Correlation of Locally-Based Performance of Asphalts with Their Physicochemical Parameters, Progress Report 2, HR-298, 1989

This project was undertaken to study the relationships between the performance of locally available asphalts and their physicochemical properties under Iowa conditions with the ultimate objective of development of a locally and performance-based asphalt specification for durable pavements. Physical and physicochemical tests were performed on three sets of asphalt samples including: (a) twelve samples from local asphalt suppliers and their TFOT residues, (b) six core samples of known service records, and (c) a total of 79 asphalts from 10 pavement projects including original, lab aged and recovered asphalts from field mixes, as well as from lab aged mixes. Tests included standard rheological tests, HP-GPC and TMA. Some specific viscoelastic tests (at 5 deg C) were run on b samples and on some a samples. DSC and X-ray diffraction studies were performed on a and b samples. Furthermore, NMR techniques were applied to some a, b and c samples. Efforts were made to identify physicochemical properties which are correlated to physical properties known to affect field performance. The significant physicochemical parameters were used as a basis for an improved performance-based trial specification for Iowa to ensure more durable pavements.

Água levemente salinizada aumenta a eficiência da larvicultura de peixes neotropicais

O objetivo deste trabalho foi avaliar o efeito de água levemente salinizada sobre a larvicultura intensiva do tambaqui, matrinxã, apaiari e piau, durante os dias iniciais de alimentação. As larvas foram mantidas em água artificialmente salinizada, em concentrações de 0 (água doce) a 14 g L-1 de NaCl (intervalo de 2,0 g L-1), e foram alimentadas com duas porções diárias de náuplios de Artemia, de acordo com protocolo para cada espécie, em delineamento inteiramente casualizado, com três repetições. Larvas de tambaqui, matrinxã e apaiari podem ser cultivadas em até 2 g L-1 de concentração salina, sem prejuízos ao crescimento e à sobrevivência. Larvas de piau foram mais tolerantes e suportaram até 4 g L-1 de concentração salina. Acima disto, a mortalidade dos peixes aumentou e chegou a 100% à concentração de 6 g L-1 (matrinxã e apaiari) e de 10 g L-1 (tambaqui). A salinização da água a 2 g L-1 proporcionou maior taxa de sobrevivência a larvas de matrinxã e maior crescimento a larvas de tambaqui, apaiari e piau. Estas duas últimas espécies apresentaram melhor crescimento com a maior quantidade de náuplios. Água salinizada a 2 g L-1 é benéfica para as espécies estudadas, pois otimiza o potencial de crescimento das larvas e o uso de náuplios de Artemia como alimento vivo.

Quantitative modelling of transcription factor binding sites

Abstract One of the most important issues in molecular biology is to understand regulatory mechanisms that control gene expression. Gene expression is often regulated by proteins, called transcription factors which bind to short (5 to 20 base pairs),degenerate segments of DNA. Experimental efforts towards understanding the sequence specificity of transcription factors is laborious and expensive, but can be substantially accelerated with the use of computational predictions. This thesis describes the use of algorithms and resources for transcriptionfactor binding site analysis in addressing quantitative modelling, where probabilitic models are built to represent binding properties of a transcription factor and can be used to find new functional binding sites in genomes. Initially, an open-access database(HTPSELEX) was created, holding high quality binding sequences for two eukaryotic families of transcription factors namely CTF/NF1 and LEFT/TCF. The binding sequences were elucidated using a recently described experimental procedure called HTP-SELEX, that allows generation of large number (> 1000) of binding sites using mass sequencing technology. For each HTP-SELEX experiments we also provide accurate primary experimental information about the protein material used, details of the wet lab protocol, an archive of sequencing trace files, and assembled clone sequences of binding sequences. The database also offers reasonably large SELEX libraries obtained with conventional low-throughput protocols.The database is available at http://wwwisrec.isb-sib.ch/htpselex/ and and ftp://ftp.isrec.isb-sib.ch/pub/databases/htpselex. The Expectation-Maximisation(EM) algorithm is one the frequently used methods to estimate probabilistic models to represent the sequence specificity of transcription factors. We present computer simulations in order to estimate the precision of EM estimated models as a function of data set parameters(like length of initial sequences, number of initial sequences, percentage of nonbinding sequences). We observed a remarkable robustness of the EM algorithm with regard to length of training sequences and the degree of contamination. The HTPSELEX database and the benchmarked results of the EM algorithm formed part of the foundation for the subsequent project, where a statistical framework called hidden Markov model has been developed to represent sequence specificity of the transcription factors CTF/NF1 and LEF1/TCF using the HTP-SELEX experiment data. The hidden Markov model framework is capable of both predicting and classifying CTF/NF1 and LEF1/TCF binding sites. A covariance analysis of the binding sites revealed non-independent base preferences at different nucleotide positions, providing insight into the binding mechanism. We next tested the LEF1/TCF model by computing binding scores for a set of LEF1/TCF binding sequences for which relative affinities were determined experimentally using non-linear regression. The predicted and experimentally determined binding affinities were in good correlation.

