Adaptation and Constraint in the Plant Reproductive Phase

Conservatism is a central theme of organismic evolution. Related species share characteristics due to their common ancestry. Some concern have been raised among evolutionary biologists, whether such conservatism is an expression of natural selection or of a constrained ability to adapt. This thesis explores adaptations and constraints within the plant reproductive phase, particularly in relation to the evolution of fleshy fruit types (berries, drupes, etc.) and the seasonal timing of flowering and fruiting. The different studies were arranged along a hierarchy of scale, with general data sets sampled among seed plants at the global scale, through more specific analyses of character evolution within the genus Rhamnus s.l. L. (Rhamnaceae), to descriptive and experimental field studies in a local population of Frangula alnus (Rhamnaceae). Apart from the field study, this thesis is mainly based on comparative methods explicitly incorporating phylogenetic relationships. The comparative study of Rhamnus s.l. species included the reconstruction of phylogenetic hypotheses based on DNA sequences. Among geographically overlapping sister clades, biotic pollination was not correlated with higher species richness when compared to wind pollinated plants. Among woody plants, clades characterized by fleshy fruit types were more species rich than their dry-fruited sister clades, suggesting that the fleshy fruit is a key innovation in woody habitats. Moreover, evolution of fleshy fruits was correlated with a change to more closed (darker) habitats. An independent contrast study within Rhamnus s.l. documented allometric relations between plant and fruit size. As a phylogenetic constraint, allometric effects must be considered weak or non-existent, though, as they did not prevail among different subclades within Rhamnus s.l. Fruit size was correlated with seed size and seed number in F. alnus. This thesis suggests that frugivore selection on fleshy fruit may be important by constraining the upper limits of fruit size, when a plant lineage is colonizing (darker) habitats where larger seed size is adaptive. Phenological correlations with fruit set, dispersal, and seed size in F. alnus, suggested that the evolution of reproductive phenology is constrained by trade-offs and partial interdependences between flowering, fruiting, dispersal, and recruitment phases. Phylogenetic constraints on the evolution of phenology were indicated by a lack of correlation between flowering time and seasonal length within Rhamnus cathartica and F. alnus, respectively. On the other hand, flowering time was correlated with seasonal length among Rhamnus s.l. species. Phenological differences between biotically and wind pollinated angiosperms also suggested adaptive change in reproductive phenology.

A novel phase variation mechanism in the meningococcus driven by a ligand-responsive repressor and differential spacing of distal promoter elements

Phase variable expression, mediated by high frequency reversible changes in the length of simple sequence repeats, facilitates adaptation of bacterial populations to changing environments and is frequently important in bacterial virulence. Here we elucidate a novel phase variable mechanism for NadA expression, an adhesin and invasin of Neisseria meningitidis. The NadR repressor protein binds to operators flanking the phase variable tract of the nadA promoter gene and contributes to the differential expression levels of phase variant promoters with different numbers of repeats, likely due to different spacing between operators. It is shown that IHF binds between these operators, and may permit looping of the promoter, allowing interaction of NadR at operators located distally or overlapping the promoter. The 4-hydroxyphenylacetic acid, a metabolite of aromatic amino acid catabolism that is secreted in saliva, induces nadA expression by inhibiting the DNA binding activity of the NadR repressor. When induced, only minor differences are evident between NadR-independent transcription levels of promoter phase variants, which are likely due to differential RNA polymerase contacts leading to altered promoter activity. These results suggest that NadA expression is under both stochastic and tight environmental-sensing regulatory control, and both regulations are mediated by the NadR repressor that and may be induced during colonization of the oropharynx where it plays a major role in the successful adhesion and invasion of the mucosa. Hence, simple sequence repeats in promoter regions may be a strategy used by host-adapted bacterial pathogens to randomly switch between expression states that may nonetheless still be induced by appropriate niche-specific signals.

[Effectiveness of Integrated Psychological Therapy for schizophrenia patients : A meta-analysis including 28 independent studies.]

Over the past 24 years, research groups in eight different countries have conducted 28 independent evaluation studies on Integrated Psychological Therapy (IPT) including 1,329 schizophrenia patients. The present study examines the effectiveness of IPT under different treatment conditions by means of a meta-analytic review. The most salient results indicate favourable mean effect sizes for IPT in comparison to control groups (placebo-attention conditions, standard care). Moreover, the superiority of IPT continues to increase during an average catamnestic phase of 8.1 months. The method obtains similarly favourable effects in different functional areas (neurocognition, social behaviour, psychopathology) and different assessment formats (expert ratings, self-reports, psychological tests). The comparison of different settings of IPT and control groups shows the superiority of IPT in any given therapy or site condition. The analysis of subsamples of inpatients, outpatients, and patients in varying rehabilitation phases reveals similarly favourable effects. Comparing only high-quality studies yields comparable results. In summary, the present meta-analysis corroborates evidence that IPT is an 'empirically validated treatment' according to American Psychiatric Association guidelines.

