The Investigation of the Low Temperature Combustion of Mesitylene and Tert-Amyl Methyl Ether by Synchrotron Photoionization Mass Spectrometry

This thesis describes the combustion experiments performed at the Chemical Dynamics Beamline of the Advanced Light Source (ALS) located at the Lawrence Berkeley National Laboratories (LBNL). The need for renewable fuel sources, the need for the study of their combustion in the contexts of homogenous charge combustion ignition (HCCI) engines can be found in Chapter 1. The components of the experimental set-up used throughout this thesis—time-of-flight mass spectrometer, Excimer laser, vacuum pumps and other components—and the components of ALS responsible in synchrotron radiation generation and processing—the linear accelerator, the booster ring, insertion devices, gas filters and monochromator are explained in Chapter 2. The data analysis method and the computational method used in the data analysis are expounded in Chapter 3. There are two combustion systems being investigated in this thesis. Mesitylene, an aromatic fuel additive, is proposed to be jet fuel, and its combustion is described in Chapter 4. Semi-biorenewable tert-amyl methyl ether (TAME) is studied in Chapter 5. Thermodynamic calculations, proposed mechanism, product identification and branching fractions are included in the analysis of the combustion of all these molecules

Properties and application of polyimide-based composites by blending surface functionalized boron nitride nanoplates

This is the peer reviewed version of the following article: Chen, Y., et al., Properties and application of polyimide-based composites by blending surface functionalized boron nitride nanoplates, Journal of Applied Polymer Science, 132 (16) which has been published in final form at http://dx.doi.org/10.1002/app.41889. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for self-archiving.This is the peer reviewed version of the article which has been published in final form at http://dx.doi.org/10.1002/app.41889. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Effect of angiotensin-converting enzyme inhibitor and angiotensin receptor blocker initiation on organ support-free days in patients hospitalized with COVID-19

IMPORTANCE Overactivation of the renin-angiotensin system (RAS) may contribute to poor clinical outcomes in patients with COVID-19. Objective To determine whether angiotensin-converting enzyme (ACE) inhibitor or angiotensin receptor blocker (ARB) initiation improves outcomes in patients hospitalized for COVID-19. DESIGN, SETTING, AND PARTICIPANTS In an ongoing, adaptive platform randomized clinical trial, 721 critically ill and 58 non–critically ill hospitalized adults were randomized to receive an RAS inhibitor or control between March 16, 2021, and February 25, 2022, at 69 sites in 7 countries (final follow-up on June 1, 2022). INTERVENTIONS Patients were randomized to receive open-label initiation of an ACE inhibitor (n = 257), ARB (n = 248), ARB in combination with DMX-200 (a chemokine receptor-2 inhibitor; n = 10), or no RAS inhibitor (control; n = 264) for up to 10 days. MAIN OUTCOMES AND MEASURES The primary outcome was organ support–free days, a composite of hospital survival and days alive without cardiovascular or respiratory organ support through 21 days. The primary analysis was a bayesian cumulative logistic model. Odds ratios (ORs) greater than 1 represent improved outcomes. RESULTS On February 25, 2022, enrollment was discontinued due to safety concerns. Among 679 critically ill patients with available primary outcome data, the median age was 56 years and 239 participants (35.2%) were women. Median (IQR) organ support–free days among critically ill patients was 10 (–1 to 16) in the ACE inhibitor group (n = 231), 8 (–1 to 17) in the ARB group (n = 217), and 12 (0 to 17) in the control group (n = 231) (median adjusted odds ratios of 0.77 [95% bayesian credible interval, 0.58-1.06] for improvement for ACE inhibitor and 0.76 [95% credible interval, 0.56-1.05] for ARB compared with control). The posterior probabilities that ACE inhibitors and ARBs worsened organ support–free days compared with control were 94.9% and 95.4%, respectively. Hospital survival occurred in 166 of 231 critically ill participants (71.9%) in the ACE inhibitor group, 152 of 217 (70.0%) in the ARB group, and 182 of 231 (78.8%) in the control group (posterior probabilities that ACE inhibitor and ARB worsened hospital survival compared with control were 95.3% and 98.1%, respectively). CONCLUSIONS AND RELEVANCE In this trial, among critically ill adults with COVID-19, initiation of an ACE inhibitor or ARB did not improve, and likely worsened, clinical outcomes. TRIAL REGISTRATION ClinicalTrials.gov Identifier: NCT0273570

