GeneID in "Drosophila"

GeneID is a program to predict genes in anonymous genomic sequences designed with a hierarchical structure. In the first step, splice sites, and start and stop codons are predicted and scored along the sequence using position weight matrices (PWMs). In the second step, exons are built from the sites. Exons are scored as the sum of the scores of the defining sites, plus the log-likelihood ratio of a Markov model for coding DNA. In the last step, from the set of predicted exons, the gene structure is assembled, maximizing the sum of the scores of the assembled exons. In this paper we describe the obtention of PWMs for sites, and the Markov model of coding DNA in Drosophila melanogaster. We also compare other models of coding DNA with the Markov model. Finally, we present and discuss the results obtained when GeneID is used to predict genes in the Adh region. These results show that the accuracy of GeneID predictions compares currently with that of other existing tools but that GeneID is likely to be more efficient in terms of speed and memory usage.

Technology Transfer of As-Built and Preliminary Surveys Using GPS, Soft Photogrammetry, and Video Logging, 2002

This research involved two studies: one to determine the local geoid to obtain mean sea level elevation from a global positioning system (GPS) to an accuracy of ±2 cm, and the other to determine the location of roadside features such as mile posts and stop signs for safety studies, geographic information systems (GIS), and maintenance applications, from video imageries collected by a van traveling at traffic speed.

SelenoDB 1.0 : a database of selenoprotein genes, proteins and SECIS elements

Selenoproteins are a diverse group of proteinsusually misidentified and misannotated in sequencedatabases. The presence of an in-frame UGA (stop)codon in the coding sequence of selenoproteingenes precludes their identification and correctannotation. The in-frame UGA codons are recodedto cotranslationally incorporate selenocysteine,a rare selenium-containing amino acid. The developmentof ad hoc experimental and, more recently,computational approaches have allowed the efficientidentification and characterization of theselenoproteomes of a growing number of species.Today, dozens of selenoprotein families have beendescribed and more are being discovered in recentlysequenced species, but the correct genomic annotationis not available for the majority of thesegenes. SelenoDB is a long-term project that aims toprovide, through the collaborative effort of experimentaland computational researchers, automaticand manually curated annotations of selenoproteingenes, proteins and SECIS elements. Version 1.0 ofthe database includes an initial set of eukaryoticgenomic annotations, with special emphasis on thehuman selenoproteome, for immediate inspectionby selenium researchers or incorporation into moregeneral databases. SelenoDB is freely available athttp://www.selenodb.org.

Guidelines for the Conversion of Urban Four-Lane Undivided Roadways to Three-Lane Two-Way Left-turn Lane Facilities, April 2001