Analyzing the effects of vertical acceleration and deceleration in multi-phase, debris-flow sediment-column experiments / by Christine Marie Williams.

Water-saturated debris flows are among some of the most destructive mass movements. Their complex nature presents a challenge for quantitative description and modeling. In order to improve understanding of the dynamics of these flows, it is important to seek a simplified dynamic system underlying their behavior. Models currently in use to describe the motion of debris flows employ depth-averaged equations of motion, typically assuming negligible effects from vertical acceleration. However, in many cases debris flows experience significant vertical acceleration as they move across irregular surfaces, and it has been proposed that friction associated with vertical forces and liquefaction merit inclusion in any comprehensive mechanical model. The intent of this work is to determine the effect of vertical acceleration through a series of laboratory experiments designed to simulate debris flows, testing a recent model for debris flows experimentally. In the experiments, a mass of water-saturated sediment is released suddenly from a holding container, and parameters including rate of collapse, pore-fluid pressure, and bed load are monitored. Experiments are simplified to axial geometry so that variables act solely in the vertical dimension. Steady state equations to infer motion of the moving sediment mass are not sufficient to model accurately the independent solid and fluid constituents in these experiments. The model developed in this work more accurately predicts the bed-normal stress of a saturated sediment mass in motion and illustrates the importance of acceleration and deceleration.

Four-window technique for measuring optical-phase-space-time-frequency tomography

A new approach, the four-window technique, was developed to measure optical phase-space-time-frequency tomography (OPSTFT). The four-window technique is based on balanced heterodyne detection with two local oscillator (LO) fields. This technique can provide independent control of position, momentum, time and frequency resolution. The OPSTFT is a Wigner distribution function of two independent Fourier transform pairs, phase-space and time-frequency. The OPSTFT can be applied for early disease detection.

Microbe sampling by mucosal dendritic cells is a discrete, MyD88-independent step in DeltainvG S. Typhimurium colitis.

Intestinal dendritic cells (DCs) are believed to sample and present commensal bacteria to the gut-associated immune system to maintain immune homeostasis. How antigen sampling pathways handle intestinal pathogens remains elusive. We present a murine colitogenic Salmonella infection model that is highly dependent on DCs. Conditional DC depletion experiments revealed that intestinal virulence of S. Typhimurium SL1344 DeltainvG mutant lacking a functional type 3 secretion system-1 (DeltainvG)critically required DCs for invasion across the epithelium. The DC-dependency was limited to the early phase of infection when bacteria colocalized with CD11c(+)CX3CR1(+) mucosal DCs. At later stages, the bacteria became associated with other (CD11c(-)CX3CR1(-)) lamina propria cells, DC depletion no longer attenuated the pathology, and a MyD88-dependent mucosal inflammation was initiated. Using bone marrow chimeric mice, we showed that the MyD88 signaling within hematopoietic cells, which are distinct from DCs, was required and sufficient for induction of the colitis. Moreover, MyD88-deficient DCs supported transepithelial uptake of the bacteria and the induction of MyD88-dependent colitis. These results establish that pathogen sampling by DCs is a discrete, and MyD88-independent, step during the initiation of a mucosal innate immune response to bacterial infection in vivo.

GOCE precise orbit determination for the entire Mission – challenges in the final mission phase

The Gravity field and steady-state Ocean Circulation Explorer (GOCE), ESA’s first Earth Explorer core mission, was launched on March 17, 2009 into a sunsynchronous dusk-dawn orbit and eventually re-entered into the Earth’s atmosphere on November 11, 2013. A precise science orbit (PSO) product was provided by the GOCE High-level Processing Facility (HPF) from the GPS high-low Satellite-to-Satellite Tracking (hl-SST) data from the beginning until the very last days of the mission. We recapitulate the PSO procedure and refer to the results achieved until the official end of the GOCE mission on October 21, 2013, where independent validations with Satellite Laser ranging (SLR) measurements confirmed a high quality of the PSO product of about 2 cm 1-D RMS. We then focus on the period after the official end of the mission, where orbits could still be determined thanks to the continuously running GPS receivers delivering high quality data until a few hours before the re-entry into the Earth’s atmosphere. We address the challenges encountered for orbit determination during these last days and report on adaptions in the PSO procedure to also obtain good orbit results at the unprecedented low orbital altitudes below 224 km.

