ESPINA: a tool for the automated segmentation and counting of synapses in large stacks of electron microscopy images

The synapses in the cerebral cortex can be classified into two main types, Gray’s type I and type II, which correspond to asymmetric (mostly glutamatergic excitatory) and symmetric (inhibitory GABAergic) synapses, respectively. Hence, the quantification and identification of their different types and the proportions in which they are found, is extraordinarily important in terms of brain function. The ideal approach to calculate the number of synapses per unit volume is to analyze 3D samples reconstructed from serial sections. However, obtaining serial sections by transmission electron microscopy is an extremely time consuming and technically demanding task. Using focused ion beam/scanning electron microscope microscopy, we recently showed that virtually all synapses can be accurately identified as asymmetric or symmetric synapses when they are visualized, reconstructed, and quantified from large 3D tissue samples obtained in an automated manner. Nevertheless, the analysis, segmentation, and quantification of synapses is still a labor intensive procedure. Thus, novel solutions are currently necessary to deal with the large volume of data that is being generated by automated 3D electron microscopy. Accordingly, we have developed ESPINA, a software tool that performs the automated segmentation and counting of synapses in a reconstructed 3D volume of the cerebral cortex, and that greatly facilitates and accelerates these processes.

Modelling the spatio-temporal pattern of primary dispersal in stone pine (Pinus pinea L.) stands in the Northern Plateau (Spain)

Natural regeneration in stone pine (Pinus pinea L.) managed forests in the Spanish Northern Plateau is not achieved successfully under current silviculture practices, constituting a main concern for forest managers. We modelled spatio-temporal features of primary dispersal to test whether (a) present low stand densities constrain natural regeneration success and (b) seed release is a climate-controlled process. The present study is based on data collected from a 6 years seed trap experiment considering different regeneration felling intensities. From a spatial perspective, we attempted alternate established kernels under different data distribution assumptions to fit a spatial model able to predict P. pinea seed rain. Due to P. pinea umbrella-like crown, models were adapted to account for crown effect through correction of distances between potential seed arrival locations and seed sources. In addition, individual tree fecundity was assessed independently from existing models, improving parameter estimation stability. Seed rain simulation enabled to calculate seed dispersal indexes for diverse silvicultural regeneration treatments. The selected spatial model of best fit (Weibull, Poisson assumption) predicted a highly clumped dispersal pattern that resulted in a proportion of gaps where no seed arrival is expected (dispersal limitation) between 0.25 and 0.30 for intermediate intensity regeneration fellings and over 0.50 for intense fellings. To describe the temporal pattern, the proportion of seeds released during monthly intervals was modelled as a function of climate variables – rainfall events – through a linear model that considered temporal autocorrelation, whereas cone opening took place over a temperature threshold. Our findings suggest the application of less intensive regeneration fellings, to be carried out after years of successful seedling establishment and, seasonally, subsequent to the main rainfall period (late fall). This schedule would avoid dispersal limitation and would allow for a complete seed release. These modifications in present silviculture practices would produce a more efficient seed shadow in managed stands.

Bruise Simulation in Peach Grading Lines as a tool for designing Improvement Strategies.

The Physical Properties Laboratory (LPF) has been working on the improvement of fruit and vegetable grading lines since 1992'. The experience shows that the improvement of grading lines for decreasing mechanical damages has to be approached from two viewpoints: 1) machinery aggressiveness, and 2) fruit susceptibility. Machinery aggressiveness can be characterized as impact probability for different impact intensities assessed by means of electronic fruits (IS-100) 2,5 . On the other hand, bruise susceptibility can be determined using different laboratory tests. A recent study from LPF4 shows that damage may arise differently in pome and in stone fruits, since: a) pome fruits are mainly stress-susceptible, while stone fruits appear to be more deformation-susceptible, and b) bruise size may be a good predictor for bruise susceptibility in pome fruits while for stone fruits bruise probability is the most relevant characteristic of bruise susceptibility. Also, this study indicates the feasibility of predicting bruise probability using several mechanical and load characterization parameters. Despite the efforts to establish damage thresholds in peachess, no simulation models are currently available for predicting bruise occurrence in grading lines.

Knowledge representation tool for cognitiveprocesses modeling

In the last decades, neuropsychological theories tend to consider cognitive functions as a result of the whole brainwork and not as individual local areas of its cortex. Studies based on neuroimaging techniques have increased in the last years, promoting an exponential growth of the body of knowledge about relations between cognitive functions and brain structures [1]. However, so fast evolution make complicated to integrate them in verifiable theories and, even more, translated in to cognitive rehabilitation. The aim of this research work is to develop a cognitive process-modeling tool. The purpose of this system is, in the first term, to represent multidimensional data, from structural and functional connectivity, neuroimaging, data from lesion studies and derived data from clinical intervention [2][3]. This will allow to identify consolidated knowledge, hypothesis, experimental designs, new data from ongoing studies and emerging results from clinical interventions. In the second term, we pursuit to use Artificial Intelligence to assist in decision making allowing to advance towards evidence based and personalized treatments in cognitive rehabilitation. This work presents the knowledge base design of the knowledge representation tool. It is compound of two different taxonomies (structure and function) and a set of tags linking both taxonomies at different levels of structural and functional organization. The remainder of the abstract is organized as follows: Section 2 presents the web application used for gathering necessary information for generating the knowledge base, Section 3 describes knowledge base structure and finally Section 4 expounds reached conclusions.

