Quantitative comparison of the in situ microbial communities in different biomes

A system to define microbial communities in different biomes requires the application of non-traditional methodology. Classical microbiological methods have severe limitations for the analysis of environmental samples. Pure-culture isolation, biochemical testing, and/or enumeration by direct microscopic counting are not well suited for the estimation of total biomass or the assessment of community composition within environmental samples. Such methods provide little insight into the in situ phenotypic activity of the extant microbiota since these techniques are dependent on microbial growth and thus select against many environmental microorganisms which are non- culturable under a wide range of conditions. It has been repeatedly documented in the literature that viable counts or direct counts of bacteria attached to sediment grains are difficult to quantitative and may grossly underestimate the extent of the existing community. The traditional tests provide little indication of the in situ nutritional status or for evidence of toxicity within the microbial community. A more recent development (MIDI Microbial Identification System), measure free and ester-linked fatty acids from isolated microorganisms. Bacterial isolates are identified by comparing their fatty acid profiles to the MIKI database which contains over 8000 entries. The application of the MIKI system to the analysis of environmental samples however, has significant drawbacks. The MIDI system was developed to identify clinical microorganisms and requires their isolation and culture on trypticase soy agar at 27{degrees}C. Since many isolates are unable to grow at these restrictive growth conditions, the system does not lend itself to identification of some environmental organisms. A more applicable methodology for environmental microbial analysis is based on the liquid extrication and separation of microbial lipids from environmental samples, followed by quantitative analysis using gas chromatography

Single-cell bioluminescence and GFP in biofilm research

Using flow cells and a combination of microscopy techniques, we can unequivocally identify single bacterial cells that express bioluminescent and fluorescent bioreporters. We have shown that, for attached cells, bioluminescence output within a bacterial strain can vary greatly from cell to cell

The response function of a sphere in a viscoelastic two-fluid medium

In order to address basic questions of importance to microrheology, we study the dynamics of a rigid sphere embedded in a model viscoelastic medium consisting of an elastic network permeated by a viscous fluid. We calculate the complete response of a single bead in this medium to an external force and compare the result to the commonly-accepted, generalized Stokes-Einstein relation (GSER). We find that our response function is well approximated by the GSER only within a particular frequency range determined by the material parameters of both the bead and the network. We then discuss the relevance of this result to recent experiments. Finally we discuss the approximations made in our solution of the response function by comparing our results to the exact solution for the response function of a bead in a viscous (Newtonian) fluid.Comment: 12 pages, 2 figure

A longitudinal study into the new and long-term use of self-monitoring blood glucose strips in the UK

Aims To determine the impact of self-monitoring blood glucose (SMBG) strip use in patients with type 2 diabetes in the UK. Methods The study period was April 1, 2004 to July 31, 2005. Data from primary care was extracted from The Health Improvement Network database. Patients identified with diabetes and matching the inclusion criteria were defined as new users of SMBG, prevalent users, or non-users. Patients were also defined as treated with insulin, with oral agents (OA), or not pharmacologically treated. Change in glycosylated hemoglobin (HbA1c) at baseline and after 12 months was compared. Results 2559 patients met the inclusion criteria. For new users, HbA1c fell by 0.59% (P=0.399) for those treated with insulin, 1.52% (P<0.001) for those treated with OA, and 0.51% (P<0.001) for no treatment. In prevalent users, changes were 0.31% (P<0.001), 0.34% (P<0.001), and 0.09% (P=0.456), respectively. In non-users, changes were 0.28% (P=0.618), 0.42% (P<0.001), and an increase of 0.05% (P=0.043), respectively. A significant decrease in mean HbA1c was associated with increasing strip use in OA patients newly initiated on strips. Conclusion This observational study showed a significant decrease in HbA1c for new users of SMBG treated either non-pharmacologically or with OA, and for prevalent users treated with insulin or OA. Reduced HbA1c with increasing strip use was observed but was only significant for OA-treated new users. This suggests that SMBG use has a role in the treatment of non-insulin treated patients with type 2 diabetes

Simulations of cubic-tetragonal ferroelastics

We study domain patterns in cubic-tetragonal ferroelastics by solving numerically equations of motion derived from a Landau model of the phase transition, including dissipative stresses. Our system sizes, of up to 256^3 points, are large enough to reveal many structures observed experimentally. Most patterns found at late stages in the relaxation are multiply banded; all three tetragonal variants appear, but inequivalently. Two of the variants form broad primary bands; the third intrudes into the others to form narrow secondary bands with the hosts. On colliding with walls between the primary variants, the third either terminates or forms a chevron. The multipy banded patterns, with the two domain sizes, the chevrons and the terminations, are seen in the microscopy of zirconia and other cubic-tetragonal ferroelastics. We examine also transient structures obtained much earlier in the relaxation; these show the above features and others also observed in experiment.Comment: 7 pages, 6 colour figures not embedded in text. Major revisions in conten

