A versatile and flexible digital pulse programmer for pulsed nuclear magnetic resonance

A versatile and flexible digital pulse programmer for two-pulse, three-pulse, saturation burst and Carr-Purcell sequences is described. Independently variable controls for pulse widths (0.2 mu s to 100 mu s), delay between pulses (0.2 mu s to 100 s) and for number of pulses (1 to 99) for the saturation burst and for the Carr-Purcell sequence, are brought to the front panel. The programmer can be used for one-shot experiments as well as for repetitive experiments.

Characterization of LRRTM and NGR gene families: Expression and functions

Some leucine-rich repeat (LRR) -containing membrane proteins are known regulators of neuronal growth and synapse formation. In this work I characterize two gene families encoding neuronal LRR membrane proteins, namely the LRRTM (leucine-rich repeat, transmembrane neuronal) and NGR (Nogo-66 receptor) families. I studied LRRTM and NGR family member's mRNA tissue distribution by RT-PCR and by in situ hybridization. Subcellular localization of LRRTM1 protein was studied in neurons and in non-neuronal cells. I discovered that LRRTM and NGR family mRNAs are predominantly expressed in the nervous system, and that each gene possesses a specific expression pattern. I also established that LRRTM and NGR family mRNAs are expressed by neurons, and not by glial cells. Within neurons, LRRTM1 protein is not transported to the plasma membrane; rather it localizes to endoplasmic reticulum. Nogo-A (RTN4), MAG, and OMgp are myelin-associated proteins that bind to NgR1 to limit axonal regeneration after central nervous system injury. To better understand the functions of NgR2 and NgR3, and to explore the possible redundancy in the signaling of myelin inhibitors of neurite growth, I mapped the interactions between NgR family and the known and candidate NgR1 ligands. I identified high-affinity interactions between RTN2-66, RTN3-66 and NgR1. I also demonstrate that Rtn3 mRNA is expressed in the same glial cell population of mouse spinal cord white matter as Nogo-A mRNA, and thus it could have a role in myelin inhibition of axonal growth. To understand how NgR1 interacts with multiple structurally divergent ligands, I aimed first to map in more detail the nature of Nogo-A:NgR1 interactions, and then to systematically map the binding sites of multiple myelin ligands in NgR1 by using a library of NgR1 expression constructs encoding proteins with one or multiple surface residues mutated to alanine. My analysis of the Nogo-A:NgR1 -interactions revealed a novel interaction site between the proteins, suggesting a trivalent Nogo-A:NgR1-interaction. Our analysis also defined a central binding region on the concave side of NgR1's LRR domain that is required for the binding of all known ligands, and a surrounding region critical for binding MAG and OMgp. To better understand the biological role of LRRTMs, I generated Lrrtm1 and Lrrtm3 knock out mice. I show here that reporter genes expressed from the targeted loci can be used for maping the neuronal connections of Lrrtm1 and Lrrtm3 expressing neurons in finer detail. With regard to LRRTM1's role in humans, we found a strong association between a 70 kb-spanning haplotype in the proposed promoter region of LRRTM1 gene and two possibly related phenotypes: left-handedness and schizophrenia. Interestingly, the responsible haplotype was linked to phenotypic variability only when paternally inherited. In summary, I identified two families of neuronal receptor-like proteins, and mapped their expression and certain protein-protein interactions. The identification of a central binding region in NgR1 shared by multiple ligands may facilitate the design and development of small molecule therapeutics blocking binding of all NgR1 ligands. Additionally, the genetic association data suggests that allelic variation upstream of LRRTM1 may play a role in the development of left-right brain asymmetry in humans. Lrrtm1 and Lrrtm3 knock out mice developed as a part of this study will likely be useful for schizophrenia and Alzheimer s disease research.

