The wide synthetic versatility of five membered rings containing phosphorus

The chemistry of cyclopentadiene rings has been widely studied. This review article deals with a similar chemistry of new compounds containing from 1 to 5 phosphorus atoms on the ring substituting the carbon atoms. The neutral rings containing one, two and three phosphorus atoms can be used as building blocks for the synthesis of new organic compounds containing phosphorus. These rings plus the anionic ones also show great potential as ligands in coordination chemistry. The aim of this article is to show how important this new area is and how diverse the chemistry related to a single type of ring can be.

Genome-wide analysis of adaptive molecular evolution in the carnivorous plant Utricularia gibba

The genome of the bladderwort Utricularia gibba provides an unparalleled opportunity to uncover the adaptive landscape of an aquatic carnivorous plant with unique phenotypic features such as absence of roots, development of water-filled suction bladders, and a highly ramified branching pattern. Despite its tiny size, the U. gibba genome accommodates approximately as many genes as other plant genomes. To examine the relationship between the compactness of its genome and gene turnover, we compared the U. gibba genome with that of four other eudicot species, defining a total of 17,324 gene families (orthogroups). These families were further classified as either 1) lineage-specific expanded/contracted or 2) stable in size. The U. gibba-expanded families are generically related to three main phenotypic features: 1) trap physiology, 2) key plant morphogenetic/developmental pathways, and 3) response to environmental stimuli, including adaptations to life in aquatic environments. Further scans for signatures of protein functional specialization permitted identification of seven candidate genes with amino acid changes putatively fixed by positive Darwinian selection in the U. gibba lineage. The Arabidopsis orthologs of these genes (AXR, UMAMIT41, IGS, TAR2, SOL1, DEG9, and DEG10) are involved in diverse plant biological functions potentially relevant for U. gibba phenotypic diversification, including 1) auxin metabolism and signal transduction, 2) flowering induction and floral meristem transition, 3) root development, and 4) peptidases. Taken together, our results suggest numerous candidate genes and gene families as interesting targets for further experimental confirmation of their functional and adaptive roles in the U. gibba's unique lifestyle and highly specialized body plan.

Wide Area Network Acceleration in Corporate Networks

There are several factors affecting network performance. Some of these can be controlled whereas the others are more fixed. These factors are studied in this thesis from the wide area network (WAN) perspective and the focus is on corporate networks. Another area of interest is the behavior of application protocols when used through WAN. The aim is to study the performance of commonly used application protocols in corporate networks. After identifying the performance problems in corporate WANs the thesis concentrates on methods for improving WAN performance. WAN acceleration is presented as a possible solution. The different acceleration methods are discussed in order to give the reader a theoretical view on how the accelerators can improve WAN performance. Guidelines on the installation of accelerators into a network are also discussed. After a general overview on accelerators is given, one accelerator vendor currently on market is selected for a further analysis. The work is also a case study where two accelerators are installed into a target company network for testing purposes. The tests are performed with three different application protocols that have been identified as critical applications for the target corporation. The aim of the tests is to serve as a proof of concept for WAN acceleration in the target network.

Balancing effluent quality, economic cost and greenhouse gas emissions during the evaluation of (plant-wide) control/operational strategies in WWTPs

The objective of this paper was to show the potential additional insight that result from adding greenhouse gas (GHG) emissions to plant performance evaluation criteria, such as effluent quality (EQI) and operational cost (OCI) indices, when evaluating (plant-wide) control/operational strategies in wastewater treatment plants (WWTPs). The proposed GHG evaluation is based on a set of comprehensive dynamic models that estimate the most significant potential on-site and off-site sources of CO2, CH4 and N2O. The study calculates and discusses the changes in EQI, OCI and the emission of GHGs as a consequence of varying the following four process variables: (i) the set point of aeration control in the activated sludge section; (ii) the removal efficiency of total suspended solids (TSS) in the primary clarifier; (iii) the temperature in the anaerobic digester; and (iv) the control of the flow of anaerobic digester supernatants coming from sludge treatment. Based upon the assumptions built into the model structures, simulation results highlight the potential undesirable effects of increased GHG production when carrying out local energy optimization of the aeration system in the activated sludge section and energy recovery from the AD. Although off-site CO2 emissions may decrease, the effect is counterbalanced by increased N2O emissions, especially since N2O has a 300-fold stronger greenhouse effect than CO2. The reported results emphasize the importance and usefulness of using multiple evaluation criteria to compare and evaluate (plant-wide) control strategies in a WWTP for more informed operational decision making

Determination of copper at wide range concentrations using instrumental features of high-resolution continuum source flame atomic absorption spectrometry

This work describes a method to determine Cu at wide range concentrations in a single run without need of further dilutions employing high-resolution continuum source flame atomic absorption spectrometry. Different atomic lines for Cu at 324.754 nm, 327.396 nm, 222.570 nm, 249.215 nm and 224.426 nm were evaluated and main figures of merit established. Absorbance measurements at 324.754 nm, 249.215 nm and 224.426 nm allows the determination of Cu in the 0.07 - 5.0 mg L-1, 5.0 - 100 mg L-1 and 100 - 800 mg L-1 concentration intervals respectively with linear correlation coefficients better than 0.998. Limits of detection were 21 µg L-1, 310 µg L-1 and 1400 µg L-1 for 324.754 nm, 249.215 nm and 224.426 nm, respectively and relative standard deviations (n = 12) were £ 2.7%. The proposed method was applied to water samples spiked with Cu and the results were in agreement at a 95% of confidence level (paired t-test) with those obtained by line-source flame atomic absorption spectrometry.