Potassium channel KCNH2 K897T polymorphism and cardiac repolarization during exercise test: The Finnish Cardiovascular Study.

Scand J Clin Lab Invest. 2007 Aug 1;:1-11 [Epub ahead of print]

Results of An International Study of Quantitative BCR/ABL Assays Using Defined RNA Samples

Molecular monitoring of BCR/ABL transcripts by real time quantitative reverse transcription PCR (qRT-PCR) is an essential technique for clinical management of patients with BCR/ABL-positive CML and ALL. Though quantitative BCR/ABL assays are performed in hundreds of laboratories worldwide, results among these laboratories cannot be reliably compared due to heterogeneity in test methods, data analysis, reporting, and lack of quantitative standards. Recent efforts towards standardization have been limited in scope. Aliquots of RNA were sent to clinical test centers worldwide in order to evaluate methods and reporting for e1a2, b2a2, and b3a2 transcript levels using their own qRT-PCR assays. Total RNA was isolated from tissue culture cells that expressed each of the different BCR/ABL transcripts. Serial log dilutions were prepared, ranging from 100 to 10-5, in RNA isolated from HL60 cells. Laboratories performed 5 independent qRT-PCR reactions for each sample type at each dilution. In addition, 15 qRT-PCR reactions of the 10-3 b3a2 RNA dilution were run to assess reproducibility within and between laboratories. Participants were asked to run the samples following their standard protocols and to report cycle threshold (Ct), quantitative values for BCR/ABL and housekeeping genes, and ratios of BCR/ABL to housekeeping genes for each sample RNA. Thirty-seven (n=37) participants have submitted qRT-PCR results for analysis (36, 37, and 34 labs generated data for b2a2, b3a2, and e1a2, respectively). The limit of detection for this study was defined as the lowest dilution that a Ct value could be detected for all 5 replicates. For b2a2, 15, 16, 4, and 1 lab(s) showed a limit of detection at the 10-5, 10-4, 10-3, and 10-2 dilutions, respectively. For b3a2, 20, 13, and 4 labs showed a limit of detection at the 10-5, 10-4, and 10-3 dilutions, respectively. For e1a2, 10, 21, 2, and 1 lab(s) showed a limit of detection at the 10-5, 10-4, 10-3, and 10-2 dilutions, respectively. Log %BCR/ABL ratio values provided a method for comparing results between the different laboratories for each BCR/ABL dilution series. Linear regression analysis revealed concordance among the majority of participant data over the 10-1 to 10-4 dilutions. The overall slope values showed comparable results among the majority of b2a2 (mean=0.939; median=0.9627; range (0.399 - 1.1872)), b3a2 (mean=0.925; median=0.922; range (0.625 - 1.140)), and e1a2 (mean=0.897; median=0.909; range (0.5174 - 1.138)) laboratory results (Fig. 1-3)). Thirty-four (n=34) out of the 37 laboratories reported Ct values for all 15 replicates and only those with a complete data set were included in the inter-lab calculations. Eleven laboratories either did not report their copy number data or used other reporting units such as nanograms or cell numbers; therefore, only 26 laboratories were included in the overall analysis of copy numbers. The median copy number was 348.4, with a range from 15.6 to 547,000 copies (approximately a 4.5 log difference); the median intra-lab %CV was 19.2% with a range from 4.2% to 82.6%. While our international performance evaluation using serially diluted RNA samples has reinforced the fact that heterogeneity exists among clinical laboratories, it has also demonstrated that performance within a laboratory is overall very consistent. Accordingly, the availability of defined BCR/ABL RNAs may facilitate the validation of all phases of quantitative BCR/ABL analysis and may be extremely useful as a tool for monitoring assay performance. Ongoing analyses of these materials, along with the development of additional control materials, may solidify consensus around their application in routine laboratory testing and possible integration in worldwide efforts to standardize quantitative BCR/ABL testing.

