Early Feasibility Assessment: A Method for Accurately Predicting Biotherapeutic Dosing to Inform Early Drug Discovery Decisions.

The application of model-informed drug discovery and development (MID3) approaches in the early stages of drug discovery can help determine feasibility of drugging a target, prioritize between targets, or define optimal drug properties for a target product profile (TPP). However, applying MID3 in early discovery can be challenging due to the lack of pharmacokinetic (PK) and pharmacodynamic (PD) data at this stage. Early Feasibility Assessment (EFA) is the application of mechanistic PKPD models, built from first principles, and parameterized by data that is readily available early in drug discovery to make effective dose predictions. This manuscript demonstrates the ability of EFA to make accurate predictions of clinical effective doses for nine approved biotherapeutics and outlines the potential of extending this approach to novel therapeutics to impact early drug discovery decisions.

A systems pharmacology model for gene therapy in sickle cell disease.

We developed a mathematical model for autologous stem cell therapy to cure sickle cell disease (SCD). Experimental therapies using this approach seek to engraft stem cells containing a curative gene. These stem cells are expected to produce a lifelong supply of red blood cells (RBCs) containing an anti-sickling hemoglobin. This complex, multistep treatment is expensive, and there is limited patient data available from early clinical trials. Our objective was to quantify the impact of treatment parameters, such as initial stem cell dose, efficiency of lentiviral transduction, and degree of bone marrow preconditioning on engraftment efficiency, peripheral RBC numbers, and anti-sickling hemoglobin levels over time. We used ordinary differential equations to model RBC production from progenitor cells in the bone marrow, and hemoglobin assembly from its constituent globin monomers. The model recapitulates observed RBC and hemoglobin levels in healthy and SCD phenotypes. Treatment simulations predict dynamics of stem cell engraftment and RBC containing the therapeutic gene product. Post-treatment dynamics show an early phase of reconstitution due to short lived stem cells, followed by a sustained RBC production from stable engraftment of long-term stem cells. This biphasic behavior was previously reported in the literature. Sensitivity analysis of the model quantified relationships between treatment parameters and efficacy. The initial dose of transduced stem cells, and the intensity of myeloablative bone marrow preconditioning are predicted to most positively impact long-term outcomes. The quantitative systems pharmacology approach used here demonstrates the value of model-assisted therapeutic design for gene therapies in SCD.

Edge Charge Neutralization of Clay for Improved Oxygen Gas Barrier in Multilayer Nanobrick Wall Thin Films.

Layer-by-layer (LbL) assembled polymer-clay multilayer thin films are known to provide transparent and flexible gas barrier. In an effort to further lower the oxygen transmission rate (OTR) of these nanobrick wall thin films, sodium chloride was introduced into montmorillonite (MMT) suspension as an "indifferent electrolyte". At pH 6.5 the amphoteric edge sites of MMT have a neutral net charge, and a moderate concentration of NaCl effectively shields the charge from neighboring platelets, allowing van der Waals forces to attract the edges to one another. This edge-to-edge bonding creates a much more tortuous path for diffusing oxygen molecules. An eight-bilayer (BL) polyethylenimine (PEI)/MMT multilayer coating (∼50 nm thick), assembled with 5 mM NaCl in the aqueous clay suspension, exhibited an order of magnitude reduction in oxygen permeability (∼4 × 10-20 cm3·cm/(cm2·Pa·s)) relative to its salt-free counterpart. This result represents the best barrier among polymer-clay bilayer systems, which is also lower than SiOx or AlxOy thin films. At higher NaCl concentration, the strong charge screening causes edge-to-face bonding among MMT nanoplatelets, which leads to misalignment in assembled films and increased OTR. This "salty-clay" strategy provides an efficient way to produce better multilayer oxygen barrier thin films by altering ionic strength of the MMT suspension. This simple modification reduces the number of layers necessary for high gas barrier, potentially making these multilayer films interesting for commercial packaging applications.