Four-lane undivided roadways in urban areas can experience a degradation of service and/or safety as traffic volumes increase. In fact, the existence of turning vehicles on this type of roadway has a dramatic effect on both of these factors. The solution identified for these problems is typically the addition of a raised median or two-way left-turn lane (TWLTL). The mobility and safety benefits of these actions have been proven and are discussed in the “Past Research” chapter of this report along with some general cross section selection guidelines. The cost and right-of-way impacts of these actions are widely accepted. These guidelines focus on the evaluation and analysis of an alternative to the typical four-lane undivided cross section improvement approach described above. It has been found that the conversion of a four-lane undivided cross section to three lanes (i.e., one lane in each direction and a TWLTL) can improve safety and maintain an acceptable level of service. These guidelines summarize the results of past research in this area (which is almost nonexistent) and qualitative/quantitative before-and-after safety and operational impacts of case study conversions located throughout the United States and Iowa. Past research confirms that this type of conversion is acceptable or feasible in some situations but for the most part fails to specifically identify those situations. In general, the reviewed case study conversions resulted in a reduction of average or 85th percentile speeds (typically less than five miles per hour) and a relatively dramatic reduction in excessive speeding (a 60 to 70 percent reduction in the number of vehicles traveling five miles per hour faster than the posted speed limit was measured in two cases) and total crashes (reductions between 17 to 62 percent were measured). The 13 roadway conversions considered had average daily traffic volumes of 8,400 to 14,000 vehicles per day (vpd) in Iowa and 9,200 to 24,000 vehicles per day elsewhere. In addition to past research and case study results, a simulation sensitivity analysis was completed to investigate and/or confirm the operational impacts of a four-lane undivided to three-lane conversion. First, the advantages and disadvantages of different corridor simulation packages were identified for this type of analysis. Then, the CORridor SIMulation (CORSIM) software was used x to investigate and evaluate several characteristics related to the operational feasibility of a four-lane undivided to three-lane conversion. Simulated speed and level of service results for both cross sections were documented for different total peak-hour traffic, access densities, and access-point left-turn volumes (for a case study corridor defined by the researchers). These analyses assisted with the identification of the considerations for the operational feasibility determination of a four -lane to three-lane conversion. The results of the simulation analyses primarily confirmed the case study impacts. The CORSIM results indicated only a slight decrease in average arterial speed for through vehicles can be expected for a large range of peak-hour volumes, access densities, and access-point left-turn volumes (given the assumptions and design of the corridor case study evaluated). Typically, the reduction in the simulated average arterial speed (which includes both segment and signal delay) was between zero and four miles per hour when a roadway was converted from a four-lane undivided to a three-lane cross section. The simulated arterial level of service for a converted roadway, however, showed a decrease when the bi-directional peak-hour volume was about 1,750 vehicles per hour (or 17,500 vehicles per day if 10 percent of the daily volume is assumed to occur in the peak hour). Past research by others, however, indicates that 12,000 vehicles per day may be the operational capacity (i.e., level of service E) of a three-lane roadway due to vehicle platooning. The simulation results, along with past research and case study results, appear to support following volume-related feasibility suggestions for four-lane undivided to three-lane cross section conversions. It is recommended that a four-lane undivided to three-lane conversion be considered as a feasible (with respect to volume only) option when bi-directional peak-hour volumes are less than 1,500 vehicles per hour, but that some caution begin to be exercised when the roadway has a bi-directional peak-hour volume between 1,500 and 1,750 vehicles per hour. At and above 1,750 vehicles per hour, the simulation indicated a reduction in arterial level of service. Therefore, at least in Iowa, the feasibility of a four-lane undivided to three-lane conversion should be questioned and/or considered much more closely when a roadway has (or is expected to have) a peak-hour volume of more than 1,750 vehicles. Assuming that 10 percent of the daily traffic occurs during the peak-hour, these volume recommendations would correspond to 15,000 and 17,500 vehicles per day, respectively. These suggestions, however, are based on the results from one idealized case xi study corridor analysis. Individual operational analysis and/or simulations should be completed in detail once a four-lane undivided to three-lane cross section conversion is considered feasible (based on the general suggestions above) for a particular corridor. All of the simulations completed as part of this project also incorporated the optimization of signal timing to minimize vehicle delay along the corridor. A number of determination feasibility factors were identified from a review of the past research, before-and-after case study results, and the simulation sensitivity analysis. The existing and expected (i.e., design period) statuses of these factors are described and should be considered. The characteristics of these factors should be compared to each other, the impacts of other potentially feasible cross section improvements, and the goals/objectives of the community. The factors discussed in these guidelines include • roadway function and environment • overall traffic volume and level of service • turning volumes and patterns • frequent-stop and slow-moving vehicles • weaving, speed, and queues • crash type and patterns • pedestrian and bike activity • right-of-way availability, cost, and acquisition impacts • general characteristics, including - parallel roadways - offset minor street intersections - parallel parking - corner radii - at-grade railroad crossings xii The characteristics of these factors are documented in these guidelines, and their relationship to four-lane undivided to three-lane cross section conversion feasibility identified. This information is summarized along with some evaluative questions in this executive summary and Appendix C. In summary, the results of past research, numerous case studies, and the simulation analyses done as part of this project support the conclusion that in certain circumstances a four-lane undivided to three-lane conversion can be a feasible alternative for the mitigation of operational and/or safety concerns. This feasibility, however, must be determined by an evaluation of the factors identified in these guidelines (along with any others that may be relevant for a individual corridor). The expected benefits, costs, and overall impacts of a four-lane undivided to three-lane conversion should then be compared to the impacts of other feasible alternatives (e.g., adding a raised median) at a particular location.

