MIMAS 3.0 is a Multiomics Information Management and Annotation System.

BACKGROUND: DNA sequence integrity, mRNA concentrations and protein-DNA interactions have been subject to genome-wide analyses based on microarrays with ever increasing efficiency and reliability over the past fifteen years. However, very recently novel technologies for Ultra High-Throughput DNA Sequencing (UHTS) have been harnessed to study these phenomena with unprecedented precision. As a consequence, the extensive bioinformatics environment available for array data management, analysis, interpretation and publication must be extended to include these novel sequencing data types. DESCRIPTION: MIMAS was originally conceived as a simple, convenient and local Microarray Information Management and Annotation System focused on GeneChips for expression profiling studies. MIMAS 3.0 enables users to manage data from high-density oligonucleotide SNP Chips, expression arrays (both 3'UTR and tiling) and promoter arrays, BeadArrays as well as UHTS data using MIAME-compliant standardized vocabulary. Importantly, researchers can export data in MAGE-TAB format and upload them to the EBI's ArrayExpress certified data repository using a one-step procedure. CONCLUSION: We have vastly extended the capability of the system such that it processes the data output of six types of GeneChips (Affymetrix), two different BeadArrays for mRNA and miRNA (Illumina) and the Genome Analyzer (a popular Ultra-High Throughput DNA Sequencer, Illumina), without compromising on its flexibility and user-friendliness. MIMAS, appropriately renamed into Multiomics Information Management and Annotation System, is currently used by scientists working in approximately 50 academic laboratories and genomics platforms in Switzerland and France. MIMAS 3.0 is freely available via http://multiomics.sourceforge.net/.

Will climate change drive alien invasive plants into areas of high protection value? An improved model-based regional assessment to prioritise the management of invasions.

Species distribution models (SDMs) studies suggest that, without control measures, the distribution of many alien invasive plant species (AIS) will increase under climate and land-use changes. Due to limited resources and large areas colonised by invaders, management and monitoring resources must be prioritised. Choices depend on the conservation value of the invaded areas and can be guided by SDM predictions. Here, we use a hierarchical SDM framework, complemented by connectivity analysis of AIS distributions, to evaluate current and future conflicts between AIS and high conservation value areas. We illustrate the framework with three Australian wattle (Acacia) species and patterns of conservation value in Northern Portugal. Results show that protected areas will likely suffer higher pressure from all three Acacia species under future climatic conditions. Due to this higher predicted conflict in protected areas, management might be prioritised for Acacia dealbata and Acacia melanoxylon. Connectivity of AIS suitable areas inside protected areas is currently lower than across the full study area, but this would change under future environmental conditions. Coupled SDM and connectivity analysis can support resource prioritisation for anticipation and monitoring of AIS impacts. However, further tests of this framework over a wide range of regions and organisms are still required before wide application.

Effect of reducing sensory and environmental stimuli during hospitalized premature infant sleep

OBJECTIVETo compare the total sleep time of premature infant in the presence or absence of reducing sensory and environmental stimuli in the neonatal unit.METHODLongitudinal study in a Neonatal Intermediate Care Unit of a public hospital in Sao Paulo. The sample consisted of 13 premature infants. We used polysomnograph and unstructured observation for data collection. We analyzed 240 and 1200 minutes corresponding to the periods of the presence and absence of environmental management, respectively. Data were compared in proportion to the total sleep time in the two moments proposed by the study.RESULTSThe total sleep time in periods without environmental management was on average 696.4 (± 112.1) minutes and with management 168.5 (± 27.9) minutes, proportionally premature infant slept an average of 70.2% during periods with no intervention and 58.0% without management (p=0.002).CONCLUSIONReducing stimulation and handling of premature infant environment periods was effective to provide greater total sleep time.