Completely organic multilayer thin film with thermoelectric power factor rivaling inorganic tellurides.

Composed exclusively of organic components, polyaniline (PANi), graphene, and double-walled nanotubes (DWNTs) are alternately deposited from aqueous solutions using a layer-by-layer assembly. The 40 quadlayer thin film (470 nm thick) exhibits electrical conductivity of 1.08 × 10(5) S m(-1) and a Seebeck coefficient of 130 µV K(-1) , producing a thermoelectric power factor of 1825 µW m(-1) K(-2) .

Nanobrick wall multilayer thin films grown faster and stronger using electrophoretic deposition.

In an effort to speed up the layer-by-layer (LbL) deposition technique, electrophoretic deposition (EPD) is employed with weak polyelectrolytes and clay nanoplatelets. The introduction of an electric field results in nearly an order of magnitude increase in thickness relative to conventional LbL deposition for a given number of deposited layers. A higher clay concentration also results with the EPD-LbL process, which produces higher modulus and strength with fewer deposited layers. A 20 quadlayer (QL) assembly of linear polyethyleneimine (LPEI)/poly(acrylic acid)/LPEI/clay has an elastic modulus of 45 GPa, tensile strength of 70 MPa, and thickness of 4.4 µm. Traditional LbL requires 40 QL to achieve the same thickness, with lower modulus and strength. This study reveals how these films grow and maintain a highly ordered nanobrick wall structure that is commonly associated with LbL deposition. Fewer layers required to achieve improved properties will open up many new opportunities for this multifunctional thin film deposition technique.

Efficient Bayesian estimates for discrimination among topologically different systems biology models.

A major effort in systems biology is the development of mathematical models that describe complex biological systems at multiple scales and levels of abstraction. Determining the topology-the set of interactions-of a biological system from observations of the system's behavior is an important and difficult problem. Here we present and demonstrate new methodology for efficiently computing the probability distribution over a set of topologies based on consistency with existing measurements. Key features of the new approach include derivation in a Bayesian framework, incorporation of prior probability distributions of topologies and parameters, and use of an analytically integrable linearization based on the Fisher information matrix that is responsible for large gains in efficiency. The new method was demonstrated on a collection of four biological topologies representing a kinase and phosphatase that operate in opposition to each other with either processive or distributive kinetics, giving 8-12 parameters for each topology. The linearization produced an approximate result very rapidly (CPU minutes) that was highly accurate on its own, as compared to a Monte Carlo method guaranteed to converge to the correct answer but at greater cost (CPU weeks). The Monte Carlo method developed and applied here used the linearization method as a starting point and importance sampling to approach the Bayesian answer in acceptable time. Other inexpensive methods to estimate probabilities produced poor approximations for this system, with likelihood estimation showing its well-known bias toward topologies with more parameters and the Akaike and Schwarz Information Criteria showing a strong bias toward topologies with fewer parameters. These results suggest that this linear approximation may be an effective compromise, providing an answer whose accuracy is near the true Bayesian answer, but at a cost near the common heuristics.

Controlling effective aspect ratio and packing of clay with pH for improved gas barrier in nanobrick wall thin films.

Polymer-clay thin films constructed via layer-by-layer (LbL) assembly, with a nanobrick wall structure (i.e., clay nanoplatelets as bricks surrounded by a polyelectrolyte mortar), are known to exhibit a high oxygen barrier. Further barrier improvement can be achieved by lowering the pH of the clay suspension in the polyethylenimine (PEI) and montmorillonite (MMT) system. In this case, the charge of the deposited PEI layer is increased in the clay suspension environment, which causes more clay to be deposited. At pH 4, MMT platelets deposit with near perfect ordering, observed with transmission electron microscopy, enabling a 5× improvement in the gas barrier for a 10 PEI/MMT bilayer thin film (85 nm) relative to the same film made with pH 10 MMT. This improved gas barrier approaches that achieved with much higher aspect ratio vermiculite clay. In essence, lower pH is generating a higher effective aspect ratio for MMT due to greater induced surface charge in the PEI layers, which causes heavier clay deposition. These flexible, transparent nanocoatings have a wide range of possible applications, from food and electronics packaging to pressurized bladders.

