25 research outputs found
Data associated with the publication: Taxonomy-based prompt engineering to generate synthetic drug-related patient portal messages
No full textThis dataset is a part of "Taxonomy-Based Prompt Engineering to Generate Synthetic Drug-Related Patient Portal Messages study". The dataset contains synthetic patient portal messages on drug related problems. The messages were generated using prompt engineering based on the taxonomy of patient-generated messages from the patient portal. This dataset aims to provide researchers with access to drug-related patient portal synthetic messages.
The dataset contains 450 generated messages, which can be categorized into 2 groups. The first group was generated from all prompt options, derived from the taxonomy, with no specific race of the patient (200 messages). The second group was generated using subset of prompt options with specific race information. This group contains 50 messages for each race, including White, American Indian or Alaska Native, Black or African American, Asian, and Native Hawaiian or Other Pacific Islander (total 250 messages). All the messages are accompanied by prompt used for generating the message, taxonomy group, medication name, race, and urgency level. <p
Non-vitamin K Antagonist Oral Anticoagulant, Warfarin, and ABC Pathway Adherence on Hierarchical Outcomes: Win Ratio Analysis of the COOL-AF Registry
No full textBackground Atrial fibrillation (AF) Better Care (ABC) pathway adherence is associated with improved outcomes. Clinical trials have shown that non-vitamin K antagonist oral anticoagulants (NOACs) are as least as effective as warfarin for stroke prevention in AF patients. The Win Ratio method, analyzing hierarchical composite outcomes considering event timing and severity, has limited data on its use in Asians. Objectives We aim to apply Win Ratio in a registry to access the comparative effectiveness of NOACs versus warfarin and ABC adherence versus nonadherence in Asian patients with AF. Methods Our study included nonvalvular AF patients from the nationwide prospective COOL-AF registry in Thailand. The NOAC-treated group was compared with the warfarin-treated group using the Win Ratio, with the following order: all-cause death, intracranial hemorrhage (ICH), ischemic stroke/transient ischemic attack/systemic embolism, non-ICH major bleeding, and myocardial infarction or heart failure. ABC pathway adherence versus nonadherence was also compared. A Win Ratio greater than 1.00 indicating a better outcome. Results The analysis included 2,568 patients, with 228 in the NOAC group and 2,340 in the warfarin group. The NOAC group had more wins than the warfarin group, with an unmatched Win Ratio of 1.64 (95% confidence interval [CI]: 1.22-2.20; p 0.001). When compared with nonadherence, ABC pathway adherence was associated with a Win Ratio of 1.57 (95% CI: 1.33 1.85; p 0.001). Conclusion This Win Ratio analysis demonstrates the significant benefits of NOACs over warfarin and ABC pathway adherence over nonadherence in reducing the composite outcome in patients with AF.</p
An Updated Global Perspective of Atrial Fibrillation: Trends, Risk Factors, and Socioeconomic Disparities
No full textSupporting Material: "The Importance of the Upper Atmosphere to CO/O<sub>2</sub> Runaway on Habitable Planets Orbiting Low-Mass Stars"
No full textHolds photochemical model outputs and processing code associated with Ranjan, Schwieterman, Leung et al. 2023 (ApJL, 958, L15). By running scripts in this repository, use can generate all plots from main text of the paper, as well as the table entries in the paper and Appendix. If you make use of this, please cite the parent ApJL article. For questions, concerns, bugreports, etc please contact [email protected]'s note: this submission is identical to the one in Zenodo listed below and is intended as an alternate long-term copy. For inquiries regarding the contents of this dataset, please contact the Corresponding Author listed in the README.txt file. Administrative inquiries (e.g., removal requests, trouble downloading, etc.) can be directed to [email protected]</p
Binding configurations of single-stranded DNA binding protein and their influence on DNA recombinase
No full textDNA inside a cell is continuously damaged through multiple mechanisms including environmental exposure to radiation, chemical agents, or UV light. Certain products of the cell's own metabolism, such as reactive oxygen species, can also damage the DNA. In the worst-case scenario, this damage results in double-stranded DNA (dsDNA) breaks. Double-stranded DNA breaks are lethal, and difficult to repair, with potential complications from genome rearrangement. To prevent this genetic instability, a cell can utilize a homologous chromosome as a template to accurately repair DSBs. This process is called homologous recombination.