Agrupación de resultados de una consulta de corpus según medidas de similitud léxica

A medida que el tamaño de un corpus aumenta, aumenta también el número de concordancias obtenidas al consultar una forma. Un número muy elevado de concordancias, de cientos o de miles, dificulta la sistematicidad de la tarea del lexicógrafo. La propuesta del artículo consiste en el uso de un sistema automático de agrupación de concordancias según su similitud léxica (es decir, qué elementos léxicos comparten), con el objetivo de presentar dichas concordancias agrupadas y asociadas a un único representante de todo el conjunto de las que son consideradas como léxicamente similares, de manera que la cardinalidad efectiva de los datos de corpus se vea reducida. El sistema se ha desarrollado teniendo en cuenta las ventajas de una arquitectura distribuida, por lo que cada una de las partes del sistema (stemming, identificación de stop words, cálculo de similitud entre concordancias, ordenación final de los datos, etc.) se ha desarrollado en módulos diferentes que pueden estar alojados en servidores, ya que las necesidades de cálculo del sistema harían que su uso desde un ordenador personal resultara muy lento.

Cytochrome P450 1A2 activity and inducibility: impact of smoking, smoking cessation and genetic polymorphisms

Aims: Cytochrome P4501A2 (CYP1A2) is involved in the metabolism of severaldrugs (clozapine, olanzapine, theopylline, caffeine, etc) and is induced by smoking.This can result in decreased plasma levels of drugs metabolized by thisisoenzyme, causing a decrease in therapeutic response. After quitting smoking,increased plasma levels can lead to adverse effects of the concerned drugs, such asconfusion and seizures, described under clozapine treatment. The present studyaimed to examine the variation of CYP1A2 activity in a large group of smokersbefore and after smoking cessation. Moreover, we aimed to determine whethergenetic polymorphisms of CYP1A2 gene could influence the inducibility ofCYP1A2. Methods: CYP1A2 activity was determined by the paraxanthine/caffeineratio in 194 smokers and in 118 of them being abstinent during a 4-weekperiod. Participants were genotyped for CYP1A2*1F (rs762551), *1D(rs35694136) and *1C (rs2069514) polymorphisms. Results: Smokers had higherCYP1A2 activity (1.55-fold; p < 0.0001). Individual change of CYP1A2 activityafter smoking cessation ranged from 1.0-fold (no change) to 7.3-fold decreasedactivity. In five participants with low initial CYP1A2 activity, an increase wasobserved after smoking cessation. During smoking, CYP1A2*1F (p = 0.005), CYP1A2*1D (p = 0.014), the number of cigarettes/day (p = 0.012), contraceptives use(p < 0.001) and - 163A/- 2467T/- 3860G haplotype (p = 0.002) influencedCYP1A2 activity, while after quitting smoking, CYP1A2*1F (p = 0.017) and contraceptives(p = 0.05) did. No influence of CYP1A2 polymorphisms on the inducibilityof CYP1A2 was observed. Conclusion: Higher CYP1A2 activity wasmeasured in smokers, but with a large interindividual variability of its inductionby smoking. Careful clinical management with the help of therapeutic drug monitoringis therefore needed for patients receiving drugs which are metabolized byCYP1A2, who stop or start smoking. Unidentified genetic variations in theCYP1A2 gene and/or in other genes controlling CYP1A2 activity and other environmentalfactors could be responsible of the observed differences in CYP1A2enzymatic activity and inducibility.

Evaluation d'une association regionale de prevention du suicide en Suisse = Evaluation of a regional association for suicide prevention in Switzerland

This article discusses the evaluation of Stop Suicide, a regional association active in youth suicide prevention in Switzerland. The first part of the article presents and discusses the activities of Stop Suicide and its national context, characterized by an absence of a general national suicide prevention program. The second part specifically focuses on the evaluation of Stop Suicide, based on interviews with the members of the association's network. The evaluation reported an assessment carried out regarding the members' general perceptions about the association and its collaborations. The article suggests the possibility of creating a branch for coordinating regional suicide prevention, and it highlights the need to evaluate the impact and effects of the activities on the population concerned, youth