A semi-analytical solution for multilayer diffusion in a composite medium consisting of a large number of layers

Diffusion in a composite slab consisting of a large number of layers provides an ideal prototype problem for developing and analysing two-scale modelling approaches for heterogeneous media. Numerous analytical techniques have been proposed for solving the transient diffusion equation in a one-dimensional composite slab consisting of an arbitrary number of layers. Most of these approaches, however, require the solution of a complex transcendental equation arising from a matrix determinant for the eigenvalues that is difficult to solve numerically for a large number of layers. To overcome this issue, in this paper, we present a semi-analytical method based on the Laplace transform and an orthogonal eigenfunction expansion. The proposed approach uses eigenvalues local to each layer that can be obtained either explicitly, or by solving simple transcendental equations. The semi-analytical solution is applicable to both perfect and imperfect contact at the interfaces between adjacent layers and either Dirichlet, Neumann or Robin boundary conditions at the ends of the slab. The solution approach is verified for several test cases and is shown to work well for a large number of layers. The work is concluded with an application to macroscopic modelling where the solution of a fine-scale multilayered medium consisting of two hundred layers is compared against an “up-scaled” variant of the same problem involving only ten layers.

Characterisation of cellulose- and lignin-based materials using x-ray scattering methods

Wood is an important material for the construction and pulping industries. Using x-ray diffraction the microfibril angle of Sitka spruce wood was studied in the first part of this thesis. Sitka spruce (Picea sitchensis [Bong.] Carr.) is native to the west coast of North America, but due to its fast growth rate, it has also been imported to Europe. So far, its nanometre scale properties have not been systematically characterised. In this thesis the microfibril angle of Sitka spruce was shown to depend significantly on the origin of the tree in the first annual rings near the pith. Wood can be further processed to separate lignin from cellulose and hemicelluloses. Solid cellulose can act as a reducer for metal ions and it is also a porous support for nanoparticles. By chemically reducing nickel or copper in the solid cellulose support it is possible to get small nanoparticles on the surfaces of the cellulose fibres. Cellulose supported metal nanoparticles can potentially be used as environmentally friendly catalysts in organic chemistry reactions. In this thesis the size of the nickel and copper containing nanoparticles were studied using anomalous small-angle x-ray scattering and wide-angle x-ray scattering. The anomalous small-angle x-ray scattering experiments showed that the crystallite size of the copper oxide nanoparticles was the same as the size of the nanoparticles, so the nanoparticles were single crystals. The nickel containing nanoparticles were amorphous, but crystallised upon heating. The size of the nanoparticles was observed to be smaller when the reduction of nickel was done in aqueous ammonium hydrate medium compared to reduction made in aqueous solution. Lignin is typically seen as the side-product of wood industries. Lignin is the second most abundant natural polymer on Earth, and it possesses potential to be a useful material for many purposes in addition to being an energy source for the pulp mills. In this thesis, the morphology of several lignins, which were produced by different separation methods from wood, was studied using small-angle and ultra small-angle x-ray scattering. It was shown that the fractal model previously proposed for the lignin structure does not apply to most of the extracted lignin types. The only lignin to which the fractal model could be applied was kraft lignin. In aqueous solutions the average shape of the low molar mass kraft lignin particles was observed to be elongated and flat. The average shape does not necessarily correspond to the shape of the individual particles because of the polydispersity of the fraction and due to selfassociation of the particles. Lignins, and especially lignosulfonate, have many uses as dispersants, binders and emulsion stabilisers. In this thesis work the selfassociation of low molar mass lignosulfonate macromolecules was observed using small-angle x-ray scattering. By taking into account the polydispersity of the studied lignosulfonate fraction, the shape of the lignosulfonate particles was determined to be flat by fitting an oblate ellipsoidal model to the scattering intensity.

