Takagi–Sugeno Fuzzy Modeling of Skin Permeability

The skin is a major exposure route for many potentially toxic chemicals. It is, therefore, important to be able to predict the permeability of compounds through skin under a variety of conditions. Available skin permeability databases are often limited in scope and not conducive to developing effective models. This sparseness and ambiguity of available data prompted the use of fuzzy set theory to model and predict skin permeability. Using a previously published database containing 140 compounds, a rule-based Takagi–Sugeno fuzzy model is shown to predict skin permeability of compounds using octanol-water partition coefficient, molecular weight, and temperature as inputs. Model performance was estimated using a cross-validation approach. In addition, 10 data points were removed prior to model development for additional testing with new data. The fuzzy model is compared to a regression model for the same inputs using both R2 and root mean square error measures. The quality of the fuzzy model is also compared with previously published models. The statistical analysis demonstrates that the fuzzy model performs better than the regression model with identical data and validation protocols. The prediction quality for this model is similar to others that were published. The fuzzy model provides insights on the relationships between lipophilicity, molecular weight, and temperature on percutaneous penetration. This model can be used as a tool for rapid determination of initial estimates of skin permeability

Takagi–Sugeno Fuzzy Modeling of Skin Permeability

The skin is a major exposure route for many potentially toxic chemicals. It is, therefore, important to be able to predict the permeability of compounds through skin under a variety of conditions. Available skin permeability databases are often limited in scope and not conducive to developing effective models. This sparseness and ambiguity of available data prompted the use of fuzzy set theory to model and predict skin permeability. Using a previously published database containing 140 compounds, a rule-based Takagi–Sugeno fuzzy model is shown to predict skin permeability of compounds using octanol-water partition coefficient, molecular weight, and temperature as inputs. Model performance was estimated using a cross-validation approach. In addition, 10 data points were removed prior to model development for additional testing with new data. The fuzzy model is compared to a regression model for the same inputs using both R2 and root mean square error measures. The quality of the fuzzy model is also compared with previously published models. The statistical analysis demonstrates that the fuzzy model performs better than the regression model with identical data and validation protocols. The prediction quality for this model is similar to others that were published. The fuzzy model provides insights on the relationships between lipophilicity, molecular weight, and temperature on percutaneous penetration. This model can be used as a tool for rapid determination of initial estimates of skin permeability

The GP Tests of Competence assessment: which part best predicts fitness to practise decisions?

BACKGROUND: The General Medical Council (GMC) conducts Tests of Competence (ToC) for doctors referred for Fitness to Practise (FtP) issues. GPs take a single best answer knowledge test, an Objective Structured Clinical Examination (OSCE), and a Simulated Surgery (SimSurg) assessment which is a simulated GP consultation. The aim of this study was to examine the similarities between OSCEs and SimSurg to determine whether each assessment contributed something unique to GP ToCs. METHODS: A mixed methods approach was used. Data were collated on 153 GPs who were required to undertake a ToC as a part of being investigated for FtP issues between February 2010 and October 2016. Using correlation analysis, we examined to what degree performance on the knowledge test, OSCE, and SimSurg related to case examiner recommendations and FtP outcomes, including the unique predictive power of these three assessments. The outcome measures were case examiner recommendations (i) not fit to practise; ii) fit to practise on a limited basis; or iii) fit to practise) as well as FtP outcomes (i) erased/removed from the register; ii) having restrictions/conditions; or iii) be in good standing). For the qualitative component, 45 GP assessors were asked to rate whether they assess the same competencies and which assessment provides better feedback about candidates. RESULTS: There was significant overlap between OSCEs and SimSurg, p < 0.001. SimSurg had additional predictive power in the presence of OSCEs and the knowledge test (p = 0.030) in distinguishing doctors from different FtP categories, while OSCEs did not (p = 0.080). Both the OSCEs (p = 0.004) and SimSurg (p < 0.001) had significant negative correlations with case examiner recommendations when accounting for the effects of the other two assessments. Inductive thematic analysis of the responses to the questionnaire showed that assessors perceived OSCEs to be better suited to target specific knowledge and skills. SimSurg was thought to produce a more global picture as the scenarios more accurately portray a patient consultation. CONCLUSION: While all three assessments are strong predictors of both case examiner recommendations and FtP outcomes, our findings suggest that the efficiency of GP ToCs can be improved by removing some of this overlapping content

