Experimental study of thermocapillary convection on a liquid bridge consisting of fluid with low Prandtl number in a floating half-zone

A device of mercury liquid bridge of floating half-zone is designed to experimentally explore thermocapillary convection and its instability of a low Prandtl number liquid. Noncontacted diagnostic techniques were developed to monitor surface flow and surface deformation. The surface flow and the influence of a growing surface film (or skin) on the flow were observed. It is shown that the film is a key factor in changing the behavior associated with the thermocapillary convection. The experiment indicates that the critical Marangoni number should be much higher than that expected by the numerical simulation. The condition and process of surface film growth are discussed. The surface oscillation of the mercury bridge wrapped with ''dirt-film'' was observed, and the characteristics and the frequency associated with this oscillation are given.

Online exercise for the design and simulation of PCR and PCR-RFLP experiments

[EN] Background: Polymerase Chain Reaction (PCR) and Restriction Fragment Length Polymorphism of PCR products (PCR-RFLP) are extensively used molecular biology techniques. An exercise for the design and simulation of PCR and PCR-RFLP experiments will be a useful educational tool. Findings: An online PCR and PCR-RFLP exercise has been create that requires users to find the target genes,compare them, design primers, search for restriction endonucleases, and finally to simulate the experiment. Each user of the service is randomly assigned a gene from Escherichia coli; to complete the exercise, users must design an experiment capable of distinguishing among E. coli strains. By applying the experimental procedure to all completely sequenced E. coli, a basic understanding of strain comparison and clustering can also be acquired. Comparison of results obtained in different experiments is also very instructive. Conclusions: The exercise is freely available at http://insilico.ehu.es/edu.

On the Selection of Non-Invasive Methods Based on Speech Analysis Oriented to Automatic Alzheimer Disease Diagnosis

The work presented here is part of a larger study to identify novel technologies and biomarkers for early Alzheimer disease (AD) detection and it focuses on evaluating the suitability of a new approach for early AD diagnosis by non-invasive methods. The purpose is to examine in a pilot study the potential of applying intelligent algorithms to speech features obtained from suspected patients in order to contribute to the improvement of diagnosis of AD and its degree of severity. In this sense, Artificial Neural Networks (ANN) have been used for the automatic classification of the two classes (AD and control subjects). Two human issues have been analyzed for feature selection: Spontaneous Speech and Emotional Response. Not only linear features but also non-linear ones, such as Fractal Dimension, have been explored. The approach is non invasive, low cost and without any side effects. Obtained experimental results were very satisfactory and promising for early diagnosis and classification of AD patients.

Die Anwendung molekulargenetischer Verfahren in der fischereiwissenschaftlichen Forschung - Trennung von Fischpopulationen

The discrimination of stocks and separate reproductive units within fish species to facilitate fisheries management based on biological data has always been a challenge to fisheries biologists. We describe the use of three different molecular genetic techniques to detect genetic differences between stocks and closely related species. Direct sequencing of the mitochondrial ND3 gene describes the relationship between different aquaculture strains and natural populations of rainbow trout and revealed genetic homogeneity within the hatchery strains. Microsatellite analyses were used to explore the differences between redfish species from the genus Sebastes and to verify populations structure within S. mentella and S. marinus. This lead to an un equivocal discrimination of the species and an indication of populations structure within those species in the North Atlantic. The Amplified Fragment Length Polymorphisum (AFLP) methodology revealed genetic differences between Baltic and North Sea dap (Limanda limanda)and a possible population structure within the North Sea.

Space-resolved spectral diagnosis of line-shaped laser-produced magnesium plasmas

Space-resolved spectra of line-shaped laser-produced magnesium plasmas in the normal direction of the target have been obtained using a pinhole crystal spectrograph. These spectra are treated by a spectrum analyzing code for obtaining the true spectra and fine structures of overlapped lines. The spatial distributions of electron temperature and density along the normal direction of the target surface have been obtained with different spectral diagnostic techniques. Especially, the electron density plateaus beyond the critical surface in line-shaped magnesium plasmas have been obtained with a fitting technique applied to the Stark-broadened Ly-alpha wings of hydrogenic ions. The difference of plasma parameters between those obtained by different diagnostic techniques is discussed. Other phenomena, such as plasma satellites, population inversion, etc., which are observed in magnesium plasmas, are also presented.