Transfusion practice in early trauma management

Introduction: Blood transfusions carry risks and complications. At the University Hospital of Lausanne the need for transfusion in early trauma resuscitation is based on clinical judgment and standard laboratory tests. We aimed to assess the transfusion practice for trauma patients during their early management. Method: Based on 2008 data from the Lausanne Trauma Registry of Acute Care (TRAC), we analyzed all adult trauma patients admitted to the shock room who received blood products or pro-coagulants in shock room and/or during their emergency operation. Demographics, physiological parameters and lab tests were recorded at arrival and at the end of anesthesiologic management. Coagulopathy was defined as PT <70%, PTT >60 sec, Fibrinogen <1 g/l or Thrombocytes <100 x 109 g/l. Results: In 2008, 323 trauma-patients were included in TRAC. 55 patients (17%) received blood products or pro-coagulants. 44 (83%) had an ISS >15 (med 29, IQR 10-35.5). 43 (78.2%) needed an emergency intervention. Coagulopathy was present in 25 patients (45.5%) at arrival vs. 30 (54.5%) after resuscitation (p = 0.446).

Effect of Tocopherol Extract, Staphylococcus carnosus Culture, and Celery Concentrate Addition on Quality Parameters of Organic and Conventional Dry-Cured Sausages

The effects of the addition to sausage mix of tocopherols (200 mg/kg), a conventional starter culture with or without Staphylococcus carnosus, celery concentrate (CP) (0.23% and 0.46%), and two doses of nitrate (70 and 140 mg/kg expressed as NaNO(3)) on residual nitrate and nitrite amounts, instrumental CIE Lab color, tocol content, oxidative stability, and overall acceptability were studied in fermented dry-cured sausages after ripening and after storage. Nitrate doses were provided by nitrate-rich CP or a chemical grade source. The lower dose complies with the EU requirements governing the maximum for ingoing amounts in organic meat products. Tocopherol addition protected against oxidation, whereas the nitrate dose, nitrate source, or starter culture had little influence on secondary oxidation values. The residual nitrate and nitrite amounts found in the sausages with the lower nitrate dose were within EU-permitted limits for organic meat products and residual nitrate can be further reduced by the presence of the S. carnosus culture. Color measurements were not affected by the CP dose. Product consumer acceptability was not affected negatively by any of the factors studied. As the two nitrate sources behaved similarly for the parameters studied, CP is a useful alternative to chemical ingredients for organic dry-cured sausage production.

Crescimento e desenvolvimento radicular do porta-enxerto de macieira Marubakaido (Malus prunifolia) micropropagado submetido à inoculação micorrízica e à poda de raízes

Com o objetivo de avaliar os efeitos da inoculação micorrízica e da poda de raízes sobre a parte aérea e sistema radicular do porta-enxerto Marubakaido, obtido in vitro, foi conduzido um estudo em câmara de crescimento. A base das plantas micropropagadas foi imersa em ácido indolbutírico e transferida para substrato à base de solo, a fim de ser enraizada ex vitro.Antes ou após a fase de enraizamento (21 dias), inoculou-se uma mistura de isolados de fungos micorrízicos arbusculares, e um terço das plantas sofreu poda de raízes. Após 51 dias, avaliaram-se colonização micorrízica, altura, massa da parte aérea e raízes, e número e comprimento de raízes de diferentes ordens. A porcentagem de colonização radicular foi maior no tratamento inoculado antes do enraizamento, que também teve os maiores valores de incremento em altura e de produção de biomassa da parte aérea. A poda de raízes causou reduções significativas na colonização micorrízica, no crescimento da parte aérea e no desenvolvimento radicular. O comprimento e a ramificação das raízes foram aumentados pela micorrização e diminuídos pela poda. Em conclusão, a poda de raízes é prejudicial e a inoculação micorrízica, antes do enraizamento, é benéfica para a produção de mudas micropropagadas do porta-enxerto Marubakaido.