Asiakastietojärjestelmän muutos lakisääteisessä lastensuojelun sosiaalityössä - jännitteistä toimijuutta

Tämän pro gradu -tutkielman tarkoituksena on ollut tavoittaa niitä vaikutuksia, joita tietojärjestelmien käytöllä on sosiaali- ja terveysalalla. Tarkastelu sijoittuu lastensuojelun sosiaalityöhön. Yhden toimintayksikön tapahtumien kuvaus ja analyysi on puheenvuoro, jolla olen pyrkinyt tavoittamaan yhteyksiä tietojärjestelmien käyttöön liittyviin yleisiin ilmiöihin. Tutkielma on tiheä kuvaus lastensuojelun sosiaalityöstä asiakastietojärjestelmän muutosvaiheessa. Tapahtumia on jäsennetty toimijuuden käsitteen kautta (Archer 2003, Heiskala, 2000). Sosiaalityöntekijän toimijuus on ollut keskiössä tutkimussuunnitelman mukaisesti. Asiakastietojärjestelmä työntyi muutosvaiheessa toimijan rooliin vaikuttaen muun muassa lastensuojelun sosiaalityön työprosesseihin. Tietojärjestelmän toimijuus vaikuttaa sosiaalityöntekijään toimijana ja työntekijän toimijan asemaan. Aineistosta nousi teoretisoinnin (Layder, 1998) kautta esille jännitteisyys näiden keskeisten toimijoiden välillä. Jännite jäsentyi kolmelle kentälle. Lainsäädännön kenttä sulkee sisäänsä organisaatiota ja sosiaalityöntekijän perustehtävää kuvaavat kentät. Kenttien sisällöissä havaitsin yhtäläisyyttä Heiskalan (2000) yhteiskunnallisia pakkoja koskevaan jaotteluun. Pakot välittyvät semioottisesti tarkastellen merkkien eli lakimerkkien, rahamerkkien ja rituaalisesti vahvistettujen symbolien välityksellä. Tutkielman aineiston pohjalta on analysoitavaksi noussut kysymys uuden julkisjohtamisen (NPM) (Harvey, 2006, Julkunen, 2006) vaikutuksista lastensuojelun sosiaalityössä. Uuden julkisjohtamisen elementit tuottavat toimintaan jännitteitä edellä kuvatuilla kolmella kentällä. Yhtä toimintayksikköä koskeva aineisto antaa viitteitä siitä, että NPM toimii lastensuojelun sosiaalityössä toimintaa ohjaavana käyttöteoriana. Käyttöteorian (Argyris & Schön, 1996) käsitteellä ymmärretään yksilön tai organisaation todellista toimintaa ohjaavaa teoriaa, mikä voi olla ristiriidassa julkilausuttujen toiminnan teorioiden kanssa. Yksilö tai organisaatio ei välttämättä ole tietoinen käyttöteorian ja julkilausutun teorian välisestä kuilusta, minkä esiin saaminen edellyttäisi reflektiota. Tutkimuskohteena on ollut Helsingin kaupungin sosiaaliviraston ruotsinkielisiä lastensuojelun palveluja tuottava yksikkö. Tutkimuksen aineisto on kerätty uuden asiakastietojärjestelmän käyttöönottovaiheessa 1.11.2008–28.2.2009. Menetelmällisesti tutkimus sijoittuu toimintatutkimukselliseen kehykseen (Carr & Kemmis, 1986). Kenttävaiheen aikana yhdistin tutkijan ja toimijan roolit työskennellen sosiaalityöntekijänä tutkimukseni kohteena olleessa yksikössä. Kirjallinen aineisto koostuu järjestelmämuutosta koskevista päätöksistä, tiedotteista ja ohjeista. Järjestelmän muutosvaiheessa kokosin aineistoa osallistuvan havainnoinnin menetelmällä. Aineistossa on mukana myös yksikön työntekijöiden kanssa tuotettua materiaalia muutosvaiheen aikaisten sisältöjen haltuun ottamiseksi, esimerkiksi työn prosessikuvauksia. Aineisto on analysoitu sisällönanalyysillä. Analyysin edetessä kävin jäsennyksistäni keskustelua toimintayksikön työntekijöiden kanssa. Tapaamisten jälkeen jatkoin analyysiä ja teoretisointia käyttäen semioottista sosiologiaa metateoriana ja aktanttimallia muutosvaihetta kuvaavien kertomusten koostamisessa. Kertomusten pohjalta jatkoin toimijuuden analyysiä subjektiaseman (Törrönen, 2000) ja toimijan aseman (Alasuutari 2007) käsitteitä käyttäen.

