Performance and Meat Quality of Broiler Chickens Reared on two Different Litter Materials and at two Stocking Densities.

1. This study evaluated the performance and meat quality of broiler chickens reared on two litter materials and at two stocking densities.2. The chicks were allotted in a completely randomised design in a 2 × 2 factorial arrangement with two litter materials (wood shavings or rice straw) and two stocking densities (24 or 30 kg/m2), with six replicates per treatment. Broiler performance, carcase yield, prime cuts, blood plasma proteins, the enzymes alanine aminotransferase and aspartate aminotransferase, edible viscera, immune organs, intestine weight and length, abdominal fat, breast meat colour, pH, weight loss by defrosting, weight loss by cooking and shear force were evaluated.3. The density of 24 kg/m2 positively influenced feed consumption and weight gain. The type of litter had a positive influence on feed conversion, with a lower value for birds raised on wood shavings.4. Breast production was improved in birds reared at a density of 24 kg/m2 when compared to birds reared at a density of 30 kg/m2. The rice straw bedding negatively affected abdominal fat (resulting in higher percentages) when compared to birds reared on wood shavings.5. The types of litter affected the enzyme aspartate aminotransferase in birds raised on wood shavings, although these values were not increased to the point of influence on the physiological functions of broilers.6. The colour of the breast meat, pH, temperature, weight loss after thawing or cooking, shear force, cholesterol, triglycerides, albumin, total proteins, glucose or alanine aminotransferase content were not influenced by the stocking densities or bedding.7. The use of wood shavings as poultry bedding at a stocking density of 24 kg/m2resulted in the best performance for broiler chickens at 42 days of age.

Aquatic macrophytes and trophic interactions: a scientometric analyses and research perspectives / Macrofitas aquáticas e interações tróficas: análise cienciométrica e perspectivas nas pesquisas

Abstract Aquatic macrophytes have a recognized role in ecosystem structuring and an important position in trophic cascades interactions, whose understanding is to improve water quality. In recent years, the number of studies on the role of aquatic macrophytes in trophic webs and interactions has increased, but South America has made little progress in research in the area. In this study, we investigated the main gaps and perspectives for future studies on macrophytes and trophic interactions, analyzing global publications, especially those conducted by South American researchers. We accessed publications using an international database (Thomson Reuters ISI-Web of Knowledge-(formerly Institute for Scientific Information)) from 1980 to 2015. We ranked each article by ecosystem and study approach, biological organization and interacting taxonomic groups (phytoplankton, periphyton, zooplankton, aquatic invertebrates, fish and birds), countries publishing in cooperation and affiliations. The results showed that published studies (n = 242) emphasizing aquatic plants in trophic interactions increased in 35 years. Comparing the contributions of the 32 countries investigated, those from South America as first affiliation, had few publications (n = 26) and in cooperation (n = 7). The largest volume of articles indexed by the researchers dealt with the dynamics and structure of aquatic assemblages, webs and trophic interactions. Ecosystems such reservoirs and wetlands have received little attention. Large numbers of studies have encompassed community-wide aquatic approaches, including in South American studies, the interactions between macrophytes, zooplankton and phytoplankton were the second most studied interactions of all indexed articles. Knowledge about trophic cascade and interactions has been successfully enhanced in several countries with the purpose of restructuring communities and restore water quality of many ecosystems. In summary, we conclude that studies in the area of trophic interactions mediated by macrophytes may be directed in a way to attenuate international asymmetries, encouraging the increase of scientific productivity in South America.

