Using functional annotations to study pairwise interactions in urinary tract infection communities

The behaviour of microbial communities depends on environmental factors and on the interactions of the community members. This is also the case for urinary tract infection (UTI) microbial communities. Here, we devise a computational approach that uses indices of complementarity and competition based on metabolic gene annotation to rapidly predict putative interactions between pair of organisms with the aim to explain pairwise growth effects. We apply our method to 66 genomes selected from online databases, which belong to 6 genera representing members of UTI communities. This resulted in a selection of metabolic pathways with high correlation for each pairwise combination between a complementarity index and the experimentally derived growth data. Our results indicated that Enteroccus spp. were most complemented in its metabolism by the other members of the UTI community. This suggests that the growth of Enteroccus spp. can potentially be enhanced by complementary metabolites produced by other community members. We tested a few putative predicted interactions by experimental supplementation of the relevant predicted metabolites. As predicted by our method, folic acid supplementation led to the increase in the population density of UTI Enterococcus isolates. Overall, we believe our method is a rapid initial in silico screening for the prediction of metabolic interactions in microbial communities

Thermal injury healing in the context of neocollagenogenesis induction: preclinical randomized experimental study

Background. The healing of skin wounds having various etiologies is known to involve a multistep process characterized by certain intercellular interactions affecting dermal cells, their attachment, migration, and differentiation. Here, recovery is interpreted as the return of dermis to its original state. The fact is, however, that the dermal extracellular matrix (ECM) is structurally impaired, which suppresses the regulatory and repository functions of the dermis, leading to the formation of a scar that inhibits several biological functions in the affected area and causes aesthetic problems associated with mobility.Objectives. To evaluate the structural features of dermis during wound healing using a calcium-containing biodegradable implant.Methods. The study used 60 rats that were inflicted with a third-degree burn injury (partially damaged dermis). The selected animals were divided into two groups: experimental and control. On post-burn day 14, a calcium-containing biodegradable implant was administered to rats from the experimental group, while a sterile saline solution was used in the control group. Material was sampled at two months (74 days) and four months (134 days). In order to assess the morphological state of the burn area, its sections were stained with hematoxylin and eosin, according to Mallory and Van-Gieson. For the selective detection of collagens, immunohistochemical tests using antibodies to collagen types I and III (Abcam, England) were employed. To characterize dermal cells, the authors used antibodies to vimentin (LabVision, USA), as well as to СD-68 (cluster of differentiation 68), α-SMA (alpha-smooth muscle actin), CD-105 (cluster of differentiation 105), and VEGF (vascular endothelial growth factor) receptors (Abcam, England). The obtained results were processed using the Statistica 6 software (StatSoft, USA).Results. The administration of a calcium-containing biodegradable filler during the burn healing process was found to ensure local fibroblast activation with the formation of collagen types I and III. When the implant residence time was prolonged up to four months, an increase in the number of macrophages expressing CD-68 receptors was observed. Of note is that these cells retained their localization, while α-SMA-expressing cells were localized in both the superficial and deep dermal compartments. The number of cells expressing CD-105 and VEGF rose as well.Conclusion. The use of the biodegradable filler is found to be promising in terms of post-burn dermal regeneration, as well as providing a dermal ECM, whose collagen network composition and assembly are similar to the original. Here, macrophages act as the primary synthesis regulators of the dermal ECM and stimulate fibroblasts, which ensures re-epithelialization and angiogenesis of the inflicted area

Stable two-dimensional solitary pulses in linearly coupled dissipative Kadomtsev-Petviashvili equations

