Plant regeneration directs changes in grassland composition after extreme drought: a 13-year study in southern Switzerland

1. The cover of plant species was recorded annually from 1988 to 2000 in nine spatially replicated plots in a species-rich, semi-natural meadow at Negrentino (southern Alps). This period showed large climatic variation and included the centennial maximum and minimum frequency of days with ≥ 10 mm of rain. 2. Changes in species composition were compared between three 4-year intervals characterized by increasingly dry weather (1988–91), a preceding extreme drought (1992–95), and increasingly wet weather (1997–2000). Redundancy analysis and anova with repeated spatial replicates were used to find trends in vegetation data across time. 3. Recruitment capacity, the potential for fast clonal growth and seasonal expansion rate were determined for abundant taxa and tested in general linear models (GLM) as predictors for rates of change in relative cover of species across the climatically defined 4-year intervals. 4. Relative cover of the major growth forms present, graminoids and forbs, changed more in the period following extreme drought than at other times. Recruitment capacity was the only predictor of species’ rates of change. 5. Following perturbation, re-colonization was the primary driver of vegetation dynamics. The dominant grasses, which lacked high recruitment from seed, therefore decreased in relative abundance. This effect persisted until the end of the study and may represent a lasting response to an extreme climatic event.

Effects of various pollutant mixtures on immune responses of the blue mussel (Mytilus edulis) collected at a salinity gradient in Danish coastal waters, links to supplementary material

The Baltic Sea is a semi-enclosed sea with a steady salinity gradient (3 per mil-30 per mil). Organisms have adapted to such low salinities, but are suspected to be more susceptible to stress. Within the frame of the integrated environmental monitoring BONUS + project "BEAST" the applicability of immune responses of the blue mussel was investigated in Danish coastal waters. The sampling sites were characterised by a salinity range (11-19 per mil) and different mixtures of contaminants (metals, PAHs and POPs), according to chemical analysis of mussel tissues. Variation partitioning (redundancy analysis) was applied to decompose salinity and contamination effects. The results indicated that cellular immune responses (total and differential haemocyte count, phagocytic activity and apoptosis) were mainly influenced by contaminants, whereas humoral factors (haemolytic activity) were mainly impacted by salinity. Hence, cellular immune functions may be suitable as biomarkers in monitoring programmes for the Baltic Sea and other geographic regions with salinity variances of the studied range.

Identification of sample-specific sequences in mammalian cDNA and genomic DNA by the novel ligation-mediated subtraction (Limes)

The representational difference analysis (RDA) and other subtraction techniques are used to enrich sample-specific sequences by elimination of ubiquitous sequences existing in both the sample of interest (tester) and the subtraction partner (driver). While applying the RDA to genomic DNA of cutaneous lymphoma cells in order to identify tumor relevant alterations, we predominantly isolated repetitive sequences and artificial repeat-mediated fusion products of otherwise independent PCR fragments (PCR hybrids). Since these products severely interfered with the isolation of tester-specific fragments, we developed a considerably more robust and efficient approach, termed ligation-mediated subtraction (Limes). In first applications of Limes, genomic sequences and/or transcripts of genes involved in the regulation of transcription, such as transforming growth factor β stimulated clone 22 related gene (TSC-22R), cell death and cytokine production (caspase-1) or antigen presentation (HLA class II sequences), were found to be completely absent in a cutaneous lymphoma line. On the assumption that mutations in tumor-relevant genes can affect their transcription pattern, a protocol was developed and successfully applied that allows the identification of such sequences. Due to these results, Limes may substitute/supplement other subtraction/comparison techniques such as RDA or DNA microarray techniques in a variety of different research fields.