Asiakastietojärjestelmän muutos lakisääteisessä lastensuojelun sosiaalityössä - jännitteistä toimijuutta

Tämän pro gradu -tutkielman tarkoituksena on ollut tavoittaa niitä vaikutuksia, joita tietojärjestelmien käytöllä on sosiaali- ja terveysalalla. Tarkastelu sijoittuu lastensuojelun sosiaalityöhön. Yhden toimintayksikön tapahtumien kuvaus ja analyysi on puheenvuoro, jolla olen pyrkinyt tavoittamaan yhteyksiä tietojärjestelmien käyttöön liittyviin yleisiin ilmiöihin. Tutkielma on tiheä kuvaus lastensuojelun sosiaalityöstä asiakastietojärjestelmän muutosvaiheessa. Tapahtumia on jäsennetty toimijuuden käsitteen kautta (Archer 2003, Heiskala, 2000). Sosiaalityöntekijän toimijuus on ollut keskiössä tutkimussuunnitelman mukaisesti. Asiakastietojärjestelmä työntyi muutosvaiheessa toimijan rooliin vaikuttaen muun muassa lastensuojelun sosiaalityön työprosesseihin. Tietojärjestelmän toimijuus vaikuttaa sosiaalityöntekijään toimijana ja työntekijän toimijan asemaan. Aineistosta nousi teoretisoinnin (Layder, 1998) kautta esille jännitteisyys näiden keskeisten toimijoiden välillä. Jännite jäsentyi kolmelle kentälle. Lainsäädännön kenttä sulkee sisäänsä organisaatiota ja sosiaalityöntekijän perustehtävää kuvaavat kentät. Kenttien sisällöissä havaitsin yhtäläisyyttä Heiskalan (2000) yhteiskunnallisia pakkoja koskevaan jaotteluun. Pakot välittyvät semioottisesti tarkastellen merkkien eli lakimerkkien, rahamerkkien ja rituaalisesti vahvistettujen symbolien välityksellä. Tutkielman aineiston pohjalta on analysoitavaksi noussut kysymys uuden julkisjohtamisen (NPM) (Harvey, 2006, Julkunen, 2006) vaikutuksista lastensuojelun sosiaalityössä. Uuden julkisjohtamisen elementit tuottavat toimintaan jännitteitä edellä kuvatuilla kolmella kentällä. Yhtä toimintayksikköä koskeva aineisto antaa viitteitä siitä, että NPM toimii lastensuojelun sosiaalityössä toimintaa ohjaavana käyttöteoriana. Käyttöteorian (Argyris ja Schön, 1996) käsitteellä ymmärretään yksilön tai organisaation todellista toimintaa ohjaavaa teoriaa, mikä voi olla ristiriidassa julkilausuttujen toiminnan teorioiden kanssa. Yksilö tai organisaatio ei välttämättä ole tietoinen käyttöteorian ja julkilausutun teorian välisestä kuilusta, minkä esiin saaminen edellyttäisi reflektiota. Tutkimuskohteena on ollut Helsingin kaupungin sosiaaliviraston ruotsinkielisiä lastensuojelun palveluja tuottava yksikkö. Tutkimuksen aineisto on kerätty uuden asiakastietojärjestelmän käyttöönottovaiheessa 1.11.2008 28.2.2009. Menetelmällisesti tutkimus sijoittuu toimintatutkimukselliseen kehykseen (Carr ja Kemmis, 1986). Kenttävaiheen aikana yhdistin tutkijan ja toimijan roolit työskennellen sosiaalityöntekijänä tutkimukseni kohteena olleessa yksikössä. Kirjallinen aineisto koostuu järjestelmämuutosta koskevista päätöksistä, tiedotteista ja ohjeista. Järjestelmän muutosvaiheessa kokosin aineistoa osallistuvan havainnoinnin menetelmällä. Aineistossa on mukana myös yksikön työntekijöiden kanssa tuotettua materiaalia muutosvaiheen aikaisten sisältöjen haltuun ottamiseksi, esimerkiksi työn prosessikuvauksia. Aineisto on analysoitu sisällönanalyysillä. Analyysin edetessä kävin jäsennyksistäni keskustelua toimintayksikön työntekijöiden kanssa. Tapaamisten jälkeen jatkoin analyysiä ja teoretisointia käyttäen semioottista sosiologiaa metateoriana ja aktanttimallia muutosvaihetta kuvaavien kertomusten koostamisessa. Kertomusten pohjalta jatkoin toimijuuden analyysiä subjektiaseman (Törrönen, 2000) ja toimijan aseman (Alasuutari 2007) käsitteitä käyttäen.

