Nonlinear primary resonance and dynamic stability in parametrically excited self-sustaining curved SWCNTs subjected to a thermal and magnetic loads

Abstract This research conducts a systematic examination of the nonlinear dynamic behaviour exhibited by curved single-walled carbon nanotubes (CSWCNTs) under parametric excitation while embedded in a nonlinear viscoelastic medium. The investigation employs nonlocal Euler–Bernoul...

Independent Predictors and a Nomogram for Postoperative Urethral Stricture After TURP in Elderly Patients: A Real-World Study

AIM: Postoperative urethral stricture is an important complication after transurethral resection of the prostate (TURP). This study aimed to identify independent predictors of urethral stricture within 3 months after TURP in elderly patients and to develop a nomogram for predicti...