The role of ribonuclease R in bacterial adaptation to cold shock

RESUMO:Os microrganismos reagem à súbita descida de temperatura através de uma resposta adaptativa específica que assegura a sua sobrevivência em condições desfavoráveis. Esta adaptação inclui alterações na composição da membrana, na maquinaria de tradução e transcrição. A resposta ao choque térmico pelo frio induz uma repressão da transcrição. No entanto, a descida de temperatura induz a produção de um grupo de proteínas específicas que ajudam a ajustar/re-ajustar o metabolismo celular às novas condições ambientais. Em E. coli o processo de adaptação demora apenas quatro horas, no qual um grupo de proteínas específicas são induzidas. Depois desde período recomeça lentamente a produção de proteínas.A ribonuclease R, uma das proteínas induzidas durante o choque térmico pelo frio, é uma das principais ribonucleases em E. coli envolvidas na degradação do RNA. É uma exoribonuclease que degrada RNA de cadeia dupla, possui funções importantes na maturação e “turnover” do RNA, libertação de ribossomas e controlo de qualidade de proteínas e RNAs. O nível celular desta enzima aumenta até dez vezes após exposição ao frio e estabiliza em células na fase estacionária. A capacidade de degradar RNA de dupla cadeia é importante a baixas temperaturas quando as estruturas de RNA estão mais estáveis. No entanto, este mecanismo é desconhecido. Embora a resposta específica ao “cold shock” tenha sido descoberta há mais de duas décadas e o número de proteínas envolvidas sugerirem que esta adaptação é rápida e simples, continuamos longe de compreender este processo. No nosso trabalho pretendemos descobrir proteínas que interactuem com a RNase R em condições ambientais diferentes através do método “TAP-tag” e espectrometria de massa. A informação obtida pode ser utilizada para deduzir algumas das novas funções da RNase R durante a adaptação bacteriana ao frio e durante a fase estacionária. Mais importante ainda, RNase R poderá ser recrutada para um complexo de proteínas de elevado peso molecular durante o “cold-shock”.------------ABSTRACT:Microorganisms react to the rapid temperature downshift with a specific adaptative response that ensures their survival in unfavorable conditions. Adaptation includes changes in membrane composition, in translation and transcription machinery. Cold shock response leads to overall repression of translation. However, temperature downshift induces production of a set of specific proteins that help to tune cell metabolism and readjust it to the new environmental conditions. For Escherichia coli the adaptation process takes only about four hours with a relatively small set of specifically induced proteins involved. After this time, protein production resumes, although at a slower rate. One of the cold inducible proteins is RNase R, one of the main E. coli ribonucleases involved in RNA degradation. RNase R is an exoribonuclease that digest double stranded RNA, serves important functions in RNA maturation and turnover, release of stalled ribosomes by trans-translation, and RNA and protein quality control. The level of this enzyme increases about ten-fold after cold induction, and it is also stabilised in cells growing in stationary phase. The RNase R ability to digest structured RNA is important at low temperatures where RNA structures are stabilized but the exact role of this mechanism remains unclear. Although specific bacterial cold shock response was discovered over two decades ago and the number of proteins involved suggests that this adaptation is fast and simple, we are still far from understanding this process. In our work we aimed to discover the proteins interacting with RNase R in different environmental conditions using TAP tag method and mass spectrometry analysis. The information obtained can be used to deduce some of the new functions of RNase R during adaptation of bacteria to cold and in stationary growth phase. Most importantly RNase R can be recruited into a high molecular mass complex of protein in cold shock.

Combining open and closed world reasoning for the semantic web

Dissertação para obtenção do Grau de Doutor em Informática

Cold Urticaria and Infectious Mononucleosis in Children

Physical urticaria includes a heterogeneous group of disorders characterized by the development of urticarial lesions and/or angioedema after exposure to certain physical stimuli. The authors present the case of a child with severe acquired cold urticaria secondary to infectious mononucleosis. Avoidance of exposure to cold was recommended; prophylactic treatment with ketotifen and cetirizine was begun and a self-administered epinephrine kit was prescribed. The results of ice cube test and symptoms significantly improved. Physical urticaria, which involves complex pathogenesis, clinical course and therapy, may be potentially life threatening. Evaluation and diagnosis are especially important in children. To our knowledge this is the first description of persistent severe cold-induced urticaria associated with infectious mononucleosis in a child.