Elucidating The Mechanism Of Nonsense Suppressor-Induced Premature Stop-Codon Readthrough In Eukaryotes

The result of nonsense mutation is premature stop-codon (PTC) in an open reading frame of a gene, resulting in truncated, inactive protein product. This leads to many diseases like cystic fibrosis, Duchenne muscular dystrophy, cancers and others. Small molecules called nonsense suppressors (NonSups) can stimulate stop-codon readthrough, inducing the ribosome to accept a near-cognate tRNA at the PTC, and restoring length and function of the protein. To elucidate the mode of action of NonSups, we have developed a pathway-specific, in vitro eukaryotic readthrough assay. Internal ribosome entry site containing mRNA from cricket-paralysis virus (CrPV-IRES) was chosen to by-pass the need for eukaryotic translation initiation factors. To understand the cap-independent translation initiation by CrPV-IRES, I measured the pseudo-translocation of CrPV-IRES and the translocation of CrPV-IRES and the first coding tRNA using fluorescence anisotropy and tRNA co-sedimentation, and translocation of the third and fourth elongation cycle using puromycin reaction with peptidyl P-site tRNA. I have shown that it is possible to produce at least a tetrapeptide using CrPV-IRES, with the caveat that the rate of translation initiation is slowed by two pseudo-translocation steps and two subsequent genuine translocation steps. To observe NonSup-stimulated PTC readthrough, I employed CrPV-IRES in a highly purified cell-free eukaryotic translational assay. Of the 16 NonSups tested, 12 exhibited readthrough activity in this assay of translational machinery activity. A closer inspection of the readthrough behaviors revealed at least two possible distinctive stop-codon readthrough mechanisms by aminoglycosides and ataluren-like molecules. To investigate the mechanism of NonSup-induced readthrough in detail, I studied three steps of translation elongation during PTC readthrough: tRNA association to the ribosome and translocation, measured by fluorescence spectroscopy, and peptide bond formation determined using thin layer electrophoresis purification of the readthrough peptide product. I found that G418, chosen as an example of an aminoglycoside, induces PTC readthrough by stimulating faster peptide bond formation. In contrast, ataluren induces PTC readthrough by inhibiting peptide release catalyzed by release factors eRF1 and eRF3. These findings will inform medicinal chemists in their utilization of rational drug design to create enhanced and safer NonSups as treatments for patients with diseases caused by nonsense mutations

Elucidating the Mechanism of Nonsense Suppressor-Induced Premature Stop-Codon Readthrough in Eukaryotes

The result of nonsense mutation is premature stop-codon (PTC) in an open reading frame of a gene, resulting in truncated, inactive protein product. This leads to many diseases like cystic fibrosis, Duchenne muscular dystrophy, cancers and others. Small molecules called nonsense suppressors (NonSups) can stimulate stop-codon readthrough, inducing the ribosome to accept a near-cognate tRNA at the PTC, and restoring length and function of the protein. To elucidate the mode of action of NonSups, we have developed a pathway-specific, in vitro eukaryotic readthrough assay. Internal ribosome entry site containing mRNA from cricket-paralysis virus (CrPV-IRES) was chosen to by-pass the need for eukaryotic translation initiation factors. To understand the cap-independent translation initiation by CrPV-IRES, I measured the pseudo-translocation of CrPV-IRES and the translocation of CrPV-IRES and the first coding tRNA using fluorescence anisotropy and tRNA co-sedimentation, and translocation of the third and fourth elongation cycle using puromycin reaction with peptidyl P-site tRNA. I have shown that it is possible to produce at least a tetrapeptide using CrPV-IRES, with the caveat that the rate of translation initiation is slowed by two pseudo-translocation steps and two subsequent genuine translocation steps. To observe NonSup-stimulated PTC readthrough, I employed CrPV-IRES in a highly purified cell-free eukaryotic translational assay. Of the 16 NonSups tested, 12 exhibited readthrough activity in this assay of translational machinery activity. A closer inspection of the readthrough behaviors revealed at least two possible distinctive stop-codon readthrough mechanisms by aminoglycosides and ataluren-like molecules. To investigate the mechanism of NonSup-induced readthrough in detail, I studied three steps of translation elongation during PTC readthrough: tRNA association to the ribosome and translocation, measured by fluorescence spectroscopy, and peptide bond formation determined using thin layer electrophoresis purification of the readthrough peptide product. I found that G418, chosen as an example of an aminoglycoside, induces PTC readthrough by stimulating faster peptide bond formation. In contrast, ataluren induces PTC readthrough by inhibiting peptide release catalyzed by release factors eRF1 and eRF3. These findings will inform medicinal chemists in their utilization of rational drug design to create enhanced and safer NonSups as treatments for patients with diseases caused by nonsense mutations