The Presence of Intra- or Subretinal Fluid during the Loading Phase in the Treatment of Exudative Age-Related Macular Degeneration with Intravitreal Ranibizumab Assessed by Optical Coherence Tomography.

PURPOSE To assess intra- and subretinal fluid during the loading phase with intravitreal ranibizumab in exudative age-related macular degeneration and to quantify the accuracy of crosshair scan spectral-domain optical coherence tomography with regard to retinal fluid. METHODS This is a retrospective study of 31 treatment-naive patients who received 3 monthly intravitreal ranibizumab injections. Visual acuity and the presence of retinal fluid were assessed at each visit using volume and crosshair scan protocols. RESULTS Visual acuity improved and central retinal thickness decreased significantly during the loading phase. However, retinal fluid persisted in two thirds of the patients. The accuracy of the crosshair scan to detect fluid was 93%. CONCLUSIONS A substantial proportion of eyes had persistent fluid after 3 months of ranibizumab injections. However, visual improvement was independent of residual fluid. Message: Crosshair scans detect relevant collections of retinal fluid accurately and may be sufficient in daily clinical practice. © 2015 S. Karger AG, Basel.

Modified 3+3 design for phase I clinical trials

Phase I clinical trial is mainly designed to determine the maximum tolerated dose (MTD) of a new drug. Optimization of phase I trial design is crucial to minimize the number of enrolled patients exposed to unsafe dose levels and to provide reliable information to the later phases of clinical trials. Although it has been criticized about its inefficient MTD estimation, nowadays the traditional 3+3 method remains dominant in practice due to its simplicity and conservative estimation. There are many new designs that have been proven to generate more credible MTD estimation, such as the Continual Reassessment Method (CRM). Despite its accepted better performance, the CRM design is still not widely used in real trials. There are several factors that contribute to the difficulties of CRM adaption in practice. First, CRM is not widely accepted by the regulatory agencies such as FDA in terms of safety. It is considered to be less conservative and tend to expose more patients above the MTD level than the traditional design. Second, CRM is relatively complex and not intuitive for the clinicians to fully understand. Third, the CRM method take much more time and need statistical experts and computer programs throughout the trial. The current situation is that the clinicians still tend to follow the trial process that they are comfortable with. This situation is not likely to change in the near future. Based on this situation, we have the motivation to improve the accuracy of MTD selection while follow the procedure of the traditional design to maintain simplicity. We found that in 3+3 method, the dose transition and the MTD determination are relatively independent. Thus we proposed to separate the two stages. The dose transition rule remained the same as 3+3 method. After getting the toxicity information from the dose transition stage, we combined the isotonic transformation to ensure the monotonic increasing order before selecting the optimal MTD. To compare the operating characteristics of the proposed isotonic method and the other designs, we carried out 10,000 simulation trials under different dose setting scenarios to compare the design characteristics of the isotonic modified method with standard 3+3 method, CRM, biased coin design (BC) and k-in-a-row design (KIAW). The isotonic modified method improved MTD estimation of the standard 3+3 in 39 out of 40 scenarios. The improvement is much greater when the target is 0.3 other than 0.25. The modified design is also competitive when comparing with other selected methods. A CRM method performed better in general but was not as stable as the isotonic method throughout the different dose settings. The results demonstrated that our proposed isotonic modified method is not only easily conducted using the same procedure as 3+3 but also outperforms the conventional 3+3 design. It can also be applied to determine MTD for any given TTL. These features make the isotonic modified method of practical value in phase I clinical trials.^

Optimal, minimax, and Bayesian two-stage designs in two-dose phase II clinical trials