Intra-Domain Cross-Talk Regulates Serine-Arginine Protein Kinase 1-Dependent Phosphorylation and Splicing Function of Transformer 2β1

Transformer 2β1 (Tra2β1) is a splicing effector protein composed of a core RNA recognition motif flanked by two arginine-serine-rich (RS) domains, RS1 and RS2. Although Tra2β1-dependent splicing is regulated by phosphorylation, very little is known about how protein kinases phosphorylate these two RS domains. We now show that the serine-arginine protein kinase-1 (SRPK1) is a regulator of Tra2β1 and promotes exon inclusion in the survival motor neuron gene 2 (SMN2). To understand how SRPK1 phosphorylates this splicing factor, we performed mass spectrometric and kinetic experiments. We found that SRPK1 specifically phosphorylates 21 serines in RS1, a process facilitated by a docking groove in the kinase domain. Although SRPK1 readily phosphorylates RS2 in a splice variant lacking the N-terminal RS domain (Tra2β3), RS1 blocks phosphorylation of these serines in the full-length Tra2β1. Thus, RS2 serves two new functions. First, RS2 positively regulates binding of the central RNA recognition motif to an exonic splicing enhancer sequence, a phenomenon reversed by SRPK1 phosphorylation on RS1. Second, RS2 enhances ligand exchange in the SRPK1 active site allowing highly efficient Tra2β1 phosphorylation. These studies demonstrate that SRPK1 is a regulator of Tra2β1 splicing function and that the individual RS domains engage in considerable cross-talk, assuming novel functions with regard to RNA binding, splicing, and SRPK1 catalysis

Trends in Use of Prescription Nonsteroidal Anti-inflammatory Medications before vs after Implementation of a Florida Law Restricting Opioid Prescribing for Acute Pain

Importance: Previous research has shown an immediate reduction in new opioid users and use after implementation of the opioid supply restriction laws. Assessment of the association between opioid restrictions and alternative treatment options, such as nonsteroidal anti-inflammatory drugs (NSAIDs), is needed to evaluate potential unintended consequences for patients requiring analgesia. Objective: To evaluate the association between an opioid restriction law in Florida and use of prescription NSAIDs. Design, Setting, and Participants: This quality improvement study used interrupted time series analyses accounting for autocorrelation to estimate immediate and trend changes in the prescribing and use of prescription NSAIDs in Florida before and after implementation of a state law limiting opioid prescriptions to a 3-day supply. Participants were enrollees in a single private health plan of a large university and health system employer in Florida from January 2015 to June 2019. Exposures: Prescriptions for NSAIDs, ascertained from pharmacy claims data. Main Outcomes and Measures: The following outcomes were calculated monthly per 1000 plan enrollees: (1) number of NSAID users; (2) mean days' supply of NSAIDs per prescription; and (3) mean number of NSAID prescriptions. Individuals were classified as NSAID users if they had at least 1 NSAID prescription in a given month. Analysis was stratified by route of NSAID administration (oral or nonoral). Results: Among 46783 NSAID users with 79089 NSAID prescriptions during the study period, the median age was 47 years (interquartile range, 35-57 years). After implementation of the opioid restriction law, the number of NSAID users immediately increased, but the difference was not significant (change, 0.82 per 1000 patients; 95% CI, -0.67 to 2.30 per 1000 patients). No significant change in the days' supply of oral NSAID users occurred (change, 0.21 days per prescription; 95% CI, -1.66 to 2.08 days per prescription). Before implementation of the law, there was a nonsignificant decreasing trend in NSAID prescriptions (rate of change, -0.03 per month per 1000 enrollees; 95% CI, -0.13 to 0.07 per month per 1000 enrollees; after implementation, there was a nonsignificant increase in the number of oral and nonoral NSAID prescriptions (change, 1.49 per 1000 enrollees; 95% CI, -3.38 to 6.37 per 1000 enrollees). Conclusions and Relevance: In this quality improvement study, prescribing and use of prescription NSAIDs did not increase after implementation of a law restricting opioid analgesic prescriptions in Florida. These findings suggest possible greater use of over-the-counter NSAIDs after implementation of the law, but further research is needed to evaluate changes in the use of nonopioid analgesics and alternative pain therapies