Elucidating The Mechanism Of Nonsense Suppressor-Induced Premature Stop-Codon Readthrough In Eukaryotes

The result of nonsense mutation is premature stop-codon (PTC) in an open reading frame of a gene, resulting in truncated, inactive protein product. This leads to many diseases like cystic fibrosis, Duchenne muscular dystrophy, cancers and others. Small molecules called nonsense suppressors (NonSups) can stimulate stop-codon readthrough, inducing the ribosome to accept a near-cognate tRNA at the PTC, and restoring length and function of the protein. To elucidate the mode of action of NonSups, we have developed a pathway-specific, in vitro eukaryotic readthrough assay. Internal ribosome entry site containing mRNA from cricket-paralysis virus (CrPV-IRES) was chosen to by-pass the need for eukaryotic translation initiation factors. To understand the cap-independent translation initiation by CrPV-IRES, I measured the pseudo-translocation of CrPV-IRES and the translocation of CrPV-IRES and the first coding tRNA using fluorescence anisotropy and tRNA co-sedimentation, and translocation of the third and fourth elongation cycle using puromycin reaction with peptidyl P-site tRNA. I have shown that it is possible to produce at least a tetrapeptide using CrPV-IRES, with the caveat that the rate of translation initiation is slowed by two pseudo-translocation steps and two subsequent genuine translocation steps. To observe NonSup-stimulated PTC readthrough, I employed CrPV-IRES in a highly purified cell-free eukaryotic translational assay. Of the 16 NonSups tested, 12 exhibited readthrough activity in this assay of translational machinery activity. A closer inspection of the readthrough behaviors revealed at least two possible distinctive stop-codon readthrough mechanisms by aminoglycosides and ataluren-like molecules. To investigate the mechanism of NonSup-induced readthrough in detail, I studied three steps of translation elongation during PTC readthrough: tRNA association to the ribosome and translocation, measured by fluorescence spectroscopy, and peptide bond formation determined using thin layer electrophoresis purification of the readthrough peptide product. I found that G418, chosen as an example of an aminoglycoside, induces PTC readthrough by stimulating faster peptide bond formation. In contrast, ataluren induces PTC readthrough by inhibiting peptide release catalyzed by release factors eRF1 and eRF3. These findings will inform medicinal chemists in their utilization of rational drug design to create enhanced and safer NonSups as treatments for patients with diseases caused by nonsense mutations

Empagliflozin in Patients with Chronic Kidney Disease

Background The effects of empagliflozin in patients with chronic kidney disease who are at risk for disease progression are not well understood. The EMPA-KIDNEY trial was designed to assess the effects of treatment with empagliflozin in a broad range of such patients. Methods We enrolled patients with chronic kidney disease who had an estimated glomerular filtration rate (eGFR) of at least 20 but less than 45 ml per minute per 1.73 m(2) of body-surface area, or who had an eGFR of at least 45 but less than 90 ml per minute per 1.73 m(2) with a urinary albumin-to-creatinine ratio (with albumin measured in milligrams and creatinine measured in grams) of at least 200. Patients were randomly assigned to receive empagliflozin (10 mg once daily) or matching placebo. The primary outcome was a composite of progression of kidney disease (defined as end-stage kidney disease, a sustained decrease in eGFR to < 10 ml per minute per 1.73 m(2), a sustained decrease in eGFR of & GE;40% from baseline, or death from renal causes) or death from cardiovascular causes. Results A total of 6609 patients underwent randomization. During a median of 2.0 years of follow-up, progression of kidney disease or death from cardiovascular causes occurred in 432 of 3304 patients (13.1%) in the empagliflozin group and in 558 of 3305 patients (16.9%) in the placebo group (hazard ratio, 0.72; 95% confidence interval [CI], 0.64 to 0.82; P < 0.001). Results were consistent among patients with or without diabetes and across subgroups defined according to eGFR ranges. The rate of hospitalization from any cause was lower in the empagliflozin group than in the placebo group (hazard ratio, 0.86; 95% CI, 0.78 to 0.95; P=0.003), but there were no significant between-group differences with respect to the composite outcome of hospitalization for heart failure or death from cardiovascular causes (which occurred in 4.0% in the empagliflozin group and 4.6% in the placebo group) or death from any cause (in 4.5% and 5.1%, respectively). The rates of serious adverse events were similar in the two groups. Conclusions Among a wide range of patients with chronic kidney disease who were at risk for disease progression, empagliflozin therapy led to a lower risk of progression of kidney disease or death from cardiovascular causes than placebo

