Machine Learning-Guided Optimization of p-Coumaric Acid Production in Yeast.

Industrial biotechnology uses Design-Build-Test-Learn (DBTL) cycles to accelerate the development of microbial cell factories, required for the transition to a biobased economy. To use them effectively, appropriate connections between the phases of the cycle are crucial. Using p-coumaric acid (pCA) production in Saccharomyces cerevisiae as a case study, we propose the use of one-pot library generation, random screening, targeted sequencing, and machine learning (ML) as links during DBTL cycles. We showed that the robustness and flexibility of the ML models strongly enable pathway optimization and propose feature importance and Shapley additive explanation values as a guide to expand the design space of original libraries. This approach allowed a 68% increased production of pCA within two DBTL cycles, leading to a 0.52 g/L titer and a 0.03 g/g yield on glucose.

Combinatorial optimization of pathway, process and media for the production of p-coumaric acid by Saccharomyces cerevisiae.

Microbial cell factories are instrumental in transitioning towards a sustainable bio-based economy, offering alternatives to conventional chemical processes. However, fulfilling their potential requires simultaneous screening for optimal media composition, process and genetic factors, acknowledging the complex interplay between the organism's genotype and its environment. This study employs statistical design of experiments to systematically explore these relationships and optimize the production of p-coumaric acid (pCA) in Saccharomyces cerevisiae. Two rounds of fractional factorial designs were used to identify factors with a significant effect on pCA production, which resulted in a 168-fold variation in pCA titre. Moreover, a significant interaction between the culture temperature and expression of ARO4 highlighted the importance of simultaneous process and strain optimization. The presented approach leverages the strengths of experimental design and statistical analysis and could be systematically applied during strain and bioprocess design efforts to unlock the full potential of microbial cell factories.

Quality of life after patient-initiated vs physician-initiated response to symptom monitoring: the SYMPRO-Lung trial.

BACKGROUND: Previous studies using patient-reported outcomes measures (PROMs) to monitor symptoms during and after (lung) cancer treatment used alerts that were sent to the health-care provider, although an approach in which patients receive alerts could be more clinically feasible. The primary aim of this study was to compare the effect of weekly PROM symptom monitoring via a reactive approach (patient receives alert) or active approach (health-care provider receives alert) with care as usual on health-related quality of life (HRQOL) at 15 weeks after start of treatment in lung cancer patients. METHODS: The SYMPRO-Lung trial is a multicenter randomized controlled trial using a stepped wedge design. Stage I-IV lung cancer patients in the reactive and active groups reported PROM symptoms weekly, which were linked to a common alerting algorithm. HRQOL was measured by the EORTC QLQ-C30 at baseline and after 15 weeks. Linear regression analyses and effect size estimates were used to assess mean QOL-C30 change scores between groups, accounting for confounding. RESULTS: A total of 515 patients were included (160 active group, 89 reactive group, 266 control group). No differences in HRQOL were observed between the reactive and active group (summary score: unstandardized beta [B] = 0.51, 95% confidence interval [CI] = -3.22 to 4.24, Cohen d effect size [ES] = 0.06; physical functioning: B = 0.25, 95% CI = -5.15 to 4.64, ES = 0.02). The combined intervention groups had statistically and clinically significantly better mean change scores on the summary score (B = 4.85, 95% CI = 1.96 to 7.73, ES = 0.57) and physical functioning (B = 7.00, 95% CI = 2.90 to 11.09, ES = 0.71) compared with the control group. CONCLUSIONS: Weekly PRO symptom monitoring statistically and clinically significantly improves HRQOL in lung cancer patients. The logistically less intensive, reactive approach may be a better fit for implementation.

SYMptom monitoring with Patient-Reported Outcomes using a web application among patients with Lung cancer in the Netherlands (SYMPRO-Lung): study protocol for a stepped-wedge randomised controlled trial.

