3D protein structure matching by patch signatures

For determining functionality dependencies between two proteins, both represented as 3D structures, it is an essential condition that they have one or more matching structural regions called patches. As 3D structures for proteins are large, complex and constantly evolving, it is computationally expensive and very time-consuming to identify possible locations and sizes of patches for a given protein against a large protein database. In this paper, we address a vector space based representation for protein structures, where a patch is formed by the vectors within the region. Based on our previews work, a compact representation of the patch named patch signature is applied here. A similarity measure of two patches is then derived based on their signatures. To achieve fast patch matching in large protein databases, a match-and-expand strategy is proposed. Given a query patch, a set of small k-sized matching patches, called candidate patches, is generated in match stage. The candidate patches are further filtered by enlarging k in expand stage. Our extensive experimental results demonstrate encouraging performances with respect to this biologically critical but previously computationally prohibitive problem.

Diel Patterns of Patch Reef Community Dynamics in a Caribbean Back-Reef System

Back-reef seascapes represent critical habitat for juvenile and adult fishes. Patch reef, seagrass, and mangrove habitats form a heterogeneous mosaic, often linked by species that use reefs as structure during the day and make foraging migrations into soft-bottom habitat at night. Artificial reefs are used to model natural patch reefs, however may not function equivalently as fish habitat. To study the relative value of natural and artificial patch reefs as fish habitat, these communities in the Sea of Abaco, Bahamas were compared using roving diver surveys and time-lapse photography. Diel turnover in fish abundance, recorded with time-lapse photography and illuminated by infrared light, was quantified across midday, dusk, and night periods to explore possible effects of reef type (artificial vs. natural) on these patterns. Diurnal communities on natural reefs exhibited greater fish abundance, species richness, and functional diversity compared to artificial reefs. Furthermore, both types of reef communities exhibited a significant shift across the diel period, characterized by a decline in total fish density at night, especially for grunts (Haemulidae). Cross-habitat foraging migrations by diurnal or nocturnal species, such as haemulids, are likely central drivers of this twilight turnover and can represent important energy and nutrient subsidies. Time-lapse surveys provided more consistent measures of reef fish assemblages for the smaller artificial reef habitats, yet underestimated abundance of certain taxa and species richness on larger patch habitats when compared to the roving diver surveys. Time-lapse photography complemented with infrared light represent a valuable non-invasive approach to studying behavior of focal species and their fine-scale temporal dynamics in shallow-reef communities.

Estudo de arranjos de antenas de microfita com Patch quase-fractal para comunicações sem fio

In this dissertation, are presented two microstrip antennas and two arrays for applications in wireless communication systems multiband. Initially, we studied an antenna and a linear array consisting of two elements identical to the patch antenna isolated. The shape of the patch used in both structures is based on fractal geometry and has multiband behavior. Next a new antenna is analyzed and a new array such as initial structure, but with the truncated ground plane, in order to obtain better bandwidths and return loss. For feeding the structures, we used microstrip transmission line. In the design of planar structures, was used HFSS software for the simulation. Next were built and measures electromagnetic parameters such as input impedance and return loss, using vector network analyzer in the telecommunications laboratory of Federal University of Rio Grande do Norte. The experimental results were compared with the simulated and showed improved return loss for the first array and also appeared a fourth band and increased directivity compared with the isolated antenna. The first two benefits are not commonly found in the literature. For structures with a truncated ground planes, the technique improved impedance matching, bandwidth and return loss when compared to the initial structure with filled ground planes. Moreover, these structures exhibited a better distribution of frequency, facilitating the adjustment of frequencies. Thus, it is expected that the planar structures presented in this study, particularly arrays may be suitable for specific applications in wireless communication systems when frequency multiband and wideband transmission signals are required.

Patch selection behaviour in the presence of environmental constraints

Habitat selection behaviour is the primary way in which organisms are able to regulate encounters with their biotic and abiotic environment. An individual chooses an area that best meets their current needs, particularly regarding safety and the presence of high-quality food. Several physical aspects of the environment can make it difficult for individuals to assess the relative habitat quality of the areas available, thus leading to suboptimal habitat selection. In this thesis, I investigated the way in which two aquatic habitat constraints - obstacles to movement between patches and turbidity - affected the ability of fish to make optimal patch choices, using threespine stickleback Gasterosteus aculeatus as a model species. Laboratory experiments showed that when movement between patches was hindered by increasingly challenging obstacles, groups of stickleback did not move as freely between the patches, and thus had greater deviations from the predictions of the Ideal Free Distribution (IFD). I also demonstrated that, unlike other species, stickleback do not use turbid environments to avoid predator detection. A trend was seen towards avoidance of a turbid food patch regardless of risk level, although this was not statistically significant. As expected, the stickleback avoided feeding in the presence of a predator regardless of water clarity. Overall, I found that both turbidity and movement constraints can have significant impacts on patch use and distribution in the threespine stickleback. Both turbidity and ease of transit will impact the distribution of ecologically important species like the threespine stickleback, and therefore should be taken into account when studying habitat selection in the wild.