Guidleines for Removal of Traffic Control Devices in Rural Areas, October 2005

It is commonly regarded that the overuse of traffic control devices desensitizes drivers and leads to disrespect, especially for low-volume secondary roads with limited enforcement. The maintenance of traffic signs is also a tort liability concern, exacerbated by unnecessary signs. The Federal Highway Administration’s (FHWA) Manual on Uniform Traffic Control Devices (MUTCD) and the Institute of Transportation Engineer’s (ITE) Traffic Control Devices Handbook provide guidance for the implementation of STOP signs based on expected compliance with right-of-way rules, provision of through traffic flow, context (proximity to other controlled intersections), speed, sight distance, and crash history. The approach(es) to stop is left to engineering judgment and is usually dependent on traffic volume or functional class/continuity of system. Although presently being considered by the National Committee on Traffic Control Devices, traffic volume itself is not given as a criterion for implementation in the MUTCD. STOP signs have been installed at many locations for various reasons which no longer (or perhaps never) met engineering needs. If in fact the presence of STOP signs does not increase safety, removal should be considered. To date, however, no guidance exists for the removal of STOP signs at two-way stop-controlled intersections. The scope of this research is ultra-low-volume (< 150 daily entering vehicles) unpaved intersections in rural agricultural areas of Iowa, where each of the 99 counties may have as many as 300 or more STOP sign pairs. Overall safety performance is examined as a function of a county excessive use factor, developed specifically for this study and based on various volume ranges and terrain as a proxy for sight distance. Four conclusions are supported: (1) there is no statistical difference in the safety performance of ultra-low-volume stop-controlled and uncontrolled intersections for all drivers or for younger and older drivers (although interestingly, older drivers are underrepresented at both types of intersections); (2) compliance with stop control (as indicated by crash performance) does not appear to be affected by the use or excessive use of STOP signs, even when adjusted for volume and a sight distance proxy; (3) crash performance does not appear to be improved by the liberal use of stop control; (4) safety performance of uncontrolled intersections appears to decline relative to stop-controlled intersections above about 150 daily entering vehicles. Subject to adequate sight distance, traffic professionals may wish to consider removal of control below this threshold. The report concludes with a section on methods and legal considerations for safe removal of stop control.

Relay card for capacitance measurements

In this bachelor's thesis a relay card for capacitance measurements was designed, built and tested. The study was made for the research and development laboratory of VTI Technologies, which manufactures capacitive silicon micro electro mechanical accelerometers and pressure sensors. As the size of the sensors is decreasing the capacitance value of the sensors also decreases. The decreased capacitance causes a need for new and more accurate measurement systems. The technology used in the instrument measuring the capacitance dictates a framework how the relay card should be designed, thus the operating principle of the instrument must be known. To achieve accurate results the measurement instrument and its functions needed to be used correctly. The relay card was designed using printed circuit board design methods that minimize interference coupling to the measurement. The relay card that was designed in this study is modular. It consists of a separate CPU card, which was used to control the add-on cards connected to it. The CPU card was controlled from a computer through a serial bus. Two add-on cards for the CPU card were designed in this study. The first one was the measurement card, which could be used to measure 32 capacitive sensors. The second add-on card was the MUX card, which could be used to switch between two measurement cards. The capacitance measurements carried out through the MUX card and the measurement cards were characterized with a series of test measurements. The test measurement data was then analysed. The relay card design was confirmed to work and offer accurate measurement results up to a measurement frequency of 10 MHz. The length of the measurement cables limited the measurement frequency.

Chylothorax in children: guidelines for diagnosis and management.