Frequency-Domain and Wide-Pulse Time-Domain Measurements of Lanthanide Luminescence and Lanthanide-Based Resonance Energy Transfer

Resonance energy transfer (RET) is a non-radiative transfer of the excitation energy from the initially excited luminescent donor to an acceptor. The requirements for the resonance energy transfer are: i) the spectral overlap between the donor emission spectrum and the acceptor absorption spectrum, ii) the close proximity of the donor and the acceptor, and iii) the suitable relative orientations of the donor emission and the acceptor absorption transition dipoles. As a result of the RET process the donor luminescence intensity and the donor lifetime are decreased. If the acceptor is luminescent, a sensitized acceptor emission appears. The rate of RET depends strongly on the donor–acceptor distance (r) and is inversely proportional to r6. The distance dependence of RET is utilized in binding assays. The proximity requirement and the selective detection of the RET-modified emission signal allow homogeneous separation free assays. The term lanthanide-based RET is used when luminescent lanthanide compounds are used as donors. The long luminescence lifetimes, the large Stokes’ shifts and the intense, sharply-spiked emission spectra of the lanthanide donors offer advantages over the conventional organic donor molecules. Both the organic lanthanide chelates and the inorganic up-converting phosphor (UCP) particles have been used as donor labels in the RET based binding assays. In the present work lanthanide luminescence and lanthanide-based resonance energy transfer phenomena were studied. Luminescence lifetime measurements had an essential role in the research. Modular frequency-domain and time-domain luminometers were assembled and used successfully in the lifetime measurements. The frequency-domain luminometer operated in the low frequency domain ( 100 kHz) and utilized a novel dual-phase lock-in detection of the luminescence. One of the studied phenomena was the recently discovered non-overlapping fluorescence resonance energy transfer (nFRET). The studied properties were the distance and temperature dependences of nFRET. The distance dependence was found to deviate from the Förster theory and a clear temperature dependence was observed whereas conventional RET was completely independent of the temperature. Based on the experimental results two thermally activated mechanisms were proposed for the nFRET process. The work with the UCP particles involved the measurement of the luminescence properties of the UCP particles synthesized in our laboratory. The goal of the UCP particle research is to develop UCP donor labels for binding assays. In the present work the effect of the dopant concentrations and the core–shell structure on the total up-conversion luminescence intensity, the red–green emission ratio, and the luminescence lifetime was studied. Also the non-radiative nature of the energy transfer from the UCP particle donors to organic acceptors was demonstrated for the first time in aqueous environment and with a controlled donor–acceptor distance.

Postcolonial Cultural Identity and the Caribbean White Creole in Jean Rhys’s Wide Sargasso Sea and Phyllis Shand Allfrey’s The Orchid House

Tutkielmassani tarkastelen, miten teokset Wide Sargasso Sea (1966) ja The Orchid House (1953) käsittelevät kulttuuri-identiteettiä henkilöhahmojen luonnissa sekä millaisia yhtäläisyyksiä ja eroja näissä esiintyy. Kulttuuri-identiteetti on yksi jälkikoloniaalisen kirjallisuudentutkimuksen keskeisimmistä teemoista. Tarkastelen tekstejä kahden keskeisen teeman kautta: nimet ja maisemakuvaukset. Molemmat teokset käyttävät näitä teemoja monipuolisesti eri identiteetin osa-alueiden kuvaamiseen. Tarkasteluni keskittyy pääasiassa teosten naispäähahmoihin, mutta käsittelen soveltuvilta osin myös muita henkilöhahmoja. Monet Jean Rhysia ja Phyllis Shand Allfreyta tutkineet kirjallisuuskriitikot ovat olleet haluttomia näkemään teosten välillä olevan yhteyden. Wide Sargasso Sean intertekstuaalinen yhteys Charlotte Brontën teokseen Jane Eyre onkin usein jättänyt hienovaraisemmat intertekstuaaliset viittaukset varjoonsa. Viimeisimpien vuosien aikana on jälkikoloniaalisen kirjallisuudentutkimuksen saralla kuitenkin ollut havaittavissa myönteisempää suhtautumista myös näihin intertekstuaalisiin viittauksiin. Lähtökohtani teosten tarkasteluun on jälkikoloniaalinen kirjallisuudentutkimus ja ensisijaisia teoreettisia lähteitäni ovat muun muassa Patrick Hoganin ja Stuart Hallin käsitykset jälkikoloniaalisesta kulttuuri-identiteetistä. Tarkastelen pääasiallisesti Karibian alueen valkoisten kreolien kulttuuri-identiteettiä. Koska kummankin teoksen keskeisimmät henkilöhahmot ovat pääasiassa naisia, myös naisnäkökulma tulee esiin tutkielmassani. Tutkielmastani käy ilmi, että teosten välillä on selkeä yhteys siinä, millaisia välineitä käytetään kulttuuri-identiteetin kuvaamiseen. Teokset liittyvät kiinteästi dominicalaiseen kirjallisuusperinteeseen, mutta yhteneväisyyksiä on havaittavissa siinä määrin, ettei niitä pystytä selittämään pelkästään samankaltaisella kulttuurisella taustalla.