Resumo Macrófitas aquáticas tem reconhecida função na estruturação de ecossistemas e importante papel nas interações tróficas em cascata, cujo entendimento é chave para melhorar a qualidade da água. Nos últimos anos, o número de estudos sobre o papel das macrófitas aquáticas nas interações e teia trófica aumentaram mas, a América do Sul progrediu pouco em pesquisas na área. Nesse estudo investigamos as principais lacunas e perspectivas para estudos futuros sobre macrófitas e interações tróficas analisando publicações mundiais, especialmente aquelas conduzidas por pesquisadores sul-americanos. Acessamos publicações usando base de dados internacional (Thomson Reuters ISI Web of Knowledge) entre 1980 a 2015. Computamos para cada artigo a organização biológica e grupos taxonômicos em interação (fitoplâncton, perifíton, zooplâncton, invertebrados aquáticos, peixes e aves), ecossistema estudado e abordagem de pesquisa, a cooperação entre países da América do Sul e demais, além das filiações. Os resultados mostraram que estudos publicados (n = 242) enfatizando plantas aquáticas em interações tróficas cresceram em 35 anos. Comparando as contribuições dos 32 países investigados, aqueles da América do Sul apresentaram baixo número de indexações (n= 26), poucos em cooperação (n= 7). O maior volume de publicações indexadas pelos pesquisadores trataram sobre a dinâmica e estrutura das assembléias aquáticas, teias e interações tróficas. Reservatórios e áreas alagadas têm recebido pouca atenção. Grande número de estudos compreeenderam abordagems de toda comunidade aquática e interações entre macrófitas, fitoplâncton, zooplâncton e peixes. Em síntese, concluimos que estudos enfatizando as interações tróficas mediadas pelas macrófitas poderão ser direcionados de maneira a atenuar assimetrias internacionais, encorajando o aumento da produtividade científica na América do Sul. O conhecimento sobre as interações tróficas em cascata tem sido desenvolvido com sucesso em diversos países cujas finalidades tem sido reestruturar comunidades e restaurar a qualidade da água de muitos ecossistemas.

Aquatic macrophytes and trophic interactions: a scientometric analyses and research perspectives.

Aquatic macrophytes have a recognized role in ecosystem structuring and an important position in trophic cascades interactions, whose understanding is to improve water quality. In recent years, the number of studies on the role of aquatic macrophytes in trophic webs and interactions has increased, but South America has made little progress in research in the area. In this study, we investigated the main gaps and perspectives for future studies on macrophytes and trophic interactions, analyzing global publications, especially those conducted by South American researchers. We accessed publications using an international database (Thomson Reuters ISI-Web of Knowledge-(formerly Institute for Scientific Information)) from 1980 to 2015. We ranked each article by ecosystem and study approach, biological organization and interacting taxonomic groups (phytoplankton, periphyton, zooplankton, aquatic invertebrates, fish and birds), countries publishing in cooperation and affiliations. The results showed that published studies (n = 242) emphasizing aquatic plants in trophic interactions increased in 35 years. Comparing the contributions of the 32 countries investigated, those from South America as first affiliation, had few publications (n = 26) and in cooperation (n = 7). The largest volume of articles indexed by the researchers dealt with the dynamics and structure of aquatic assemblages, webs and trophic interactions. Ecosystems such reservoirs and wetlands have received little attention. Large numbers of studies have encompassed community-wide aquatic approaches, including in South American studies, the interactions between macrophytes, zooplankton and phytoplankton were the second most studied interactions of all indexed articles. Knowledge about trophic cascade and interactions has been successfully enhanced in several countries with the purpose of restructuring communities and restore water quality of many ecosystems. In summary, we conclude that studies in the area of trophic interactions mediated by macrophytes may be directed in a way to attenuate international asymmetries, encouraging the increase of scientific productivity in South America.

Aquatic macrophytes and trophic interactions: a scientometric analyses and research perspectives

