Aquatic plant community in porto primavera reservoir

Aiming to identify the populations of aquatic plants present in the Porto Primavera reservoir and evaluate the behavior of Hydrilla verticillata colonization of this water body a survey was carried out in 2007. The data was based on presence or absence, only were assessed the presence or absence of the species and the data were subjected to cluster analysis to establish differences in distribution and occurrence of populations. The community of aquatic plants showed 24 species distributed in 16 botanical families. Cyperaceae and Pontederiaceae were the most representative in terms of species richness. The submerged macrophyte Hydrilla verticillata showed the highest frequency of occurrence in the water body, showing a different behavior from the other populations of the water body. Species like Eichhornia crassipes, Eichhornia azurea, Typha dominguensis and Oxycaryum cubense also showed different behavior in relation to other populations within the community, forming large populations in lagoons and backwater areas.

Developing Bioimage Informatics – from Microscopy to Software Solutions – with alpha2beta1 Integrin as a Case Study

Biokuvainformatiikan kehittäminen – mikroskopiasta ohjelmistoratkaisuihin – sovellusesimerkkinä α2β1-integriini Kun ihmisen genomi saatiin sekvensoitua vuonna 2003, biotieteiden päätehtäväksi tuli selvittää eri geenien tehtävät, ja erilaisista biokuvantamistekniikoista tuli keskeisiä tutkimusmenetelmiä. Teknologiset kehitysaskeleet johtivat erityisesti fluoresenssipohjaisten valomikroskopiatekniikoiden suosion räjähdysmäiseen kasvuun, mutta mikroskopian tuli muuntua kvalitatiivisesta tieteestä kvantitatiiviseksi. Tämä muutos synnytti uuden tieteenalan, biokuvainformatiikan, jonka on sanottu mahdollisesti mullistavan biotieteet. Tämä väitöskirja esittelee laajan, poikkitieteellisen työkokonaisuuden biokuvainformatiikan alalta. Väitöskirjan ensimmäinen tavoite oli kehittää protokollia elävien solujen neliulotteiseen konfokaalimikroskopiaan, joka oli yksi nopeimmin kasvavista biokuvantamismenetelmistä. Ihmisen kollageenireseptori α2β1-integriini, joka on tärkeä molekyyli monissa fysiologisissa ja patologisissa prosesseissa, oli sovellusesimerkkinä. Työssä saavutettiin selkeitä visualisointeja integriinien liikkeistä, yhteenkeräytymisestä ja solun sisään siirtymisestä, mutta työkaluja kuvainformaation kvantitatiiviseen analysointiin ei ollut. Väitöskirjan toiseksi tavoitteeksi tulikin tällaiseen analysointiin soveltuvan tietokoneohjelmiston kehittäminen. Samaan aikaan syntyi biokuvainformatiikka, ja kipeimmin uudella alalla kaivattiin erikoistuneita tietokoneohjelmistoja. Tämän väitöskirjatyön tärkeimmäksi tulokseksi muodostui näin ollen BioImageXD, uudenlainen avoimen lähdekoodin ohjelmisto moniulotteisten biokuvien visualisointiin, prosessointiin ja analysointiin. BioImageXD kasvoi yhdeksi alansa suurimmista ja monipuolisimmista. Se julkaistiin Nature Methods -lehden biokuvainformatiikkaa käsittelevässä erikoisnumerossa, ja siitä tuli tunnettu ja laajalti käytetty. Väitöskirjan kolmas tavoite oli soveltaa kehitettyjä menetelmiä johonkin käytännönläheisempään. Tehtiin keinotekoisia piidioksidinanopartikkeleita, joissa oli "osoitelappuina" α2β1-integriinin tunnistavia vasta-aineita. BioImageXD:n avulla osoitettiin, että nanopartikkeleilla on potentiaalia lääkkeiden täsmäohjaussovelluksissa. Tämän väitöskirjatyön yksi perimmäinen tavoite oli edistää uutta ja tuntematonta biokuvainformatiikan tieteenalaa, ja tämä tavoite saavutettiin erityisesti BioImageXD:n ja sen lukuisten julkaistujen sovellusten kautta. Väitöskirjatyöllä on merkittävää potentiaalia tulevaisuudessa, mutta biokuvainformatiikalla on vakavia haasteita. Ala on liian monimutkainen keskimääräisen biolääketieteen tutkijan hallittavaksi, ja alan keskeisin elementti, avoimen lähdekoodin ohjelmistokehitystyö, on aliarvostettu. Näihin seikkoihin tarvitaan useita parannuksia,