Dinoflagellates of multicorer surface sediments

Only very few studies focus on recent calcareous dinoflagellate cyst diversity, geographic distribution and ecology, so that information on the distribution patterns and environmental affinities of individual cyst species is extremely limited. This information is, however, essential if we want to use calcareous dinoflagellate cysts for palaeoenvironmental reconstruction. Surface sediment samples from the generally oligotrophic western equatorial Atlantic Ocean, offshore northeast Brazil, were therefore quantitatively analysed for their calcareous dinoflagellate cyst content, including the calcareous vegetative coccoid Thoracosphaera heimii. Seven calcareous dinoflagellate cyst species/morphotypes and T. heimii were encountered in high concentrations throughout the area. Substantial differences in the distribution patterns were observed. The highest concentrations of cysts are found in sediments of the more oligotrophic, oceanic regions, beyond the influence of Amazon River discharge waters. Dinoflagellates producing calcareous cysts thus appear to be capable of surviving low nutrient concentrations and produce large numbers of cysts in relatively stable and predictable environments affected by minimal seasonality. To test for the environmental affinities of individual species, distribution patterns in surface sediments were compared with temperature, salinity, density and stratification gradients within the upper water column (0-100 m) over different times of the year, using principal components analysis and redundancy analysis. T. heimii and four of the seven encountered cyst species (Sphaerodinella? albatrosiana, two morphotypes of Sphaerodinella? tuberosa and Scrippsiella regalis) relate to these parameters significantly and the variations in the cyst associations appear to be associated with the different surface water currents characterising the area. The results imply that calcareous dinoflagellate cyst distributions can potentially be used to distinguish between different open oceanic environments and they could, therefore, be useful in tracing water mass movements throughout the late Quaternary.

A developmental intervention science outreach research approach to promoting positive youth development

Recent intervention efforts in promoting positive identity in troubled adolescents have begun to draw on the potential for an integration of the self-construction and self-discovery perspectives in conceptualizing identity processes, as well as the integration of quantitative and qualitative data analytic strategies. This study reports an investigation of the Changing Lives Program (CLP), using an Outcome Mediation (OM) evaluation model, an integrated model for evaluating targets of intervention, while theoretically including a Self-Transformative Model of Identity Development (STM), a proposed integration of self-discovery and self-construction identity processes. This study also used a Relational Data Analysis (RDA) integration of quantitative and qualitative analysis strategies and a structural equation modeling approach (SEM), to construct and evaluate the hypothesized OM/STM model. The CLP is a community supported positive youth development intervention, targeting multi-problem youth in alternative high schools in the Miami Dade County Public Schools (M-DCPS). The 259 participants for this study were drawn from the CLP’s archival data file. The model evaluated in this study utilized three indices of core identity processes (1) personal expressiveness, (2) identity conflict resolution, and (3) informational identity style that were conceptualized as mediators of the effects of participation in the CLP on change in two qualitative outcome indices of participants’ sense of self and identity. Findings indicated the model fit the data (χ2 (10) = 3.638, p = .96; RMSEA = .00; CFI = 1.00; WRMR = .299). The pattern of findings supported the utilization of the STM in conceptualizing identity processes and provided support for the OM design. The findings also suggested the need for methods capable of detecting and rendering unique sample specific free response data to increase the likelihood of identifying emergent core developmental research concepts and constructs in studies of intervention/developmental change over time in ways not possible using fixed response methods alone.

