Identification of Conserved Splicing Motifs in Mutually Exclusive Exons of 15 Insect Species

Background: During alternative splicing, the inclusion of an exon in the final mRNA molecule is determined by nuclear proteins that bind cis-regulatory sequences in a target pre-mRNA molecule. A recent study suggested that the regulatory codes of individual RNA-binding proteins may be nearly immutable between very diverse species such as mammals and insects. The model system Drosophila melanogaster therefore presents an excellent opportunity for the study of alternative splicing due to the availability of quality EST annotations in FlyBase. Methods: In this paper, we describe an in silico analysis pipeline to extract putative exonic splicing regulatory sequences from a multiple alignment of 15 species of insects. Our method, ESTs-to-ESRs (E2E), uses graph analysis of EST splicing graphs to identify mutually exclusive (ME) exons and combines phylogenetic measures, a sliding window approach along the multiple alignment and the Welch’s t statistic to extract conserved ESR motifs. Results: The most frequent 100% conserved word of length 5 bp in different insect exons was “ATGGA”. We identified 799 statistically significant “spike” hexamers, 218 motifs with either a left or right FDR corrected spike magnitude p-value < 0.05 and 83 with both left and right uncorrected p < 0.01. 11 genes were identified with highly significant motifs in one ME exon but not in the other, suggesting regulation of ME exon splicing through these highly conserved hexamers. The majority of these genes have been shown to have regulated spatiotemporal expression. 10 elements were found to match three mammalian splicing regulator databases. A putative ESR motif, GATGCAG, was identified in the ME-13b but not in the ME-13a of Drosophila N-Cadherin, a gene that has been shown to have a distinct spatiotemporal expression pattern of spliced isoforms in a recent study. Conclusions: Analysis of phylogenetic relationships and variability of sequence conservation as implemented in the E2E spikes method may lead to improved identification of ESRs. We found that approximately half of the putative ESRs in common between insects and mammals have a high statistical support (p < 0.01). Several Drosophila genes with spatiotemporal expression patterns were identified to contain putative ESRs located in one exon of the ME exon pairs but not in the other.

Estudo da sinterização e oxidação anódica na produção de um capacitor eletrolítico de nióbio

It seeks to find an alternative to the current tantalum electrolytic capacitors in the market due to its high cost. Niobium is a potential replacement for be lighter and cheaper than tantalum. They belong to the same table group periodically and thus exhibit several physical and chemical properties similar. Niobium is used in many technologically important applications, and Brazil has the largest reserves, around 96%. These electrolytic capacitors have high specific capacitance, so they can store high energy in small volumes compared to other types of capacitors. This is the main attraction of this type of capacitor because is growing demand in the production of capacitors with capacitance specifies increasingly high, this because of the miniaturization of various devices such as GPS devices, televisions, computers, phones and many others. The production route of the capacitor was made by powder metallurgy. The initial niobium poder was first characterized by XRD, SEM and laser particle size to then be sieved into particle size 400mesh. The powder was then compacted at pressure of 150MPa and sintered at 1400, 1450 and 1500°C using two sintering time 30 and 60min. Sintering is an important part of the process as it affects properties as porosity and surface cleaning of the samples, which greatly affected the quality of the capacitor. After sintering the samples were underwent a process of anodic oxidation (anodizing), which created a thin film of niobium pentoxide over the whole surface of the sample, this film is the dielectric capacitor. The anodizing process variables influenced a lot in film formation and consequently the capacitor. The samples were characterized by electrical measurements of capacitance, loss factor and ESR (equivalent series resistance). The sintering has affected the porosity and in turn the specific area of the samples. The capacitor area is directly related to the capacitance, that is, the higher the specific area is the capacitance. Higher sintering temperatures decrease the surface area but eliminate as many impurities. The best results were obtained at a temperature of 1400°C with 60 minutes. The most interesting results were compared with the specific capacitance and ESR for all samples.

Estudo da sinterização e oxidação anódica na produção de um capacitor eletrolítico de nióbio

