Single molecule experiments were performed on DNA, a model polymer, and entangled DNA networks to explore diffusion within complex polymeric fluids and their linear and non- linear viscoelasticity. DNA molecules of varying length and topology were prepared using biological methods. An ensemble of individual molecules were then fluorescently labeled and tracked in blends of entangled linear and circular DNA to examine the dependence of diffusion on polymer length, topology, and blend ratio. Diffusion was revealed to possess a non-monotonic dependence on the blend ratio, which we believe to be due to a second-order effect where the threading of circular polymers by their linear counterparts greatly slows the mobility of the system. Similar methods were used to examine the diffusive and conformational behavior of DNA within highly crowded environments, comparable to that experienced within the cell. A previously unseen gamma distributed elongation of the DNA in the presence of crowders, proposed to be due to entropic effects and crowder mobility, was observed. Additionally, linear viscoelastic properties of entangled DNA networks were explored using active microrheology. Plateau moduli values verified for the first time the predicted independence from polymer length. However, a clear bead-size dependence was observed for bead radii less than ̃3x the tube radius, a newly discovered limit, above which microrheology results are within the continuum limit and may access the bulk properties of the fluid. Furthermore, the viscoelastic properties of entangled DNA in the non-linear regime, where the driven beads actively deform the network, were also examined. By rapidly driving a bead through the network utilizing optical tweezers, then removing the trap and tracking the bead's subsequent motion we are able to model the system as an over-damped harmonic oscillator and find the elasticity to be dominated by stress-dependent entanglements

Many challenges related to carbon-dioxide ([Formula: see text]) sequestration in subsurface rock are linked to the injection of fluids through induced or existing fracture networks and how these fluids are altered through geochemical interactions. Here, we demonstrate that fluid mixing and carbonate mineral distributions in fractures are controlled by gravity-driven chemical dynamics. Using optical imaging and numerical simulations, we show that a density contrast between two miscible fluids causes the formation of a low-density fluid runlet that increases in areal extent as the fracture inclination decreases from 90[Formula: see text] (vertical fracture plane) to 30[Formula: see text]. The runlet is sustained over time and the stability of the runlet is controlled by the gravity-driven formation of 3D vortices that arise in a laminar flow regime. When homogeneous precipitation was induced, calcium carbonate covered the entire surface for horizontal fractures (0[Formula: see text]). However, for fracture inclinations greater than 10[Formula: see text], the runlet formation limited the areal extent of the precipitation to less than 15% of the fracture surface. These insights suggest that the ability to sequester [Formula: see text] through mineralization along fractures will depend on the fracture orientation relative to gravity, with horizontal fractures more likely to seal uniformly.

Abstract Background Administration of recombinant G-CSF following cytoreductive therapy enhances the recovery of myeloid cells, minimizing the risk of opportunistic infection. Free G-CSF, however, is expensive, exhibits a short half-life, and has poor biological activity in vivo. Methods We evaluated whether the biological activity of G-CSF could be improved by pre-association with anti-G-CSF mAb prior to injection into mice. Results We find that the efficacy of G-CSF therapy can be enhanced more than 100-fold by pre-association of G-CSF with an anti-G-CSF monoclonal antibody (mAb). Compared with G-CSF alone, administration of G-CSF/anti-G-CSF mAb complexes induced the potent expansion of CD11b+Gr-1+ myeloid cells in mice with or without concomitant cytoreductive treatment including radiation or chemotherapy. Despite driving the dramatic expansion of myeloid cells, in vivo antigen-specific CD8+ T cell immune responses were not compromised. Furthermore, injection of G-CSF/anti-G-CSF mAb complexes heightened protective immunity to bacterial infection. As a measure of clinical value, we also found that antibody complexes improved G-CSF biological activity much more significantly than pegylation. Conclusions Our findings provide the first evidence that antibody cytokine complexes can effectively expand myeloid cells, and furthermore, that G-CSF/anti-G-CSF mAb complexes may provide an improved method for the administration of recombinant G-CSF.

Despite clinical potential and recent advances, durable immunotherapeutic ablation of solid tumors is not routinely achieved. IL15 expands natural killer cell (NK), natural killer T cell (NKT) and CD8(+) T-cell numbers and engages the cytotoxic program, and thus is under evaluation for potentiation of cancer immunotherapy. We found that short-term therapy with IL15 bound to soluble IL15 receptor α-Fc (IL15cx; a form of IL15 with increased half-life and activity) was ineffective in the treatment of autochthonous PyMT murine mammary tumors, despite abundant CD8(+) T-cell infiltration. Probing of this poor responsiveness revealed that IL15cx only weakly activated intratumoral CD8(+) T cells, even though cells in the lung and spleen were activated and dramatically expanded. Tumor-infiltrating CD8(+) T cells exhibited cell-extrinsic and cell-intrinsic resistance to IL15. Our data showed that in the case of persistent viral or tumor antigen, single-agent systemic IL15cx treatment primarily expanded antigen-irrelevant or extratumoral CD8(+) T cells. We identified exhaustion, tissue-resident memory, and tumor-specific molecules expressed in tumor-infiltrating CD8(+) T cells, which may allow therapeutic targeting or programming of specific subsets to evade loss of function and cytokine resistance, and, in turn, increase the efficacy of IL2/15 adjuvant cytokine therapy. Cancer Immunol Res; 4(9); 799-811. ©2016 AACR.