Cognitive competence and life course change in multi-problem adolescents

The dissertation reports on two studies. The purpose of Study I was to develop and evaluate a measure of cognitive competence (the Critical Problem Solving Skills Scale – Qualitative Extension) using Relational Data Analysis (RDA) with a multi-ethnic, adolescent sample. My study builds on previous work that has been conducted to provide evidence for the reliability and validity of the RDA framework in evaluating youth development programs (Kurtines et al., 2008). Inter-coder percent agreement among the TOC and TCC coders for each of the category levels was moderate to high, with a range of .76 to .94. The Fleiss' kappa across all category levels was from substantial agreement to almost perfect agreement, with a range of .72 to .91. The correlation between the TOC and the TCC demonstrated medium to high correlation, with a range of r(40)=.68, p<.001 to r(40)=.79, p<.001. Study II reports an investigation of a positive youth development program using an Outcome Mediation Cascade (OMC) evaluation model, an integrated model for evaluating the empirical intersection between intervention and developmental processes. The Changing Lives Program (CLP) is a community supported positive youth development intervention implemented in a practice setting as a selective/indicated program for multi-ethnic, multi-problem at risk youth in urban alternative high schools in the Miami Dade County Public Schools (M-DCPS). The 259 participants for this study were drawn from the CLP's archival data file. The study used a structural equation modeling approach to construct and evaluate the hypothesized model. Findings indicated that the hypothesized model fit the data (χ2 (7) = 5.651, p = .83; RMSEA = .00; CFI = 1.00; WRMR = .319). My study built on previous research using the OMC evaluation model (Eichas, 2010), and the findings are consistent with the hypothesis that in addition to having effects on targeted positive outcomes, PYD interventions are likely to have progressive cascading effects on untargeted problem outcomes that operate through effects on positive outcomes.

Participation in a positive youth development program and multi -problem alternative high school students' transformative goals: An investigation of the theoretical and methodological utility and validity of the Transformative Goal Attainment (TGAS)

There is a growing body of literature that provides evidence for the efficacy of positive youth development programs in general and preliminary empirical support for the efficacy of the Changing Lives Program (CLP) in particular. This dissertation sought to extend previous efforts to develop and preliminarily examine the Transformative Goal Attainment Scale (TGAS) as a measure of participant empowerment in the promotion of positive development. Consistent with recent advances in the use of qualitative research methods, this dissertation sought to further investigate the utility of Relational Data Analysis (RDA) for providing categorizations of qualitative open-ended response data. In particular, a qualitative index of Transformative Goals, TG, was developed to complement the previously developed quantitative index of Transformative Goal Attainment (TGA), and RDA procedures for calculating reliability and content validity were refined. Second, as a Stage I pilot/feasibility study this study preliminarily examined the potentially mediating role of empowerment, as indexed by the TGAS, in the promotion of positive development. ^ Fifty-seven participants took part in this study, forty CLP intervention participants and seventeen control condition participants. All 57 participants were administered the study's measures just prior to and just following the fall 2003 semester. This study thus used a short-term longitudinal quasi-experimental research design with a comparison control group. ^ RDA procedures were refined and applied to the categorization of open-ended response data regarding participants' transformative goals (TG) and future possible selves (PSQ-QE). These analyses revealed relatively strong, indirect evidence for the construct validity of the categories as well as their theoretically meaningful structural organization, thereby providing sufficient support for the utility of RDA procedures in the categorization of qualitative open-ended response data. ^ In addition, transformative goals (TG) and future possible selves (PSQ-QE), and the quantitative index of perceived goal attainment (TGA) were evaluated as potential mediators of positive development by testing their relationships to other indices of positive intervention outcome within a four-step method involving both analysis of variance (ANOVA and RMANOVAs) and regression analysis. Though more limited in scope than the efforts at the development and refinement of the measures of these mediators, the results were also promising. ^

Metacommunity Structure Along Resource and Disturbance Gradients in Everglades Wetlands

We evaluated metacommunity hypotheses of landscape arrangement (indicative of dispersal limitation) and environmental gradients (hydroperiod and nutrients) in structuring macroinvertebrate and fish communities in the southern Everglades. We used samples collected at sites from the eastern boundary of the southern Everglades and from Shark River Slough, to evaluate the role of these factors in metacommunity structure. We used eigenfunction spatial analysis to model community structure among sites and distance-based redundancy analysis to partition the variability in communities between spatial and environmental filters. For most animal communities, hydrological parameters had a greater influence on structure than nutrient enrichment, however both had large effects. The influence of spatial effects indicative of dispersal limitation was weak and only periphyton infauna appeared to be limited by regional dispersal. At the landscape scale, communities were well-mixed, but strongly influenced by hydrology. Local-scale species dominance was influenced by water-permanence and nutrient enrichment. Nutrient enrichment is limited to water inflow points associated with canals, which may explain its impact in this data set. Hydroperiod and nutrient enrichment are controlled by water managers; our analysis indicates that the decisions they make have strong effects on the communities at the base of the Everglades food web.