It seeks to find an alternative to the current tantalum electrolytic capacitors in the market due to its high cost. Niobium is a potential replacement for be lighter and cheaper than tantalum. They belong to the same table group periodically and thus exhibit several physical and chemical properties similar. Niobium is used in many technologically important applications, and Brazil has the largest reserves, around 96%. These electrolytic capacitors have high specific capacitance, so they can store high energy in small volumes compared to other types of capacitors. This is the main attraction of this type of capacitor because is growing demand in the production of capacitors with capacitance specifies increasingly high, this because of the miniaturization of various devices such as GPS devices, televisions, computers, phones and many others. The production route of the capacitor was made by powder metallurgy. The initial niobium poder was first characterized by XRD, SEM and laser particle size to then be sieved into particle size 400mesh. The powder was then compacted at pressure of 150MPa and sintered at 1400, 1450 and 1500°C using two sintering time 30 and 60min. Sintering is an important part of the process as it affects properties as porosity and surface cleaning of the samples, which greatly affected the quality of the capacitor. After sintering the samples were underwent a process of anodic oxidation (anodizing), which created a thin film of niobium pentoxide over the whole surface of the sample, this film is the dielectric capacitor. The anodizing process variables influenced a lot in film formation and consequently the capacitor. The samples were characterized by electrical measurements of capacitance, loss factor and ESR (equivalent series resistance). The sintering has affected the porosity and in turn the specific area of the samples. The capacitor area is directly related to the capacitance, that is, the higher the specific area is the capacitance. Higher sintering temperatures decrease the surface area but eliminate as many impurities. The best results were obtained at a temperature of 1400°C with 60 minutes. The most interesting results were compared with the specific capacitance and ESR for all samples.

Preparação e caracterização de biomateriais poliméricos para avaliação da viabilidade de uso como phantom biológico

The theoretical and experimental developments in the biomaterials area have been directly applied to different fields of Medicine (odontology, regenerative medicine and radiotherapy). These advances have focused both for diagnosing diseases such as for quantifying degrees of progression. From the perspective of these studies, biomaterials are being designed and manufactured for application in various areas of science, provided advances in diagnostic radiology, radiotherapy dosimetry and calibration of radiotherapy equipment. Develop a phantom from a biomaterial has become a great ally of medicine in the treat patients with oncological diseases, allowing better performance of the equipment in order to reduce damage to healthy tissue due to excessive exposure to radiation. This work used polymers: chitosan and gelatin, for making the polymeric structures and controlled for different types of production and processing, characterizing and evaluating the biopolymer by physical techniques (STL, SEM and DEI) and therefore analyze applicability as phantom mouse lung. It was possible to evaluate the morphology of biomaterials quantitatively by scanning electron microscopy associated with imaging technique. The relevance of this work focuses on developing a phantom from polymeric biomaterials that can act as phantom providing high image contrast when subjected to analysis. Thus, the choice of DEI technique is satisfactory since it is an imaging technique of X-ray high resolution. The images obtained by DEI have shown the details of the internal microstructure of the biomaterial produced which have ≈ 10 μm dimension. The phantoms had made density ranging from 0.08 a 0.13 g/cm3.

Does attendance affect grade? An analysis of first year economics students in Ireland

This paper examines the relationship between attendance and grade, controlling for other factors, in first year economics courses in University College Cork. Determinants of both class attendance and grade are specified and estimated. We find that attendance is low, at least by comparison with US evidence. Hours worked and travel time are among the factors affecting class attendance. Class attendance, and especially tutorial attendance has a positive and diminishing marginal effect on grade, while hours worked in a part-time job have a significant negative effect on grade.

Radiation Dose to the Lens of the Eye from Computed Tomography Scans of the Head

While it is well known that exposure to radiation can result in cataract formation, questions still remain about the presence of a dose threshold in radiation cataractogenesis. Since the exposure history from diagnostic CT exams is well documented in a patient’s medical record, the population of patients chronically exposed to radiation from head CT exams may be an interesting area to explore for further research in this area. However, there are some challenges in estimating lens dose from head CT exams. An accurate lens dosimetry model would have to account for differences in imaging protocols, differences in head size, and the use of any dose reduction methods.

The overall objective of this dissertation was to develop a comprehensive method to estimate radiation dose to the lens of the eye for patients receiving CT scans of the head. This research is comprised of a physics component, in which a lens dosimetry model was derived for head CT, and a clinical component, which involved the application of that dosimetry model to patient data.

The physics component includes experiments related to the physical measurement of the radiation dose to the lens by various types of dosimeters placed within anthropomorphic phantoms. These dosimeters include high-sensitivity MOSFETs, TLDs, and radiochromic film. The six anthropomorphic phantoms used in these experiments range in age from newborn to adult.