Abstract Aquatic macrophytes have a recognized role in ecosystem structuring and an important position in trophic cascades interactions, whose understanding is to improve water quality. In recent years, the number of studies on the role of aquatic macrophytes in trophic webs and interactions has increased, but South America has made little progress in research in the area. In this study, we investigated the main gaps and perspectives for future studies on macrophytes and trophic interactions, analyzing global publications, especially those conducted by South American researchers. We accessed publications using an international database (Thomson Reuters ISI-Web of Knowledge-(formerly Institute for Scientific Information)) from 1980 to 2015. We ranked each article by ecosystem and study approach, biological organization and interacting taxonomic groups (phytoplankton, periphyton, zooplankton, aquatic invertebrates, fish and birds), countries publishing in cooperation and affiliations. The results showed that published studies (n = 242) emphasizing aquatic plants in trophic interactions increased in 35 years. Comparing the contributions of the 32 countries investigated, those from South America as first affiliation, had few publications (n = 26) and in cooperation (n = 7). The largest volume of articles indexed by the researchers dealt with the dynamics and structure of aquatic assemblages, webs and trophic interactions. Ecosystems such reservoirs and wetlands have received little attention. Large numbers of studies have encompassed community-wide aquatic approaches, including in South American studies, the interactions between macrophytes, zooplankton and phytoplankton were the second most studied interactions of all indexed articles. Knowledge about trophic cascade and interactions has been successfully enhanced in several countries with the purpose of restructuring communities and restore water quality of many ecosystems. In summary, we conclude that studies in the area of trophic interactions mediated by macrophytes may be directed in a way to attenuate international asymmetries, encouraging the increase of scientific productivity in South America.

Resumo Macrófitas aquáticas tem reconhecida função na estruturação de ecossistemas e importante papel nas interações tróficas em cascata, cujo entendimento é chave para melhorar a qualidade da água. Nos últimos anos, o número de estudos sobre o papel das macrófitas aquáticas nas interações e teia trófica aumentaram mas, a América do Sul progrediu pouco em pesquisas na área. Nesse estudo investigamos as principais lacunas e perspectivas para estudos futuros sobre macrófitas e interações tróficas analisando publicações mundiais, especialmente aquelas conduzidas por pesquisadores sul-americanos. Acessamos publicações usando base de dados internacional (Thomson Reuters ISI Web of Knowledge) entre 1980 a 2015. Computamos para cada artigo a organização biológica e grupos taxonômicos em interação (fitoplâncton, perifíton, zooplâncton, invertebrados aquáticos, peixes e aves), ecossistema estudado e abordagem de pesquisa, a cooperação entre países da América do Sul e demais, além das filiações. Os resultados mostraram que estudos publicados (n = 242) enfatizando plantas aquáticas em interações tróficas cresceram em 35 anos. Comparando as contribuições dos 32 países investigados, aqueles da América do Sul apresentaram baixo número de indexações (n= 26), poucos em cooperação (n= 7). O maior volume de publicações indexadas pelos pesquisadores trataram sobre a dinâmica e estrutura das assembléias aquáticas, teias e interações tróficas. Reservatórios e áreas alagadas têm recebido pouca atenção. Grande número de estudos compreeenderam abordagems de toda comunidade aquática e interações entre macrófitas, fitoplâncton, zooplâncton e peixes. Em síntese, concluimos que estudos enfatizando as interações tróficas mediadas pelas macrófitas poderão ser direcionados de maneira a atenuar assimetrias internacionais, encorajando o aumento da produtividade científica na América do Sul. O conhecimento sobre as interações tróficas em cascata tem sido desenvolvido com sucesso em diversos países cujas finalidades tem sido reestruturar comunidades e restaurar a qualidade da água de muitos ecossistemas.

The use of 185 MBq and 740 MBq of 153-samarium hydroxyapatite for knee synovectomy in haemophilia.

The penetration of beta energy of 153-samarium ((153) Sm) (0.8 MeV) is not only appropriate for synovectomy of median articulations but is possible to improve the radiobiological effect using increased activities. The aim of this study was to assess the effectiveness of 185 MBq and 740 MBq of 153-samarium hydroxyapatite ((153) Sm-HA) in knees of haemophilic patients. Thirty-one patients--36 knees, 30 males, were divided into two groups without coinjection of corticosteroid: A - 14 patients (17 knees) treated with intra-articular dose of 185 MBq of (153) Sm-HA, average age 23 years; B--17 patients (19 knees) with 740 MBq of (153) Sm-HA, average age 21.3 years. The evaluation before and after 1 year of synovectomy used the following criteria: reduction in the number of haemarthroses and use of the coagulation factor and improvement in articular motility. Adverse-effects occurrence was considered too. Early and late scintigraphic studies were performed after synoviorthesis and no joint immobilization was recommended. The reduction in haemarthrosis and use of coagulation factor were: group 1--31.3% and 25%; group 2--81.5% and 79% with P < 0.001 respectively; no significant improvement in knees motility was noted for both groups. Four cases of mild reactional synovitis were observed in each group. The scintigraphic control showed homogenous distribution of the radiopharmaceuticals with no articular escape; the material was considered safe by its permanence in the articulation. We have significant improvement in the synovectomy of haemophilic knees with 740 MBq of (153) Sm-HA; the less penetration of its beta radiation was compensated by the increased biological effect with the higher used activity.