SobekCM’s Community Ecosystems & Socio-Technical Practices

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

What is behind the OpenDOAR? New Development and Community Benefits

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Building Successful, Open Repository Software Ecosystems: Technology and Community

Panel at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Weed Community in a Raw Sugarcane Renovation Area Submitted to Different Soil Managements

The objective of this study was to evaluate the weed community in a raw sugarcane renovation area with three soil managements and peanut sowing in succession. The experiment was conducted during the 2007/08 season on a raw sugarcane area harvested without prior burning in the last five cuts. A randomized block design with treatments arranged in a split plot and arranged in four replications was used. The main treatments consisted of three cropping systems: conventional tillage, minimum tillage and direct planting, and subplots consisted in the absence (resting) or presence of crop rotation with peanuts. After 135 days from planting peanuts and 180 days of sugarcane harvest, the number of weeds m-2 was counted and the shoot dry biomass of the weeds collected was determined. The data were interpreted by analysis of variance and the means were compared by Tukey's test at 5% probability so that phytosociological indices a, b, c e d were calculated. The use of soil conservation tillage and peanut in rotation with sugarcane in the renovation areas is effective in controlling weeds and suppression of weed species difficult to control like Cyperus rotundus, Commelina bengalensis, Urochloa plantaginea, and Digitaria nuda.

Islandora Archipelago: Update on the Project & Community

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Open Preservation: Community Approaches to Ensuring Long-Term Access to Digital Collections

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Diameter and height distributions in a gallery forest tree community and some of its main species in central Brazil over a six-year period (1985-1991)

(Diameter and height distributions in a gallery forest tree community and some of its main species in central Brazil over a six-year period (1985-1991)). The diameter and height structure were studied over six years in approximately 64 ha of the Gama gallery forest in Brasília, DF. Trees from 10 cm dbh were measured every three years from 1985 in 151 (10 x 20 m) permanent plots. Natural regeneration (individuals under 10 cm dbh) was measured in subplots within the 200 m² plots. Most individuals and species were under 45 cm diameter and 20 m high while the maximum diameter for individual species ranged from 30 to 95 cm. The diameter structure was typical of a mixed tropical forest with the number of individuals decreasing with increasing size classes and showing little change over the six years. The most abundant species occupy different positions in the canopy and have different size structures.

How to Hack the DSpace Community

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

A museum object repository using LIDO schema

Poster at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Diversity and structure of the tree community of a fragment of tropical secondary forest of the brazilian Atlantic Forest domain 15 and 40 years after logging

Two adjacent tracts of tropical secondary forest, situated in Itambé do Mato Dentro, south-eastern Brazil, which had been regenerating for 15 and 40 years after clearing, were compared with the purpose of detecting differences in species diversity and composition, species guild composition (regeneration, stratification and dispersion), and stand structure. Four and three 1,125 m² plots laid on the 15- and 40-year-old stands, respectively, sampled 2,430 trees with diameter at the base of the stem > 5 cm. The number of species (S = 199) was high for this forest type and significantly higher for the older stand. Tree density was significantly higher in the younger stand, particularly for smaller trees, whereas the two stands did not differ in both basal area and volume per hectare. Trees of shade-tolerant and understory species were significantly more abundant in the older stand. Though sharing a large proportion of species (49%), the two stands differed significantly in the abundance of many species. Live stumps probably contributed to the relatively quick restoration of some forest characteristics, particularly species diversity, basal area and volume.

