Rapid establishment of the European Bank for induced Pluripotent Stem Cells (EBiSC):The Hot Start experience

A fast track “Hot Start” process was implemented to launch the European Bank for Induced Pluripotent Stem Cells (EBiSC) to provide early release of a range of established control and disease linked human induced pluripotent stem cell (hiPSC) lines. Established practice amongst consortium members was surveyed to arrive at harmonised and publically accessible Standard Operations Procedures (SOPs) for tissue procurement, bio-sample tracking, iPSC expansion, cryopreservation, qualification and distribution to the research community. These were implemented to create a quality managed foundational collection of lines and associated data made available for distribution. Here we report on the successful outcome of this experience and work flow for banking and facilitating access to an otherwise disparate European resource, with lessons to benefit the international research community. eTOC: The report focuses on the EBiSC experience of rapidly establishing an operational capacity to procure, bank and distribute a foundational collection of established hiPSC lines. It validates the feasibility and defines the challenges of harnessing and integrating the capability and productivity of centres across Europe using commonly available resources currently in the field

Mutual features for pattern classification

The mean of a data set is one trivial representation of data from one class. This thesis discusses mutual interdependence analysis (MIA) that is successfully used to extract moreinvolved representations, or “mutual features”, accounting for samples in the class. MIA aims to extract a common or mutual signature that is invariant to changes in the inputs. For example, a mutual feature is a speaker signature under varying channel conditions or a face signature under varying illumination conditions. By definition, the mutual feature is a linear combination of class examples that is equally correlated with all training samples in the class. An equivalent view is to find a direction to project the dataset such that projection lengths are maximally correlated. The MIA optimization criterion is presented from the perspectives of canonical correlation analysis and Bayesian estimation. This allows to state and solve the criterion for mutual features concisely and to infer other properties of its closed form, unique solution under various statistical assumptions. Moreover, a generalized MIA solution (GMIA) is defined that enables utilization of a priori knowledge. MIA and GMIA work well even if the mutual signature accounts only for a small part of the energy in the inputs. Real world problems do notexactly fit the signal model of an equally correlated common signature. Therefore, the behavior of MIA is analyzed in situations where its model does not exactly fit. For these situations it is shown that GMIA continues to extract meaningful information. Furthermore, the GMIA result is compared to ubiquitous signal processing methods. It is shown that GMIA extends these current tools visualizing previously hidden information. The utility of both MIA and GMIA is demonstrated on two standard pattern recognition problems: text–independent speaker verification and illumination–independent face recognition. For example, GMIA achieves an equal error rate (EER) of 4.0% in the text–independent speaker verification application on the full NTIMIT database of 630 speakers. On the other hand, for illumination–independent face recognition, MIA achieves an identification error rate of 7.4% in exhaustive leave–one–out tests on the Yale database. Overall, MIA and GMIA are found to achieve competitive pattern classification performance to other modern algorithms

Gas Turbine Exhaust Temperature Measurement Approach Using Time-Frequency Controlled Sources

Siemens has developed a novel approach for measuring the process gas temperature leaving the power turbine in their heavy industrial gas turbine engines using active acoustic tomography. Siemens has deployed this measurement technique on two test engines of different power ranges and different combustion and exhaust duct configurations. These engine tests have demonstrated that this technology is effective and robust. All working parts are outside the heat effective zone so, unlike the traditional intrusive point temperature measurement method, sensors are easily replaceable during engine operation. Bulk exhaust temperature is used in performance testing of industrial gas turbine engines and is a critical measurement for power production. Temperature distribution information in the exhaust plane is valuable for safe engine operation and can be used to prevent lifetime reduction due to hotspots or to monitor the burner flames. Siemens used broadband sound sources for the previously reported acoustic pyrometer experiments. This paper extends this work utilizing sparse time-frequency encoded sources to improve the robustness of time of flight estimation in the high noise area of the turbine exhaust. The goal is to achieve a higher signal to noise ratio between the emitted and received signals by focusing the acoustic energy into narrow time-frequency bins that are little affected by turbine noise. Different acoustic patterns are tested and compared to the previously used broadband source both in laboratory experiments and a turbine test bed. The patterns are evaluated regarding their noise robustness, sound pressure levels and narrow autocorrelation which are important for accurate time of flight estimation in high noise environments

Trade-off between benefits, harms and economic efficiency of low-dose CT lung cancer screening: a microsimulation analysis of nodule management strategies in a population-based setting

