An optimal Bayesian predictive probability design for phase II clinical trials with simple and complicated endpoints

Most existing phase II clinical trial designs focus on conventional chemotherapy with binary tumor response as the endpoint. The advent of novel therapies, such as molecularly targeted agents and immunotherapy, has made the endpoint of phase II trials more complicated, often involving ordinal, nested, and coprimary endpoints. We propose a simple and flexible Bayesian optimal phase II predictive probability (OPP) design that handles binary and complex endpoints in a unified way. The Dirichlet-multinomial model is employed to accommodate different types of endpoints. At each interim, given the observed interim data, we calculate the Bayesian predictive probability of success, should the trial continue to the maximum planned sample size, and use it to make the go/no-go decision. The OPP design controls the type I error rate, maximizes power or minimizes the expected sample size, and is easy to implement, because the go/no-go decision boundaries can be enumerated and included in the protocol before the onset of the trial. Simulation studies show that the OPP design has satisfactory operating characteristics.     

Rational design and synthesis of molecularly imprinted polymers (MIP) for purifying tylosin by seeded precipitation polymerization

A useful approach was proposed to easily synthesize molecularly imprinted adsorbent for the purification of tylosin from broth. Firstly, by molecular simulation based on density functional theory, methacrylic acid was chosen as a functional monomer by comparing the binding energy. Second, a novel method of polymerization based on precipitation polymerization with added seeds was used in water-mixed solvent for the preparation of water-compatible micron-sized MIP. Its static adsorption capacity for tylosin in aqueous solution was estimated to be 106.5 mg/g with the highest imprinting factor (IF) of 3.6. The selectivity coefficient (α) of tylosin to desmycosin was 3.3. The antibiotic in fermentation broth could be purified by means of molecularly imprinted solid phase extraction (MISPE), which allows MIP to be used for the purification of tylosin from a complex sample.     

Workflow optimization in a clinical laboratory using Lean management principles in the pre-analytical phase

BackgroundThe application of the Lean methodology in clinical laboratories can improve workflow and user satisfaction through the efficient delivery of analytical results. The purpose of this study was to optimise delivery times of the test results at a clinical laboratory, using Lean management principles in the pre-analytical phase.MethodsA prospective study with a quasi-experimental design was implemented. Staff functions were restructured and sample flows were modified. Delivery times of clinical results (glucose and haematocrit; 6648 data) from the Medicine and Adult Emergency services for years 2017 and 2018 were compared.ResultsA reduction (p < 0.05) in turnaround times in the delivery of glucose test results at the adult emergency service was observed (84 to 73 min, 13%, pre and post). In addition, there was a non-significant reduction in the turnaround times for glucose (Medicine) and haematocrit in both services. In the analytical and post-analytical phase (not intervened), an increase in turnaround times was observed in some cases.ConclusionsOther studies have indicated that the application of the Lean methodology in clinical laboratories improves workflow, increasing effectiveness and efficiency. This study showed an improvement in the delivery time of test results (glucose - Emergency), giving rise to a culture of cooperation and continuous improvement. It would, however, be essential to address the management model integrating the analytical and post-analytical phases.     

Phase separation liquid-liquid extraction for the quantification of 8-iso-Prostaglandin F2 Alpha in human plasma by LC-MS/MS

BackgroundReactive oxygen species (ROS) are produced in the body during normal metabolism by means of enzymes and non-enzymatic chemical reduction of molecular oxygen. In case of the prevalence of ROS formation over their elimination, highly reactive free radicals can be accumulated and can cause multiple damages to the biomolecules and cells. Determination of isoprostanes in biological matrices is most often used to register free radical damage and requires selective, sensitive and specific techniques.MethodsThis study presents the development and validation of the LC-MS/MS method for the determination of 8-iso-Prostaglandin F2α in human plasma utilising a modified liquid-liquid extraction procedure with phase separation.ResultsModified sample preparation procedure assured higher extraction yield, clear separation of organic layer from the plasma water phase and protein precipitates, and better-purified product for instrumental analysis. Linearity was validated in the range 0.1-5.0 µg/L with R2 > 0.996; normalised matrix varied between 86.0% and 108.3%, accuracy ranged from 90.4 % to 113.9% and precision both within runs and between runs was less than 7%. With a run time of 10 min, a throughput of over 50 samples per working day could be performed.ConclusionsThe method meets all the current industrial validation criteria and allows the accurate and precise determination of 8-iso-PGF2α in human plasma at diagnostically significant concentration range.     