Sistemas da qualidade no ensino superior : contributos para modelos de melhoria da qualidade e responsabilidade social

A gestão das Instituições de Ensino Superior está a ser repensada num contexto de globalização tendo em conta a missão destas, a responsabilidade e a sua cultura (ou culturas), impondo-se novos modelos de gestão e governação. A Qualidade e a Responsabilidade Social do Ensino Superior constituem um tema pertinente e actual. As transformações estruturais que as sociedades atravessam aconselham e justificam da parte do Ensino Superior uma atitude consentânea com as necessidades daquelas. Os desafios que, as Instituições de Ensino Superior enfrentam, exigem novas perspectivas estratégicas e nova visão perante cenários de incerteza que surgem a nível mundial, desempenhando a liderança um papel fundamental na qualidade destas instituições. Neste sentido, lança-se no presente estudo, a seguinte questão: Que Modelos de Gestão e Governação contribuem para a melhoria da Qualidade no Ensino Superior? A metodologia utilizada para a realização deste estudo passa pelo delineamento de uma estratégia com cinco fases: elaboração de um plano ajustável à evolução do trabalho, levantamento do estado da arte de uma forma gradual, trabalho de pesquisa e criação, escrita da tese e análise crítica e reflexão. Para além de outros aspectos relevantes no domínio do Ensino Superior, foram estudados diversos modelos, Modelos de Excelência, modelos para implementação de Sistemas de Gestão da Qualidade, Gestão Ambiental, Gestão da Segurança e Saúde do Trabalho, Gestão de Risco; entre outros. Criaram-se diversos Indicadores de Responsabilidade Social neste contexto e foi feito um estudo piloto no âmbito da Responsabilidade Social em Instituições de Ensino Superior. Por último, destacaram-se as conclusões que decorrem do estudo piloto efectuado, bem como reflexões que surgem da investigação teórica realizada. O estudo piloto efectuado permitiu concluir, por exemplo, que existem indícios de algum alheamento no seio das Instituições às temáticas relacionadas com os princípios éticos e com a educação ambiental. Por outro lado, uma grande parte dos indivíduos inquiridos disseram não ter qualquer opinião quando confrontados com questões sobre Participação Social Responsável, Investigação Socialmente Útil e Gestão Social do Conhecimento. Conclui-se que as questões para as pessoas ainda são muito vagas, daí que, faça sentido o debate de todas estas questões, bem como estudos que contribuam para uma mudança de paradigma relativamente à educação, e em particular no Ensino Superior, com vista à qualidade, num sentido abrangente.

Sistemas da qualidade no ensino superior : contributos para modelos de melhoria da qualidade e responsabilidade social

The management of Higher Education Institutions is being rethought, with the mission and culture of the institutions changing due to globalization, resulting in new models of management and governance. The quality of Higher Education and its obligations to society are of current importance. The structural changes that the society has gone through requires a response in higher education that matches the changing needs of the society. Higher Education Institutions require new perspectives and a new strategic vision to cope with the uncertainty arising at a global scale, and this plays a role in their quality and whether they are leading institutions. Thus the following question arises: Which forms of management and governance contribute to the improvement of quality in higher education? The methodology for this study was designed with five stages: preparation of a plan of work within the thesis, the gradual progression to understanding the up-to-date understanding of Higher Education Research, generating research hypotheses and creating further understanding, writing the thesis with critical analysis and reflection. In addition to other relevant issues in higher education, different models were studied: Models of excellence, Models for implementation of Quality Management Systems, Environmental Management, Occupational Health and Safety Management, Risk Management, among others. Several indicators of Social Responsibility were created in this context and a pilot study was conducted in the area of Social Responsibility in Higher Education Institutions. Finally the conclusions resulting from the pilot study are presented and questions arising from the theoretical research are discussed. For example, the pilot study showed that there are indicators of a lack of understanding within the institutions to issues related to ethical and environmental education. Moreover, a large proportion of respondents said individuals have no opinion when confronted with questions on Responsible Social Involvement and Social Research and Social Management of Useful Knowledge. It is concluded that people have a vague awareness of these issues, so these concepts are new to them.