Rapid restoration of visual pigment and function with oral retinoid in a mouse model of childhood blindness

Mutations in the retinal pigment epithelium gene encoding RPE65 are a cause of the incurable early-onset recessive human retinal degenerations known as Leber congenital amaurosis. Rpe65-deficient mice, a model of Leber congenital amaurosis, have no rod photopigment and severely impaired rod physiology. We analyzed retinoid flow in this model and then intervened by using oral 9-cis-retinal, attempting to bypass the biochemical block caused by the genetic abnormality. Within 48 h, there was formation of rod photopigment and dramatic improvement in rod physiology, thus demonstrating that mechanism-based pharmacological intervention has the potential to restore vision in otherwise incurable genetic retinal degenerations.

Piperonylic Acid, a Selective, Mechanism-Based Inactivator of the trans-Cinnamate 4-Hydroxylase: A New Tool to Control the Flux of Metabolites in the Phenylpropanoid Pathway1

Piperonylic acid (PA) is a natural molecule bearing a methylenedioxy function that closely mimics the structure of trans-cinnamic acid. The CYP73A subfamily of plant P450s catalyzes trans-cinnamic acid 4-hydroxylation, the second step of the general phenylpropanoid pathway. We show that when incubated in vitro with yeast-expressed CYP73A1, PA behaves as a potent mechanism-based and quasi-irreversible inactivator of trans-cinnamate 4-hydroxylase. Inactivation requires NADPH, is time dependent and saturable (KI = 17 μm, kinact = 0.064 min−1), and results from the formation of a stable metabolite-P450 complex absorbing at 427 nm. The formation of this complex is reversible with substrate or other strong ligands of the enzyme. In plant microsomes PA seems to selectively inactivate the CYP73A P450 subpopulation. It does not form detectable complexes with other recombinant plant P450 enzymes. In vivo PA induces a sharp decrease in 4-coumaric acid concomitant to cinnamic acid accumulation in an elicited tobacco (Nicotiana tabacum) cell suspension. It also strongly decreases the formation of scopoletin in tobacco leaves infected with tobacco mosaic virus.

A Divine Round Trip: the Literary and Christological Function of the Descent/Ascent Leitmotif in the Gospel of John

The thesis of this dissertation is that the Descent/Ascent Leitmotif, which includes the language of not only descending and ascending, but also going, coming, and being sent, performs a significant literary and christological function in the Gospel of John. The Evangelist's Descent/Ascent Leitmotif becomes the Gospel's organizing principal, drawing together a constellation of verbs and a number of themes, including Jesus-Son's origin, identity, relationship to God, authority, signs and works, life, and glory. In the introductory chapter, after providing a layout of the dissertation, the discussion turns to the spacial dimensions and christological importance of the vertical and horizontal depictions of the descending, ascending, coming, going, and being sent verbs. The focus of chapter two is to explain and illustrate, using a version of the Cinderella story, a method that serves to identify the Leitmotif and the verbs, motifs, and themes the Leitmotif draws within its constellation. This approach, titled a thematic structural method, integrates works from thematic scholars Horst Daemmrich and Eugene Falk with works from literary structural scholars A. J Greimas and Roland Barthes, and is a tool to analyze the influence of the Leitmotif as the Gospel's organizing principal on the relationships between the Leitmotif and numerous themes from which John's Christology emerges. The task of chapter three is to explain the rationale for the selection of the Leitmotif's verbs of descending, ascending, coming, going, and being sent. Chapters four and five investigate how the Evangelist, with the repetition of the Leitmotif, constructs his narrative to tell the story of the historical Jesus and shape the Evangelist's Christology. Additionally, the focus is to analyze the transforming influences of the Descent/Ascent Leitmotif on the themes of Jesus-Son's origin, identity, relationship to the Father, and authority, through his signs and works, life, and glory. The Descent/Ascent Leitmotif depicts a divine round trip, and the emphasis of chapter six is to examine the role of the Leitmotif in Jesus-Son's departure from the world and return to God. The Evangelist's use of the Leitmotif in Jesus' prayer to the Father (John 17) and the promise of the Paraclete are included in this chapter. Due to the Descent/Ascent Leitmotif's inherent spatial overtones, elements related to Jesus' return, including heaven, world, the hour, and his form after his resurrection, are explored from a cosmological and ontological perspective.