Sodium atoms and clusters on graphite: a density functional study

Sodium atoms and clusters (N<5) on graphite (0001) are studied using density functional theory, pseudopotentials and periodic boundary conditions. A single Na atom is observed to bind at a hollow site 2.45 A above the surface with an adsorption energy of 0.51 eV. The small diffusion barrier of 0.06 eV indicates a flat potential energy surface. Increased Na coverage results in a weak adsorbate-substrate interaction, which is evident in the larger separation from the surface in the cases of Na_3, Na_4, Na_5, and the (2x2) Na overlayer. The binding is weak for Na_2, which has a full valence electron shell. The presence of substrate modifies the structures of Na_3, Na_4, and Na_5 significantly, and both Na_4 and Na_5 are distorted from planarity. The calculated formation energies suggest that clustering of atoms is energetically favorable, and that the open shell clusters (e.g. Na_3 and Na_5) can be more abundant on graphite than in the gas phase. Analysis of the lateral charge density distributions of Na and Na_3 shows a charge transfer of about 0.5 electrons in both cases.Comment: 20 pages, 6 figure

A systematic review of the quality of evidence of ablative therapy for small renal masses

Purpose: We critically assessed the methodological and reporting quality of published studies of ablative techniques for small renal masses. Materials and Methods: We performed a systematic PubMed® and EMBASE® literature search from January 1966 to March 2010 to identify all full text, original research publications on ablative therapy for renal masses. Six reviewers working independently in 3 teams performed duplicate data abstraction using Strengthening the Reporting of Observational Studies in Epidemiology criteria, which were pilot tested in a separate sample. Results: A total of 117 original research publications published in a 15-year period (1995 to 2009) met eligibility criteria. No randomized, controlled trials were identified. All studies were observational and 88.9 had 1 arm with no comparison group. Median sample size was 18 patients (IQR 5.5, 40.0) and 53.8 of studies included 20 or fewer patients. Median followup was 14.0 months (IQR 8.0, 23.8) and only 19.7 of studies had an average followup of greater than 24 months. Of the studies 20.5 mentioned the number of operators involved and only 6.0 provided information on their experience level. Of the studies 66.7 addressed the recurrence rate. Disease specific and overall survival was reported in only 15.4 and 16.2 of studies, respectively. Conclusions: The published literature on the therapeutic efficacy of ablative therapy for renal masses is largely limited to uncontrolled, 1-arm observational studies. In the absence of higher quality evidence ablative therapy outside research studies should be limited to select patients who are not candidates for surgical intervention. © 2012 American Urological Association Education and Research, Inc

STING agonist promotes CAR T cell trafficking and persistence in breast cancer

CAR T therapy targeting solid tumors is restrained by limited infiltration and persistence of those cells in the tumor microenvironment (TME). Here, we developed approaches to enhance the activity of CAR T cells using an orthotopic model of locally advanced breast cancer. CAR T cells generated from Th/Tc17 cells given with the STING agonists DMXAA or cGAMP greatly enhanced tumor control, which was associated with enhanced CAR T cell persistence in the TME. Using single-cell RNA sequencing, we demonstrate that DMXAA promoted CAR T cell trafficking and persistence, supported by the generation of a chemokine milieu that promoted CAR T cell recruitment and modulation of the immunosuppressive TME through alterations in the balance of immune-stimulatory and suppressive myeloid cells. However, sustained tumor regression was accomplished only with the addition of anti-PD-1 and anti-GR-1 mAb to Th/Tc17 CAR T cell therapy given with STING agonists. This study provides new approaches to enhance adoptive T cell therapy in solid tumors

Testing "microscopic" theories of glass-forming liquids

We assess the validity of "microscopic" approaches of glass-forming liquids based on the sole k nowledge of the static pair density correlations. To do so we apply them to a benchmark provided by two liquid models that share very similar static pair density correlation functions while disp laying distinct temperature evolutions of their relaxation times. We find that the approaches are unsuccessful in describing the difference in the dynamical behavior of the two models. Our study is not exhausti ve, and we have not tested the effect of adding corrections by including for instance three-body density correlations. Yet, our results appear strong enough to challenge the claim that the slowd own of relaxation in glass-forming liquids, for which it is well established that the changes of the static structure factor with temperature are small, can be explained by "microscopic" appr oaches only requiring the static pair density correlations as nontrivial input.Comment: 10 pages, 7 figs; Accepted to EPJE Special Issue on The Physics of Glasses. Arxiv version contains an addendum to the appendix which does not appear in published versio