Remarkable karyotypic homogeneity in a widespread tropical fish species: Hoplosternum littorale (Siluriformes, Callichthyidae).

The first chromosomal data in Hoplosternum littorale from an isolated South American drainage in north-eastern Brazil are presented. All specimens were characterized by a diploid number (2n) of 60 chromosomes divided into three metacentric, one submetacentric and 26 acrocentric pairs; single nucleolar organizer regions (NOR) on the sixth pair; centromeric and interstitial heterochromatin; GC-rich sites on four large acrocentric chromosomes, including the NOR-bearing pair, and 5S ribosomal genes at terminal region on short arms of two acrocentric pairs. These data are invariably similar to previous reports in H. littorale from distant localities throughout South America, which contrasts with the chromosomal diversity of Callichthyidae and reinforces the role of human activities on the dispersal and colonization of this fish.

Hydrogels containing rutin intended for cutaneous administration: efficacy in wound healing in rats.

OBJECTIVE: Development of a hydrogel containing rutin at 0.025% (w/w) and evaluation of its in vivo efficacy in cutaneous wound healing in rats. METHODS: Hydrogels were prepared using Carbopol Ultrez® 10 NF and an aqueous dispersion of rutin in polysorbate 80. Hydrogels were characterized by means of pH measurement, rheological and spreadability analysis and rutin content determination by liquid chromatography. The in vivo healing effect was evaluated through the regression of skin lesions in rats and by analysis of oxidative stress. RESULTS AND DISCUSSION: Hydrogels showed adequate pH values (5.50-6.50) and pseudoplastic non-Newtonian behavior. After 5 days of treatment of wounds, hydrogels containing rutin presented a higher decrease in the wound area compared to the control hydrogels. Analysis of the oxidative stress showed a decrease in lipid peroxidation and protein carbonyl content as well as an increase in catalase activity after the treatment with the hydrogel containing rutin. Furthermore, this treatment increased total protein levels. CONCLUSION: This study shows for the first time the feasibility of using dermatological formulations containing rutin to improve skin wound healing.

Clinical evaluation after 1 year of 153-samarium hydroxyapatite synovectomy in patients with haemophilic arthropathy.

The aim is to evaluate the efficiency of the treatment with 153-samarium hydroxyapatite (153-Sm-HA) in haemophilic arthropathy. Thirty-one patients (30 males) with ages ranging from 8 to 34 years (average age = 20.6 years) were treated with fixed intra-articular dose of 185 MBq (5 mCi) and divided into two groups: infantile-juvenile (13 patients with up to 18 years of age, an average age of 12.7 years and arthropathy evolution of 7.8 years), and adult (18 patients older than 18 years, an average age of 24 years and arthropathy evolution of 18.7 years). The clinical evaluation before and after 1 year of synovectomy used the following criteria: subjective (pain through visual scale, articulation inspection), objective (articular movement through flexion level, sensitivity to palpation and leakage through joint circumference), reduction on the use of the coagulation factor, number of haemarthrosis, and the occurrence of adverse effects. The results were classified as: 1, good (remission from 70% to 100% of manifestations); 2, moderate (remission from 40% to 69%); and 3, poor (remission from 0% to 39%). Seventy-eight joints were tested: 15 knees, 36 elbows, 24 ankles, 1 shoulder and 2 hips. Early scintigraphic (1-2 h) and late scintigraphic (24-72 h) studies were performed after synoviorthesis. The cost of the procedure per joint was also estimated. No significant difference in the synoviorthesis result between groups was observed. The results were good for 75% of elbows, 87.5% of ankles and 40% of knees; the reduction in haemarthrosis and use of the coagulation factor was respectively 78% and 80% for elbows, 82% and 85% for ankles and 30% and 35% for knees. Four cases of reactional synovitis were observed in the 31 patients. The scintigraphic control showed homogeneous distribution of the material with no articular escape. The use of 153 Sm-HA in the treatment of the haemophilic arthropathy is effective for intermediate-size joints (elbows and ankles), but less effective for knees. Moreover, this treatment presents an excellent safety profile and accessible cost.

