A Kalman Filter Approach for Biomolecular Systems with Noise Covariance Updating

An important part of system modeling is determining parameter values, particularly for biomolecular systems, where direct measurements of individual parameters are typically hard. While Extended Kalman Filters have been used for this purpose, the choice of the process noise covariance is generally unclear. In this chapter, we address this issue for biomolecular systems using a combination of Monte Carlo simulations and experimental data, exploiting the dependence of the process noise covariance on the states and parameters, as given in the Langevin framework. We adapt a Hybrid Extended Kalman Filtering technique by updating the process noise covariance at each time step based on estimates. We compare the performance of this framework with different fixed values of process noise covariance in biomolecular system models, including an oscillator model, as well as in experimentally measured data for a negative transcriptional feedback circuit. We find that the Extended Kalman Filter with such process noise covariance update is closer to the optimality condition in the sense that the innovation sequence becomes white and in achieving a balance between the mean square estimation error and parameter convergence time. The results of this chapter may help in the use of Extended Kalman Filters for systems where process noise covariance depends on states and/or parameters.Comment: 23 pages, 9 figure

The United States COVID-19 Forecast Hub dataset

Academic researchers, government agencies, industry groups, and individuals have produced forecasts at an unprecedented scale during the COVID-19 pandemic. To leverage these forecasts, the United States Centers for Disease Control and Prevention (CDC) partnered with an academic research lab at the University of Massachusetts Amherst to create the US COVID-19 Forecast Hub. Launched in April 2020, the Forecast Hub is a dataset with point and probabilistic forecasts of incident cases, incident hospitalizations, incident deaths, and cumulative deaths due to COVID-19 at county, state, and national, levels in the United States. Included forecasts represent a variety of modeling approaches, data sources, and assumptions regarding the spread of COVID-19. The goal of this dataset is to establish a standardized and comparable set of short-term forecasts from modeling teams. These data can be used to develop ensemble models, communicate forecasts to the public, create visualizations, compare models, and inform policies regarding COVID-19 mitigation. These open-source data are available via download from GitHub, through an online API, and through R packages

Studies on Texturing of Polyester Viscose Spun Yarn by Simultaneous Setting of Both the Components

91-94<span style="font-size:11.0pt;line-height:115%; font-family:" calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-fareast-font-family:="" "times="" new="" roman";mso-fareast-theme-font:minor-fareast;mso-hansi-theme-font:="" minor-latin;mso-bidi-font-family:"times="" roman";color:black;mso-ansi-language:="" en-us;mso-fareast-language:en-us;mso-bidi-language:ar-sa"="">Texturing of polyester-viscose blended yarn has been accomplished through heat setting of polyester and crosslinking of viscose by a single-stage rapid cure technique. Two resins, Finish KVS new (Sandoz) (dimethylol dihydroxycthy1cne urea based resin with built-in catalyst) and resin U-4750(BASF) (a polyfunctional urethane resin) were used as crosslinking agents for setting the deformation. The efficiency of both the resins has been studied as a function of curing period, temperature and catalyst and resin concentrations. It is observed that a curing temperature of 210-220oC and a curing period of 30 see are optimum for both the resins. With lesser amount of resin <span style="font-size:11.0pt; line-height:115%;font-family:" calibri","sans-serif";mso-ascii-theme-font:minor-latin;="" mso-fareast-font-family:"times="" new="" roman";mso-fareast-theme-font:minor-fareast;="" mso-hansi-theme-font:minor-latin;mso-bidi-font-family:arial;color:black;="" mso-ansi-language:en-us;mso-fareast-language:en-us;mso-bidi-language:ar-sa"="">+ catalyst in the padding bath, KVS gives a stronger yarn than U-4750 resin for an equivalent crimp rigidity value.</span

Quality characteristics of tasar (tussah) silk yarn

128-135<span style="font-size:11.0pt;line-height:115%; font-family:" calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-fareast-font-family:="" "times="" new="" roman";mso-fareast-theme-font:minor-fareast;mso-hansi-theme-font:="" minor-latin;mso-bidi-font-family:calibri;mso-bidi-theme-font:minor-latin;="" color:black;mso-ansi-language:en-us;mso-fareast-language:en-us;mso-bidi-language:="" ar-sa"="">Four commercially available tasar silk yarns have been characterized on the basis of physical and mechanical properties<span style="font-size: 11.0pt;line-height:115%;font-family:" calibri","sans-serif";mso-ascii-theme-font:="" minor-latin;mso-fareast-font-family:"times="" new="" roman";mso-fareast-theme-font:="" minor-fareast;mso-hansi-theme-font:minor-latin;mso-bidi-font-family:calibri;="" mso-bidi-theme-font:minor-latin;color:#111111;mso-ansi-language:en-us;="" mso-fareast-language:en-us;mso-bidi-language:ar-sa"="">. Machine-reeled and organzine (double-twisted) yarns show the highest and lowest value of evenness respectively. Neps contribute maximum towards imperfections in comparison to thick and thin places. Though the tenacity values of brin are almost similar for all the yarns, the changes occur when the brins are converted into yarn. The yarns are more extensible than brins. The modulii of the brins are always higher than those of the corresponding yarns. All tasar yarns show rectangular cross-section of brin.</span

Studies on cooking of tussah silk cocoon

61-67<span style="font-size:11.0pt;line-height:115%; font-family:" calibri","sans-serif";mso-ascii-theme-font:minor-latin;mso-fareast-font-family:="" "times="" new="" roman";mso-fareast-theme-font:minor-fareast;mso-hansi-theme-font:="" minor-latin;mso-bidi-font-family:calibri;mso-bidi-theme-font:minor-latin;="" mso-ansi-language:en-us;mso-fareast-language:en-us;mso-bidi-language:ar-sa"="">An attempt bas been made to optimize the cooking conditions of tussah silk cocoon (Antheraea mylitta D.) with ethylenediamine using the Box and Behnken factorial design for three variables and three levels for each variable. It is observed that the duration and temperature of treatment as well as the concentration of ethylenediamine significantly influence the cocoon shell weight loss and silk filament recovery. Silk recovery improves with the shell weight loss of up to 11.5% after which no further improvement in silk recovery is observed. The mechanical properties of tussah silk filament have very little correlation with the process parameters. For better silk recovery, the following cooking conditions are recommended: ethylenediamine, 10% on the weight of cocoon; temperature, 80ᵒC; duration of treatment, 30 min; and meterial-to-liquor ratio, 1:30. Different races of tussah silk cocoon require adjustment in the duration of treatment. The hardness of water up to 1100 ppm has no significant effect on the recovery of silk in ethylenediamine cooking system.</span