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Full-Text Articles in Engineering
Optfill: A Tool For Infeasible Cycle-Free Gapfilling Of Stoichiometric Metabolic Models, Wheaton L. Schroeder, Rajib Saha
Optfill: A Tool For Infeasible Cycle-Free Gapfilling Of Stoichiometric Metabolic Models, Wheaton L. Schroeder, Rajib Saha
Mid-America Transportation Center: Final Reports and Technical Briefs
Stoichiometric metabolic modeling, particularly genome-scale models (GSMs), is now an indispens- able tool for systems biology. The model reconstruction process typically involves collecting informa- tion from public databases; however, incomplete systems knowledge leaves gaps in any reconstruc- tion. Current tools for addressing gaps use databases of biochemical functionalities to address gaps on a per-metabolite basis and can provide multiple solutions but cannot avoid thermodynami- cally infeasible cycles (TICs), invariably requiring lengthy manual curation. To address these limita- tions, this work introduces an optimization-based multi-step method named OptFill, which performs TIC-avoiding whole-model gapfilling. We applied OptFill to three fictional prokaryotic models …
Corrigendum To “Heavy Metal Ion Detection On A Microspot Electrode Using An Optical Electrochemical Probe” [Electrochem. Commun. 86 (2018) 94–98], Santanu Roy, Abhijeet Prasad, Rahul Tevatia, Ravi Saraf
Corrigendum To “Heavy Metal Ion Detection On A Microspot Electrode Using An Optical Electrochemical Probe” [Electrochem. Commun. 86 (2018) 94–98], Santanu Roy, Abhijeet Prasad, Rahul Tevatia, Ravi Saraf
Mid-America Transportation Center: Final Reports and Technical Briefs
The authors regret to inform an error. Ravi F. Saraf of this pub- lication discloses financial interest in Vajra Instrument as its founder and President. In accordance with its Conflict of Interest policy, the University of Nebraska-Lincoln’s Conflict of Interest in Research Committee has determined that this must be disclosed. The authors would like to apologise for any inconvenience caused.
An Integrated Computational And Experimental Study To Investigate Staphylococcus Aureus Metabolism, Mohammad Mazharul Islam, Vinai C. Thomas, Matthew Van Beek, Jong-Sam Ahn, Abdulelah A. Alqarzaee, Chunyi Zhou, Paul D. Fey, Kenneth W. Bayles, Rajib Saha
An Integrated Computational And Experimental Study To Investigate Staphylococcus Aureus Metabolism, Mohammad Mazharul Islam, Vinai C. Thomas, Matthew Van Beek, Jong-Sam Ahn, Abdulelah A. Alqarzaee, Chunyi Zhou, Paul D. Fey, Kenneth W. Bayles, Rajib Saha
Mid-America Transportation Center: Final Reports and Technical Briefs
Staphylococcus aureus is a metabolically versatile pathogen that colonizes nearly all organs of the human body. A detailed and comprehensive knowledge of staphylococcal metabolism is essential to understand its pathogenesis. To this end, we have reconstructed and experimentally validated an updated and enhanced genome-scale metabolic model of S. aureus USA300_FPR3757. The model combined genome annotation data, reaction stoichiometry, and regulation information from biochemical databases and previous strain-specific models. Reactions in the model were checked and fixed to ensure chemical balance and thermodynamic consistency. To further refine the model, growth assessment of 1920 nonessential mutants from the Nebraska Transposon Mutant Library …
Calibrating The Highway Capacity Manual Arterial Travel Time Reliability Model, Ernest Tufuor, Laurence Rilett, Li Zhao
Calibrating The Highway Capacity Manual Arterial Travel Time Reliability Model, Ernest Tufuor, Laurence Rilett, Li Zhao
Mid-America Transportation Center: Final Reports and Technical Briefs
The latest edition of the Highway Capacity Manual (HCM-6) includes, for the first time, a methodology for estimating and predicting the average travel time distribution (TTD) of urban streets. Travel time reliability (TTR) metrics can then be estimated from the TTD. The HCM-6 explicitly considers five key sources of travel time variability. A literature search showed no evidence that the HCM-6 TTR model has ever been calibrated with empirical travel time data. More importantly, previous research showed that the HCM-6 underestimated the empirical TTD variability by 70% on a testbed in Lincoln, Nebraska. In other words, the HCM-6 TTR metrics …
Analysis Of Component Errors In The Highway Capacity Manual Travel Time Reliability Estimations For Urban Streets, Ernest Tufuor, Laurence Rilett
Analysis Of Component Errors In The Highway Capacity Manual Travel Time Reliability Estimations For Urban Streets, Ernest Tufuor, Laurence Rilett
Mid-America Transportation Center: Final Reports and Technical Briefs
The Highway Capacity Manual 6th edition (HCM6) includes a new methodology to estimate and predict the distribution of average travel times (TTD) for urban streets. The TTD can then be used to estimate travel time reliability (TTR) metrics. Previous research on a 0.5-mi testbed showed statistically significant differences between the HCM6 estimated TTD and the corresponding empirical TTD. The difference in average travel time was 4 s that, while statistically significant, is not important from a practical perspective. More importantly, the TTD variance was underestimated by 70%. In other words, the HCM6 results reflected a more reliable testbed than field …