A two-dimensional (2D) generalization of the stabilized Kuramoto - Sivashinsky (KS) system is presented. It is based on the Kadomtsev-Petviashvili (KP) equation including dissipation of the generic (Newell -- Whitehead -- Segel, NWS) type and gain. The system directly applies to the description of gravity-capillary waves on the surface of a liquid layer flowing down an inclined plane, with a surfactant diffusing along the layer's surface. Actually, the model is quite general, offering a simple way to stabilize nonlinear waves in media combining the weakly-2D dispersion of the KP type with gain and NWS dissipation. Parallel to this, another model is introduced, whose dissipative terms are isotropic, rather than of the NWS type. Both models include an additional linear equation of the advection-diffusion type, linearly coupled to the main KP-NWS equation. The extra equation provides for stability of the zero background in the system, opening a way to the existence of stable localized pulses. The consideration is focused on the case when the dispersive part of the system of the KP-I type, admitting the existence of 2D localized pulses. Treating the dissipation and gain as small perturbations and making use of the balance equation for the field momentum, we find that the equilibrium between the gain and losses may select two 2D solitons, from their continuous family existing in the conservative counterpart of the model (the latter family is found in an exact analytical form). The selected soliton with the larger amplitude is expected to be stable. Direct simulations completely corroborate the analytical predictions.Comment: a latex text file and 16 eps files with figures; Physical Review E, in pres

Construction of Special Solutions for Nonintegrable Systems

The Painleve test is very useful to construct not only the Laurent series solutions of systems of nonlinear ordinary differential equations but also the elliptic and trigonometric ones. The standard methods for constructing the elliptic solutions consist of two independent steps: transformation of a nonlinear polynomial differential equation into a nonlinear algebraic system and a search for solutions of the obtained system. It has been demonstrated by the example of the generalized Henon-Heiles system that the use of the Laurent series solutions of the initial differential equation assists to solve the obtained algebraic system. This procedure has been automatized and generalized on some type of multivalued solutions. To find solutions of the initial differential equation in the form of the Laurent or Puiseux series we use the Painleve test. This test can also assist to solve the inverse problem: to find the form of a polynomial potential, which corresponds to the required type of solutions. We consider the five-dimensional gravitational model with a scalar field to demonstrate this.Comment: LaTeX, 14 pages, the paper has been published in the Journal of Nonlinear Mathematical Physics (http://www.sm.luth.se/math/JNMP/

Constraints on new interactions from neutron scattering experiments

Constraints for the constants of hypothetical Yukawa-type corrections to the Newtonian gravitational potential are obtained from analysis of neutron scattering experiments. Restrictions are obtained for the interaction range between 10^{-12} and 10^{-7} cm, where Casimir force experiments and atomic force microscopy are not sensitive. Experimental limits are obtained also for non-electromagnetic inverse power law neutron-nucleus potential. Some possibilities are discussed to strengthen these constraints.Comment: 18 pages, 3 figure

Development of the Acellular Dermal Matrix and Experimental Substantiation of Its Use in the Anterior Abdominal Wall hernia Repair

Objective: To develop a biological implant that is an acellular dermal matrix (ADM), evaluate its use as a support material in tensionfree hernioplasty for ventral hernia, and compare it to that of the commercially available implant PermacolTM.   Materials and methods: ADM was derived from the porcine dermis (Landrace breed) decellularized using detergents and enzymes. The quality of devitalization was assessed in vitro. We performed sublay hernioplasty in 4-month-old Landrace pigs using ADM (experimental group) and PermacolTM (control group). The specimens were explanted on day 120 of the experiment for histological and immunohistochemical examination.   Results: All cellular elements were removed by the detergent-enzymatic treatment of the dermis; the native architecture of the dermis was slightly disrupted. The specimens of the commercially available chemically cross-linked biomaterial PermacolTM had better mechanical properties than ADM specimens; however, there were no significant differences in terms of cytotoxicity. The state of the tissues after the explantation (number of fibroblasts and endothelial cells) showed no differences in the result of using ADM and PermacolTM. In 120 days, the materials integrated into the tissues without the formation of adhesions or inflammation.   Conclusions: Our findings show that ADM does not have cytotoxic properties, has adequate biomechanical parameters to effectively reinforce supporting soft tissues, does not cause an inflammatory response during implantation, and integrates fully into tissues. Our study demonstrates the effectiveness and utility of the developed ADM in surgical treatment of anterior abdominal wall defects

Geography of non-melanoma skin cancer and ecological associations with environmental risk factors in England.

This is the author's peer reviewed version of the article. Please cite the published, final version which is available via the DOI link in this record.This study investigates the geography of non-melanoma skin cancer (NMSC) in England, and ecological associations with three widespread environmental hazards: radon, arsenic and ultraviolet radiation from the sun.European Regional Development FundEuropean Social Fund Convergence Programme for Cornwall and the Isles of Scill