Valoración experiencial del aprendizaje tras formación virtual.

[eng] An observable study on the behaviour in the laboratory of Pharmaceutical Technology II (pharmaceutical pilot plant), with two groups of students of 3rd course (proactive aptitude and valuation of the"knowledge to do acquired") is carried out. The variable between groups is that one has realised a training (by means of self-study of an interactive application multimedia, especially designed), without tutorship on behalf the teacher in front of the other group that carried out the same training with the same material but with the guide of the teacher in the computer lab. On the one hand it is valued if there is some effect differentiator between both types of training, by means of the accounting of the correct results obtained in a previous test to the entrance in the pilot plant and by another one the valuation that the professors made responsible for the groups of practices in situ. The results demonstrate the previous hypothesis that there must not be significant differences between the groups, beyond the inherent ones to personality of the students itself (interest and personal implication by the subject). On the other hand the test for the observation in the laboratory did not facilitate the distinction of objective differences. [spa] Se lleva a cabo un estudio observacional sobre el comportamiento de los estudiantes (aptitud pro-activa y valoración del “saber hacer adquirido”) en el laboratorio de Tecnología Farmacéutica II (planta piloto farmacéutica) de dos grupos de estudiantes de 3er curso. La variable entre los dos grupos es que uno ha realizado una formación no presencial (mediante el autoestudio de una aplicación interactiva multimedia, especialmente diseñada), sin tutoría por parte del profesor, frente al otro grupo que llevó a cabo la misma formación con el mismo material pero con la guía del profesor en el aula de informática. Por una parte se valora si hay algún efecto diferenciador entre ambos tipos de formación, mediante la contabilización de los resultados correctos obtenidos en un test previo a la entrada en la planta piloto y por otro la valoración que hicieron los profesores responsables de los grupos de prácticas in situ. Los resultados demuestran la hipótesis previa de que no debían existir diferencias significativas entre los grupos, más allá de las inherentes a la propia personalidad de los estudiantes (interés e implicación personal por el tema). Por otra parte el test para la observación en el laboratorio no facilitó la distinción de diferencias objetivas.

Structured running program for health and performance promotion in hospital employees.

Introduction Our institution (University hospital) is encouraging physical activities for health through various popular sporting events in the city of Lausanne, the biggest of which is a road race of 2, 4, 10 and 20km. Objective To create an efficient and sustainable training program in preparation of the race for a group of motivated hospital employees without any prior experience with structured training and to identifying the benefits and limitations encountered.. Methods Subjects of various fitness levels were recruited by add and agreed to undergo lab and field testing before a 12-week 3 times/week running program, based on maximal aerobic speed (MAS-30/30 sec intervals), running technique exercises and endurance training. The interval session was the only one supervised. Their goal was the 10km (11 subjects) and the 20km (6 subjects). Results A group of 17 subjects (7 male and 10 female), mean age 36.6±7.3 years, VO2max 44.0±5.5 ml/kg/min, filed test interval MAS 15.1±2.4 km/h started the program. 2 were lost because of injury (while skiing). Adherence to interval sessions was excellent, although 3 weekly training sessions proved to be difficult for most of the subjects. Performance in the race was satisfying for all of them, 6/7 subjects having improved their running time from the previous year, the others participated for the first time and 7/8 completed the race satisfyingly, one DNF-ed because of sinusitis. Repeat MAS field test was available for 6 subjects, who improved by 5.9% (p<0.01). Subjectively, all of the participants were very satisfied with improvement, interaction with colleagues from various professions, and with self achievement and confidence. Conclusions Implementation of a structured training program for recreational or non-athletes can be very successful in creating a better self-confidence, a better working environment inside a hospital facility and obviously in improvement of physical fitness and athletic performance. Above all, it can only encourage health institutions to promote the health of their own employees through physical activity, which can allow people to connect through sports. As a result, subjects in this study tend to encourage other employees to be more active and are hungry for more advice and continued offers for physical activities benefiting both them and the institution through better efficiency at work and less absenteeism common to more active people.