Horizontal and vertical tree community structure in a lowland atlantic rain forest, southeastern Brazil

The horizontal and vertical tree community structure in a lowland Atlantic Rain Forest was investigated through a phytosociological survey in two 0.99 ha plots in the Intervales State Park, São Paulo State. All trees > 5 cm diameter at breast height were recorded. 3,078 individuals belonging to 172 species were identified and recorded. The Shannon diversity index was H' = 3.85 nat.ind.-1. The Myrtaceae family showed the greatest floristic richness (38 species) and the highest density (745 individuals) in the stand. Euterpe edulis Mart. had the highest importance value (33.98%) accounting for 21.8% of all individuals recorded. The quantitative similarity index was higher than the qualitative index, showing little structural variation between plots. However, the large number of uncommon species resulted in pronounced floristic differences. A detrended correspondence analysis (DCA) generated three arbitrary vertical strata. Stratum A (> 26 m), where Sloanea guianensis (Aubl.) Benth. and Virola bicuhyba (Schott. ex A.DC.) Warb. were predominant showed the lowest density. Stratum B (8 m < h < 26 m) had the greatest richness and diversity, and stratum C (< 8 m) showed the highest density. Euterpe edulis, Guapira opposita (Vell.) Reitz, Garcinia gardneriana (Planch. & Triana) Zappi, and Eugenia mosenii (Kausel) Sobral were abundant in strata B and C. The occurrence of strata in tropical forests is discussed and we recommend the use of DCA for others studies of the vertical distribution of tropical forest tree communities.

Forest spatial heterogeneity and palm richness, abundance and community composition in Terra Firme forest, Central Amazon

The mechanisms that maintain tree diversity in tropical rain forests are still in debate. Variations in forest structural components produce forest microenvironmental heterogeneity, which in turn may affect plant performance and have been scarcely analyzed in the Amazon. Palms are widespread in the Neotropical rainforests and have relatively well known taxonomy, apart from being ecologically and economically important. The understanding of how palms respond to variation in the forest structural components may help to explain their abundance and richness in a given area. In this study, we describe a palm community and analyze how it is affected by forest microenvironmental heterogeneity. In a pristine "Terra Firme" forest at Reserva Ducke, Manaus, we recorded all adult palm trees in twenty 100 × 10 m plots. In the same plots we recorded the variation in canopy openness, the leaflitter thickness and counted all non-palm forest trees. A total of 713 individuals in 29 palm species were found. The three most abundant species were Astrocaryum sciophilum (Miq.) Pulle, A. gynacanthum Mart. and Attalea attaleoides (Barb. Rodr.) Wess. Boer. The most locally abundant species were also very frequent or occurred in a larger number of plots. There were no significant effects of litter depth, forest canopy openness and forest tree abundance on palm richness. However, in areas where leaf litter was thicker a significant lower number of palm trees occurred. In microsites where proportionally more incident light was reaching the forest understory, due to higher canopy opening, significantly more palm trees were present.

The succession dynamics of a macroalgal community after a flood disturbance in a tropical stream from São Paulo State, southeastern Brazil

The succession dynamics of a macroalgal community in a tropical stream (20º58' S and 49º25' W) was investigated after disturbance by a sequence of intensive rains. High precipitation levels caused almost complete loss of the macroalgal community attached to the substratum and provided a strong pressure against its immediate re-establishment. After this disturbance, a weekly sampling program from May 1999 to January 2000 was established to investigate macroalgal recolonization. The community changed greatly throughout the succession process. The number of species varied from one to seven per sampling. Global abundance of macroalgal community did not reveal a consistent temporal pattern of variation. In early succession stages, the morphological form of tufts dominated, followed by unbranched filaments. Latter succession stages showed the almost exclusive occurrence of gelatinous forms, including filaments and colonies. The succession trajectory was mediated by phosphorus availability in which community composition followed a scheme of changes in growth forms. However, we believe that deterministic and stochastic processes occur in lotic ecosystems, but they are dependent on the length of time considered in the succession analyses.