INTRODUCTION: Lung cancer and its treatment cause a wide range of symptoms impacting the patients' health-related quality of life (HRQoL). The use of patient-reported outcomes (PRO) to monitor symptoms during and after cancer treatment has been shown not only to improve symptom management but also to improve HRQoL and overall survival (OS). Collectively, these results favour implementation of PRO-symptom monitoring in daily clinical care. However, these promising outcomes have been obtained under trial conditions in which patients were selected based on stringent inclusion criteria, and in countries with a dissimilar healthcare system than in the Netherlands.The primary aim of the SYMptom monitoring with Patient-Reported Outcomes using a web application among patients with Lung cancer in the Netherlands (SYMPRO-Lung) study is to evaluate the effect of PRO-symptom monitoring during and after lung cancer treatment on HRQoL in daily clinical practice. Secondary objectives include assessing the effect of PRO-symptom monitoring on progression-free survival, OS, the incidence and grade of PRO symptoms, medication adherence, implementation fidelity and cost-effectiveness. METHODS AND ANALYSIS: The SYMPRO-Lung study is a prospective, multicentre trial with a stepped wedge cluster randomised design. Study participants (n=292 intervention, n=292 controls) include patients with lung cancer (stages I-IV) starting treatment with surgery, systemic treatment, targeted treatment and/or radiotherapy.Every participating centre will consecutively switch from the control period to the intervention period, in which patients report their symptoms weekly via an online tool. In the intervention group, we evaluate two alert approaches: the active and reactive approach. If the symptoms exceed a predefined threshold, an alert is sent to the healthcare provider (active approach) or to the patient (reactive approach). Both the control and intervention group complete HRQoL questionnaires at 4 time points: at baseline, 15 weeks, 6 months and 1-year post treatment). Differences in HRQoL between the groups will be compared using linear mixed modelling analyses, accounting for within-centre clustering, potential time effects and confounding. ETHICS AND DISSEMINATION: The study protocol was approved by the Institutional Review Board and the Medical Ethics Committee of the Amsterdam UMC (under number NL 68440.029.18) and the institutional review boards of the participating study sites. The dissemination of the results will be conducted through publication in peer-reviewed journals and through scientific conferences. TRIAL REGISTRATION NUMBER: Trial register identifier: Netherlands Trial register Trial NL7897. Date of registration: 24 July 2019. https://www.trialregister.nl/trial/7897.

Imatinib in patients with severe COVID-19: a randomised, double-blind, placebo-controlled, clinical trial.

BACKGROUND: The major complication of COVID-19 is hypoxaemic respiratory failure from capillary leak and alveolar oedema. Experimental and early clinical data suggest that the tyrosine-kinase inhibitor imatinib reverses pulmonary capillary leak. METHODS: This randomised, double-blind, placebo-controlled, clinical trial was done at 13 academic and non-academic teaching hospitals in the Netherlands. Hospitalised patients (aged ≥18 years) with COVID-19, as confirmed by an RT-PCR test for SARS-CoV-2, requiring supplemental oxygen to maintain a peripheral oxygen saturation of greater than 94% were eligible. Patients were excluded if they had severe pre-existing pulmonary disease, had pre-existing heart failure, had undergone active treatment of a haematological or non-haematological malignancy in the previous 12 months, had cytopenia, or were receiving concomitant treatment with medication known to strongly interact with imatinib. Patients were randomly assigned (1:1) to receive either oral imatinib, given as a loading dose of 800 mg on day 0 followed by 400 mg daily on days 1-9, or placebo. Randomisation was done with a computer-based clinical data management platform with variable block sizes (containing two, four, or six patients), stratified by study site. The primary outcome was time to discontinuation of mechanical ventilation and supplemental oxygen for more than 48 consecutive hours, while being alive during a 28-day period. Secondary outcomes included safety, mortality at 28 days, and the need for invasive mechanical ventilation. All efficacy and safety analyses were done in all randomised patients who had received at least one dose of study medication (modified intention-to-treat population). This study is registered with the EU Clinical Trials Register (EudraCT 2020-001236-10). FINDINGS: Between March 31, 2020, and Jan 4, 2021, 805 patients were screened, of whom 400 were eligible and randomly assigned to the imatinib group (n=204) or the placebo group (n=196). A total of 385 (96%) patients (median age 64 years [IQR 56-73]) received at least one dose of study medication and were included in the modified intention-to-treat population. Time to discontinuation of ventilation and supplemental oxygen for more than 48 h was not significantly different between the two groups (unadjusted hazard ratio [HR] 0·95 [95% CI 0·76-1·20]). At day 28, 15 (8%) of 197 patients had died in the imatinib group compared with 27 (14%) of 188 patients in the placebo group (unadjusted HR 0·51 [0·27-0·95]). After adjusting for baseline imbalances between the two groups (sex, obesity, diabetes, and cardiovascular disease) the HR for mortality was 0·52 (95% CI 0·26-1·05). The HR for mechanical ventilation in the imatinib group compared with the placebo group was 1·07 (0·63-1·80; p=0·81). The median duration of invasive mechanical ventilation was 7 days (IQR 3-13) in the imatinib group compared with 12 days (6-20) in the placebo group (p=0·0080). 91 (46%) of 197 patients in the imatinib group and 82 (44%) of 188 patients in the placebo group had at least one grade 3 or higher adverse event. The safety evaluation revealed no imatinib-associated adverse events. INTERPRETATION: The study failed to meet its primary outcome, as imatinib did not reduce the time to discontinuation of ventilation and supplemental oxygen for more than 48 consecutive hours in patients with COVID-19 requiring supplemental oxygen. The observed effects on survival (although attenuated after adjustment for baseline imbalances) and duration of mechanical ventilation suggest that imatinib might confer clinical benefit in hospitalised patients with COVID-19, but further studies are required to validate these findings. FUNDING: Amsterdam Medical Center Foundation, Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ZonMW, and the European Union Innovative Medicines Initiative 2.

