model-based model-free

ColE1-like plasmid vectors are widely used for expression of recombinant genes in E. coli. For these vectors, segregation of individual plasmids into daughter cells during cell division appears to be random, making them susceptible to loss over time when no mechanisms ensuring their maintenance are present. Here we use the plasmid pGFPuv in a recA relA strain as a sensitized model to study factors affecting plasmid stability in the context of recombinant gene expression. We find that in this model, plasmid stability can be restored by two types of genetic modifications to the plasmid origin of replication (ori) sequence: point mutations and a novel 269 nt duplication at the 5' end of the plasmid ori, which we named DAS (duplicated anti-sense) ori...

Neurotoxicity testing still relies on ethically debated, expensive and time consuming in vivo experiments, which are unsuitable for high-throughput toxicity screening. There is thus a clear need for a rapid in vitro screening strategy that is preferably based on human-derived neurons to circumvent interspecies translation. Recent availability of commercially obtainable human induced pluripotent stem cell (hiPSC)-derived neurons and astrocytes holds great promise in assisting the transition from the current standard of rat primary cortical cultures to an animal-free alternative...

Potent adjuvants are highly demanded for most protein and peptides based vaccine candidates in clinical development. Recognition of viral single stranded (ss)RNA by innate toll-like receptors 7/8 in dendritic cells results in a cytokine environment supportive to the establishment of long lasting antibody responses and Th1 oriented T cell immunity. To fully exploit the immunestimulatory properties of ssRNA, it needs to be adequately formulated to ensure its optimal delivery to dendritic cells in the vaccine draining lymph nodes...

BACKGROUND: Emerging evidence indicates that individuals after an episode of acute pancreatitis (AP) are at an increased risk of developing metabolic derangements. While the link between general obesity and insulin resistance (IR) is well established, only a few studies have investigated the association between abdominal obesity and IR. The aim of this study was to investigate the associations between abdominal obesity and several indices of IR in individuals after an episode of AP. METHODS: Patients were eligible for this cross-sectional study if they were previously admitted with a primary diagnosis of AP based on the recent international guidelines...

OBJECTIVES: To evaluate emergency department use and outcomes of neuroimaging for headache in a free-standing children's hospital system. STUDY DESIGN: We prospectively enrolled children aged 6-18 years who presented to the emergency department with a chief complaint of headache from September 2015 to September 2016. Standardized data collection was performed in real time, including telephone follow-up as needed, and imaging outcome was determined through a chart review...

Viruses persist outside their hosts in a variety of forms, from naked virions to virus protected in sloughed tissues or carcasses, and for a range of times, all of which affect the likelihood and importance of transmission from the environment. This review synthesizes the literature on environmental persistence of viruses in the genus Ranavirus (family Iridoviridae), which are large double-stranded DNA viruses of ectothermic, often aquatic or semiaquatic vertebrates. Ranaviruses have been associated with mass mortality events in natural and captive settings around the world, and with population and community-wide declines in Europe...

Improvement of problematic dissolution and solubility properties of a model drug, furosemide, was investigated for poly(amidoamine) (PAMAM) dendrimer complexes of the drug. Full and half generation dendrimers with amino and ester terminals respectively, were studied. In vitro release performance of these complexes was investigated at drug loads ranging 5-60% using simulated gastric fluids. Full generation dendrimers accommodated higher drug loads, outperformed half-generation complexes, and free drug. Pharmacokinetic studies in rats indicated that the dendrimer complexes markedly improved in the bioavailability of the drug compared to the unformulated drug...

In this work, the stepwise synthesis of interpenetrating polymer network (IPN) strategy was developed in an attempt to fabricate novel hydrogels consisting of sugarcane bagasse cellulose (SBC), carboxymethylcellulose (CMC) and poly (N-isopropylacrylamide) (PNIPAm) as a dual-responsive drug carrier. The pretreated and dissolved SBC was pre-crosslinked using epichlorohydrin in the presence of CMC, followed by in-situ free-radical polymerization of NIPAm in the presence of N,N'-Methylene-bis(acrylamide) as a crosslinking agent...

The plant shoot system consists of reproductive organs such as inflorescences, buds and fruits, and the vegetative leaves and stems. In this study, the reproductive part of the Jatropha curcas shoot system, which includes the aerial shoots, shoots bearing the inflorescence and inflorescence were investigated in regard to gene-to-gene interactions underpinning yield-related biological processes. An RNA-seq based sequencing of shoot tissues performed on an Illumina HiSeq. 2500 platform generated 18 transcriptomes...

OBJECTIVE: Patients with eosinophilic granulomatosis with polyangiitis (EGPA) frequently experience relapses, which lead to cumulative organ damage. In this retrospective observational study, we aimed to reveal the risk factors for relapse in EGPA. METHODS: A total of 188 Japanese patients with EGPA diagnosed between 1996 and 2015 were identified from medical records in 10 hospitals. The diagnosis was based on the American College of Rheumatology 1990 criteria or Lanham's criteria...