Sistemas da qualidade no ensino superior : contributos para modelos de melhoria da qualidade e responsabilidade social

The management of Higher Education Institutions is being rethought, with the mission and culture of the institutions changing due to globalization, resulting in new models of management and governance. The quality of Higher Education and its obligations to society are of current importance. The structural changes that the society has gone through requires a response in higher education that matches the changing needs of the society. Higher Education Institutions require new perspectives and a new strategic vision to cope with the uncertainty arising at a global scale, and this plays a role in their quality and whether they are leading institutions. Thus the following question arises: Which forms of management and governance contribute to the improvement of quality in higher education? The methodology for this study was designed with five stages: preparation of a plan of work within the thesis, the gradual progression to understanding the up-to-date understanding of Higher Education Research, generating research hypotheses and creating further understanding, writing the thesis with critical analysis and reflection. In addition to other relevant issues in higher education, different models were studied: Models of excellence, Models for implementation of Quality Management Systems, Environmental Management, Occupational Health and Safety Management, Risk Management, among others. Several indicators of Social Responsibility were created in this context and a pilot study was conducted in the area of Social Responsibility in Higher Education Institutions. Finally the conclusions resulting from the pilot study are presented and questions arising from the theoretical research are discussed. For example, the pilot study showed that there are indicators of a lack of understanding within the institutions to issues related to ethical and environmental education. Moreover, a large proportion of respondents said individuals have no opinion when confronted with questions on Responsible Social Involvement and Social Research and Social Management of Useful Knowledge. It is concluded that people have a vague awareness of these issues, so these concepts are new to them.

Sistemas da qualidade no ensino superior : contributos para modelos de melhoria da qualidade e responsabilidade social

The management of Higher Education Institutions is being rethought, with the mission and culture of the institutions changing due to globalization, resulting in new models of management and governance. The quality of Higher Education and its obligations to society are of current importance. The structural changes that the society has gone through requires a response in higher education that matches the changing needs of the society. Higher Education Institutions require new perspectives and a new strategic vision to cope with the uncertainty arising at a global scale, and this plays a role in their quality and whether they are leading institutions. Thus the following question arises: Which forms of management and governance contribute to the improvement of quality in higher education? The methodology for this study was designed with five stages: preparation of a plan of work within the thesis, the gradual progression to understanding the up-to-date understanding of Higher Education Research, generating research hypotheses and creating further understanding, writing the thesis with critical analysis and reflection. In addition to other relevant issues in higher education, different models were studied: Models of excellence, Models for implementation of Quality Management Systems, Environmental Management, Occupational Health and Safety Management, Risk Management, among others. Several indicators of Social Responsibility were created in this context and a pilot study was conducted in the area of Social Responsibility in Higher Education Institutions. Finally the conclusions resulting from the pilot study are presented and questions arising from the theoretical research are discussed. For example, the pilot study showed that there are indicators of a lack of understanding within the institutions to issues related to ethical and environmental education. Moreover, a large proportion of respondents said individuals have no opinion when confronted with questions on Responsible Social Involvement and Social Research and Social Management of Useful Knowledge. It is concluded that people have a vague awareness of these issues, so these concepts are new to them.

Glyphosate behavior in a Rhodic Oxisol under no-till and conventional agricultural systems

The behavior of glyphosate in a Rhodic Oxisol, collected from fields under no-till and conventional management systems in Ponta Grossa, Parana state (Brazil) was investigated. Both agricultural systems had been in production for 23 years. Glyphosate mineralization, soil-bound forms, sorption and desorption kinetics, sorption/desorption batch experiments, and soil glyphosate phythoavailability (to Panicum maximum) were determined. The mineralization experiment was set up in a completely randomized design with a 2 x 2 factorial scheme (two management systems and two 14C radiolabelled positions in the glyphosate), with five replicates. 14CO2 evolution was measured in 7-day intervals during 63 days. The glyphosate sorption kinetics was investigated in a batch experiment, employing a glyphosate concentration of 0.84 mg L-1. The equilibration solution was 0.01 mol L-1 CaCl2 and the equilibration times were 0, 10, 30, 60, 120, 240, and 360 min. Sorption/desorption of glyphosate was also investigated using equilibrium batch experiments. Five different concentrations of the herbicide were used for sorption (0.42, 0.84, 1.68, 3.36, and 6.72 mg L-1) and one concentration for desorption. Glyphosate phytoavailability was analyzed in a 2 x 5 factorial scheme with two management systems and five glyphosate concentrations added to soil (0, 4.2, 8.4, 42.0, and 210.0 µg g-1) in a completely randomized design. Phytotoxicity symptoms in P. maximum were evaluated for different periods. The soil under both management systems showed high glyphosate sorption, which impeded its desorption and impaired the mineralization in the soil solution. Practically the total amount of the applied glyphosate was quickly sorbed (over 90 % sorbed within 10 min). Glyphosate bound to residues did not have adverse effects on P. maximum growth. The mineralization of glyphosate was faster under no-till and aminomethylphosphonic acid was the main glyphosate metabolite.