Optimal pulse spacing for dynamical decoupling in the presence of a purely dephasing spin bath

Maintaining quantum coherence is a crucial requirement for quantum computation; hence protecting quantum systems against their irreversible corruption due to environmental noise is an important open problem. Dynamical decoupling (DD) is an effective method for reducing decoherence with a low control overhead. It also plays an important role in quantum metrology, where, for instance, it is employed in multiparameter estimation. While a sequence of equidistant control pulses the Carr-Purcell-Meiboom-Gill (CPMG) sequence] has been ubiquitously used for decoupling, Uhrig recently proposed that a nonequidistant pulse sequence the Uhrig dynamic decoupling (UDD) sequence] may enhance DD performance, especially for systems where the spectral density of the environment has a sharp frequency cutoff. On the other hand, equidistant sequences outperform UDD for soft cutoffs. The relative advantage provided by UDD for intermediate regimes is not clear. In this paper, we analyze the relative DD performance in this regime experimentally, using solid-state nuclear magnetic resonance. Our system qubits are C-13 nuclear spins and the environment consists of a H-1 nuclear spin bath whose spectral density is close to a normal (Gaussian) distribution. We find that in the presence of such a bath, the CPMG sequence outperforms the UDD sequence. An analogy between dynamical decoupling and interference effects in optics provides an intuitive explanation as to why the CPMG sequence performs better than any nonequidistant DD sequence in the presence of this kind of environmental noise.

Structure and dynamics of protein excited states with millisecond lifetimes

An in-depth understanding of biological processes often requires detailed atomic resolution structures of the molecules involved. However in solution where most of these processes occur the conformation of biomolecules like RNA, DNA and proteins is not static but fluctuates. Routinely used structural techniques like X-ray crystallography, NMR spectroscopy and cryo-electron microscopy have almost always been used to determine the structure of the dominant conformation or obtain an average structure of the biomolecule in solution with very little detailed information regarding the dynamics of these molecules in solution. Over the last few years, NMR based methods have been developed to study the dynamics of these biomolecules in solution in a site-specific manner with the aim of generating structures of the different conformations that these molecules can adopt in solution. One powerful technique is the Carr-Purcell-Meiboom-Gill (CPMG) relaxation dispersion experiment, which can be used to detect and characterize protein excited states that are populated for as less as 0.5% of the time with ∼0.5–10 millisecond lifetimes. Due to recent advances in NMR pulse sequences and labeling methodology, it is now possible to determine the structures of these transiently populated excited states with millisecond lifetimes by obtaining accurate chemical shifts, residual dipolar couplings (RDCs) and residual chemical shift anisotropies (RCSAs) of these excited states. In these excited states the dynamics of some methyl containing residues can also be studied.