In this review, we discuss the opportunity for repurposing drugs for use in l-DOPA-induced dyskinesia (LID) in Parkinson's disease. LID is a particularly suitable indication for drug repurposing given its pharmacological diversity, translatability of animal-models, availability of Phase II proof-of-concept (PoC) methodologies and the indication-specific regulatory environment. A compound fit for repurposing is defined as one with appropriate human safety-data as well as animal safety, toxicology and pharmacokinetic data as found in an Investigational New Drug (IND) package for another indication...

The absolute intrinsic hydration free energy GH+ ,wat ◦ of the proton, the surface electric potential jump χwat ◦ upon entering bulk water, and the absolute redox potential VH+ ,wat ◦ of the reference hydrogen electrode are cornerstone quantities for formulating single-ion thermodynamics on absolute scales. They can be easily calculated from each other but remain fundamentally elusive, i.e., they cannot be determined experimentally without invoking some extra-thermodynamic assumption (ETA). The Born model provides a natural framework to formulate such an assumption (Born ETA), as it automatically factors out the contribution of crossing the water surface from the hydration free energy...

The charge-dependent structure of interfacial water at the n-Ge(100)-aqueous perchlorate interface was studied by controlling the electrode potential. Specifically, a joint attenuated total reflection infrared spectroscopy and electrochemical experiment was used in 0.1M NaClO4 at pH ≈ 1-10. The germanium surface transformation to an H-terminated surface followed the thermodynamic Nernstian pH dependence and was observed throughout the entire pH range. A singular value decomposition-based spectra deconvolution technique coupled to a sigmoidal transition model for the potential dependence of the main components in the spectra shows the surface transformation to be a two-stage process...

We study the solvation free energy of two different conformations (helix and extended) of two different peptides (deca-alanine and deca-glycine) in two different solvents (water and aqueous guanidinium chloride, GdmCl). The free energies are obtained using the quasichemical organization of the potential distribution theorem, an approach that naturally provides the repulsive (solvophobic or cavity) and attractive (solvophilic) contributions to solvation. The solvophilic contribution is further parsed into a chemistry contribution arising from solute interaction with the solvent in the first solvation shell and a long-range contribution arising from non-specific interactions between the solute and the solvent beyond the first solvation shell...

The aim of the present paper is to provide a quantitative prediction of the stretch-induced crystallization in natural rubber, the exclusive reason for its history-dependent thermomechanical features. A constitutive model based on a micromechanism inspired molecular chain approach is formulated within the context of the thermodynamic framework. The molecular configuration of the partially crystallized single chain is analyzed and calculated by means of some statistical mechanical methods. The random thermal oscillation of the crystal orientation, considered as a continuous random variable, is treated by means of a representative angle...

Recently a discrete unified gas kinetic scheme (DUGKS) in a finite-volume formulation based on the Boltzmann model equation has been developed for gas flows in all flow regimes. The original DUGKS is designed for flows of single-species gases. In this work, we extend the DUGKS to flows of binary gas mixtures of Maxwell molecules based on the Andries-Aoki-Perthame kinetic model [P. Andries et al., J. Stat. Phys. 106, 993 (2002)JSTPBS0022-471510.1023/A:1014033703134. A particular feature of the method is that the flux at each cell interface is evaluated based on the characteristic solution of the kinetic equation itself; thus the numerical dissipation is low in comparison with that using direct reconstruction...

There is increasing evidence that dense networks occur in on-line social networks, recommendation networks and in the brain. In addition to being dense, these networks are often also scale-free, i.e., their degree distributions follow P(k)∝k^{-γ} with γ∈(1,2]. Models of growing networks have been successfully employed to produce scale-free networks using preferential attachment, however these models can only produce sparse networks as the numbers of links and nodes being added at each time step is constant...

When a spatially uniform system that displays a liquid-crystal ordering on a two-dimensional surface is confined inside a rectangular box, the liquid crystal direction field develops inhomogeneous textures accompanied by topological defects because of the geometric frustrations. We show that the rich variety of nematic textures and defect patterns found in recent experimental and theoretical studies can be classified by the solutions of the rather fundamental, extended Onsager model. This is critically examined based on the determined free energies of different defect states, as functions of a few relevant, dimensionless geometric parameters...

Lattice Boltzmann (LB) models used for the computation of fluid flows represented by the Navier-Stokes (NS) equations on standard lattices can lead to non-Galilean-invariant (GI) viscous stress involving cubic velocity errors. This arises from the dependence of their third-order diagonal moments on the first-order moments for standard lattices, and strategies have recently been introduced to restore Galilean invariance without such errors using a modified collision operator involving corrections to either the relaxation times or the moment equilibria...

BACKGROUND: Dose reduction in obese cancer patients has been replaced by fully weight-based dosing recommendations. No data, however, are available on the effects of dose reduction in obese stage III colon cancer patients undergoing adjuvant chemotherapy. METHODS: Survival outcomes and toxicity data of obese (body mass index [BMI] ≥30 kg/m2 ), stage III colon cancer patients treated within the phase III PETACC 3 trial comparing leucovorin, 5-FU (LV5FU2) with LV5FU2 plus irinotecan were analysed retrospectively according to chemotherapy dosing at first infusion (i...