Buprenorphine Use Trends Following Removal of Prior Authorization Policies for the Treatment of Opioid Use Disorder in 2 State Medicaid Programs

Importance: State Medicaid programs have implemented initiatives to expand treatment coverage for opioid use disorder (OUD); however, some Medicaid programs still require prior authorizations (PAs) for filling buprenorphine prescriptions. Objective: To evaluate the changes in buprenorphine use for OUD among Medicaid enrollees in states that completely removed buprenorphine PA requirements. Design, Setting, and Participants: This retrospective cross-sectional study analyzed the immediate and trend changes on buprenorphine use during 2013 to 2020 associated with removal of PA requirements using a controlled interrupted time series analysis to account for autocorrelation. Data were collected from Medicaid State Drug Utilization Data for 2 states (California and Illinois) that completely removed a buprenorphine PA during the study period, and buprenorphine prescriptions for OUD treatment were identified among Medicaid enrollees. Main Outcomes and Measures: Quarterly total number of buprenorphine prescriptions for each state was calculated, and stratification analyses were conducted by dosage form (films and tablets). Results: Among the 2 state Medicaid programs (California and Illinois) that removed buprenorphine PAs, there was a total of 702643 and 415115 eligible buprenorphine prescription claims, respectively. After removing PA requirements for buprenorphine, there was an immediate increase that was not statistically significant (rate ratio [RR], 1.11; 95% CI, 0.76-1.61) in the number of all buprenorphine prescriptions in California and a statistically significant increase (RR, 6.99; 95% CI, 4.67-10.47) in the number of all buprenorphine prescriptions in Illinois relative to the change in the control states (Alabama, Florida, Idaho, Kansas, Mississippi, Nevada, South Dakota, and Wyoming). Additionally, there was a statistically significant decreasing trend in the number of all buprenorphine prescriptions in California (RR, 0.88; 95% CI, 0.82-0.94) and a statistically significant increasing trend in Illinois (RR, 1.11; 95% CI, 1.05-1.19) relative to the trend in control states. Conclusions and Relevance: In this cross-sectional study, removal of buprenorphine PA requirements was associated with a statistically significant increase in the number of buprenorphine prescription fills among Medicaid populations in 1 of the 2 included states

Comparing novelty of designs from biological-inspiration with those from brainstorming

This research aims to understand the significance of biological-analogies in fostering novelty by comparing biological-analogies with other design methods for idea generation. Among other design methods, brainstorming was chosen here as benchmark. Four studies were conducted to compare: (i) the levels of abstraction at which concepts were ideated using biological inspiration (represented using biocards) with that using traditional brainstorming; and (ii) the novelty of concepts produced by using these two design methods. Concepts produced in these studies were evaluated for levels of abstraction at which they were ideated, average novelty, and proportion of high-novelty concepts. Results suggest that concepts generated using biocards were ideated at higher abstraction levels than those using brainstorming, but neither were at the highest abstraction levels. The average novelty of concepts produced using biocards was found to be greater than that using brainstorming; however, no statistically significant difference was found in the proportion of high-novelty concepts. We suspect the lack of biological knowledge and cultural difference among the subjects involved in our studies as the two reasons behind the results. The results demonstrate that the design methods substantially influence the novelty of concepts generated, while indicating the need for better training in effective use of biological-analogies

Improving biomass production and saccharification in Brachypodium distachyon through overexpression of a sucrose-phosphate synthase from sugarcane