Abstract Background In lung cancer screening, a nodule management protocol describes nodule assessment and thresholds for nodule size and growth rate to identify patients who require immediate diagnostic evaluation or additional imaging exams. The Netherlands-Leuvens Screening Trial and the National Lung Screening Trial used different selection criteria and nodule management protocols. Several modelling studies have reported variations in screening outcomes and cost-effectiveness across selection criteria and screening intervals; however, the effect of variations in the nodule management protocol remains uncertain. This study evaluated the effects of the eligibility criteria and nodule management protocols on the benefits, harms and cost-effectiveness of lung screening scenarios in a population-based setting in Germany. Methods We developed a modular microsimulation model: a biological module simulated individual histories of lung cancer development from carcinogenesis onset to death; a screening module simulated patient selection, screening-detection, nodule management protocols, diagnostic evaluation and screening outcomes. Benefits included mortality reduction, life years gained and averted lung cancer deaths. Harms were costs, false positives and overdiagnosis. The comparator was no screening. The evaluated 76 screening scenarios included variations in selection criteria and thresholds for nodule size and growth rate. Results Five years of annual screening resulted in a 9.7–12.8% lung cancer mortality reduction in the screened population. The efficient scenarios included volumetric assessment of nodule size, a threshold for a volume of 300 mm3 and a threshold for a volume doubling time of 400 days. Assessment of volume doubling time is essential for reducing overdiagnosis and false positives. Incremental cost-effectiveness ratios of the efficient scenarios were 16,754–23,847 euro per life year gained and 155,287–285,630 euro per averted lung cancer death. Conclusions Lung cancer screening can be cost-effective in Germany. Along with the eligibility criteria, the nodule management protocol influences screening performance and cost-effectiveness. Definition of the thresholds for nodule size and nodule growth in the nodule management protocol should be considered in detail when defining optimal screening strategies

Crystallization and preliminary analysis of the NqrA and NqrC subunits of the Na⁺-translocating NADH:ubiquinone oxidoreductase from Vibrio cholerae

The Na+-translocating NADH:ubiquinone oxidoreductase (Na+-NQR) from Vibrio cholerae is a membrane protein complex consisting of six different subunits NqrA-NqrF. The major domains of the NqrA and NqrC subunits were heterologously expressed in Escherichia coli and crystallized. The structure of NqrA1-377 was solved in space groups C2221 and P21 by SAD phasing and molecular replacement at 1.9 and 2.1 Å resolution, respectively. NqrC devoid of the transmembrane helix was co-expressed with ApbE to insert the flavin mononucleotide group covalently attached to Thr225. The structure was determined by molecular replacement using apo-NqrC of Parabacteroides distasonis as search model at 1.8 Å resolution

Droplet-based vitrification of adherent human induced pluripotent stem cells on alginate microcarrier influenced by adhesion time and matrix elasticity

The gold standard in cryopreservation is still conventional slow freezing of single cells or small aggregates in suspension, although major cell loss and limitation to non-specialised cell types in stem cell technology are known drawbacks. The requirement for rapidly available therapeutic and diagnostic cell types is increasing constantly. In the case of human induced pluripotent stem cells (hiPSCs) or their derivates, more sophisticated cryopreservation protocols are needed to address this demand. These should allow a preservation in their physiological, adherent state, an efficient re-cultivation and upscaling upon thawing towards high-throughput applications in cell therapies or disease modelling in drug discovery. Here, we present a novel vitrification based method for adherent hiPSCs, designed for automated handling by microfluidic approaches and with ready-to-use potential e.g. in suspension-based bioreactors after thawing. Modifiable alginate microcarriers serve as a growth surface for adherent hiPSCs that were cultured in a suspension-based bioreactor and subsequently cryopreserved via droplet-based vitrification in comparison to conventional slow freezing. Soft (0.35%) versus stiff (0.65%) alginate microcarriers in concert with adhesion time variation have been examined. Findings revealed specific optimal conditions leading to an adhesion time and growth surface (matrix) elasticity depen dent hypothesis on cryo-induced damaging regimes for adherent cell types. Deviations from the found optimum parameters give rise to membrane ruptures assessed via SEM and major cell loss after adherent vitrification. Applying the optimal conditions, droplet-based vitrification was superior to conventional slow freezing. A decreased microcarrier stiffness was found to outperform stiffer material regarding cell recovery, whereas the stemness characteristics of rewarmed hiPSCs were preserved