Work stress prevention needs of employees and supervisors.

BACKGROUND: Work stress prevention can reduce health risks for individuals, as well as organisational and societal costs. The success of work stress interventions depends on proper implementation. Failure to take into account the needs of employees and supervisors can hinder intervention implementation. This study aimed to explore employee and supervisor needs regarding organisational work stress prevention. METHODS: Semi-structured telephone interviews were conducted with employees (n = 7) and supervisors (n = 8) from different sectors, such as the finance, health care, and services industry. The interviews focused on respondents' needs regarding the prevention of work stress within an organisational setting. Performing thematic analysis, topics and themes were extracted from the verbatim transcribed interviews using Atlas.ti. RESULTS: Both employees and supervisors reported a need for: 1) communication about work stress, 2) attention for determinants of work stress, 3) supportive circumstances (prerequisites) for work stress prevention, 4) involvement of various stakeholders in work stress prevention, and 5) availability of work stress prevention measures. Both employees and supervisors expressed the need for supervisors to communicate about work stress. Employees and supervisors reported similar psychosocial work factors that should be targeted for prevention (e.g., social support and autonomy). There was greater variety in the sub-themes within communication about work stress and supportive circumstances for work stress prevention in supervisor responses, and greater variety in the sub-themes within availability of work stress prevention measures in employee responses. CONCLUSIONS: Both employees and supervisors were explicit about who should take part in communication about work stress, what prerequisites for work stress prevention should exist, and which stakeholders should be involved. These results can inform work stress prevention practice, supporting selection and implementation of interventions. TRIAL REGISTRATION: This study was registered in the Netherlands National Trial Register, trial code: NTR5527 .

Stress Prevention@Work: a study protocol for the evaluation of a multifaceted integral stress prevention strategy to prevent employee stress in a healthcare organization: a cluster controlled trial.

BACKGROUND: Adequate implementation of work-related stress management interventions can reduce or prevent work-related stress and sick leave in organizations. We developed a multifaceted integral stress-prevention strategy for organizations from several sectors that includes a digital platform and collaborative learning network. The digital platform contains a stepwise protocol to implement work-related stress-management interventions. It includes stress screeners, interventions and intervention providers to facilitate access to and the selection of matching work-related stress-management interventions. The collaborative learning network, including stakeholders from various organizations, plans meetings focussing on an exchange of experiences and good practices among organizations for the implementation of stress prevention measures. This paper describes the design of an integral stress-prevention strategy, Stress Prevention@Work, and the protocol for the evaluation of: 1) the effects of the strategy on perceived stress and work-related outcomes, and 2) the barriers and facilitators for implementation of the strategy. METHODS: The effectiveness of Stress Prevention@Work will be evaluated in a cluster controlled trial, in a large healthcare organization in the Netherlands, at six and 12 months. An independent researcher will match teams on working conditions and size and allocate the teams to the intervention or control group. Teams in the intervention group will be offered Stress Prevention@Work. For each intervention team, one employee is responsible for applying the strategy within his/her team using the digital platform and visiting the collaborative learning network. Using a waiting list design, the control group will be given access to the strategy after 12 months. The primary outcome is the employees' perceived stress measured by the stress subscale of the Depression, Anxiety, and Stress Scale (DASS-21). Secondary outcome measures are job demands, job resources and the number of preventive stress measures implemented at the team level. Alongside the trial, a process evaluation, including barriers and facilitators of the implementation of Stress Prevention@Work, will be conducted in one healthcare organisation. DISCUSSION: If Stress Prevention@Work is found to be effective in one healthcare organisation, further implementation on a broader scale might lead to increased productivity and decreased stress and sick leave in other organizations. Results are expected in 2018. TRIAL REGISTRATION: NTR5527 . Registered 7 Dec 2015.