Phase separation of chromatin and small RNA pathways in plants

Gene expression can be modulated by epigenetic mechanisms, including chromatin modifications and small regulatory RNAs. These pathways are unevenly distributed within a cell and usually take place in specific intracellular regions. Unfortunately, the fundamental driving force and biological relevance of such spatial differentiation is largely unknown. Liquid–liquid phase separation (LLPS) is a natural propensity of demixing liquid phases and has been recently suggested to mediate the formation of biomolecular condensates that are relevant to diverse cellular processes. LLPS provides a mechanistic explanation for the self-assembly of subcellular structures by which the efficiency and specificity of certain cellular reactions are achieved. In plants, LLPS has been observed for several key factors in the chromatin and small RNA pathways. For example, the formation of facultative and obligate heterochromatin involves the LLPS of multiple relevant factors. In addition, phase separation is observed in a set of proteins acting in microRNA biogenesis and the small interfering RNA pathway. In this Focused Review, we highlight and discuss the recent findings regarding phase separation in the epigenetic mechanisms of plants.     

Improved visualization of X-ray phase contrast volumetric data through artifact-free integrated differential images

Artifacts arising when differential phase images are integrated is a common problem to several X-ray phase-based experimental techniques. The combination of noise and insufficient sampling of the high-frequency differential phase signal leads to the formation of streak artifacts in the projections, translating into poor image quality in the tomography slices. In this work, we apply a non-iterative integration algorithm proven to reduce streak artifacts in planar (2D) images to a differential phase tomography scan. We report on how the reduction of streak artifacts in the projections improves the quality of the tomography slices, especially in the directions different from the reconstruction plane. Importantly, the method is compatible with large tomography datasets in terms of computation time.     

Synthetic biomolecular condensates to engineer eukaryotic cells

The compartmentalization of specific functions into specialized organelles is a key feature of eukaryotic life. In particular, dynamic biomolecular condensates that are not membrane enclosed offer exciting opportunities for synthetic biology. In recent years, multiple approaches to generate and control condensates have been reported. Notably, multiple orthogonally translating organelles were designed that enable precise protein engineering inside living cells. Despite being built from only very few components, orthogonal translation can be engineered with subresolution precision at different places inside the same cell to create mammalian cells with multiple expanded genetic codes. This provides a pathway to engineer multiple proteins with multiple and distinct functionalities inside living eukaryotes and provides a general strategy toward spatially orthogonal enzyme engineering.     

Cell‐extracellular matrix interactions in the fluidic phase direct the topology and polarity of self‐organized epithelial structures

IntroductionIn vivo, cells are surrounded by extracellular matrix (ECM). To build organs from single cells, it is generally believed that ECM serves as scaffolds to coordinate cell positioning and differentiation. Nevertheless, how cells utilize cell‐ECM interactions for the spatiotemporal coordination to different ECM at the tissue scale is not fully understood.MethodsHere, using in vitro assay with engineered MDCK cells expressing H2B‐mCherry (nucleus) and gp135/Podocalyxin‐GFP (apical marker), we show in multi‐dimensions that such coordination for epithelial morphogenesis can be determined by cell‐soluble ECM interaction in the fluidic phase.ResultsThe coordination depends on the native topology of ECM components such as sheet‐like basement membrane (BM) and type I collagen (COL) fibres: scaffold formed by BM (COL) facilitates a close‐ended (open‐ended) coordination that leads to the formation of lobular (tubular) epithelium. Further, cells form apicobasal polarity throughout the entire lobule/tubule without a complete coverage of ECM at the basal side, and time‐lapse two‐photon scanning imaging reveals the polarization occurring early and maintained through the lobular expansion. During polarization, gp135‐GFP was converged to the apical surface collectively in the lobular/tubular structures, suggesting possible intercellular communications. Under suspension culture, the polarization was impaired with multi‐lumen formation in the tubules, implying the importance of ECM biomechanical microenvironment.ConclusionOur results suggest a biophysical mechanism for cells to form polarity and coordinate positioning at tissue scale, and in engineering epithelium through cell‐soluble ECM interaction and self‐assembly.     

Small heat shock protein 22 kDa can modulate the aggregation and liquid–liquid phase separation behavior of tau

Alzheimer''s disease is a progressive fatal neurodegenerative disease with no cure or effective treatments. The hallmarks of disease include extracellular plaques and intracellular tangles of aggregated protein. The intracellular tangles consist of the microtubule associated protein tau. Preventing the pathological aggregation of tau may be an important therapeutic approach to treat disease. In this study we show that small heat shock protein 22 kDa (Hsp22) can prevent the aggregation of tau in vitro. Additionally, tau can undergo liquid–liquid phase separation (LLPS) in the presence of crowding reagents which causes it to have an increased aggregation rate. We show that Hsp22 can modulate both the aggregation and LLPS behavior of tau in vitro.