Stochastic modeling for characterisation of biofilm development with discrete detachment events (sloughing).

The monitoring of biofilm development at a small-scale is often observed to be a stochastic process. This raises important issues concerning the reproducibility of biofilm growth monitoring experiments. By realising that there are limits to the latter, a model of biofilm accumulation curves that takes into account the dynamics of seemingly random fluctuations resulting from sloughing events is proposed. The model is derived from a stochastic differential equation (SDE) based on the logistic equation, adding a stochastic term for the sloughing events and measurement noise. Experimental light absorbance data that correlate with biofilm biomass obtained from the development of phototrophic biofilms are analysed to illustrate the use of SDE modeling.

Noblest of all metals is structurally unstable at high pressure.

In a series of experiments in externally electrically heated diamond anvil cells we demonstrate that at pressures above approximately 240 GPa gold adopts a hexagonal-close-packed structure. Ab initio calculations predict that at pressures about 250 GPa different stacking sequences of close-packed atomic layers in gold become virtually degenerate in energy, strongly supporting the experimental observations.

Illustration of a common framework for relating multiple typing methods by application to macrolide-resistant Streptococcus pyogenes.

The studies that correlate the results obtained by different typing methodologies rely solely on qualitative comparisons of the groups defined by each methodology. We propose a framework of measures for the quantitative assessment of correspondences between different typing methods as a first step to the global mapping of type equivalences. A collection of 325 macrolide-resistant Streptococcus pyogenes isolates associated with pharyngitis cases in Portugal was used to benchmark the proposed measures. All isolates were characterized by macrolide resistance phenotyping, T serotyping, emm sequence typing, and pulsed-field gel electrophoresis (PFGE), using SmaI or Cfr9I and SfiI. A subset of 41 isolates, representing each PFGE cluster, was also characterized by multilocus sequence typing (MLST). The application of Adjusted Rand and Wallace indices allowed the evaluation of the strength and the directionality of the correspondences between the various typing methods and showed that if PFGE or MLST data are available one can confidently predict the emm type (Wallace coefficients of 0.952 for both methods). In contrast, emm typing was a poor predictor of PFGE cluster or MLST sequence type (Wallace coefficients of 0.803 and 0.655, respectively). This was confirmed by the analysis of the larger data set available from http://spyogenes.mlst.net and underscores the necessity of performing PFGE or MLST to unambiguously define clones in S. pyogenes.

Natural history of drug-resistant clones of Streptococcus pneumoniae colonizing healthy children in Portugal.

A total of 3,539 Streptococcus pneumoniae (Pn) were recovered from 4,969 nasopharyngeal samples of children attending 13 day-care centers (DCCs) located in Lisbon, Portugal, during a surveillance study from January, 2001, through March, 2003, integrated in the European intervention project (EURIS, European Resistance Intervention Study). All Pn isolates were tested for anti-biotyping and drug-resistant pneumococci (DRPn) were further tested by serotyping and pulsed-field gel electrophoresis (PFGE). Overall carriage of Pn was very high (71.2%) and 39.9% of the isolates were resistant to antimicrobials (22.5% with decreased susceptibility to penicillin and 17.4% susceptible to penicillin and resistant to other antimicrobials). Serotypes 6B, 14, 23 F, 19F, and 19 A were prevalent among the 1,287 DRPn and 5.8% of the isolates were non-typeable. Eighty PFGE patterns were identified among 1,285 DRPn, and 93.1% of the DRPn belonged to 26 major clonal types that comprised: Pneumococcal Molecular Epidemiology Network (PMEN) clones (76.3%), Portuguese (PT)-DCC clones, previously detected in 1996-1999 (14.3%), and EURIS PT-DCC new clones, identified for the first time in the EURIS study, during 2001-2003 (9.4%). Comparing with previous Portuguese surveillance studies carried out since 1996, we observed that carriage increased from 47% to 71%, but no major changes were detected on the prevalence of pneumococcal serotypes. Moreover, although PMEN clones were predominant in all DCCs, in the present study the majority of them were gradually decreasing in time whereas several PT-DCC and new clones seemed to be increasing.