(Table 1) Physical oceanography during Lance cruise LA99/2 in the marginal ice zone of the Barents Sea

Zooplankton was studied on eight stations in the marginal ice zone (MIZ) of the Barents Sea, in May 1999, along two transects across the ice edge. On each station, physical background measurements and zooplankton samples were taken every 6 h over a 24 h period at five discrete depth intervals. Cluster analysis revealed separation of open water stations from all ice stations as well as high similarity level among replicates belonging to particular station. Based on five replicates per station, analysis of variance (ANOVA) confirmed significant differences (P < 0.05) in abundances of the main mesozooplankton taxa among stations. Relations between the zooplankton community and environmental parameters were established using redundancy analysis (CANOCO). In total, 55% of mesozooplankton variability within studied area was explained by eight variables with significant conditional effects: depth stratum, fluorescence, temperature, salinity, bottom depth, latitude, bloom situation, and ice concentration. GLM models supported supposition about clear and negative relationship between concentration of Oithona similis, and overall mesozooplankton diversity The analyses showed a dynamic relationship between mesozooplankton distribution and hydrological conditions on short-term scale. Furthermore, our study demonstrated that variability in the physical environment of dynamic MIZ of the Barents Sea has measurable effect on the Arctic pelagic ecosystem.

Cognitive Competence and Life Course Change in Multi-Problem Adolescents

The dissertation reports on two studies. The purpose of Study I was to develop and evaluate a measure of cognitive competence (the Critical Problem Solving Skills Scale – Qualitative Extension) using Relational Data Analysis (RDA) with a multi-ethnic, adolescent sample. My study builds on previous work that has been conducted to provide evidence for the reliability and validity of the RDA framework in evaluating youth development programs (Kurtines et al., 2008). Inter-coder percent agreement among the TOC and TCC coders for each of the category levels was moderate to high, with a range of .76 to .94. The Fleiss’ kappa across all category levels was from substantial agreement to almost perfect agreement, with a range of .72 to .91. The correlation between the TOC and the TCC demonstrated medium to high correlation, with a range of r(40)=.68, p Study II reports an investigation of a positive youth development program using an Outcome Mediation Cascade (OMC) evaluation model, an integrated model for evaluating the empirical intersection between intervention and developmental processes. The Changing Lives Program (CLP) is a community supported positive youth development intervention implemented in a practice setting as a selective/indicated program for multi-ethnic, multi-problem at risk youth in urban alternative high schools in the Miami Dade County Public Schools (M-DCPS). The 259 participants for this study were drawn from the CLP’s archival data file. The study used a structural equation modeling approach to construct and evaluate the hypothesized model. Findings indicated that the hypothesized model fit the data (χ2 (7) = 5.651, p = .83; RMSEA = .00; CFI = 1.00; WRMR = .319). My study built on previous research using the OMC evaluation model (Eichas, 2010), and the findings are consistent with the hypothesis that in addition to having effects on targeted positive outcomes, PYD interventions are likely to have progressive cascading effects on untargeted problem outcomes that operate through effects on positive outcomes.