The substitution of fossil by renewable energy sources is a major strategy in reducing CO2 emission and mitigating climate change. In the transport sector, which is still mainly dependent on liquid fuels, the production of second generation ethanol from lignocellulosic feedstock is a promising strategy to substitute fossil fuels. The main prerequisites on designated crops for increased biomass production are high biomass yield and optimized saccharification for subsequent use in fermentation processes. We tried to address these traits by the overexpression of a sucrose-phosphate synthase gene (SoSPS) from sugarcane (Saccharum officinarum) in the model grass Brachypodium distachyon. The resulting transgenic B. distachyon lines not only revealed increased plant height at early growth stages but also higher biomass yield from fully senesced plants, which was increased up to 52 % compared to wild-type. Additionally, we determined higher sucrose content in senesced leaf biomass from the transgenic lines, which correlated with improved biomass saccharification after conventional thermo-chemical pretreatment and enzymatic hydrolysis. Combining increased biomass production and saccharification efficiency in the generated B. distachyon SoSPS overexpression lines, we obtained a maximum of 74 % increase in glucose release per plant compared to wild-type. Therefore, we consider SoSPS overexpression as a promising approach in molecular breeding of energy crops for optimizing yields of biomass and its utilization in second generation biofuel production

Hypoxia leads to significant changes in alternative splicing and elevated expression of CLK splice factor kinases in PC3 prostate cancer cells

© 2018 The Author(s). Background: Mounting evidence suggests that one of the ways that cells adapt to hypoxia is through alternative splicing. The aim of this study was firstly to examine the effect of hypoxia on the alternative splicing of cancer associated genes using the prostate cancer cell line PC3 as a model. Secondly, the effect of hypoxia on the expression of several regulators of splicing was examined. Methods: PC3 cells were grown in 1% oxygen in a hypoxic chamber for 48 h, RNA extracted and sent for high throughput PCR analysis at the RNomics platform at the University of Sherbrooke, Canada. Genes whose exon inclusion rate PSI (ψ) changed significantly were identified, and their altered exon inclusion rates verified by RT-PCR in three cell lines. The expression of splice factors and splice factor kinases in response to hypoxia was examined by qPCR and western blotting. The splice factor kinase CLK1 was inhibited with the benzothiazole TG003. Results: In PC3 cells the exon inclusion rate PSI (ψ) was seen to change by >25% in 12 cancer-associated genes; MBP, APAF1, PUF60, SYNE2, CDC42BPA, FGFR10P, BTN2A2, UTRN, RAP1GDS1, PTPN13, TTC23 and CASP9 (caspase 9). The expression of the splice factors SRSF1, SRSF2, SRSF3, SAM68, HuR, hnRNPA1, and of the splice factor kinases SRPK1 and CLK1 increased significantly in hypoxia. We also observed that the splice factor kinase CLK3, but not CLK2 and CLK4, was also induced in hypoxic DU145 prostate, HT29 colon and MCF7 breast cancer cell lines. Lastly, we show that the inhibition of CLK1 in PC3 cells with the benzothiazole TG003 increased expression of the anti-apoptotic isoform caspase 9b. Conclusions: Significant changes in alternative splicing of cancer associated genes occur in prostate cancer cells in hypoxic conditions. The expression of several splice factors and splice factor kinases increases during hypoxia, in particular the Cdc-like splice factor kinases CLK1 and CLK3. We suggest that in hypoxia the elevated expression of these regulators of splicing helps cells adapt through alternative splicing of key cancer-associated genes. We suggest that the CLK splice factor kinases could be targeted in cancers in which hypoxia contributes to resistance to therapy

Downregulation of Cinnamyl-Alcohol Dehydrogenase in Switchgrass by RNA Silencing Results in Enhanced Glucose Release after Cellulase Treatment

Cinnamyl alcohol dehydrogenase (CAD) catalyzes the last step in monolignol biosynthesis and genetic evidence indicates CAD deficiency in grasses both decreases overall lignin, alters lignin structure and increases enzymatic recovery of sugars. To ascertain the effect of CAD downregulation in switchgrass, RNA mediated silencing of CAD was induced through Agrobacterium mediated transformation of cv. “Alamo” with an inverted repeat construct containing a fragment derived from the coding sequence of PviCAD2. The resulting primary transformants accumulated less CAD RNA transcript and protein than control transformants and were demonstrated to be stably transformed with between 1 and 5 copies of the T-DNA. CAD activity against coniferaldehyde, and sinapaldehyde in stems of silenced lines was significantly reduced as was overall lignin and cutin. Glucose release from ground samples pretreated with ammonium hydroxide and digested with cellulases was greater than in control transformants. When stained with the lignin and cutin specific stain phloroglucinol-HCl the staining intensity of one line indicated greater incorporation of hydroxycinnamyl aldehydes in the lignin