Differenzierung von Kammmuscheln durch DNA-Analyse

Abstract In the last years scallops have reached a considerable popularity and the import of scallops into the EU has increased about 20 % over the last fi ve years from some 50.000 t to nearly 63.000 t in the year 2010. Scallops are fi shed or farmed, and traded as fresh or deep frozen product. Recently investigation of scallop products of various origins by determining the species using molecular biological techniques showed that the species had been mislabelled in a considerable proportion of samples. Determination of the species was performed by PCR-based DNA-analysis of mitochondrial DNA followed by (i) sequencing the PCR product and (ii) comparison of the DNA sequence with entries in GenBank using BLAST. The deduced sequences of the analysed samples were considerably different from each other allowing the unambiguous assignment of samples to a certain species. Kurzfassung Die Nachfrage von Kammmuscheln in der EU hat in den letzten fünf Jahren erheblich zugenommen. Der Import stieg von knapp 53.000 t im Jahr 2005 um 20% auf annähernd 63.000 t im Jahr 2010. Gehandelt werden Kammmuscheln sowohl als frische als auch als Tiefkühlware aus Wildfängen und Aquakultur. Untersuchungen von Kammmuschel-Proben aus verschiedenen Ursprungsländern und Bestimmung der Spezies auf molekularbiologischer Basis zeigten, dass ein erheblicher Anteil der Proben falsch deklariert war. Die Bestimmung der Spezies erfolgte durch Vervielfältigung eines Abschnitts des 16S rRNA Gens durch Polymerase- Kettenreaktion (PCR), anschließender Sequenzanalyse der PCR-Produkte und Vergleich der DNA Sequenzen untereinander und mit Dateneintragungen in GenBank. Die DNA-Sequenzen der ermittelten Abschnitte der 16S rRNA der Proben unterschieden sich erheblich voneinander und erlaubten eine eindeutige Zuordnung zu jeweils einer Spezies.

Hanseníase neural, aspectos diagnósticos da forma neural pura e mecanismos imunopatogênicos da lesão do nervo na doença. Participação de quimiocinas CCL2 e CXCL10 e metaloproteinases 2 e 9

O diagnóstico da hanseníase neural pura baseia-se em dados clínicos e laboratoriais do paciente, incluindo a histopatologia de espécimes de biópsia de nervo e detecção de DNA de Mycobacterium leprae (M. leprae) pelo PCR. Como o exame histopatológico e a técnica PCR podem não ser suficientes para confirmar o diagnóstico, a imunomarcação de lipoarabinomanana (LAM) e/ou Glicolipídio fenólico 1 (PGL1) - componentes de parede celular de M. leprae foi utilizada na primeira etapa deste estudo, na tentativa de detectar qualquer presença vestigial do M. leprae em amostras de nervo sem bacilos. Além disso, sabe-se que a lesão do nervo na hanseníase pode diretamente ser induzida pelo M. leprae nos estágios iniciais da infecção, no entanto, os mecanismos imunomediados adicionam severidade ao comprometimento da função neural em períodos sintomáticos da doença. Este estudo investigou também a expressão imuno-histoquímica de marcadores envolvidos nos mecanismos de patogenicidade do dano ao nervo na hanseníase. Os imunomarcadores selecionados foram: quimiocinas CXCL10, CCL2, CD3, CD4, CD8, CD45RA, CD45RO, CD68, HLA-DR, e metaloproteinases 2 e 9. O estudo foi desenvolvido em espécimes de biópsias congeladas de nervo coletados de pacientes com HNP (n=23 / 6 BAAR+ e 17 BAAR - PCR +) e pacientes diagnosticados com outras neuropatias (n=5) utilizados como controle. Todas as amostras foram criosseccionadas e submetidas à imunoperoxidase. Os resultados iniciais demonstraram que as 6 amostras de nervos BAAR+ são LAM+/PGL1+. Já entre as 17 amostras de nervos BAAR-, 8 são LAM+ e/ou PGL1+. Nas 17 amostras de nervos BAAR-PCR+, apenas 7 tiveram resultados LAM+ e/ou PGL1+. A detecção de imunorreatividade para LAM e PGL1 nas amostras de nervo do grupo HNP contribuiu para a maior eficiência diagnóstica na ausência recursos a diagnósticos moleculares. Os resultados da segunda parte deste estudo mostraram que foram encontradas imunoreatividade para CXCL10, CCL2, MMP2 e MMP9 nos nervos da hanseníase, mas não em amostras de nervos com outras neuropatias. Além disso, essa imunomarcação foi encontrada predominantemente em células de Schwann e em macrófagos da população celular inflamatória nos nervos HNP. Os outros marcadores de ativação imunológica foram encontrados em leucócitos (linfócitos T e macrófagos) do infiltrado inflamatório encontrados nos nervos. A expressão de todos os marcadores, exceto CXCL10, apresentou associação com a fibrose, no entanto, apenas a CCL2, independentemente dos outros imunomarcadores, estava associada a esse excessivo depósito de matriz extracelular. Nenhuma diferença na frequência da imunomarcação foi detectada entre os subgrupos BAAR+ e BAAR-, exceção feita apenas às células CD68+ e HLA-DR+, que apresentaram discreta diferença entre os grupos BAAR + e BAAR- com granuloma epitelioide. A expressão de MMP9 associada com fibrose é consistente com os resultados anteriores do grupo de pesquisa. Estes resultados indicam que as quimiocinas CCL2 e CXCL10 não são determinantes para o estabelecimento das lesões com ou sem bacilos nos em nervo em estágios avançados da doença, entretanto, a CCL2 está associada com o recrutamento de macrófagos e com o desenvolvimento da fibrose do nervo na lesão neural da hanseníase.