Antiguo Oriente: Cuadernos del Centro de Estudios de Historia del Antiguo Oriente, 2006, n° 4 (número completo)

How old is the Kingdom of Edom? A review of new evidence and recent discussion / Eveline Van Der Steen ; Piotr Bienkowski -- A problem of pedubasts? / Dan´El Kahn -- Le ciel selon l´Hymne Orphique à Ouranos et selon des textes funéraires égyptiens (PT, CT, BD): une brève comparaison préliminaire / Amanda–Alice Marvelia -- An epigraphic reanalysis of Two Stelae from Firs Intermediate Period Dendera in the Cairo Museum / Tracy Musacchio -- Mass production in Mesopotamia / Morris Silver -- Iron Age “negative” pottery: a reassessment / Juan Manuel Tebes -- The Cordage from the 2001- Season of the excavations at Berenike (Egyptian Red Sea Coast): preliminary results / André J. Veldmeijer -- Article review. Carr, David M., Writing of the Tablet of the Heart: origins of scripture and literature / Itamar Singer -- Reseñas bibliográficas -- Política editorial

Preliminary guide to the identification of the early life history stages of Gerreid fishes of the Western Central Atlantic

The family Gerreidae contains four genera and 13 species that occur in the western central North Atlantic. Adult gerreids are small to medium size fishes that are abundant in coastal waters, bays, and estuaries in tropical and warm temperate regions and sometimes occur in freshwaters. They are generally associate~ with grassy or open bottoms, but not with reefs. Gerreids are silvery fishes, with deeply forked tails, and extremely protrusible mouth that points downward when protracted. They apparently feed on bottom-dwelling organisms and at least one species (Eucinostomus gula) shows a distinct transition, during the juvenile period, from a planktivore (exclusively copepods) to a carnivore that includes a diet of almost solely polychaetes (Carr & Adams, 1973; Robins and Ray, 1987; Murdy et al., 1997). (PDF contains 10 pages)

Sediment Quality in Puget Sound Year 3 - Southern Puget Sound

As a component of a three-year cooperative effort of the Washington State Department of Ecology and the National Oceanic and Atmospheric Administration, surficial sediment samples from 100 locations in southern Puget Sound were collected in 1999 to determine their relative quality based on measures of toxicity, chemical contamination, and benthic infaunal assemblage structure. The survey encompassed an area of approximately 858 km2, ranging from East and Colvos Passages south to Oakland Bay, and including Hood Canal. Toxic responses were most severe in some of the industrialized waterways of Tacoma’s Commencement Bay. Other industrialized harbors in which sediments induced toxic responses on smaller scales included the Port of Olympia, Oakland Bay at Shelton, Gig Harbor, Port Ludlow, and Port Gamble. Based on the methods selected for this survey, the spatial extent of toxicity for the southern Puget Sound survey area was 0% of the total survey area for amphipod survival, 5.7% for urchin fertilization, 0.2% for microbial bioluminescence, and 5- 38% with the cytochrome P450 HRGS assay. Measurements of trace metals, PAHs, PCBs, chlorinated pesticides, other organic chemicals, and other characteristics of the sediments, indicated that 20 of the 100 samples collected had one or more chemical concentrations that exceeded applicable, effects-based sediment guidelines and/or Washington State standards. Chemical contamination was highest in eight samples collected in or near the industrialized waterways of Commencement Bay. Samples from the Thea Foss and Middle Waterways were primarily contaminated with a mixture of PAHs and trace metals, whereas those from Hylebos Waterway were contaminated with chlorinated organic hydrocarbons. The remaining 12 samples with elevated chemical concentrations primarily had high levels of other chemicals, including bis(2-ethylhexyl) phthalate, benzoic acid, benzyl alcohol, and phenol. The characteristics of benthic infaunal assemblages in south Puget Sound differed considerably among locations and habitat types throughout the study area. In general, many of the small embayments and inlets throughout the study area had infaunal assemblages with relatively low total abundance, taxa richness, evenness, and dominance values, although total abundance values were very high in some cases, typically due to high abundance of one organism such as the polychaete Aphelochaeta sp. N1. The majority of the samples collected from passages, outer embayments, and larger bodies of water tended to have infaunal assemblages with higher total abundance, taxa richness, evenness, and dominance values. Two samples collected in the Port of Olympia near a superfund cleanup site had no living organisms in them. A weight-of-evidence approach used to simultaneously examine all three “sediment quality triad” parameters, identified 11 stations (representing 4.4 km2, 0.5% of the total study area) with sediment toxicity, chemical contamination, and altered benthos (i.e., degraded sediment quality), 36 stations (493.5 km2, 57.5% total study area) with no toxicity or chemical contamination (i.e., high sediment quality), 35 stations (274.1 km2, 32.0% total study area) with one impaired sediment triad parameter (i.e., intermediate/high sediment quality), and 18 stations (85.7km2, 10.0% total study area) with two impaired sediment parameters (i.e., intermediate/degraded quality sediments). Generally, upon comparison, the number of stations with degraded sediments based upon the sediment quality triad of data was slightly greater in the central Puget Sound than in the northern and southern Puget Sound study areas, with the percent of the total study area degraded in each region decreasing from central to north to south (2.8, 1.3 and 0.5%, respectively). Overall, the sediments collected in Puget Sound during the combined 1997-1999 surveys were among the least contaminated relative to other marine bays and estuaries studied by NOAA using equivalent methods. (PDF contains 351 pages)