Homologous recombination begins when an enzyme complex binds to a blunt end of a dsDNA break. The complex unzips the dsDNA through its helicase activity, and simultaneously cleaves the newly-generated 5' end of the ssDNA. This process leaves the remaining ssDNA strand exposed to the surrounding environment and prone to nucleolytic and chemical attacks. Cells have evolved single-stranded DNA binding (SSB) proteins to wrap and protect this ssDNA. In E. coli, SSB is known to wrap ssDNA in a variety of binding configurations, or modes. Three different binding modes, (SSB)65, (SSB)56, and (SSB)35, which wraps 65, 56, and 35 nucleotides (nt) respectively, have been observed in vitro Previous studies have suggested that SSB binding in different modes may exhibit different levels of binding cooperativity. SSBs in the (SSB)65 binding mode form isolated clusters (limited cooperativity), while SSBs in the (SSB)35 binding mode form long filaments (unlimited cooperativity). These different levels of binding cooperativity have been proposed to be used selectively in different DNA metabolic processes, including DNA replication, recombination, and repair.
In homologous recombination, recombinase RecA must bind and form nucleoprotein filaments on the ssDNA, in direct competition with SSB. Prior studies have shown that RecA is capable of forming filaments on ssDNA wrapped by SSBs in the (SSB)65 binding mode, but filament formation on ssDNA wrapped by SSBs in the (SSB)35 binding mode is inhibited. Recent single-molecule studies have been conducted to investigate this competitive process, but the detailed mechanisms remain unclear.
Here, we use high-resolution optical tweezers with simultaneous fluorescence microscopy to observe directly the activity of ssDNA-SSB, ssDNA-RecA, and ssDNA-SSB-RecA complexes under tension, and characterize their mechanical properties. The instrument allows us to simultaneously probe and visualize the interactions of RecA and SSB with ssDNA in real time and with nanometer resolution.
We confirm that individuals SSBs bind and compact ssDNA in discrete modes. Under low tension (1-3 pN), a single SSB wraps ssDNA in the (SSB)65 or (SSB)56 binding mode. At higher tension (4-8 pN), SSB exhibits transient wrapping-unwrapping, switching between the (SSB)56, (SSB)35, and (SSB)17 wrapping modes. When multiple SSBs are present on the ssDNA, the SSBs form isolated clusters in those solution conditions that favor the (SSB)65 binding mode. The configuration of the SSBs changes to a long and stable filament when solution conditions that favor the (SSB)35 binding mode are used.
In the absence of SSB, RecAs nucleate filament rapidly on ssDNA. The nucleation rate of RecA is slowed down by several times when RecA is added to ssDNA coated with isolated clusters of SSBs in the (SSB)56 mode. The nucleation rate of RecA decreases further when long and stable filaments of SSBs in the (SSB)35 binding mode are present on the ssDNA. The same experiments also demonstrate that RecA is capable of removing these SSBs from the ssDNA in a step-wise manner.
Our results reveal the importance of SSB binding modes and their oligomerization to DNA recombination, and further confirm that (SSB)65/(SSB)56 binding modes are more likely to facilitate the activity of recombinase RecA during the DNA repair. The (SSB)35 binding mode, on the contrary, inhibits RecA filament formation, and is believed to not play an important role in this recombination process.Submission published under a 24 month embargo labeled 'U of I only', the embargo will last until 2017-05-01The student, Sukrit Suksombat, accepted the attached license on 2015-04-22 at 12:19.The student, Sukrit Suksombat, submitted this Dissertation for approval on 2015-04-22 at 12:32.This Dissertation was approved for publication on 2015-04-22 at 14:31.DSpace SAF Submission Ingestion Package generated from Vireo submission #8021 on 2015-07-22 at 14:18:35Made available in DSpace on 2015-07-22T22:33:46Z (GMT). No. of bitstreams: 2
SUKSOMBAT-DISSERTATION-2015.pdf: 14609855 bytes, checksum: fb5f9dee2ab7bf9b7274297805574813 (MD5)
LICENSE.txt: 4213 bytes, checksum: b5c96d34c463c81ef7f031abed4c4770 (MD5)
Previous issue date: 2015-04-22Embargo set by: Seth Robbins for item 79895
Lift date: 2017-07-22T22:34:16Z
Reason: Author requested U of Illinois access only (OA after 2yrs) in Vireo ETD systemU of I Only Restriction Lifted for Item 79895 on 2017-07-23T09:15:34Z
Renal function decline in Asian patients with atrial fibrillation with warfarin and non-vitamin K antagonist oral anticoagulants:A report from the COOL-AF registry