Background: For most cytotoxic and biologic anti-cancer agents, the response rate of the drug is commonly assumed to be non-decreasing with an increasing dose. However, an increasing dose does not always result in an appreciable increase in the response rate. This may especially be true at high doses for a biologic agent. Therefore, in a phase II trial the investigators may be interested in testing the anti-tumor activity of a drug at more than one (often two) doses, instead of only at the maximum tolerated dose (MTD). This way, when the lower dose appears equally effective, this dose can be recommended for further confirmatory testing in a phase III trial under potential long-term toxicity and cost considerations. A common approach to designing such a phase II trial has been to use an independent (e.g., Simon's two-stage) design at each dose ignoring the prior knowledge about the ordering of the response probabilities at the different doses. However, failure to account for this ordering constraint in estimating the response probabilities may result in an inefficient design. In this dissertation, we developed extensions of Simon's optimal and minimax two-stage designs, including both frequentist and Bayesian methods, for two doses that assume ordered response rates between doses. ^ Methods: Optimal and minimax two-stage designs are proposed for phase II clinical trials in settings where the true response rates at two dose levels are ordered. We borrow strength between doses using isotonic regression and control the joint and/or marginal error probabilities. Bayesian two-stage designs are also proposed under a stochastic ordering constraint. ^ Results: Compared to Simon's designs, when controlling the power and type I error at the same levels, the proposed frequentist and Bayesian designs reduce the maximum and expected sample sizes. Most of the proposed designs also increase the probability of early termination when the true response rates are poor. ^ Conclusion: Proposed frequentist and Bayesian designs are superior to Simon's designs in terms of operating characteristics (expected sample size and probability of early termination, when the response rates are poor) Thus, the proposed designs lead to more cost-efficient and ethical trials, and may consequently improve and expedite the drug discovery process. The proposed designs may be extended to designs of multiple group trials and drug combination trials.^

Development and evaluation of a video-based modeling strategy for the dissemination phase of a school health tobacco -use prevention program

Even the best school health education programs will be unsuccessful if they are not disseminated effectively in a manner that encourages classroom adoption and implementation. This study involved two components: (1) the development of a videotape intervention to be used in the dissemination phase of a 4-year, NCI-funded diffusion study and (2) the evaluation of that videotape intervention strategy in comparison with a print (information transfer) strategy. Conceptualization has been guided by Social Learning Theory, Diffusion Theory, and communication theory. Additionally, the PRECEDE Framework has been used. Seventh and 8th grade classroom teachers from Spring Branch Independent School District in west Houston participated in the evaluation of the videotape and print interventions using a 57-item preadoption survey instrument developed by the UT Center for Health Promotion Research and Development. Two-way ANOVA was used to study individual score differences for five outcome variables: Total Scale Score (comprised of 57 predisposing, enabling, and reinforcing items), Adoption Characteristics Subscale, Attitude Toward Innovation Subscale, Receptivity Toward Innovation, and Reinforcement Subscale. The aim of the study is to compare the effect upon score differences of video and print interventions alone and in combination. Seventy-three 7th and 8th grade classroom teachers completed the study providing baseline and post-intervention measures on factors related to the adoption and implementation of tobacco-use prevention programs. Two-way ANOVA, in relation to the study questions, found significant scoring differences for those exposed to the videotape intervention alone for both the Attitude Toward Innovation Subscale and the Receptivity to Adopt Subscale. No significant results were found to suggest that print alone influences favorable scoring differences between baseline and post-intervention testing. One interaction effect was found suggesting video and print combined are more effective for influencing favorable scoring differences for the Reinforcement for the Adoption Subscale.^ This research is unique in that it represents a newly emerging field in health promotion communications research with implications for Social Learning Theory, Diffusion Theory, and communication science that are applicable to the development of improved school health interventions. ^

Gotland Deep (Baltic Sea) independent age model based on Palaeomagnetic Secular Variation (PSV) and lead (Pb) deposition profiles

Dating of sediment cores from the Baltic Sea has proven to be difficult due to uncertainties surrounding the 14C reservoir age and a scarcity of macrofossils suitable for dating. Here we present the results of multiple dating methods carried out on cores in the Gotland Deep area of the Baltic Sea. Particular emphasis is placed on the Littorina stage (8 ka ago to the present) of the Baltic Sea and possible changes in the 14C reservoir age of our dated samples. Three geochronological methods are used. Firstly, palaeomagnetic secular variations (PSV) are reconstructed, whereby ages are transferred to PSV features through comparison with varved lake sediment based PSV records. Secondly, lead (Pb) content and stable isotope analysis are used to identify past peaks in anthropogenic atmospheric Pb pollution. Lastly, 14C determinations were carried out on benthic foraminifera (Elphidium spec.) samples from the brackish Littorina stage of the Baltic Sea. Determinations carried out on smaller samples (as low as 4 µg C) employed an experimental, state-of-the-art method involving the direct measurement of CO2 from samples by a gas ion source without the need for a graphitisation step - the first time this method has been performed on foraminifera in an applied study. The PSV chronology, based on the uppermost Littorina stage sediments, produced ten age constraints between 6.29 and 1.29 cal ka BP, and the Pb depositional analysis produced two age constraints associated with the Medieval pollution peak. Analysis of PSV data shows that adequate directional data can be derived from both the present Littorina saline phase muds and Baltic Ice Lake stage varved glacial sediments. Ferrimagnetic iron sulphides, most likely authigenic greigite (Fe3S4), present in the intermediate Ancylus Lake freshwater stage sediments acquire a gyroremanent magnetisation during static alternating field (AF) demagnetisation, preventing the identification of a primary natural remanent magnetisation for these sediments. An inferred marine reservoir age offset (deltaR) is calculated by comparing the foraminifera 14C determinations to a PSV & Pb age model. This deltaR is found to trend towards younger values upwards in the core, possibly due to a gradual change in hydrographic conditions brought about by a reduction in marine water exchange from the open sea due to continued isostatic rebound.