Magnitude and extent of chemical contamination and toxicity in sediments of Biscayne Bay and vicinity

The toxicity of sediments in Biscayne Bay and many adjoining tributaries was determined as part of a bioeffects assessments program managed by NOAA’s National Status and Trends Program. The objectives of the survey were to determine: (1) the incidence and degree of toxicity of sediments throughout the study area; (2) the spatial patterns (or gradients) in chemical contamination and toxicity, if any, throughout the study area; (3) the spatial extent of chemical contamination and toxicity; and (4) the statistical relationships between measures of toxicity and concentrations of chemicals in the sediments. The survey was designed to characterize sediment quality throughout the greater Biscayne Bay area. Surficial sediment samples were collected during 1995 and 1996 from 226 randomly-chosen locations throughout nine major regions. Laboratory toxicity tests were performed as indicators of potential ecotoxicological effects in sediments. A battery of tests was performed to generate information from different phases (components) of the sediments. Tests were selected to represent a range in toxicological endpoints from acute to chronic sublethal responses. Toxicological tests were conducted to measure: reduced survival of adult amphipods exposed to solid-phase sediments; impaired fertilization success and abnormal morphological development in gametes and embryos, respectively, of sea urchins exposed to pore waters; reduced metabolic activity of a marine bioluminescent bacteria exposed to organic solvent extracts; induction of a cytochrome P-450 reporter gene system in exposures to solvent extracts; and reduced reproductive success in marine copepods exposed to solid-phase sediments. Contamination and toxicity were most severe in several peripheral canals and tributaries, including the lower Miami River, adjoining the main axis of the bay. In the open basins of the bay, chemical concentrations and toxicity generally were higher in areas north of the Rickenbacker Causeway than south of it. Sediments from the main basins of the bay generally were less toxic than those from the adjoining tributaries and canals. The different toxicity tests, however, indicated differences in severity, incidence, spatial patterns, and spatial extent in toxicity. The most sensitive test among those performed on all samples, a bioassay of normal morphological development of sea urchin embryos, indicated toxicity was pervasive throughout the entire study area. The least sensitive test, an acute bioassay performed with a benthic amphipod, indicated toxicity was restricted to a very small percentage of the area. Both the degree and spatial extent of chemical contamination and toxicity in this study area were similar to or less severe than those observed in many other areas in the U.S. The spatial extent of toxicity in all four tests performed throughout the bay were comparable to the “national averages” calculated by NOAA from previous surveys conducted in a similar manner. Several trace metals occurred in concentrations in excess of those expected in reference sediments. Mixtures of substances, including pesticides, petroleum constituents, trace metals, and ammonia, were associated statistically with the measures of toxicity. Substances most elevated in concentration relative to numerical guidelines and associated with toxicity included polychlorinated biphenyls, DDT pesticides, polynuclear aromatic hydrocarbons, hexachloro cyclohexanes, lead, and mercury. These (and other) substances occurred in concentrations greater than effects-based guidelines in the samples that were most toxic in one or more of the tests. (PDF contains 180 pages)