No full textBackground: The objective of this study was to compare the risk of estimated glomerular filtration rate (eGFR) decline between atrial fibrillation (AF) patients with direct oral anticoagulants (DOACs) and warfarin. Methods: We studied patients with nonvalvular AF from a prospective multicenter national AF registry in Thailand. Patients with missing eGFR data or eGFR less than 30 mL/min/1.73 m 2 were excluded. Follow-up data including eGFR were collected every 6 months until 3 years. eGFR decline was assessed by eGFR slope. We compared eGFR slope between patients who received DOACs and warfarin at baseline. In the warfarin group, we assessed the impact of good anticoagulation control by time in the therapeutic range (TTR). Results: A total of 1708 patients were studied (mean age 68.1 years; 42.6% female). Patients with DOACs had a significantly slower rate of eGFR decline compared to warfarin. The eGFR slope was 2.32 mL/min/1.73 m 2 per year in the warfarin group (95% CI: 3.09 to 1.55), and 1.31 mL/min/1.73 m 2 per year in the DOAC group (95% CI: 1.97 to 0.64). The effect of OAC type on the eGFR slope remained significant even after the adjustment of baseline variables including baseline eGFR. There was no difference in GFR decline as reflected by eGFR slope when comparing warfarin patients with TTR <65% and ≥65%. Conclusion: In this prospective cohort of Asian patients with AF, DOACs were associated with a slower rate of eGFR decline when compared with warfarin. In the latter group, this was irrespective of the quality of anticoagulation control.</p
Cytomegalovirus enterocolitis with subsequent diagnosis of coexisting new-onset inflammatory bowel disease
No full textEnd-to-End Motion Planning: A Data Driven Approach for Mobile Robot Navigation
No full textA lot research has been conducted in the field of autonomous navigation of mobile robots with focus on Robot Vision and Robot Motion Planning. However, most of the classical navigation solutions require several steps of data pre-processing and hand tuning of parameters, with separate modules for vision, localization, planning and control. All these modules work independently and make their own parameter assumptions to optimize their own performance without taking into account the effect these assumptions have on the performance of rest of the modules. Hence, even though each module in the whole system tries to achieve an optimal performance for the task it has been assigned, the lack of interdependence exhibited by these modules for decision making means that the overall performance of the whole system is sub-optimal in most of the cases. An alternating approach for addressing these issues is to train certain parts of the vision module to incorporate partial tasks from the planning module. Deep Learning architectures have achieved great success in the field of pattern recognition and object detection and as a result are usually being deployed to design such a module that jointly learns to carry out perception and path planning. This master's thesis, making use of Deep Learning, proposes an End-to-End Learning architecture that learns to directly map raw sensor readings to control commands for a ground based mobile robot. The research makes use of the simulation of Jackal UGV from Clearpath Robotics and the proposed network is able to produce collision free trajectories for the robot to navigate in it's environment.Mechanical Engineering | Systems and Contro
Clinical phenotype classification to predict risk and optimize the management of patients with atrial fibrillation using the Atrial fibrillation Better Care (ABC) pathway: A report from the COOL-AF registry
No full textBackground: Phenotypic classification is a method of grouping patients with similar phenotypes.Aim: We aimed to use phenotype classification based on a clustering process for risk stratification of patients with non-valvular atrial fibrillation (AF) and second, to assess the benefit of the Atrial Fibrillation Better Care (ABC) pathway.Methods: Patients with AF were prospectively enrolled from 27 hospitals in Thailand from 2014 to 2017, and followed up every 6 months for 3 years. Cluster analysis was performed from 46 variables using the hierarchical clustering using the Ward minimum variance method. Outcomes were a composite of all-cause death, ischemic stroke/systemic embolism, acute myocardial infarction and heart failure.Results: A total of 3405 patients were enrolled (mean age 67.8 ± 11.3 years, 58.2% male). During the mean follow-up of 31.8 ± 8.7 months. Three clusters were identified: Cluster 1 had the highest risk followed by Cluster 3 and Cluster 2 with a hazard ratio (HR) and 95% confidence interval (CI) of composite outcomes of 2.78 (2.25, 3.43), P < 0.001 for Cluster 1 and 1.99 (1.63, 2.42), P < 0.001 for Cluster 3 compared with Cluster 2. Management according to the ABC pathway was associated with reductions in adverse clinical outcomes especially those who belonged to Clusters 1 and 3 with HR and 95%CI of the composite outcome of 0.54 (0.40, 073), P < 0.001 for Cluster 1 and 0.49 (0.38, 0.63), P < 0.001 for Cluster 3.Conclusion: Phenotypic classification helps in risk stratification and prognostication. Compliance with the ABC pathway was associated with improved clinical outcomes