Fine-grained sedimentary rocks – namely mudrocks, including their laminated fissile variety — shales – make up about two thirds of all sedimentary rocks in the Earth's crust and a quarter of the continental land mass. Organic-rich shales and mudstones are the source rocks and reservoirs for conventional and unconventional hydrocarbon resources. Mudrocks are relied upon as natural barriers for geological carbon storage and nuclear waste disposal. Consideration of mudrock multi-scale physics and multi-scale spatial and temporal behavior is vital to address emergent phenomena in shale formations perturbed by engineering activities. Unique physical characteristics of shales arise as a result of their layered and highly heterogeneous and anisotropic nature, low permeability fabric, compositional complexity, and nano-scale confined chemical environments. Barriers of lexicon among geoscientists and engineers impede the development and use of conceptual models for the coupled thermal-hydraulic-mechanical-chemical-biological (THMCB) processes in mudrock formations. This manuscript reviews the THMCB process couplings, resulting emergent behavior, and key modeling approaches. We identify future research priorities, in particular fundamental knowledge gaps in understanding the phase behavior under nano-scale confinement, coupled chemo-mechanical effects on fractures, the interplay between physical and chemical processes and their rates, and issues of non-linearity and heterogeneity. We develop recommendations for future research and integrating multi-disciplinary conceptual models for the coupled multi-scale multi-physics behavior of mudrocks. Consistent conceptual models across disciplines are essential for predicting emergent processes in the subsurface, such as self-focusing of flow, time-dependent deformation (creep), fracture network development, and wellbore stability.

Our limited understanding of mineral reactive surface area contributes to significant uncertainties in quantitative simulations of reactive chemical transport in subsurface processes. Continuum formulations for reactive transport typically use a number of different approximations for reactive surface area, including geometric, specific, and effective surface area. In this study, reactive surface area estimates are developed and evaluated for their ability to predict dissolution rates in a well-stirred flow-through reactor experiment using disaggregated samples from the Nagaoka pilot CO2 injection site (Japan). The disaggregated samples are reacted with CO2 acidified synthetic brine under conditions approximating the field conditions and the evolution of solute concentrations in the reactor effluent is tracked over time. The experiments, carried out in fluid-dominated conditions at a pH of 3.2 for 650 h, resulted in substantial dissolution of the sample and release of a disproportionately large fraction of the divalent cations. Traditional reactive surface area estimation methods, including an adjusted geometric surface area and a BET-based surface area, are compared to a newly developed image-based method. Continuum reactive transport modeling is used to determine which of the reactive surface area models provides the best match with the effluent chemistry from the well-stirred reactor. The modeling incorporates laboratory derived mineral dissolution rates reported in the literature and the initial modal mineralogy of the Nagaoka sediment was determined from scanning electron microscopy (SEM) characterization. The closest match with the observed steady-state effluent concentrations was obtained using specific surface area estimates from the image-based approach supplemented by literature-derived BET measurements. To capture the evolving effluent chemistry, particularly over the first 300 h of the experiment, it was also necessary to account for the grain size distribution in the sediment and the presence of a highly reactive volcanic glass phase that shows preferential cation leaching.

Purpose

To evaluate, in a phase 2 study, the safety and efficacy of induction gemcitabine, oxaliplatin, and cetuximab followed by selective capecitabine-based chemoradiation in patients with borderline resectable or unresectable locally advanced pancreatic cancer (BRPC or LAPC, respectively).

Methods and materials

Patients received gemcitabine and oxaliplatin chemotherapy repeated every 14 days for 6 cycles, combined with weekly cetuximab. Patients were then restaged; "downstaged" patients with resectable disease underwent attempted resection. Remaining patients were treated with chemoradiation consisting of intensity modulated radiation therapy (54 Gy) and concurrent capecitabine; patients with borderline resectable disease or better at restaging underwent attempted resection.

Results

A total of 39 patients were enrolled, of whom 37 were evaluable. Protocol treatment was generally well tolerated. Median follow-up for all patients was 11.9 months. Overall, 29.7% of patients underwent R0 surgical resection (69.2% of patients with BRPC; 8.3% of patients with LAPC). Overall 6-month progression-free survival (PFS) was 62%, and median PFS was 10.4 months. Median overall survival (OS) was 11.8 months. In patients with LAPC, median OS was 9.3 months; in patients with BRPC, median OS was 24.1 months. In the group of patients who underwent R0 resection (all of which were R0 resections), median survival had not yet been reached at the time of analysis.

Conclusions

This regimen was well tolerated in patients with BRPC or LAPC, and almost one-third of patients underwent R0 resection. Although OS for the entire cohort was comparable to that in historical controls, PFS and OS in patients with BRPC and/or who underwent R0 resection was markedly improved.