Maize response to nitrogen fertilization timing in two tillage systems in a soil with high organic matter content

No-tillage systems, associated to black oat as preceding cover crop, have been increasingly adopted. This has motivated anticipated maize nitrogen fertilization, transferring it from the side-dress system at the stage when plants have five to six expanded leaves to when the preceding cover crop is eliminated or to maize sowing. This study was conducted to evaluate the effects of soil tillage system and timing of N fertilization on maize grain yield and agronomic efficiency of N applied to a soil with high organic matter content. A three-year field experiment was conducted in Lages, state of Santa Catarina, from 1999 onwards. Treatments were set up in a split plot arrangement. Two soil tillage systems were tested in the main plots: conventional tillage (CT) and no-tillage (NT). Six N management systems were assessed in the split-plots: S1 - control, without N application; S2 - all N (100 kg ha-1) applied at oat desiccation; S3 - all N applied at maize sowing; S4 - all N side-dressed when maize had five expanded leaves (V5 growth stage); S5 - 1/3 of N rate applied at maize sowing and 2/3 at V5; S6 - 2/3 of nitrogen rate applied at maize sowing and 1/3 at V5. Maize response to the time and form of splitting N was not affected by the soil tillage system. Grain yield ranged from 6.0 to 11.8 t ha-1. The anticipation of N application (S2 and S3) decreased grain yield in two of three years. In the rainiest early spring season (2000/2001) of the experiment, S4 promoted an yield advantage of 2.2 t ha-1 over S2 and S3. Application of total N rate before or at sowing decreased the number of kernels produced per ear in 2000/2001 and 2001/2002 and the number of ears produced per area in 2001/2002, resulting in reduced grain yield. The agronomic efficiency of applied N (kg grain increase/kg of N applied) ranged from 13.9 to 38.8 and was always higher in the S4 than in the S2 and S3 N systems. Short-term N immobilization did not reduce grain yield when no N was applied before or at maize sowing in a soil with high organic matter content, regardless of the soil tillage system.

Characterization of soil structure and porosity under long-term conventional tillage and no-tillage systems

Different management systems tend to modify soil structure and porosity over the years. The aim of this study was to study modifications in the morphostructure and porosity of dystroferric Red Latosol (Oxisol) under conventional tillage and no-tillage over a 31- year period. The study began with the description of soil profiles based on the cropping profile method, to identify the most compact structures, define sample collection points for physical and chemical analysis, and determine the water retention curve. A forest soil profile was described and used as reference. The results showed that, under conventional tillage, the microaggregate structure of the Oxisol was fragmented between 0 and 0.20 m, and compact (bulk density = 1.52 Mg m-3) in the sub-surface layer between 0.20 and 0.50 m. Under no-tillage, the structure became compacted (bulk density = 1.40 Mg m-3) between 0 and 0.60 m, but contained fissures and biopores. The volume of the class with a pore diameter of > 100 µm under no-tillage was limited, but practically non-existent in the conventional management system. On the other hand, the classes with a pore diameter of < 100 µm were not affected by the type of soil management system.

Postharvest nitrous oxide emissions from a subtropical oxisol as influenced by summer crop residues and their management

Nitrous oxide (N2O) is the most important non-CO2 greenhouse gas and soil management systems should be evaluated for their N2O mitigation potential. This research evaluated a long-term (22 years) experiment testing the effect of soil management systems on N2O emissions in the postharvest period (autumn) from a subtropical Rhodic Hapludox at the research center FUNDACEP, in Cruz Alta, state of Rio Grande do Sul. Three treatments were evaluated, one under conventional tillage with soybean residues (CTsoybean) and two under no-tillage with soybean (NTsoybean) and maize residues (NTmaize). N2O emissions were measured eight times within 24 days (May 2007) using closed static chambers. Gas flows were obtained based on the relations between gas concentrations in the chamber at regular intervals (0, 15, 30, 45 min) analyzed by gas chromatography. After soybean harvest, accumulated N2O emissions in the period were approximately three times higher in the untilled soil (164 mg m-2 N) than under CT (51 mg m-2 N), with a short-lived N2O peak of 670 mg m-2 h-1 N. In contrast, soil N2O emissions in NT were lower after maize than after soybean, with a N2O peak of 127 g m-2 h-1 N. The multivariate analysis of N2O fluxes and soil variables, which were determined simultaneously with air sampling, demonstrated that the main driving variables of soil N2O emissions were soil microbial activity, temperature, water-filled pore space, and NO3- content. To replace soybean monoculture, crop rotation including maize must be considered as a strategy to decrease soil N2O emissions from NT soils in Southern Brazil in a Autumn.