Assessment of band-based similarity coefficients for automatic type and subtype classification of microbial isolates analyzed by pulsed-field gel electrophoresis.

Pulsed-field gel electrophoresis (PFGE) has been the typing method of choice for strain identification in epidemiological studies of several bacterial species of medical importance. The usual procedure for the comparison of strains and assignment of strain type and subtype relies on visual assessment of band difference number, followed by an incremental assignment to the group hosting the most similar type previously seen. Band-based similarity coefficients, such as the Dice or the Jaccard coefficient, are then used for dendrogram construction, which provides a quantitative assessment of strain similarity. PFGE type assignment is based on the definition of a threshold linkage value, below which strains are assigned to the same group. This is typically performed empirically by inspecting the hierarchical cluster analysis dendrogram containing the strains of interest. This approach has the problem that the threshold value selected is dependent on the linkage method used for dendrogram construction. Furthermore, the use of a linkage method skews the original similarity values between strains. In this paper we assess the goodness of classification of several band-based similarity coefficients by comparing it with the band difference number for PFGE type and subtype classification using receiver operating characteristic curves. The procedure described was applied to a collection of PFGE results for 1,798 isolates of Streptococcus pneumoniae, which documented 96 types and 396 subtypes. The band-based similarity coefficients were found to perform equally well for type classification, but with different proportions of false-positive and false-negative classifications in their minimal false discovery rate when they were used for subtype classification.

Modelling of the extractive membrane bioreactor process based on natural fluorescence fingerprints and process operation history.

A method for non-mechanistic and non-linear modelling of complex biological processes is presented, using the example of the extractive membrane bioreactor (EMB). The model is based on artificial neural networks (ANN), which are able to predict the state of the process from a combination of reactor operational parameters and natural fluorescence fingerprints. Current as well as historic process operation is included in the ANN input vector, in order to account for lag-times within the reactor system and for biofilm dynamics that are dependent on process history. The model is especially relevant for practitioners, as it does not require assumptions on underlying process mechanisms, and it relies on routinely available operational data and on an easy-to-install, non-invasive, in-situ, on-line monitoring method. Moreover, it focuses on the prediction of overall process performance parameters, which are of immediate relevance in practice. The developed model was able to predict the process state very well. Sensitivity analysis revealed that the main impact on process performance stems from process operation rather than the physiological state of the biological culture, and that in the EMB configuration employed process operation history decisively impacts on the process outcome.

Trends in drug resistance, serotypes, and molecular types of Streptococcus pneumoniae colonizing preschool-age children attending day care centers in Lisbon, Portugal: a summary of 4 years of annual surveillance.