Hierarchical spatial segregation of two Mediterranean vole species : the role of patch-network structure and matrix composition

Acknowledgments This study was financed by FEDER funds through the Programa Operacional Factores de Competitividade— COMPETE, and National funds through the Portuguese Foundation for Science and Technology—FCT, within the scope of the projects PERSIST (PTDC/BIA-BEC/105110/2008), NETPERSIST (PTDC/ AAG-MAA/3227/2012), and MateFrag (PTDC/BIA-BIC/6582/2014). RP was supported by the FCT grant SFRH/BPD/73478/2010 and SFRH/BPD/109235/2015. PB was supported by EDP Biodiversity Chair. We thank Rita Brito and Marta Duarte for help during field work. We thank Chris Sutherland, Douglas Morris, William Morgan, and Richard Hassall for critical reviews of early versions of the paper. We also thank two anonymous reviewers for helpful comments to improve the paper.

Development of a dissolvable microneedle influenza vaccine patch

Delivery of large molecular weight biological molecules to the epidermis and dermis is constrained by the tough outer layer of the epidermis, the stratum corneum (sc). Microneedle technologies attempt to overcome this physical barrier using sharp micron-size projections to penetrate the sc. Dissolvable microneedles (DMN), are a particular microneedle design whereby the needle structure is composed of a soluble matrix that upon application to the skin, dissolves releasing the vaccine load into skin. This thesis examines (1) the formulation and processing considerations around DMN fabrication, (2) the immunogenicity of DMN containing trivalent influenza vaccine (TIV) in pre-clinical mouse and pig models and (3) the thermostability of these DMN formulations during storage. The results demonstrate the importance of formulation for microneedle formation and mechanical strength. Trehalose and polyvinylalcohol based formulations produced optimal microneedle structures and were amenable to piezoelectric dispensing; allowing for precise multi-layered DMN to be fabricated. The effect of drying conditions was assessed and found to be critical for DMN mechanical strength and skin penetration. The antibody responses to TIV generated by DMN-mediated vaccination were comparable or greater to those induced by immunization with a commercial TIV via the IM route in mice. DMN mediated immunisation resulted in a significantly broader humoral response to heterotypic influenza viruses compared to IM delivery. Stored at 40°C, a licensed seasonal influenza vaccine incorporated into DMN array was thermostable for at least 6 month as determined by Single Radial Immunodiffusion and immunogenicity in mice. The thesis advances the field of DMN influenza vaccination by elucidating important processing and formulation considerations in the fabrication of highly reproducible DMN. It also demonstrated that DMN can induce broader, larger humoral responses than conventional IM administration while demonstrating enhanced accelerated stability. Crucially, this works advances an automated fabrication system that will allow for clinical translation of DMN.

Modified patch repair of femoral hernia after inguinal herniorrhaphy

Background and aim. It has been reported that femoral hernias are rather common after a previous repair of inguinal hernia. We herein present a modified patch repair technique for large femoral hernias that develop after a Lichtenstein operation for ipsilateral inguinal hernia. Patients and methods. The modified technique for femoral hernia was applied to three patients who had a Lichtenstein repair for inguinal hernia. All patients were male. Hernia sac is dissected completely and sent back into to the preperitoneal space. Special attention should be given to the prevascular component of the sac. It is dissected as deep as possible into the preperitoneal space over the femoral vein. The defect is quite wide in this particular type of femoral hernia following Lichtenstein repair. A prosthetic patch that matches the defect is prepared. The medial edge of the mesh is configured to correspond to the pubic corner and lacunar ligament. The lateral margin of the patch is cut to create several petals for inverting the mesh above and medial to the femoral vein to prevent prevascular herniation. The mesh is secured to inguinal ligament, ilioinguinal tract, lacunar ligament, and Cooper ligament. Few sutures are put on the pubic corner and lacunar ligament. Results. One patient was discharged after two hours, other two stayed overnight. Readmission because of seroma development was recorded in two cases where standard polypropylene meshes were used. No complication was observed in the other patient who received lightweight meshes. No early recurrences were recorded after 4, 9, and 30 months. Conclusion. Femoral recurrence after previous inguinal hernia repair seems to be a specific entity. It has a prevascular component and the hernia defect can be much larger than that of a primary femoral hernia. A patch repair with infra-inguinal approach can be a valuable alternative with low complication rate.