Design a computer programming learning environment for Massive Open Online Courses

Teaching and learning computer programming is as challenging as difficult. Assessing the work of students and providing individualised feedback to all is time-consuming and error prone for teachers and frequently involves a time delay. The existent tools and specifications prove to be insufficient in complex evaluation domains where there is a greater need to practice. At the same time Massive Open Online Courses (MOOC) are appearing revealing a new way of learning, more dynamic and more accessible. However this new paradigm raises serious questions regarding the monitoring of student progress and its timely feedback. This paper provides a conceptual design model for a computer programming learning environment. This environment uses the portal interface design model gathering information from a network of services such as repositories and program evaluators. The design model includes also the integration with learning management systems, a central piece in the MOOC realm, endowing the model with characteristics such as scalability, collaboration and interoperability. This model is not limited to the domain of computer programming and can be adapted to any complex area that requires systematic evaluation with immediate feedback.

Reconstrução de Superfícies usando um Scanner 3D de Luz Estruturada

Ao longo dos últimos anos, os scanners 3D têm tido uma utilização crescente nas mais variadas áreas. Desde a Medicina à Arqueologia, passando pelos vários tipos de indústria, ´e possível identificar aplicações destes sistemas. Essa crescente utilização deve-se, entre vários factores, ao aumento dos recursos computacionais, à simplicidade e `a diversidade das técnicas existentes, e `as vantagens dos scanners 3D comparativamente com outros sistemas. Estas vantagens são evidentes em áreas como a Medicina Forense, onde a fotografia, tradicionalmente utilizada para documentar objectos e provas, reduz a informação adquirida a duas dimensões. Apesar das vantagens associadas aos scanners 3D, um factor negativo é o preço elevado. No âmbito deste trabalho pretendeu-se desenvolver um scanner 3D de luz estruturada económico e eficaz, e um conjunto de algoritmos para o controlo do scanner, para a reconstrução de superfícies de estruturas analisadas, e para a validação dos resultados obtidos. O scanner 3D implementado ´e constituído por uma câmara e por um projector de vídeo ”off-the-shelf”, e por uma plataforma rotativa desenvolvida neste trabalho. A função da plataforma rotativa consiste em automatizar o scanner de modo a diminuir a interação dos utilizadores. Os algoritmos foram desenvolvidos recorrendo a pacotes de software open-source e a ferramentas gratuitas. O scanner 3D foi utilizado para adquirir informação 3D de um crânio, e o algoritmo para reconstrução de superfícies permitiu obter superfícies virtuais do crânio. Através do algoritmo de validação, as superfícies obtidas foram comparadas com uma superfície do mesmo crânio, obtida por tomografia computorizada (TC). O algoritmo de validação forneceu um mapa de distâncias entre regiões correspondentes nas duas superfícies, que permitiu quantificar a qualidade das superfícies obtidas. Com base no trabalho desenvolvido e nos resultados obtidos, é possível afirmar que foi criada uma base funcional para o varrimento de superfícies 3D de estruturas, apta para desenvolvimento futuro, mostrando que é possível obter alternativas aos métodos comerciais usando poucos recursos financeiros.

Conceção e Execução de Estruturas Metálicas

O presente relatório diz respeito ao trabalho desenvolvido ao longo de seis meses em ambiente de estágio curricular na empresa O FELIZ – Metalomecânica, S.A.. O objetivo principal deste trabalho foi o conhecimento resultante de uma experiência num ambiente industrial no sector das construções metálicas. Pela especificidade do setor, foi desenvolvido um estudo no âmbito da conceção e execução (na componente de fabrico) de estruturas. O relatório que resulta deste trabalho de estágio tem como referência um caso de estudo de uma estrutura metálica. O caso de estudo realizado é referente a um pavilhão industrial standard, e possui dimensões em planta de 60 x 25 metros e cércea total de 9,0 metros, para o qual foi efetuado um breve dimensionamento de toda a estrutura metálica principal. O edifício será constituído por um sistema de pórtico simples formado por perfis laminados a quente normalizados de secção IPE e de aço de classe S275. Posteriormente, e com recurso a software apropriado de detalhamento de estruturas metálicas, foi desenvolvido um modelo 3D de toda a estrutura metálica do edifício. Neste modelo estão presentes todos os elementos constituintes da estrutura, bem como algumas das características físicas e mecânicas de cada peça elementar. Por fim, e com base no modelo anterior foram gerados e editados todos os desenhos 2D para o fabrico da estrutura, incluindo os desenhos de montagem da estrutura.