System-wide approaches to uncover Th2 cell lineage commitment

T helper (Th) cells are vital regulators of the adaptive immune system. When activated by presentation of cognate antigen, Th cells demonstrate capacity to differentiate into functionally distinct effector cell subsets. The Th2 subset is required for protection against extracellular parasites, such as helminths, but is also closely linked to pathogenesis of asthma and allergies. The intracellular molecular signal transduction pathways regulating T helper cell subset differentiation are still incompletely known. Moreover, great majority of studies regarding Th2 differentiation have been conducted with mice models, while studies with human cells have been fewer in comparison. The goal of this thesis was to characterize molecular mechanisms promoting the development of Th2 phenotype, focusing specifically on human umbilical cord blood T cells as an experimental model. These primary cells, activated and differentiated to Th2 cells in vitro, were investigated by complementary system-wide approaches, targeting levels of mRNA, proteins, and lipid molecules. Specifically, the results indicated IL4-regulated recruitment of nuclear protein, and described novel components of the Th2-promoting STAT6 enhanceosome complex. Furthermore, the development of the activated effector cell phenotype was found to correlate with remodeling of the cellular lipidome. These findings will hopefully advance the understanding of human Th2 cell lineage commitment and development of Th2-associated disease states.

From library repository to university-wide service: Stanford Digital Repository as a case study

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

Scalable Feature Selection Applications for Genome-Wide Association Studies of Complex Diseases

Personalized medicine will revolutionize our capabilities to combat disease. Working toward this goal, a fundamental task is the deciphering of geneticvariants that are predictive of complex diseases. Modern studies, in the formof genome-wide association studies (GWAS) have afforded researchers with the opportunity to reveal new genotype-phenotype relationships through the extensive scanning of genetic variants. These studies typically contain over half a million genetic features for thousands of individuals. Examining this with methods other than univariate statistics is a challenging task requiring advanced algorithms that are scalable to the genome-wide level. In the future, next-generation sequencing studies (NGS) will contain an even larger number of common and rare variants. Machine learning-based feature selection algorithms have been shown to have the ability to effectively create predictive models for various genotype-phenotype relationships. This work explores the problem of selecting genetic variant subsets that are the most predictive of complex disease phenotypes through various feature selection methodologies, including filter, wrapper and embedded algorithms. The examined machine learning algorithms were demonstrated to not only be effective at predicting the disease phenotypes, but also doing so efficiently through the use of computational shortcuts. While much of the work was able to be run on high-end desktops, some work was further extended so that it could be implemented on parallel computers helping to assure that they will also scale to the NGS data sets. Further, these studies analyzed the relationships between various feature selection methods and demonstrated the need for careful testing when selecting an algorithm. It was shown that there is no universally optimal algorithm for variant selection in GWAS, but rather methodologies need to be selected based on the desired outcome, such as the number of features to be included in the prediction model. It was also demonstrated that without proper model validation, for example using nested cross-validation, the models can result in overly-optimistic prediction accuracies and decreased generalization ability. It is through the implementation and application of machine learning methods that one can extract predictive genotype–phenotype relationships and biological insights from genetic data sets.

Implementation of hospital-wide computer information system :a case study of this change process

This case study examines the impact of a computer information system as it was being implemented in one Ontario hospital. The attitudes of a cross section of the hospital staff acted as a barometer to measure their perceptions of the implementation process. With The Mississauga Hospital in the early stages of an extensive computer implementation project, the opportunity existed to identify staff attitudes about the computer system, overall knowledge and compare the findings with the literature. The goal of the study was to develop a greater base about the affective domain in the relationship between people and the computer system. Eight exploratory questions shaped the focus of the investigation. Data were collected from three sources: a survey questionnaire, focused interviews, and internal hospital documents. Both quantitative and qualitative data were analyzed. Instrumentation in the study consisted of a survey distributed at two points in time to randomly selected hospital employees who represented all staff levels.Other sources of data included hospital documents, and twenty-five focused interviews with staff who replied to both surveys. Leavitt's socio-technical system, with its four subsystems: task, structure, technology, and people was used to classify staff responses to the research questions. The study findings revealed that the majority of respondents felt positive about using the computer as part of their jobs. No apparent correlations were found between sex, age, or staff group and feelings about using the computer. Differences in attitudes, and attitude changes were found in potential relationship to the element of time. Another difference was found in staff group and perception of being involved in the decision making process. These findings and other evidence about the role of change agents in this change process help to emphasize that planning change is one thing, managing the transition is another.