Low-temperature thermal reduction of graphene oxide nanobrick walls: unique combination of high gas barrier and low resistivity in fully organic polyelectrolyte multilayer thin films.

Layer-by-layer assembly from aqueous solutions was used to construct multilayer thin films (<200 nm) comprising polyethylenimine and graphene oxide. Low-temperature (175 °C) thermal reduction of these films improved gas barrier properties (e.g., lower permeability than SiOx), even under high humidity conditions, and enhanced their electrical conductivity to 1750 S/m. The flexible nature of the aforementioned thin films, along with their excellent combination of transport properties, make them ideal candidates for use in a broad range of electronics and packaging applications.

Thick growing multilayer nanobrick wall thin films: super gas barrier with very few layers.

Recent work with multilayer nanocoatings composed of polyelectrolytes and clay has demonstrated the ability to prepare super gas barrier layers from water that rival inorganic CVD-based films (e.g., SiOx). In an effort to reduce the number of layers required to achieve a very low oxygen transmission rate (OTR (<0.01 cc/m(2)·day·atm)) in these nanocoatings, buffered cationic chitosan (CH) and vermiculite clay (VMT) were deposited using layer-by-layer (LbL) assembly. Buffering the chitosan solution and its rinse with 50 mM Trizma base increased the thickness of these films by an order of magnitude. The OTR of a 1.6-µm-thick, six-bilayer film was 0.009 cc/m(2)·day·atm, making this the best gas barrier reported for such a small number of layers. This simple modification to the LbL process could likely be applied more universally to produce films with the desired properties much more quickly.

Shift-Time Polyelectrolyte Multilayer Assembly: Fast Film Growth and High Gas Barrier with Fewer Layers by Adjusting Deposition Time.

In an effort to reduce deposition time and number of layers needed to achieve high gas barrier, multilayer films were deposited using 1 s exposures for the first four bilayers (BLs) and 1 min for subsequent dips. Thin-film assemblies of polyethylenimine (PEI) and poly(acrylic acid) (PAA) were deposited onto poly(ethylene terephthalate) [PET] using the layer-by-layer deposition process. Varying the exposure time of PET to polyelectrolyte solutions (i.e., dip time) significantly alters the growth rate of the multilayer thin films. The PEI/PAA system grows linearly with 1 s dip times and exponentially with longer times. Eight bilayers (650 nm) were required to achieve an undetectable oxygen transmission rate (<0.005 cm3/(m2·day)) using 1 min deposition steps, but this barrier was obtained with only 6 BLs (552 nm) using 1s deposition of the initial layers, reducing total deposition time by 73%. This "shift-time" concept makes layer-by-layer assembly much faster and more commercially feasible.

Convergence in parameters and predictions using computational experimental design.

Typically, biological models fitted to experimental data suffer from significant parameter uncertainty, which can lead to inaccurate or uncertain predictions. One school of thought holds that accurate estimation of the true parameters of a biological system is inherently problematic. Recent work, however, suggests that optimal experimental design techniques can select sets of experiments whose members probe complementary aspects of a biochemical network that together can account for its full behaviour. Here, we implemented an experimental design approach for selecting sets of experiments that constrain parameter uncertainty. We demonstrated with a model of the epidermal growth factor-nerve growth factor pathway that, after synthetically performing a handful of optimal experiments, the uncertainty in all 48 parameters converged below 10 per cent. Furthermore, the fitted parameters converged to their true values with a small error consistent with the residual uncertainty. When untested experimental conditions were simulated with the fitted models, the predicted species concentrations converged to their true values with errors that were consistent with the residual uncertainty. This paper suggests that accurate parameter estimation is achievable with complementary experiments specifically designed for the task, and that the resulting parametrized models are capable of accurate predictions.