Frequency of toxocara infection in children attended by the health public service of Maringá, south Brazil

The lack of specific laboratorial diagnosis methods and precise symptoms makes the toxocariasis a neglected disease in Public Health Services. This study aims to determine the frequency of Toxocara spp. infection in children attended by the Health Public Service of Hospital Municipal de Maringá, South Brazil. To evaluate the association of epidemiological and clinical data, an observational and cross-section study was carried out. From 14,690 attended children/year aged from seven month to 12 years old, 450 serum samples were randomly collected from September/2004 to September/2005. A questionnaire was used to evaluate epidemiological, clinical and hematological data. An ELISA using Toxocara canis larval excretory-secretory products as antigen detected 130 (28.8%) positive sera, mainly between children from seven month to five years old (p = 0.0016). Significant correlation was observed between positive serology for Toxocara, and frequent playing in sandbox at school or daycare center (p = 0.011) and the presence of a cat at home (p = 0.056). From the families, 50% were dog owners which exposed soil backyards. Eosinophilia (p = 0.776), and signs and symptoms analyzed (fever p = 0.992, pneumonia p = 0.289, cold-like symptoms p = 0.277, cough p = 0.783, gastrointestinal problems p = 0.877, migraine p = 0.979, abdominal pain p = 0.965, joint pain p = 0.686 and skin rash p = 0.105) could not be related to the presence of anti-Toxocara antibodies. Therefore, two asthmatics children showed titles of 1:10,240 and accentuated eosinophilia (p = 0.0001). The authors emphasize the needs of prevention activities.

Defeitos do Tubo Neural. Experiência de 10 Anos numa Maternidade Central

OBJECTIVES: 1) To determine trends in prevalence of neural tube defects and the impact of therapeutic abortion. 2) To review perinatal management of spina bifida. DESIGN: All spontaneous and therapeutic abortions, still births and live births affected by neural tube defects registered in Alfredo da Costa Maternity in Lisbon, from 1983 to 1992, were retrospectively analysed. RESULTS: Eighty-two cases with neural tube defects are reported and myelomeningocele and anencephaly++ were the most frequent ones. Total prevalence for all defects was 0.78:1000 births with a small upward trend during the last two years. Birth prevalence was 0.6:1000, with a clear downward trend, due to therapeutic abortion. Prenatal diagnosis improved significantly, from 9% of all defects detected in 1983-87 to 77.5% in 1988-92. Since 1989, all cases of anencephaly were detected before birth. Most cases of spina bifida were vaginally delivered, and elective cesarean section occurred in 4. Early closure of the defect was undertaken in 87.6% of the newborns with open spina bifida. CONCLUSION: While total prevalence of neural tube defects remained stable, with only a small upward trend, prenatal diagnosis and therapeutic abortion resulted in a 56.3% fall in birth prevalence. Optimal management of open spina bifida demands a multidisciplinary team with an individual program for each case.