Role of amphiregulin in mammary gland development

Abstract Ovarian hormones are key regulators of postnatal mammary gland development and are linked to breast carcinogenesis. In particular, estrogens induce mammary epithelial cells to proliferate at the onset of puberty, leading to the elongation of the rudimental ductal tree into the fatty stromal tissue. Elucidating the molecular events underlying estrogen mitogenic activity in the mammary gland is of value in understanding how the deregulation of this signalling pathway can lead to breast tumorigenesis. Our lab has recently shown that estrogen induces mammary proliferation via epithelial estrogen receptor alpha (ERα) by a paracrine mechanism. Based on the finding that several EGF receptor (EGFR) ligands are able to substitute for estrogens and that amphiregulin (Areg), one of these ligands, is required during mammary development, we have hypothesized that Areg is a key mediator of estrogen induced paracrine signalling during ductal morphogenesis. Our analysis of the Areg -/- mice mammary phenotype reveals that epithelial Areg is required at the onset of puberty for epithelial proliferation, terminal end bud (TEB) formation and, subsequently, ductal elongation. Hormonal stimulation experiments show that among the EGFR ligands, only Arég is specifically controlled by estrogen at the transcriptional level, via ERα, in the mammary gland. Moreover, Areg is required for the estrogen-induced mammotrophic effects of epithelial proliferation and ductal elongation. We have shown that ectopic Areg expression in ERα -/- mammary epithelial cells is sufficient to induce ductal morphogenesis. Our transplantations experiment show that when Areg -/- cells are in the presence of wt cells they contribute to all aspects of ductal development, suggesting that this growth factor acts in a paracrine fashion. Moreover, this result shows that Areg -/- epithelial cells are not intrinsically impaired in proliferation. Our transplantation experiment carried out under physiological conditions confirmed previous reports showing that stromal EGFR is needed for ductal morphogenesis. This suggests that estrogen-driven Areg signalling involves an epithelium-stroma crosstalk. Thus, these data confirmed our hypothesis of Areg being an important estrogen mediator during ductal morphogenesis. Résumé Les hormones ovariennes, régulatrices clés du développement post-natal de la glande mammaire, sont également liées à la carcinogénèse du sein. En particulier, l'oestrogène induit la division des cellules épithéliales au début de la puberté. Cette prolifération amène à l'élongation du réseau canalaire rudimentaire et permet l'invasion du compartiment stromal. L'élucidation des mécanismes moléculaires responsables de l'activité mitogénique de l'oestrogène dans la glande mammaire est précieuse pour une meilleure compréhension du développement du cancer du sein. Notre laboratoire a récemment démontré que l'cestrogène induit la prolifération des cellules épithéliales par un signal paracrine, grâce au récepteur à l'oestrogène alpha (ERα). En se basant sur le fait que plusieurs ligands du récepteur à l'EGF (EGFR) sont capables de se substituer à l'cestrogène et d'induire la prolifération épithéliale et qu'amphiregulin (Areg), un de ces ligands, est essentielle au développement de la glande mammaire, nous avons émi l'hypothèse que Areg est un médiateur essentiel du signal paracrine induit par l'oestrogène pendant la croissance du système canalaire. Nos analyses phénotypiques des glandes mammaires issues de souris transgéniques Areg -/- démontrent que cette protéine est indispensable à la prolifération des cellules épithéliales mammaires au début de la puberté et à la formation des bourgeons terminaux qui conduisent à l'élongation des canaux. Nos expériences de stimulations hormonales démontrent que, parmi l'ensemble des ligands du EGFR, seule Areg est contrôlée au niveau transcriptionnel par l'cestrogène dans la glande mammaire, ceci via le récepteur ERα. De plus, Areg est essentielle pour le effets mammotrophique induit par l'cestrogène, à savoir la prolifération épithéliál et la croissance du système canalaire. Par ailleurs, l'expression ectopique d'Areg dans des cellules epithéliales mammaires de souris transgéniques ERα -/- est suffisante pour permettre la formation du réseau canalaire. En présence de cellules normales, les cellules dépourvues du gène d'Areg contribuent à la formation des canaux. Cette expérience suggère que ce facteur de croissance agit de manière paracrine. De plus, ce résultat montre que les cellules épithéliales Areg -/- conservent leur potentiel prolifératif. Nos expériences de transplantation, réalisées dans des conditions physiologiques, ont confirmé des précédentes études qui montraient que le récepteur stromal à l'EGF est nécessaire pour la morphogénèse du système canalaire. Ceci suggère que la voie de signalisation activée par l'oestrogène et dépendante d' implique une communication entre l'épithélium et le stroma. Ainsi, ces résultats valident notre hypothèse puisqu'ils confirment Areg en tant que médiateur majeur de l'oestrogène dans la morphogénèse du système canalaire.