Pedotransfer functions to estimate proctor test parameters under different tillage systems

The Proctor test is time-consuming and requires sampling of several kilograms of soil. Proctor test parameters were predicted in Mollisols, Entisols and Vertisols of the Pampean region of Argentina under different management systems. They were estimated from a minimum number of readily available soil properties (soil texture, total organic C) and management (training data set; n = 73). The results were used to generate a soil compaction susceptibility model, which was subsequently validated using a second group of independent data (test data set; n = 24). Soil maximum bulk density was estimated as follows: Maximum bulk density (Mg m-3) = 1.4756 - 0.00599 total organic C (g kg-1) + 0.0000275 sand (g kg-1) + 0.0539 management. Management was equal to 0 for uncropped and untilled soils and 1 for conventionally tilled soils. The established models predicted the Proctor test parameters reasonably well, based on readily available soil properties. Tillage systems induced changes in the maximum bulk density regardless of total organic matter content or soil texture. The lower maximum apparent bulk density values under no-tillage require a revision of the relative compaction thresholds for different no-tillage crops.

Carbon stock and its compartments in a subtropical oxisol under long-term tillage and crop rotation systems

Soil organic matter (SOM) plays a crucial role in soil quality and can act as an atmospheric C-CO2 sink under conservationist management systems. This study aimed to evaluate the long-term effects (19 years) of tillage (CT-conventional tillage and NT-no tillage) and crop rotations (R0-monoculture system, R1-winter crop rotation, and R2- intensive crop rotation) on total, particulate and mineral-associated organic carbon (C) stocks of an originally degraded Red Oxisol in Cruz Alta, RS, Southern Brazil. The climate is humid subtropical Cfa 2a (Köppen classification), the mean annual precipitation 1,774 mm and mean annual temperature 19.2 ºC. The plots were divided into four segments, of which each was sampled in the layers 0-0.05, 0.05-0.10, 0.10-0.20, and 0.20-0.30 m. Sampling was performed manually by opening small trenches. The SOM pools were determined by physical fractionation. Soil C stocks had a linear relationship with annual crop C inputs, regardless of the tillage systems. Thus, soil disturbance had a minor effect on SOM turnover. In the 0-0.30 m layer, soil C sequestration ranged from 0 to 0.51 Mg ha-1 yr-1, using the CT R0 treatment as base-line; crop rotation systems had more influence on soil stock C than tillage systems. The mean C sequestration rate of the cropping systems was 0.13 Mg ha-1 yr-1 higher in NT than CT. This result was associated to the higher C input by crops due to the improvement in soil quality under long-term no-tillage. The particulate C fraction was a sensitive indicator of soil management quality, while mineral-associated organic C was the main pool of atmospheric C fixed in this clayey Oxisol. The C retention in this stable SOM fraction accounts for 81 and 89 % of total C sequestration in the treatments NT R1 and NT R2, respectively, in relation to the same cropping systems under CT. The highest C management index was observed in NT R2, confirming the capacity of this soil management practice to improve the soil C stock qualitatively in relation to CT R0. The results highlighted the diversification of crop rotation with cover crops as a crucial strategy for atmospheric C-CO2 sequestration and SOM quality improvement in highly weathered subtropical Oxisols.