Using auditory hallucinations as a therapeutic tool.

This paper integrates psychodynamic and cognitive theories understanding of schizophrenia and the function of auditory hallucinations to propose five principles for the successful treatment of auditory hallucinations within schizophrenia; connection, education, collaboration, empowerment, and independence. Pharmacological and biological research is acknowledged and integrated into psychological treatment using case information based on an autobiographical novel by a person diagnosed with schizophrenia.

Reverse engineering as a teaching tool: the corneal topographer

Póster presentado en EDULEARN12, International Conference on Education and New Learning Technologies, Barcelona, 2nd-4th July 2012.

Reverse engineering as a teaching tool: the corneal topographer

Reverse engineering is the process of discovering the technological principles of a device, object or system through analysis of its structure, function, and operation. From a device used in clinical practice, as the corneal topographer, reverse engineering will be used to infer physical principles and laws. In our case, reverse engineering involves taking this mechanical device apart and analyzing its working detail. The initial knowledge of the application and usefulness of the device provides a motivation that, together with the combination of theory and practice, will help the students to understand and learn concepts studied in different subjects in the Optics and Optometry degree. These subjects belong to both the core and compulsory subjects of the syllabus of first and second year of the degree. Furthermore, the experimental practice is used as transverse axis that relates theoretical concepts, technology transfer and research.

Ecosystem structure, function, and composition in rangelands are negatively affected by livestock grazing

Reports of positive or neutral effects of grazing on plant species richness have prompted calls for livestock grazing to be used as a tool for managing land for conservation. Grazing effects, however, are likely to vary among different response variables, types, and intensity of grazing, and across abiotic conditions. We aimed to examine how grazing affects ecosystem structure, function, and composition. We compiled a database of 7615 records reporting an effect of grazing by sheep and cattle on 278 biotic and abiotic response variables for published studies across Australia. Using these data, we derived three ecosystem measures based on structure, function, and composition, which were compared against six contrasts of grazing pressure, ranging from low to heavy, two different herbivores (sheep, cattle), and across three different climatic zones. Grazing reduced structure (by 35%), function (24%), and composition (10%). Structure and function (but not composition) declined more when grazed by sheep and cattle together than sheep alone. Grazing reduced plant biomass (40%), animal richness (15%), and plant and animal abundance, and plant and litter cover (25%), but had no effect on plant richness nor soil function. The negative effects of grazing on plant biomass, plant cover, and soil function were more pronounced in drier environments. Grazing effects on plant and animal richness and composition were constant, or even declined, with increasing aridity. Our study represents a comprehensive continental assessment of the implications of grazing for managing Australian rangelands. Grazing effects were largely negative, even at very low levels of grazing. Overall, our results suggest that livestock grazing in Australia is unlikely to produce positive outcomes for ecosystem structure, function, and composition or even as a blanket conservation tool unless reduction in specific response variables is an explicit management objective.

Radiolarian-based bransfer function for the estimation of sea surface temperatures in the Southern Ocean (Atlantic Sector)

A new radiolarian-based transfer function for sea surface temperature (SST) estimations has been developed from 23 taxa and taxa groups in 53 surface sediment samples recovered between 35° and 72°S in the Atlantic sector of the Southern Ocean. For the selection of taxa and taxa groups ecological information from water column studies was considered. The transfer function allows the estimation of austral summer SST (December-March) ranging between -1 and 18°C with a standard error of estimate of 1.2°C. SST estimates from selected late Pleistocene squences were sucessfully compared with independend paleotemperature estimates derived from a diatom transfer function. This shows that radiolarians provide an excellent tool for paleotemperature reconstructions in Pleistocene sediments of the Southern Ocean.

Function and Regulation of Cytochrome P450 4V2 and the Implications in Bietti’s Crystalline Dystrophy

Thesis (Ph.D.)--University of Washington, 2016-06

Defining Atoh1 function and regulation in avian supporting cells during auditory hair cell regeneration

Thesis (Ph.D.)--University of Washington, 2016-06

Fractal analysis as a tool for studying specialization in neuronal structure: The study of the evolution of the primate cerebral cortex and human intellect

We review recent findings that, using fractal analysis, have demonstrated systematic regional and species differences in the branching complexity of neocortical pyramidal neurons. In particular, attention is focused on how fractal analysis is being applied to the study of specialization in pyramidal cell structure during the evolution of the primate cerebral cortex. These studies reveal variation in pyramidal cell phenotype that cannot be attributed solely to increasing brain volume. Moreover, the results of these studies suggest that the primate cerebral cortex is composed of neurons of different structural complexity. There is growing evidence to suggest that regional and species differences in neuronal structure influence function at both the cellular and circuit levels. These data challenge the prevailing dogma for cortical uniformity.