Analysis and Control of Robot Manipulators with Kinematic Redundancy

A closed-form solution formula for the kinematic control of manipulators with redundancy is derived, using the Lagrangian multiplier method. Differential relationship equivalent to the Resolved Motion Method has been also derived. The proposed method is proved to provide with the exact equilibrium state for the Resolved Motion Method. This exactness in the proposed method fixes the repeatability problem in the Resolved Motion Method, and establishes a fixed transformation from workspace to the joint space. Also the method, owing to the exactness, is demonstrated to give more accurate trajectories than the Resolved Motion Method. In addition, a new performance measure for redundancy control has been developed. This measure, if used with kinematic control methods, helps achieve dexterous movements including singularity avoidance. Compared to other measures such as the manipulability measure and the condition number, this measure tends to give superior performances in terms of preserving the repeatability property and providing with smoother joint velocity trajectories. Using the fixed transformation property, Taylor's Bounded Deviation Paths Algorithm has been extended to the redundant manipulators.

Functional XPB/RAD25 redundancy in Arabidopsis genome: characterization of AtXPB2 and expression analysis

The xeroderma pigmentosum complementation group B (XPB) protein is involved in both DNA repair and transcription in human cells. It is a component of the transcription factor IIH (TFIIH) and is responsible for DNA helicase activity during nucleotide (nt) excision repair (NER). Its high evolutionary conservation has allowed identification of homologous proteins in different organisms, including plants. In contrast to other organisms, Arabidopsis thaliana harbors a duplication of the XPB orthologue (AtXPB1 and AtXPB2), and the proteins encoded by the duplicated genes are very similar (95% amino acid identity). Complementation assays in yeast rad25 mutant strains suggest the involvement of AtXPB2 in DNA repair, as already shown for AtXPB1, indicating that these proteins may be functionally redundant in the removal of DNA lesions in A. thaliana. Although both genes are expressed in a constitutive manner during the plant life cycle, Northern blot analyses suggest that light modulates the expression level of both XPB copies, and transcript levels increase during early stages of development. Considering the high similarity between AtXPB1 and AtXPB2 and that both of predicted proteins may act in DNA repair, it is possible that this duplication may confer more flexibility and resistance to DNA damaging agents in thale cress. (C) 2004 Elsevier B.V. All rights reserved.

Análise por técnica de RDA (Representational Difference Analysis) da expressão gênica diferencial, para a identificação de fatores genéticos associados à produção de etanol em linhagem de Saccharomyces cerevisae

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Tackling redundancy in text summarization through different levels of language analysis

One of the main challenges to be addressed in text summarization concerns the detection of redundant information. This paper presents a detailed analysis of three methods for achieving such goal. The proposed methods rely on different levels of language analysis: lexical, syntactic and semantic. Moreover, they are also analyzed for detecting relevance in texts. The results show that semantic-based methods are able to detect up to 90% of redundancy, compared to only the 19% of lexical-based ones. This is also reflected in the quality of the generated summaries, obtaining better summaries when employing syntactic- or semantic-based approaches to remove redundancy.

Functional XPB/RAD25 redundancy in Arabidopsis genome: characterization of AtXPB2 and expression analysis

The xeroderma pigmentosum complementation group B (XPB) protein is involved in both DNA repair and transcription in human cells. It is a component of the transcription factor IIH (TFIIH) and is responsible for DNA helicase activity during nucleotide (nt) excision repair (NER). Its high evolutionary conservation has allowed identification of homologous proteins in different organisms, including plants. In contrast to other organisms, Arabidopsis thaliana harbors a duplication of the XPB orthologue (AtXPB1 and AtXPB2), and the proteins encoded by the duplicated genes are very similar (95% amino acid identity). Complementation assays in yeast rad25 mutant strains suggest the involvement of AtXPB2 in DNA repair, as already shown for AtXPB1, indicating that these proteins may be functionally redundant in the removal of DNA lesions in A. thaliana. Although both genes are expressed in a constitutive manner during the plant life cycle, Northern blot analyses suggest that light modulates the expression level of both XPB copies, and transcript levels increase during early stages of development. Considering the high similarity between AtXPB1 and AtXPB2 and that both of predicted proteins may act in DNA repair, it is possible that this duplication may confer more flexibility and resistance to DNA damaging agents in thale cress. (C) 2004 Elsevier B.V. All rights reserved.