Successful control program to implement the appropriate antibiotic prophylaxis for cesarean section

OBJECTIVE: Describe implementation of a successful program to reduce doses (cefazolin 2 to 1 g) used for antimicrobial prophylaxis. METHODS: Evaluation of an intervention program to reduce prophylactic antimicrobial doses. The intervention included weekly staff discussions, automatic dispensation of 1g-vial of cefazolin by the pharmacy unless expressly requested by surgeon and increase in post-discharge surveillance as a strategy to reassure surgeons of the safety of the reduction. In the pre and post intervention periods, a prospective study of antimicrobial consumption and surgical site infections were measured. RESULTS: There were 5,164 and 5,204 deliveries in 2001-2002 and 2003-2004, respectively; 1,524 (29.5%) and 1,363 (26%) were cesarean sections. There was a 45% decrease in cefazolin vials used on average per cesarean section (2.29 to 1.25). Patients evaluated increased from 16% to 67% and the SSI rates in both periods were 3.34% to 2.42%, respectively. CONCLUSION: An ample intervention, including administrative and educational measures, led to high compliance with dose reduction and saved more than US$4,000 in cefazolin, considered important because government reimbursement in Brazil for cesarean section is $80.

Significance of Biogenic Amines in Cold-Smoked Fish and Their Relation to Microbiological Characteristics of Products Available in Portuguese Retail Markets

Studies on microbial characterization of cold-smoked salmon and salmon trout during cold storage were performed on samples available in the Portuguese market. Samples were also classified microbiologically according to guidelines for ready-to-eat (RTE) products. Further investigations on sample variability and microbial abilities to produce tyramine and histamine were also performed. The coefficient of variation for viable counts of different groups of microorganisms of samples collected at retail market point was high in the first 2 wk of storage, mainly in the Enterobacteriaceae group and aerobic plate count (APC), suggesting that microbiological characteristics of samples were different in numbers, even within the same batch from the same producer. This variation seemed to be decreased when storage and temperature were controlled under lab conditions. The numbers of Enterobacteriaceae were influenced by storage temperature, as indicated by low microbial numbers in samples from controlled refrigeration. Lactic acid bacteria (LAB) and Enterobacteriaceae were predominant in commercial products, a significant percentage of which were tyramine and less histamine producers. These results might be influenced by (1) the technological processes in the early stages of production, (2) contamination during the smoking process, and (3) conditions and temperature fluctuations during cold storage at retail market point of sale.

Massive Open Online Course management: learning science and engineering through peer-reviewed projects

Massive Open Online Courses (MOOC) are gaining prominence in transversal teaching-learning strategies. However, there are many issues still debated, namely assessment, recognized largely as a cornerstone in Education. The large number of students involved requires a redefinition of strategies that often use approaches based on tasks or challenging projects. In these conditions and due to this approach, assessment is made through peer-reviewed assignments and quizzes online. The peer-reviewed assignments are often based upon sample answers or topics, which guide the student in the task of evaluating peers. This chapter analyzes the grading and evaluation in MOOCs, especially in science and engineering courses, within the context of education and grading methodologies and discusses possible perspectives to pursue grading quality in massive e-learning courses.

In situ measured cross section geometry of old timber structures and its influence on structural safety

Old timber structures may show significant variation in the cross section geometry along the same element, as a result of both construction methods and deterioration. As consequence, the definition of the geometric parameters in situ may be both time consuming and costly. This work presents the results of inspections carried out in different timber structures. Based on the obtained results, different simplified geometric models are proposed in order to efficiently model the geometry variations found. Probabilistic modelling techniques are also used to define safety parameters of existing timber structures, when subjected to dead and live loads, namely self-weight and wind actions. The parameters of the models have been defined as probabilistic variables, and safety of a selected case study was assessed using the Monte Carlo simulation technique. Assuming a target reliability index, a model was defined for both the residual cross section and the time dependent deterioration evolution. As a consequence, it was possible to compute probabilities of failure and reliability indices, as well as, time evolution deterioration curves for this structure. The results obtained provide a proposal for definition of the cross section geometric parameters of existing timber structures with different levels of decay, using a simplified probabilistic geometry model and considering a remaining capacity factor for the decayed areas. This model can be used for assessing the safety of the structure at present and for predicting future performance.