Are residential and nursing homes adequately screening overseas healthcare workers?

BACKGROUND: There has been significant growth in the number of healthcare workers born outside the UK or recruited to the UK from countries with a high prevalence of TB, Hepatitis and other blood borne infections. Government policy recognises the need for occupational health procedures to facilitate treatment for these individuals and to reduce the risk of transmission of disease to patients.The aim of this study was to undertake a survey of nursing and residential homes in South East England, to assess whether homes had occupational health screening policies for healthcare workers who have originated from overseas, and what level of occupational health screening had been undertaken on these employees. METHODS: An anonymous survey was sent to all 500 homes in West Sussex assessing occupational health practices for "overseas health care workers", defined as health care workers who had been born outside the UK. RESULTS: Only one employer (0.8%) reported they had an occupational health screening policy specific for healthcare workers who originate from overseas. Over 80% of homes who had recruited directly had no evidence of screening results for HIV, TB, Hepatitis B and C. The commonest countries of origin for staff were the UK, Philippines, Poland, South Africa, Zimbabwe, and India. CONCLUSION: This study suggests that screening of overseas healthcare workers is not routine practice for residential or nursing care homes and requires further input from Primary Care Trust's, Health Care Commission, Commission for Social Care Inspection, and Professional bodies.

Overexpression of the cytosolic form of phosphoenolpyruvate carboxykinase (GTP) in skeletal muscle repatterns energy metabolism in the mouse.

Transgenic mice, containing a chimeric gene in which the cDNA for phosphoenolpyruvate carboxykinase (GTP) (PEPCK-C) (EC 4.1.1.32) was linked to the alpha-skeletal actin gene promoter, express PEPCK-C in skeletal muscle (1-3 units/g). Breeding two founder lines together produced mice with an activity of PEPCK-C of 9 units/g of muscle (PEPCK-C(mus) mice). These mice were seven times more active in their cages than controls. On a mouse treadmill, PEPCK-C(mus) mice ran up to 6 km at a speed of 20 m/min, whereas controls stopped at 0.2 km. PEPCK-C(mus) mice had an enhanced exercise capacity, with a VO(2max) of 156 +/- 8.0 ml/kg/min, a maximal respiratory exchange ratio of 0.91 +/- 0.03, and a blood lactate concentration of 3.7 +/- 1.0 mm after running for 32 min at a 25 degrees grade; the values for control animals were 112 +/- 21 ml/kg/min, 0.99 +/- 0.08, and 8.1 +/- 5.0 mm respectively. The PEPCK-C(mus) mice ate 60% more than controls but had half the body weight and 10% the body fat as determined by magnetic resonance imaging. In addition, the number of mitochondria and the content of triglyceride in the skeletal muscle of PEPCK-C(mus) mice were greatly increased as compared with controls. PEPCK-C(mus) mice had an extended life span relative to control animals; mice up to an age of 2.5 years ran twice as fast as 6-12-month-old control animals. We conclude that overexpression of PEPCK-C repatterns energy metabolism and leads to greater longevity.

A fluorescent high-throughput assay for double-stranded DNA: the RediPlate PicoGreen assay.

The fluorescent PicoGreen reagent for detection and quantitation of double-stranded DNA has been adapted for high-throughput screening: the RediPlate PicoGreen double-stranded DNA assay format. In the RediPlate PicoGreen assay format, the PicoGreen reagent is predistributed and co-dried into either 96- or 384-well microplates with the excipient trehalose. The user resuspends the dried reagents upon adding DNA, and measures the resulting fluorescence after a five minute incubation. Replicate fluorescence measurements on nominally identical wells have less than a 5% coefficient of variation. The assay is linear from 5 to 500 ng/ml DNA in a 200 micro l volume. The RediPlate PicoGreen assay format retains the advantages of the original PicoGreen reagent - sensitivity, speed, and specificity - but in a high-throughput format.