Total nitrogen from solid phase in the Jena Experiment (Main Experiment up to 30cm depth, year 2008)

This data set contains measurements of total nitrogen from the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. Soil sampling and analysis: Stratified soil sampling was performed in April 2008 to a depth of 30 cm. Three independent samples per plot were taken using a split tube sampler with an inner diameter of 4.8 cm (Eijkelkamp Agrisearch Equipment, Giesbeek, the Netherlands). Soil samples were segmented to a depth resolution of 5 cm in the field, giving six depth subsamples per core, and made into composite samples per depth. Sampling locations were less than 30 cm apart from sampling locations in other years. Samples were dried at 40°C. All soil samples were passed through a sieve with a mesh size of 2 mm. Because of much higher proportions of roots in the soil, the samples were further sieved to 1 mm according to common root removal methods. No additional mineral particles were removed by this procedure. Total nitrogen concentration was analyzed on ball-milled subsamples (time 4 min, frequency 30 s-1) by an elemental analyzer at 1150°C (Elementaranalysator vario Max CN; Elementar Analysensysteme GmbH, Hanau, Germany).

Total nitrogen from solid phase in the Jena Experiment (Block 2 Main Experiment up to 100cm depth, year 2002)

This data set contains measurements of total nitrogen from the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. Soil sampling and analysis: Stratified soil sampling to a depth of 1m was performed before sowing in April 2002. Three independent samples per plot were taken of all plots in block 2 using a motor-driven soil column cylinder (Cobra, Eijkelkamp, 8.3 cm in diameter). Soil samples were dried at 40°C and segmented to a depth resolution of 5 cm giving 20 depth subsamples per core. All samples were analyzed independently. All soil samples were passed through a sieve with a mesh size of 2 mm. Rarely present visible plant remains were removed using tweezers. Total nitrogen concentration was analyzed on ball-milled subsamples (time 4 min, frequency 30 s-1) by an elemental analyzer at 1150°C (Elementaranalysator vario Max CN; Elementar Analysensysteme GmbH, Hanau, Germany).

Total nitrogen from solid phase in the Jena Experiment (Main Experiment up to 30cm depth, year 2004)

This data set contains measurements of total nitrogen from the main experiment plots of a large grassland biodiversity experiment (the Jena Experiment; see further details below). In the main experiment, 82 grassland plots of 20 x 20 m were established from a pool of 60 species belonging to four functional groups (grasses, legumes, tall and small herbs). In May 2002, varying numbers of plant species from this species pool were sown into the plots to create a gradient of plant species richness (1, 2, 4, 8, 16 and 60 species) and functional richness (1, 2, 3, 4 functional groups). Plots were maintained by bi-annual weeding and mowing. Soil sampling and analysis: Stratified soil sampling was performed in April 2004 to a depth of 30 cm. Three independent samples per plot were taken using a split tube sampler with an inner diameter of 4.8 cm (Eijkelkamp Agrisearch Equipment, Giesbeek, the Netherlands). Soil samples were segmented to a depth resolution of 5 cm in the field, giving six depth subsamples per core, and made into composite samples per depth. Sampling locations were less than 30 cm apart from sampling locations in other years. Samples were dried at 40°C. All soil samples were passed through a sieve with a mesh size of 2 mm. Because of much higher proportions of roots in the soil, the samples were further sieved to 1 mm according to common root removal methods. No additional mineral particles were removed by this procedure. Total nitrogen concentration was analyzed on ball-milled subsamples (time 4 min, frequency 30 s-1) by an elemental analyzer at 1150°C (Elementaranalysator vario Max CN; Elementar Analysensysteme GmbH, Hanau, Germany).