Publications by authors named "Timothy J Lee"

Article Synopsis
  • Early detection of cell type changes in genitourinary tract diseases is a clinical challenge, as current assays often lack the detailed cellular insight that invasive biopsies provide.
  • Researchers studied cell-free RNA (cfRNA) from urine samples of healthy individuals and kidney stone patients, aiming to improve understanding of cell type contributions and the urine metabolome.
  • The analysis revealed that urine transcriptome can discern contributions from various cell types and highlighted specific metabolic pathways linked to kidney function, indicating noninvasive urine analysis could serve as a useful tool in diagnosing related diseases.
View Article and Find Full Text PDF

Purpose: Accurate documentation of lesions during transurethral resection of bladder tumors (TURBT) is essential for precise diagnosis, treatment planning, and follow-up care. However, optimizing schematic documentation techniques for bladder lesions has received limited attention.

Materials And Methods: This prospective observational study used a cMDX-based documentation system that facilitates graphical representation, a lesion-specific questionnaire, and heatmap analysis with a posterization effect.

View Article and Find Full Text PDF

Most low-mass stars form in stellar clusters that also contain massive stars, which are sources of far-ultraviolet (FUV) radiation. Theoretical models predict that this FUV radiation produces photodissociation regions (PDRs) on the surfaces of protoplanetary disks around low-mass stars, which affects planet formation within the disks. We report James Webb Space Telescope and Atacama Large Millimeter Array observations of a FUV-irradiated protoplanetary disk in the Orion Nebula.

View Article and Find Full Text PDF

Danionella cerebrum (DC) is a promising vertebrate animal model for systems neuroscience due to its small adult brain volume and inherent optical transparency, but the scope of their cognitive abilities remains an area of active research. In this work, we established a behavioral paradigm to study visual spatial navigation in DC and investigate their navigational capabilities and strategies. We initially observed that adult DC exhibit strong negative phototaxis in groups but less so as individuals.

View Article and Find Full Text PDF

Urine is assayed alongside blood in medicine, yet current clinical diagnostic tests utilize only a small fraction of its total biomolecular repertoire, potentially foregoing high-resolution insights into human health and disease. In this work, we characterized the joint landscapes of transcriptomic and metabolomic signals in human urine. We also compared the urine transcriptome to plasma cell-free RNA, identifying a distinct cell type repertoire and enrichment for metabolic signal.

View Article and Find Full Text PDF

Purpose: Development of intelligence systems for bladder lesion detection is cost intensive. An efficient strategy to develop such intelligence solutions is needed.

Materials And Methods: We used four deep learning models (ConvNeXt, PlexusNet, MobileNet, and SwinTransformer) covering a variety of model complexity and efficacy.

View Article and Find Full Text PDF

This study aims to advance the theoretical understanding of the contextual antecedents underlying abusive supervision. It provides a fresh perspective on how subordinates' perceptions of an abusive supervision climate are shaped in temporary work environments. By developing a robust model, this research examines the relationships between temporary organizational characteristics (i.

View Article and Find Full Text PDF

Background: The clinical documentation of cystoscopy includes visual and textual materials. However, the secondary use of visual cystoscopic data for educational and research purposes remains limited due to inefficient data management in routine clinical practice.

Methods: A conceptual framework was designed to document cystoscopy in a standardized manner with three major sections: data management, annotation management, and utilization management.

View Article and Find Full Text PDF

Background: The clinical documentation of cystoscopy includes visual and textual materials. However, the secondary use of visual cystoscopic data for educational and research purposes remains limited due to inefficient data management in routine clinical practice.

Methods: A conceptual framework was designed to document cystoscopy in a standardized manner with three major sections: data management, annotation management, and utilization management.

View Article and Find Full Text PDF

Objectives: Providing high-quality care in the appropriate setting to optimize value is a worthy goal of an efficient health system. Consequences of managing nonurgent complaints in the emergency department (ED) have been described including inefficiency, loss of the primary care-patient relationship, and delayed care for other ED patients. The purpose of this initiative was to redirect nonurgent patients arriving in the ED to their primary care office for a same-day visit, and the SMART AIM was to increase redirected patients from 0% of those eligible to 30% in a 12-month period.

View Article and Find Full Text PDF

Processing full-length cystoscopy videos is challenging for documentation and research purposes. We therefore designed a surgeon-guided framework to extract short video clips with bladder lesions for more efficient content navigation and extraction. Screenshots of bladder lesions were captured during transurethral resection of bladder tumor, then manually labeled according to case identification, date, lesion location, imaging modality, and pathology.

View Article and Find Full Text PDF

A highly accurate CO dipole moment surface (DMS), Ames-2021, is reported along with CO infrared (IR) intensity comparisons approaching a 1-4‰ level of agreement and uncertainty. The Ames-2021 DMS was accurately fitted from CCSD(T) finite-field dipoles computed with the aug-cc-pVXZ (X = T, Q, 5) basis for C atom and the d-aug-cc-pVXZ (X = T, Q, 5) basis for O atoms, and extrapolated to the one particle basis set limit. Fitting σ is 3.

View Article and Find Full Text PDF

Identifying new nitrogenated hydrocarbon molecules in the interstellar medium (ISM) is challenging because of the lack of comprehensive spectroscopic data from experiments. In this computational work, we focus on investigating the structures, relative energies, spectroscopic constants, and energy landscape of the cyclic isomers of diazirine (c-CHN) using quantum chemical methods. Density functional theory (DFT) methods and coupled cluster theory with singles and doubles including perturbative triples [CCSD(T)] and CCSD(T) with the explicitly correlated F12b correction [CCSD(T)-F12b] were employed for this purpose along with large correlation consistent cc-pVTZ, cc-pVQZ, and cc-pV5Z basis sets.