Long-term C-CO2 emissions and carbon crop residue mineralization in an oxisol under different tillage and crop rotation systems

Soil C-CO2 emissions are sensitive indicators of management system impacts on soil organic matter (SOM). The main soil C-CO2 sources at the soil-plant interface are the decomposition of crop residues, SOM turnover, and respiration of roots and soil biota. The objectives of this study were to evaluate the impacts of tillage and cropping systems on long-term soil C-CO2 emissions and their relationship with carbon (C) mineralization of crop residues. A long-term experiment was conducted in a Red Oxisol in Cruz Alta, RS, Brazil, with subtropical climate Cfa (Köppen classification), mean annual precipitation of 1,774 mm and mean annual temperature of 19.2 ºC. Treatments consisted of two tillage systems: (a) conventional tillage (CT) and (b) no tillage (NT) in combination with three cropping systems: (a) R0- monoculture system (soybean/wheat), (b) R1- winter crop rotation (soybean/wheat/soybean/black oat), and (c) R2- intensive crop rotation (soybean/ black oat/soybean/black oat + common vetch/maize/oilseed radish/wheat). The soil C-CO2 efflux was measured every 14 days for two years (48 measurements), by trapping the CO2 in an alkaline solution. The soil gravimetric moisture in the 0-0.05 m layer was determined concomitantly with the C-CO2 efflux measurements. The crop residue C mineralization was evaluated with the mesh-bag method, with sampling 14, 28, 56, 84, 112, and 140 days after the beginning of the evaluation period for C measurements. Four C conservation indexes were used to assess the relation between C-CO2 efflux and soil C stock and its compartments. The crop residue C mineralization fit an exponential model in time. For black oat, wheat and maize residues, C mineralization was higher in CT than NT, while for soybean it was similar. Soil moisture was higher in NT than CT, mainly in the second year of evaluation. There was no difference in tillage systems for annual average C-CO2 emissions, but in some individual evaluations, differences between tillage systems were noticed for C-CO2 evolution. Soil C-CO2 effluxes followed a bi-modal pattern, with peaks in October/November and February/March. The highest emission was recorded in the summer and the lowest in the winter. The C-CO2 effluxes were weakly correlated to air temperature and not correlated to soil moisture. Based on the soil C conservation indexes investigated, NT associated to intensive crop rotation was more C conserving than CT with monoculture.

Microbial biomass and soil chemical properties under different land use systems in northeastern Pará

The increase in agricultural production in the Brazilian Amazon region is mostly a result of the agricultural frontier expansion, into areas previously influenced by humans or of native vegetation. At the same time, burning is still used to clear areas in small-scale agricultural systems, leading to a loss of the soil productive capacity shortly after, forcing the opening of new areas. This study had the objective of evaluating the effect of soil preparation methods that involve plant residue shredding, left on the surface or incorporated to the soil, with or without chemical fertilization, on the soil chemical and biological properties. The experiment was conducted in 1995, in an experimental field of Yellow Latosol (Oxisol) of the Embrapa Amazônia Oriental, northeastern Pará (Brazil). The experiment was arranged in randomized blocks, in a 2x6 factorial design, with two management systems and six treatments evaluated twice. The management systems consisted of rice (Oriza sativa), followed by cowpea (Vigna unguiculata) with manioc (Manihot esculenta). In the first system the crops were planted in two consecutive cycles, followed by a three-year fallow period (natural regrowth); the second system consisted of one cultivation cycle and was left fallow for three years. The following treatments were applied to the secondary forest vegetation: slash and burn, fertilized with NPK (Q+NPK); slash and burn, without fertilizer NPK (Q-NPK); cutting and shredding, leaving the residues on the soil surface, fertilized with NPK (C+NPK); cutting and shredding, leaving residues on the soil surface, without fertilizer (C-NPK); cutting and shredding, with residue incorporation and fertilized with NPK (I+NPK); cutting and shredding, with residue incorporation and without NPK fertilizer (I-NPK). The soil was sampled in the rainier season (April 2006) and in the drier season (September 2006), in the 0-0.1 m layer. From each plot, 10 simple samples were collected in order to generate a composite sample. In the more intensive management system the contents of microbial C (Cmic) and microbial N (Nmic) were higher, while the C (Corg) level was higher in the less intensive system. The treatments with highest Cmic and Nmic levels were those with cutting, shredding and distribution of biomass on the soil surface. Under both management systems, the chemical characteristics were in ranges that classify the soil as little fertile, although P and K (in the rainy season) were higher in the less intensive management system.