Of the nasopharyngeal cultures recovered from 942 day care center (DCC) attendees in Lisbon, Portugal, 591 (62%) yielded Streptococcus pneumoniae during a surveillance performed in February and March of 1999. Forty percent of the isolates were resistant to one or more antimicrobial agents. In particular, 2% were penicillin resistant and 20% had intermediate penicillin resistance. Multidrug resistance to macrolides, lincosamides, and tetracycline was the most frequent antibiotype (17% of all isolates). Serotyping and molecular typing by pulsed-field gel electrophoresis were performed for 202 out of 237 drug-resistant pneumococci (DRPn). The most frequent serotypes were 6B (26%), 14 (22%), 19F (16%), 23F (10%), and nontypeable (12%). The majority (67%) of the DRPn strains were representatives of nine international clones included in the Pneumococcal Molecular Epidemiology Network; eight of them had been detected in previous studies. Fourteen novel clones were identified, corresponding to 26% of the DRPn strains. The remaining 7% of the strains were local clones detected in our previous studies. Comparison with studies conducted since 1996 in Portuguese DCCs identified several trends: (i) the rate of DRPn frequency has fluctuated between 40 and 50%; (ii) the serotypes most frequently recovered have remained the same; (iii) nontypeable strains appear to be increasing in frequency; and (iv) a clone of serotype 33F emerged in 1999. Together, our observations highlight that the nasopharynxes of children in DCCs are a melting pot of successful DRPn clones that are important to study and monitor if we aim to gain a better understanding on the epidemiology of this pathogen.

Local correlation of expression profiles with gene annotations--proof of concept for a general conciliatory method.

MOTIVATION: Integrated analysis of expression data and gene ontology annotations is a prime example of biological data that need co-explanatory interpretation. This particular application is used to validate a new method for integrated analysis of varied biological information. RESULTS: The proposed method consists of determining local correlation coefficients and the corresponding P-values calculated per biological entity. This measure considers the combined intensity and significance of the agreement or disagreement, between two data sources about the same biological entity. The method is applied to the integrated analysis of gene expression and annotation of two gene sets, one from yeast and other from mouse. The potential of the method to generate accurate mechanistic hypothesis is also demonstrated. Specially, negative correlation results pose a new kind of biological hypothesis. Method performance was compared with annotation enrichment methods, and optimal conditions for the superiority of local correlation results are discussed.

Automated biofilm morphology quantification from confocal laser scanning microscopy imaging.

In spite of the immediate visual appeal of confocal laser scanning microscopy images, the extraction of accurate reconstitutions of biofilm morphology requires a lengthy and computational intensive succession of processing steps. However, once performed, it provides ample reward by enabling the quantitative study of biofilm structure. A software suite of image processing tools for full automation of biofilm morphology quantification was developed by integrating preprocessing, segmentation and morphology quantification operations. This software toolbox was implemented in a web server and a user friendly interface was developed to facilitate image submission, storage and sharing, its access being unrestricted for scientific applications. The image bioinformatics tool which results from the integration of the processing operations can be accessed at http://www.itqb.unl.pt:111/clsmip/. Its use is described in this paper and is illustrated with an example of processing of experimental data describing the growth of a mixed species dentrifying biofilm.

Monitoring of biofilm reactors using natural fluorescence fingerprints.

Natural fluorescence as a method to monitor biofilm processes was studied, using the example of an extractive membrane bioreactor for the degradation of 3-chloro-4 methylaniline and 1,2-dichloroethane. Non-invasive, on-line, in-situ 2D fluorometry monitoring was employed to elicit biofilm process status. The fluorescence fingerprints were deconvoluted in a pattern recognition approach using artificial neural networks (ANN) through association with key process performance parameters.

Nutrient removal in a sequencing batch reactor operated with short anaerobic/aerobic cycles.

A single sequencing batch reactor operated with short intermittent aeration cycles was used to simultaneously remove carbon, nitrogen and phosphorus. The complete cycle, comprising feeding, anaerobiosis, aerobiosis, settling and decanting, was only 36 minutes long. The system has shown high and stable nutrient removal at 30 degrees C with acetate as carbon source and it has proved to be rather robust and dynamic, efficiently adapting to most of the changes in operating parameters tested: presence of nitrate in the feeding medium, different substrates (propionate and butyrate), temperature and nutrient shock loads. For the optimum conditions used, a removal efficiency of over 90% was obtained for each nutrient. Description of the population kinetics was obtained for each operating condition, by performing batch tests. Kinetic and stoichiometric parameters were used to infer the relative contribution of each group of microorganisms on SBR performance. Compared to the traditional SBR operated with cycles of 6 hours, the use of short intermittent aeration cycles of 36 minutes corresponds to a 40% reduction on aeration time.