View Article and Find Full Text PDF

The characteristics of the CH stretching and out-of-plane bending modes in polycyclic aromatic hydrocarbon molecules are investigated using anharmonic density functional theory (DFT) coupled to a vibrational second-order perturbation treatment taking resonance effects into account. The results are used to calculate the infrared emission spectrum of vibrationally excited species in the collision-less environment of interstellar space. This model follows the energy cascade as the molecules relax after the absorption of a UV photon in order to calculate the detailed profiles of the infrared bands.

View Article and Find Full Text PDF

The profile of the 11.2 μm feature of the infrared (IR) cascade emission spectra of polycyclic aromatic hydrocarbon (PAH) molecules is investigated using a vibrational anharmonic method. Several factors are found to affect the profile including: the energy of the initially absorbed ultraviolet (UV) photon, the density of vibrational states, the anharmonic nature of the vibrational modes, the relative intensities of the vibrational modes, the rotational temperature of the molecule, and blending with nearby features.

View Article and Find Full Text PDF

Objective: The objective of this review is to investigate overall survival in patients with human papillomavirus positive oropharyngeal squamous cell carcinoma (HPV+ OPSCC) comparing standard- versus reduced-dose radiotherapy.

Introduction: The improved survival of patients with HPV+ compared to HPV-negative OPSCC has raised the question of reducing the total radiation treatment dose delivered to patients with HPV+ OPSCC. A de-escalated radiotherapy protocol may provide equal oncological benefit, with reduced adverse events/toxicity.

View Article and Find Full Text PDF

The recent detection of ethynyl-functionalized cyclopropenylidene (c-CHCH) has initiated the search for other functional forms of cyclopropenylidene (c-CH) in space. There is existing gas-phase rotational spectroscopic data for cyano-cyclopropenylidene (c-CHCN), but the present work provides the first anharmonic vibrational spectral data for that molecule, as well as the first full set of both rotational and vibrational spectroscopic data for fluoro- and chloro-cyclopropenylidenes (c-CHF and c-CHCl). All three molecules have fundamental vibrational frequencies with substantial infrared intensities.

View Article and Find Full Text PDF

Objectives: The risk of bladder cancer (BCa) diagnosis and recurrence necessitates cystoscopy. Improved risk stratification may inform personalized triage and surveillance strategies. We aim to develop a urinary mRNA biomarker panel for risk stratification in patients undergoing BCa screening and surveillance.

View Article and Find Full Text PDF

ConspectusWe review the Best Theory + Reliable High-Resolution Experiment (BTRHE) strategy for obtaining highly accurate molecular rovibrational line lists with InfraRed (IR) intensities. The need for highly accurate molecular rovibrational line lists is twofold: (a) assignment of the many rovibrational lines for common stable molecules especially those that exhibit a large amplitude motion, such as NH, or have a high density of states such as SO; and (b) characterization of the atmospheres of exoplanets, which will be one of the main areas of research in astronomy in the coming decades. The first motivation arises due to the need to eliminate lines due to common molecules in an astronomical observation in order to identify lines from new molecules, while the second motivation arises due to the need to obtain accurate molecular opacities in order to characterize the atmosphere of an exoplanet.

View Article and Find Full Text PDF

More than 30 years ago two groups independently identified a problem in the calculation of the out-of-plane bending (OPB) vibrational frequencies for the ethylene molecule using correlated electronic structure methods. Several studies have been done in the meantime to try and understand and resolve this issue. In so doing this problem has been found to be far more insidious than previously realized for acetylene-like and benzene-like molecules, which can become non-linear and non-planar, respectively.

View Article and Find Full Text PDF

The CcCR quartic force field (QFF) methodology is capable of computing B and C rotational constants to within 35 MHz (0.14%) of experiment for triatomic and larger molecules with at least two heavy atoms. Additionally, the same constants for molecules with four or more atoms agree to within 20 MHz (0.

View Article and Find Full Text PDF

The growth mechanisms of organic molecules in an ionizing environment such as the interstellar medium are not completely understood. Here we examine by means of ab initio molecular dynamics (AIMD) simulations and density functional theory (DFT) computations the possibility of bond formation and molecular growth upon ionization of van der Waals clusters of pure HCN clusters, and mixed clusters of HCN and HCCH, both of which are widespread in the interstellar medium. Ionization of van der Waals clusters can potentially lead to growth in low temperature and low-density environments.

View Article and Find Full Text PDF

The challenges associated with the out-of-plane bending problem in multiply-bonded hydrocarbon molecules can be mitigated in quartic force field analyses by varying the step size in the out-of-plane coordinates. Carbon is a highly prevalent element in astronomical and terrestrial environments, but this major piece of its spectra has eluded theoretical examinations for decades. Earlier explanations for this problem focused on method and basis set issues, while this work seeks to corroborate the recent diagnosis as a numerical instability problem related to the generation of the potential energy surface.

View Article and Find Full Text PDF

Hydrofluorocarbons (HFCs) are potent greenhouse gases that are potential substitutes for ozone depleting substances. The Kigali amendment lists 17 HFCs that are currently in commercial use to be regulated under the Montreal Protocol. Future commercial applications may explore the use of other HFCs, most of which currently lack an evaluation of their climate metrics.

View Article and Find Full Text PDF

Despite the generally hostile nature of the environments involved, chemistry does occur in space. Molecules are seen in environments that span a wide range of physical and chemical conditions and that clearly were created by a multitude of chemical processes, many of which differ substantially from those associated with traditional equilibrium chemistry. The wide range of environmental conditions and processes involved with chemistry in space yields complex populations of materials, and because the elements H, C, O, and N are among the most abundant in the universe, many of these are organic in nature, including some of direct astrobiological interest.

View Article and Find Full Text PDF