Teaching mathematics using Massive Open Online Courses

Distance learning - where students take courses (attend classes, get activities and other sort of learning materials) while being physically separated from their instructors, for larger part of the course duration - is far from being a “new event”. Since the middle of the nineteenth century, this has been done through Radio, Mail and TV, taking advantage of the full educational potential that these media resources had to offer at the time. However, in recent times we have, at our complete disposal, the “magic wonder” of communication and globalization - the Internet. Taking advantage of a whole new set of educational opportunities, with a more or less unselfish “look” to economic interests, focusing its concern on a larger and collective “welfare”, contributing to the development of a more “equitable” world, with regard to educational opportunities, the Massive Open Online Courses (MOOCs) were born and have become an important feature of the higher education in recent years. Many people have been talking about MOOCs as a potential educational revolution, which has arrived from North America, still growing and spreading, referring to its benefits and/or disadvantages. The Polytechnic Institute of Porto, also known as IPP, is a Higher Education Portuguese institution providing undergraduate and graduate studies, which has a solid history of online education and innovation through the use of technology, and it has been particularly interested and focused on MOOC developments, based on an open educational policy in order to try to implement some differentiated learning strategies to its actual students and as a way to attract future ones. Therefore, in July 2014, IPP launched the first Math MOOC on its own platform. This paper describes the requirements, the resulting design and implementation of a mathematics MOOC, which was essentially addressed to three target populations: - pre-college students or individuals wishing to update their Math skills or that need to prepare for the National Exam of Mathematics; - Higher Education students who have not attended in High School, this subject, and who feel the need to acquire basic knowledge about some of the topics covered; - High School Teachers who may use these resources with their students allowing them to develop teaching methodologies like "Flipped Classroom” (available at http://www.opened.ipp.pt/). The MOOC was developed in partnership with several professors from several schools from IPP, gathering different math competences and backgrounds to create and put to work different activities such video lectures and quizzes. We will also try to briefly discuss the advertising strategy being developed to promote this MOOC, since it is not offered through a main MOOC portal, such as Coursera or Udacity.

Interface Humana Músculo-Facial

Esta dissertação tem como principal objetivo a criação de uma interface humana, baseada na eletromiografia dos músculos orbicular do olho e frontalis. O algoritmo de programação do microcontrolador ATmega2560 deteta o piscar de olhos voluntário, conta o número de vezes que este acontece e verifica se preenche os requisitos necessários à execução de um comando. Para este efeito foram utilizados elétrodos para a captação do sinal eletromiográfico. O sinal analógico é condicionado pela Shield ECG/EMG da Olimex sendo enviado para o arduíno ATmega2560. Este microcontrolador administra todos os atuadores, dos quais o mais importante é um painel de comandos (quatro comandos diferentes), no qual existe um ponteiro motorizado que indica qual a ação a realizar. O código de execução é extremamente simples:  se o utilizador piscar os olhos três vezes, o ponteiro movimenta-se para a secção do painel imediatamente à direita; e  se o utilizador piscar os olhos quatro vezes, o ponteiro movimenta-se para a secção do painel imediatamente à esquerda. Os testes realizados com este dispositivo indicam que os utilizadores demoram menos de 10 minutos a aprender a utilizar e executar todos os comandos do painel. Apenas num dos testes realizados o dispositivo não funcionou. Dos utilizadores que realizaram o teste:  vários usam óculos;  um idoso com graves problemas auditivos, cegueira parcial e dificuldades locomotoras;  nenhum foi incapaz de piscar, pelo menos, um dos olhos voluntariamente; e  a maioria referiu que, com alguma concentração e principalmente se ouvirem o bip sonoro, a aprendizagem de utilização torna-se muito fácil. Apesar dos limites impostos à concretização de um projeto deste tipo (dos quais se evidenciam as dificuldades em conseguir voluntários com paralisia medular, bem como os limites orçamentais), pode-se afirmar que este dispositivo é eficaz e seria uma mais valia quando implementado num cenário de paralisia medular (total ou parcial). A melhoria de qualidade de vida de um utilizador com estes problemas físicos, ou outros que lhe comprometam a locomoção é garantida. O cenário em que vivem é tremendamente limitado sendo urgente criar soluções para tornar estas vidas mais cómodas. Com os devidos aplicativos, o utilizador poderia abrir portas ou janelas, acender ou apagar luzes, pedir ajuda, ajustar a posição da cama, controlar cadeiras de rodas, entre outros. É neste sentido que surge a minha motivação de criar algo que ajude estas pessoas.