First, the lens dose from five clinically relevant head CT protocols was measured in the anthropomorphic phantoms with MOSFET dosimeters on two state-of-the-art CT scanners. The volume CT dose index (CTDIvol), which is a standard CT output index, was compared to the measured lens doses. Phantom age-specific CTDIvol-to-lens dose conversion factors were derived using linear regression analysis. Since head size can vary among individuals of the same age, a method was derived to estimate the CTDIvol-to-lens dose conversion factor using the effective head diameter. These conversion factors were derived for each scanner individually, but also were derived with the combined data from the two scanners as a means to investigate the feasibility of a scanner-independent method. Using the scanner-independent method to derive the CTDIvol-to-lens dose conversion factor from the effective head diameter, most of the fitted lens dose values fell within 10-15% of the measured values from the phantom study, suggesting that this is a fairly accurate method of estimating lens dose from the CTDIvol with knowledge of the patient’s head size.

Second, the dose reduction potential of organ-based tube current modulation (OB-TCM) and its effect on the CTDIvol-to-lens dose estimation method was investigated. The lens dose was measured with MOSFET dosimeters placed within the same six anthropomorphic phantoms. The phantoms were scanned with the five clinical head CT protocols with OB-TCM enabled on the one scanner model at our institution equipped with this software. The average decrease in lens dose with OB-TCM ranged from 13.5 to 26.0%. Using the size-specific method to derive the CTDIvol-to-lens dose conversion factor from the effective head diameter for protocols with OB-TCM, the majority of the fitted lens dose values fell within 15-18% of the measured values from the phantom study.

Third, the effect of gantry angulation on lens dose was investigated by measuring the lens dose with TLDs placed within the six anthropomorphic phantoms. The 2-dimensional spatial distribution of dose within the areas of the phantoms containing the orbit was measured with radiochromic film. A method was derived to determine the CTDIvol-to-lens dose conversion factor based upon distance from the primary beam scan range to the lens. The average dose to the lens region decreased substantially for almost all the phantoms (ranging from 67 to 92%) when the orbit was exposed to scattered radiation compared to the primary beam. The effectiveness of this method to reduce lens dose is highly dependent upon the shape and size of the head, which influences whether or not the angled scan range coverage can include the entire brain volume and still avoid the orbit.

The clinical component of this dissertation involved performing retrospective patient studies in the pediatric and adult populations, and reconstructing the lens doses from head CT examinations with the methods derived in the physics component. The cumulative lens doses in the patients selected for the retrospective study ranged from 40 to 1020 mGy in the pediatric group, and 53 to 2900 mGy in the adult group.

This dissertation represents a comprehensive approach to lens of the eye dosimetry in CT imaging of the head. The collected data and derived formulas can be used in future studies on radiation-induced cataracts from repeated CT imaging of the head. Additionally, it can be used in the areas of personalized patient dose management, and protocol optimization and clinician training.

MRI-Guided Radiation Therapy: Investigating the Accuracy of Treatment Delivery

Purpose: To develop, evaluate and apply a novel high-resolution 3D remote dosimetry protocol for validation of MRI guided radiation therapy treatments (MRIdian® by ViewRay®). We demonstrate the first application of the protocol (including two small but required new correction terms) utilizing radiochromic 3D plastic PRESAGE® with optical-CT readout.

Methods: A detailed study of PRESAGE® dosimeters (2kg) was conducted to investigate the temporal and spatial stability of radiation induced optical density change (ΔOD) over 8 days. Temporal stability was investigated on 3 dosimeters irradiated with four equally-spaced square 6MV fields delivering doses between 10cGy and 300cGy. Doses were imaged (read-out) by optical-CT at multiple intervals. Spatial stability of ΔOD response was investigated on 3 other dosimeters irradiated uniformly with 15MV extended-SSD fields with doses of 15cGy, 30cGy and 60cGy. Temporal and spatial (radial) changes were investigated using CERR and MATLAB’s Curve Fitting Tool-box. A protocol was developed to extrapolate measured ΔOD readings at t=48hr (the typical shipment time in remote dosimetry) to time t=1hr.

Results: All dosimeters were observed to gradually darken with time (<5% per day). Consistent intra-batch sensitivity (0.0930±0.002 ΔOD/cm/Gy) and linearity (R2=0.9996) was observed at t=1hr. A small radial effect (<3%) was observed, attributed to curing thermodynamics during manufacture. The refined remote dosimetry protocol (including polynomial correction terms for temporal and spatial effects, CT and CR) was then applied to independent dosimeters irradiated with MR-IGRT treatments. Excellent line profile agreement and 3D-gamma results for 3%/3mm, 10% threshold were observed, with an average passing rate 96.5%± 3.43%.

Conclusion: A novel 3D remote dosimetry protocol is presented capable of validation of advanced radiation treatments (including MR-IGRT). The protocol uses 2kg radiochromic plastic dosimeters read-out by optical-CT within a week of treatment. The protocol requires small corrections for temporal and spatially-dependent behaviors observed between irradiation and readout.