STUDY OBJECTIVE: To establish guidelines for the diagnosis and management of chylothorax in children. DESIGN: Retrospective study. PATIENTS: Fifty-one patients with a diagnosis of chylothorax. Twelve patients were excluded because of incomplete data or incorrect diagnosis. The following parameters were analyzed: triglyceride level, total cell number, and lymphocyte percentage; amount of pleural effusion on day of diagnosis, day 5, and day 14; and total time of pleural effusion. Prospectively, the same parameters were analyzed in a control group of 10 patients with pleural drainage. INTERVENTION: Patients with chylothorax were treated primarily with fat-free oral nutrition; if chyle did not stop, total parenteral nutrition with total enteric rest was started. If conservative therapy was not successful, pleurodesis was performed. RESULTS: In children with chylothorax triglyceride, triglyceride content ranged from 0.56 to 26.6 mmol/L; all values except one were > 1.1 mmol/L. In 36 of 39 patients (92%), the cell count was > 1,000 cells/microL. In 33 of 39 patients (85%), lymphocytes were > 90%. In patients without chylothorax triglyceride, triglyceride levels ranged from 0.1 to 0.71 mmol/L (median, 0.38 mmol/L) and cell count was from 20 to 1400 cells/microL (median, 322 cells/microL), with a maximum of 60% lymphocytes. With fat-free nutrition, chyle disappeared in 29 of 39 patients. Five patients died, and five required pleurodesis. CONCLUSIONS: Pleural effusion in children is chyle when it contains > 1.1 mmol/L triglycerides (with oral fat intake) and has a total cell count > or 1,000 cells/microL, with a lymphocyte fraction > 80%. Chylous effusions usually last long; however, after 6 weeks, the majority of the effusions (29 of 39 patients) had ceased. Late surgical interventions reduce the number of thoracotomies substantially, but can lead to very long hospitalization times. Early surgical interventions (after < 3 weeks) lead to a high number of thoracotomies, but certainly reduce hospitalization time.

Avaliação da Qualidade do Transporte Colectivo Urbano, na Cidade da Praia, e a Satisfação dos Utentes

A qualidade nas organizações de serviço tem-se tornado num tópico de muita importância, sendo reconhecida como uma variável estratégica para aumentar a sua eficácia e eficiência, ganhar vantagem competitiva e conduzir à satisfação dos seus clientes. Promover uma escala apropriada, que reflicta convenientemente as percepções e as expectativas dos clientes, deve ser uma preocupação tanto dos gestores de empresas como das agências governativas. O presente estudo empírico desenvolve e analisa uma escala de medição da qualidade de serviço, através da aplicação do modelo SERVQUAL, desenvolvido por Parasuraman et al. (1985, 1988, 1991), e adaptado para o serviço de transporte colectivo urbano de passageiros (TCUP). O procedimento levado a efeito na presente investigação apresenta 4 fases e 9 etapas, com a combinação do paradigma de Churchill (1979) e entrevistas focus group. A escala final SERVQUAL adaptada, com 23 itens, e as dimensões obtidas indicam que a mesma é altamente fiável (0,891) e válida, demonstrando assim que o procedimento seguido é aplicável e que os seus itens foram desenhados de acordo com as condições do sector. A pesquisa exploratória foi conduzida em Cabo Verde, na cidade da Praia, em Setembro de 2008, com 230 utentes regulares do serviço de TCUP. Os dados confirmam a existência de gaps, encontrando-se a maioria dos inquiridos (67%) insatisfeita com esse serviço. A análise factorial confirmou a existência de cinco dimensões, que determinam a qualidade de serviço no TCUP, na Praia, pela seguinte ordem de importância: “aparência física dos veículos/conforto”, “atenção personalizada/desempenho dos colaboradores”, “empatia”, “conveniência do serviço”, e, por último, “equipamento tangível”. Service quality has become a topic of great importance and it is recognized as a strategic variable to increase its efficiency and effectiveness in getting competitive advantage and leading to customer satisfaction. To seek a proper scale that can reflect perceptions and customers’ expectations accurately should be a concern for business managers as well as government agencies. Present empirical study develops and analyzes a measurement scale of quality service, through the application of SERVQUAL model developed by Parasuraman et al. (1985, 1988, 1991) and adapted for the urban passenger transportation. The procedure followed in present research indicates four phases and nine steps in connection to Churchill paradigm (1979) and focus group interview. The adapted final SERVQUAL scale, with 23 items, and the dimensions obtained indicated that it is highly reliable (0.891) and valid, showing this way that the procedure followed is applicable and their items were drawn according to the sector conditions. This exploratory research was performed in Cape Verde, at Praia in September 2008 with 230 regular’s users of bus service. The data confirms the existence of gaps and that the majority of the inquired are not pleased (67%) with their bus service. The factorial analysis confirms the existence of five dimensions, which determines the service quality in the bus service at Praia according to the following order of importance : “physical appearance of the bus/confort”, “personalized attention/results from the collaborators”, “empathy”, “service convenience” and lastly “tangible equipment”.