Evaluation of prognostic risk models for postoperative pulmonary complications in adult patients undergoing major abdominal surgery: a systematic review and international external validation cohort study

Background Stratifying risk of postoperative pulmonary complications after major abdominal surgery allows clinicians to modify risk through targeted interventions and enhanced monitoring. In this study, we aimed to identify and validate prognostic models against a new consensus definition of postoperative pulmonary complications. Methods We did a systematic review and international external validation cohort study. The systematic review was done in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. We searched MEDLINE and Embase on March 1, 2020, for articles published in English that reported on risk prediction models for postoperative pulmonary complications following abdominal surgery. External validation of existing models was done within a prospective international cohort study of adult patients (≥18 years) undergoing major abdominal surgery. Data were collected between Jan 1, 2019, and April 30, 2019, in the UK, Ireland, and Australia. Discriminative ability and prognostic accuracy summary statistics were compared between models for the 30-day postoperative pulmonary complication rate as defined by the Standardised Endpoints in Perioperative Medicine Core Outcome Measures in Perioperative and Anaesthetic Care (StEP-COMPAC). Model performance was compared using the area under the receiver operating characteristic curve (AUROCC). Findings In total, we identified 2903 records from our literature search; of which, 2514 (86·6%) unique records were screened, 121 (4·8%) of 2514 full texts were assessed for eligibility, and 29 unique prognostic models were identified. Nine (31·0%) of 29 models had score development reported only, 19 (65·5%) had undergone internal validation, and only four (13·8%) had been externally validated. Data to validate six eligible models were collected in the international external validation cohort study. Data from 11 591 patients were available, with an overall postoperative pulmonary complication rate of 7·8% (n=903). None of the six models showed good discrimination (defined as AUROCC ≥0·70) for identifying postoperative pulmonary complications, with the Assess Respiratory Risk in Surgical Patients in Catalonia score showing the best discrimination (AUROCC 0·700 [95% CI 0·683–0·717]). Interpretation In the pre-COVID-19 pandemic data, variability in the risk of pulmonary complications (StEP-COMPAC definition) following major abdominal surgery was poorly described by existing prognostication tools. To improve surgical safety during the COVID-19 pandemic recovery and beyond, novel risk stratification tools are required. Funding British Journal of Surgery Society

Global economic burden of unmet surgical need for appendicitis

Background There is a substantial gap in provision of adequate surgical care in many low- and middle-income countries. This study aimed to identify the economic burden of unmet surgical need for the common condition of appendicitis. Methods Data on the incidence of appendicitis from 170 countries and two different approaches were used to estimate numbers of patients who do not receive surgery: as a fixed proportion of the total unmet surgical need per country (approach 1); and based on country income status (approach 2). Indirect costs with current levels of access and local quality, and those if quality were at the standards of high-income countries, were estimated. A human capital approach was applied, focusing on the economic burden resulting from premature death and absenteeism. Results Excess mortality was 4185 per 100 000 cases of appendicitis using approach 1 and 3448 per 100 000 using approach 2. The economic burden of continuing current levels of access and local quality was US $92 492 million using approach 1 and$73 141 million using approach 2. The economic burden of not providing surgical care to the standards of high-income countries was $95 004 million using approach 1 and$75 666 million using approach 2. The largest share of these costs resulted from premature death (97.7 per cent) and lack of access (97.0 per cent) in contrast to lack of quality. Conclusion For a comparatively non-complex emergency condition such as appendicitis, increasing access to care should be prioritized. Although improving quality of care should not be neglected, increasing provision of care at current standards could reduce societal costs substantially