Field applications of the second-generation Environmental Sample Processor (ESP) for remote detection of harmful algae: 2006-2007

We assess the application of the second-generation Environmental Sample Processor (ESP) for the detection of harmful algal bloom (HAB) species in field and laboratory settings using two molecular probe techniques: a sandwich hybridization assay (SHA) and fluorescent in situ hybridization (FISH). During spring 2006, the first time this new instrument was deployed, the ESP successfully automated application of DNA probe arrays for various HAB species and other planktonic taxa, but non-specific background binding on the SHA probe array support made results interpretation problematic. Following 2006, the DNA array support membrane that we were using was replaced with a different membrane, and the SHA chemistry was adjusted. The sensitivity and dynamic range of these modifications were assessed using 96-well plate and ESP array SHA formats for several HAB species found commonly in Monterey Bay over a range of concentrations; responses were significantly correlated (p < 0.01). Modified arrays were deployed in 2007. Compared to 2006, probe arrays showed improved signal:noise, and remote detection of various HAB species was demonstrated. We confirmed that the ESP and affiliated assays can detect HAB populations at levels below those posing human health concerns, and results can be related to prevailing environmental conditions in near real-time.

The coastal environment and human health: microbial indicators, pathogens, sentinels and reservoirs

Innovative research relating oceans and human health is advancing our understanding of disease-causing organisms in coastal ecosystems. Novel techniques are elucidating the loading, transport and fate of pathogens in coastal ecosystems, and identifying sources of contamination. This research is facilitating improved risk assessments for seafood consumers and those who use the oceans for recreation. A number of challenges still remain and define future directions of research and public policy. Sample processing and molecular detection techniques need to be advanced to allow rapid and specific identification of microbes of public health concern from complex environmental samples. Water quality standards need to be updated to more accurately reflect health risks and to provide managers with improved tools for decision-making. Greater discrimination of virulent versus harmless microbes is needed to identify environmental reservoirs of pathogens and factors leading to human infections. Investigations must include examination of microbial community dynamics that may be important from a human health perspective. Further research is needed to evaluate the ecology of non-enteric water-transmitted diseases. Sentinels should also be established and monitored, providing early warning of dangers to ecosystem health. Taken together, this effort will provide more reliable information about public health risks associated with beaches and seafood consumption, and how human activities can affect their exposure to disease-causing organisms from the oceans.

Corrosion of carbon steel influenced by anaerobic biofilm in natural seawater

The bacteria in the anaerobic biofilm on rusted carbon steel immersed in natural seawater were characterized by culturing and molecular biology techniques. Two types of anaerobic bacterium, sulfate-reducing bacteria (SRB) Desulfovibrio caledoniensis and iron-reducing bacteria Clostridium sp. uncultured were found. The compositions of the rust layer were also analyzed and we found that iron oxide and sulfate green rust were the major components. To investigate the corrosion mechanisms, electrochemical impedance spectra was obtained based on the isolated sulfate-reducing bacteria and mixed bacteria cultured from rust layer in laboratory culture conditions. We found that single species produced iron sulfide and accelerated corrosion, but mixed species produced sulfate green rust and inhibited corrosion. The anaerobic corrosion mechanism of steel was proposed and its environmental significance was discussed. (c) 2008 Elsevier Ltd. All rights reserved.