How Doing Business Jeopardizes Institutional Reform

Simplifying business formalization and eliminating outdated formalities is often a good way of improving the institutional environment for firms. Unfortunately, the World Bank's Doing Business project is harming such policies by promoting a reform agenda that gives them priority even in countries lacking functional business registers, so that the reformed registers keep producing valueless information, but faster. Its methodology also promotes biased measurements that impede proper consideration of the essential tradeoffs in the design of formalization institutions. If Doing Business is to stop jeopardizing its true objectives and contribute positively to scientific progress, institutional reform and economic development, then its aims, governance and methodology need to change.

Per què llegim Homer i toquem Bach? Una comparació entre clàssics des de la relativització de la tradició en el repertori oboístic

L'objectiu d'aquest projecte és dur a terme una comparació entre els clàssics que trobem en el món literari i musical, i els clàssics que hem acabat establint al llarg de la tradició en el repertori de l'oboè. A partir d'una recerca i anàlisi de les característiques que defineixen els clàssics, farem un recorregut al llarg de la història del repertori de l'oboè, per adonar-nos que les obres que toquem avui han estat determinades per un context històric i social molt concret, així com per l'aparició d'altres instruments, la influència dels enregistraments i dels oboistes, el paper del músic en cada època... Conclourem, finalment, que els clàssics, pel fet de ser-ho, guarden dins seu un secret inexhaurible i atemporal, però que cal anar amb compte perquè –especialment en el món musical i de l'oboè– correm el risc d'esgotar-los i de deixar de percebre el seu valor.

Assessment of diesel exhaust particulate exposure and surface characteristics in association with levels of oxidative stress biomarkers

Exposure to PM10 and PM2.5 (particulate matter with aerodynamic diameter smaller than 10 μm and 2.5 μm, respectively) is associated with a range of adverse health effects, including cancer, pulmonary and cardiovascular diseases. Surface characteristics (chemical reactivity, surface area) are considered of prime importance to understand the mechanisms which lead to harmful effects. A hypothetical mechanism to explain these adverse effects is the ability of components (organics, metal ions) adsorbed on these particles to generate Reactive Oxygen Species (ROS), and thereby to cause oxidative stress in biological systems (Donaldson et al., 2003). ROS can attack almost any cellular structure, like DNA or cellular membrane, leading to the formation of a wide variety of degradation products which can be used as a biomarker of oxidative stress. The aim of the present research project is to test whether there is a correlation between the exposure to Diesel Exhaust Particulate (DEP) and the oxidative stress status. For that purpose, a survey has been conducted in real occupational situations where workers were exposed to DEP (bus depots). Different exposure variables have been considered: - particulate number, size distribution and surface area (SMPS); - particulate mass - PM2.5 and PM4 (gravimetry); - elemental and organic carbon (coulometry); - total adsorbed heavy metals - iron, copper, manganese (atomic adsorption); - surface functional groups present on aerosols (Knudsen flow reactor). (Demirdjian et al., 2005). Several biomarkers of oxidative stress (8-hydroxy-2'-deoxyguanosine and several aldehydes) have been determined either in urine or serum of volunteers. Results obtained during the sampling campaign in several bus depots indicated that the occupational exposure to particulates in these places was rather low (40-50 μg/m3 for PM4). Size distributions indicated that particles are within the nanometric range. Surface characteristics of sampled particles varied strongly, depending on the bus depot. They were usually characterized by high carbonyl and low acidic sites content. Among the different biomarkers which have been analyzed within the framework of this study, mean levels of 8- hydroxy-2'-deoxyguanosine and several aldehydes (hexanal, heptanal, octanal, nonanal) increased during two consecutive days of exposure for non-smokers. In order to bring some insight into the relation between the particulate characteristics and the formation of ROS by-products, biomarkers levels will be discussed in relation with exposure variables.

Roundabouts, 2006

Roundabouts are intersections that direct traffic in a counterclockwise direction around a center island. They have no stop signs or traffic signals. Yield signs, directional signs, and pavement markings guide traffic through the intersection.