A statistical approach to virtual cellular experiments: improved causal discovery using accumulation IDA (aIDA)

Motivation: We address the following question: Does inhibition of the expression of a gene X in a cellular assay affect the expression of another gene Y? Rather than inhibiting gene X experimentally, we aim at answering this question computationally using as the only input observational gene expression data. Recently, a new statistical algorithm called Intervention calculus when the Directed acyclic graph is Absent (IDA), has been proposed for this problem. For several biological systems, IDA has been shown to outcompete regression-based methods with respect to the number of true positives versus the number of false positives for the top 5000 predicted effects. Further improvements in the performance of IDA have been realized by stability selection, a resampling method wrapped around IDA that enhances the discovery of true causal effects. Nevertheless, the rate of false positive and false negative predictions is still unsatisfactorily high. Results: We introduce a new resampling approach for causal discovery called accumulation IDA (aIDA). We show that aIDA improves the performance of causal discoveries compared to existing variants of IDA on both simulated and real yeast data. The higher reliability of top causal effect predictions achieved by aIDA promises to increase the rate of success of wet lab intervention experiments for functional studies

The influence on quality of life of intermittent scheduling in first- and second-line chemotherapy of patients with HER2-negative advanced breast cancer

Background: The Stop&Go study randomized patients with advanced breast cancer to intermittent (two times four) or continuous (eight subsequent cycles) first- and second-line chemotherapy. Methods: QoL was measured with RAND-36 questionnaires every 12 weeks. The primary objective was to estimate differences in changes from baseline between intermittent and continuous treatment. An effect size of 0.5 SD (5 points) was considered clinically meaningful. Results: A total of 398 patients were included with a median follow-up of 11.4 months (IQR 5.6–22.2). Mean physical QoL baseline scores were 38.0 resp. 38.2, and mental scores 45.0 resp. 42.4 for intermittent and continuous treatm

Degeneration of penicillin production in ethanol-limited chemostat cultivations of Penicillium chrysogenum:A systems biology approach

Background: In microbial production of non-catabolic products such as antibiotics a loss of production capacity upon long-term cultivation (for example chemostat), a phenomenon called strain degeneration, is often observed. In this study a systems biology approach, monitoring changes from gene to produced flux, was used to study degeneration of penicillin production in a high producing Penicillium chrysogenum strain during prolonged ethanol-limited chemostat cultivations. Results: During these cultivations, the biomass specific penicillin production rate decreased more than 10-fold in less than 22 generations. No evidence was obtained for a decrease of the copy number of the penicillin gene cluster, nor a significant down regulation of the expression of the penicillin biosynthesis genes. However, a strong down regulation of the biosynthesis pathway of cysteine, one of the precursors of penicillin, was observed. Furthermore the protein levels of the penicillin pathway enzymes L-alpha-(d-aminoadipyl)-L-alpha-cystenyl-D-alpha-valine synthetase (ACVS) and isopenicillin-N synthase (IPNS), decreased significantly. Re-cultivation of fully degenerated cells in unlimited batch culture and subsequent C-limited chemostats did only result in a slight recovery of penicillin production. Conclusions: Our findings indicate that the observed degeneration is attributed to a significant decrease of the levels of the first two enzymes of the penicillin biosynthesis pathway, ACVS and IPNS. This decrease is not caused by genetic instability of the penicillin amplicon, neither by down regulation of the penicillin biosynthesis pathway. Furthermore no indications were obtained for degradation of these enzymes as a result of autophagy. Possible causes for the decreased enzyme levels could be a decrease of the translation efficiency of ACVS and IPNS during degeneration, or the presence of a culture variant impaired in the biosynthesis of functional proteins of these enzymes, which outcompeted the high producing part of the population

Early extracorporeal CPR for refractory out-of-hospital cardiac arrest

BACKGROUNDExtracorporeal cardiopulmonary resuscitation (CPR) restores perfusion and oxy-genation in a patient who does not have spontaneous circulation. The evidencewith regard to the effect of extracorporeal CPR on survival with a favorable neu-rologic outcome in refractory out-of-hospital cardiac arrest is inconclusive.METHODSIn this multicenter, randomized, controlled trial conducted in the Netherlands, weassigned patients with an out-of-hospital cardiac arrest to receive extracorporealCPR or conventional CPR (standard advanced cardiac life support). Eligible patientswere between 18 and 70 years of age, had received bystander CPR, had an initialventricular arrhythmia, and did not have a return of spontaneous circulationwithin 15 minutes after CPR had been initiated. The primary outcome was sur-vival with a favorable neurologic outcome, defined as a Cerebral PerformanceCategory score of 1 or 2 (range, 1 to 5, with higher scores indicating more severedisability) at 30 days. Analyses were performed on an intention-to-treat basis.RESULTSOf the 160 patients who underwent randomization, 70 were assigned to receiveextracorporeal CPR and 64 to receive conventional CPR; 26 patients who did notmeet the inclusion criteria at hospital admission were excluded. At 30 days, 14 pa-tients (20%) in the extracorporeal-CPR group were alive with a favorable neuro-logic outcome, as compared with 10 patients (16%) in the conventional-CPR group(odds ratio, 1.4; 95% confidence interval, 0.5 to 3.5; P = 0.52). The number of seri-ous adverse events per patient was similar in the two groups.CONCLUSIONSIn patients with refractory out-of-hospital cardiac arrest, extracorporeal CPR andconventional CPR had similar effects on survival with a favorable neurologic out-come. (Funded by the Netherlands Organization for Health Research and Develop-ment and Maquet Cardiopulmonary [Getinge]; INCEPTION ClinicalTrials.govnumber, NCT03101787.)Cardiolog

Biological Industrial waste-water treatment minimizing biomass Production and maximizing biomass Concentration

Applied Science