Estudo da suscetibilidade aos antibióticos em isolados de Enterobacteriaceae provenientes de suiniculturas Portuguesas

Projeto de Pós-Graduação/Dissertação apresentado à Universidade Fernando Pessoa como parte dos requisitos para obtenção do grau de Mestre em Ciências Farmacêuticas

Patient-based outcome assessment instruments in acupuncture research.

BACKGROUND: Outcome assessment can support the therapeutic process by providing a way to track symptoms and functionality over time, providing insights to clinicians and patients, as well as offering a common language to discuss patient behavior/functioning. OBJECTIVES: In this article, we examine the patient-based outcome assessment (PBOA) instruments that have been used to determine outcomes in acupuncture clinical research and highlight measures that are feasible, practical, economical, reliable, valid, and responsive to clinical change. The aims of this review were to assess and identify the commonly available PBOA measures, describe a framework for identifying appropriate sets of measures, and address the challenges associated with these measures and acupuncture. Instruments were evaluated in terms of feasibility, practicality, economy, reliability, validity, and responsiveness to clinical change. METHODS: This study was a systematic review. A total of 582 abstracts were reviewed using PubMed (from inception through April 2009). RESULTS: A total of 582 citations were identified. After screening of title/abstract, 212 articles were excluded. From the remaining 370 citations, 258 manuscripts identified explicit PBOA; 112 abstracts did not include any PBOA. The five most common PBOA instruments identified were the Visual Analog Scale, Symptom Diary, Numerical Pain Rating Scales, SF-36, and depression scales such as the Beck Depression Inventory. CONCLUSIONS: The way a questionnaire or scale is administered can have an effect on the outcome. Also, developing and validating outcome measures can be costly and difficult. Therefore, reviewing the literature on existing measures before creating or modifying PBOA instruments can significantly reduce the burden of developing a new measure.

Automatic segmentation of seven retinal layers in SDOCT images congruent with expert manual segmentation.

Segmentation of anatomical and pathological structures in ophthalmic images is crucial for the diagnosis and study of ocular diseases. However, manual segmentation is often a time-consuming and subjective process. This paper presents an automatic approach for segmenting retinal layers in Spectral Domain Optical Coherence Tomography images using graph theory and dynamic programming. Results show that this method accurately segments eight retinal layer boundaries in normal adult eyes more closely to an expert grader as compared to a second expert grader.

Integrative Genomics Reveals a Role for GNA13 in Lymphomagenesis

Lymphomas comprise a diverse group of malignancies derived from immune cells. High throughput sequencing has recently emerged as a powerful and versatile method for analysis of the cancer genome and transcriptome. As these data continue to emerge, the crucial work lies in sorting through the wealth of information to hone in on the critical aspects that will give us a better understanding of biology and new insight for how to treat disease. Finding the important signals within these large data sets is one of the major challenges of next generation sequencing.

In this dissertation, I have developed several complementary strategies to describe the genetic underpinnings of lymphomas. I begin with developing a better method for RNA sequencing that enables strand-specific total RNA sequencing and alternative splicing profiling in the same analysis. I then combine this RNA sequencing technique with whole exome sequencing to better understand the global landscape of aberrations in these diseases. Finally, I use traditional cell and molecular biology techniques to define the consequences of major genetic alterations in lymphoma.

Through this analysis, I find recurrent silencing mutations in the G alpha binding protein GNA13 and associated focal adhesion proteins. I aim to describe how loss-of-function mutations in GNA13 can be oncogenic in the context of germinal center B cell biology. Using in vitro techniques including liquid chromatography-mass spectrometry and knockdown and overexpression of genes in B cell lymphoma cell lines, I determine protein binding partners and downstream effectors of GNA13. I also develop a transgenic mouse model to study the role of GNA13 in the germinal center in vivo to determine effects of GNA13 deletion on germinal center structure and cell migration.

Thus, I have developed complementary approaches that span the spectrum from discovery to context-dependent gene models that afford a better understanding of the biological function of aberrant events and ultimately result in a better understanding of disease.

Assessing the viability of studying motion indicators of autism spectrum disorders in infants at high and low risk for ASD using a passive motion capture system

Gemstone Team AMIRA