WiBed, A Platform for Commodity Wireless Testbeds

Testbeds are a stage between the simulation and the production stages. To this end they must be as close as possible to production environments (i.e. real hardware, on the field deployments) while also keeping the traits of experimentation facilities (i.e. fault tolerance, ease of deployment, testing and data collection). This paper presents WiBed, a FOSS platform for WiFi testbeds based on OpenWRT Linux made to run oncommodity IEEE802.11 WiFi routers part of the Community-lab.net project, a global testbed for Community networks. WiBedhas been designed to support realistic low layer network exper-iments (according to the OSI model). This work recolects thedetails of the architecture, design and implementation of WiBed consolidated during its operation as a testbed. In addition to a set of routing experimentation results obtained during the Wireless Battlemesh v7 where WiBed was used as testbed platform.

Estudi de l’efecte de l’aigua de reg en la producció i qualitat de préssec per a industria (4rt any experimental)

El Projecte forma part d’un estudi plurianual, en el que participen l’ETSEA UdL, el centre UdL - IRTA de R+D i les empreses INDULLEIDA, S.A. i LAB – FERRER. Es tracta d’un projecte INIA de R+D el qual es centra en l’estudi i desenvolupament de diferents estratègies de reg i de diferents estratègies d’adobat nitrogenat. El present PFC es centra en l’estudi de les estratègies de reg. D’aquesta manera s’estableixen 3 tractaments diferents de reg (un tractament de reg complert i dos tractaments de reg deficitari controlat) i s’estudia la resposta del cultiu en relació a la producció i qualitat del fruit.

In silico pathway reconstruction: Iron-sulfur cluster biogenesis in Saccharomyces cerevisiae

Background: Current advances in genomics, proteomics and other areas of molecular biology make the identification and reconstruction of novel pathways an emerging area of great interest. One such class of pathways is involved in the biogenesis of Iron-Sulfur Clusters (ISC). Results: Our goal is the development of a new approach based on the use and combination of mathematical, theoretical and computational methods to identify the topology of a target network. In this approach, mathematical models play a central role for the evaluation of the alternative network structures that arise from literature data-mining, phylogenetic profiling, structural methods, and human curation. As a test case, we reconstruct the topology of the reaction and regulatory network for the mitochondrial ISC biogenesis pathway in S. cerevisiae. Predictions regarding how proteins act in ISC biogenesis are validated by comparison with published experimental results. For example, the predicted role of Arh1 and Yah1 and some of the interactions we predict for Grx5 both matches experimental evidence. A putative role for frataxin in directly regulating mitochondrial iron import is discarded from our analysis, which agrees with also published experimental results. Additionally, we propose a number of experiments for testing other predictions and further improve the identification of the network structure. Conclusion: We propose and apply an iterative in silico procedure for predictive reconstruction of the network topology of metabolic pathways. The procedure combines structural bioinformatics tools and mathematical modeling techniques that allow the reconstruction of biochemical networks. Using the Iron Sulfur cluster biogenesis in S. cerevisiae as a test case we indicate how this procedure can be used to analyze and validate the network model against experimental results. Critical evaluation of the obtained results through this procedure allows devising new wet lab experiments to confirm its predictions or provide alternative explanations for further improving the models.

Dynamic drag modeling of submerged aquatic vegetation canopy flows

Vegetation has a profound effect on flow and sediment transport processes in natural rivers, by increasing both skin friction and form drag. The increase in drag introduces a drag discontinuity between the in-canopy flow and the flow above, which leads to the development of an inflection point in the velocity profile, resembling a free shear layer. Therefore, drag acts as the primary driver for the entire canopy system. Most current numerical hydraulic models which incorporate vegetation rely either on simple, static plant forms, or canopy-scaled drag terms. However, it is suggested that these are insufficient as vegetation canopies represent complex, dynamic, porous blockages within the flow, which are subject to spatially and temporally dynamic drag forces. Here we present a dynamic drag methodology within a CFD framework. Preliminary results for a benchmark cylinder case highlight the accuracy of the method, and suggest its applicability to more complex cases.