Sampling-Design Effects on Properties of Species-Area Relationships - A Case Study from Estonian Dry Grassland Communities

Despite widespread use of species-area relationships (SARs), dispute remains over the most representative SAR model. Using data of small-scale SARs of Estonian dry grassland communities, we address three questions: (1) Which model describes these SARs best when known artifacts are excluded? (2) How do deviating sampling procedures (marginal instead of central position of the smaller plots in relation to the largest plot; single values instead of average values; randomly located subplots instead of nested subplots) influence the properties of the SARs? (3) Are those effects likely to bias the selection of the best model? Our general dataset consisted of 16 series of nested-plots (1 cm(2)-100 m(2), any-part system), each of which comprised five series of subplots located in the four corners and the centre of the 100-m(2) plot. Data for the three pairs of compared sampling designs were generated from this dataset by subsampling. Five function types (power, quadratic power, logarithmic, Michaelis-Menten, Lomolino) were fitted with non-linear regression. In some of the communities, we found extremely high species densities (including bryophytes and lichens), namely up to eight species in 1 cm(2) and up to 140 species in 100 m(2), which appear to be the highest documented values on these scales. For SARs constructed from nested-plot average-value data, the regular power function generally was the best model, closely followed by the quadratic power function, while the logarithmic and Michaelis-Menten functions performed poorly throughout. However, the relative fit of the latter two models increased significantly relative to the respective best model when the single-value or random-sampling method was applied, however, the power function normally remained far superior. These results confirm the hypothesis that both single-value and random-sampling approaches cause artifacts by increasing stochasticity in the data, which can lead to the selection of inappropriate models.

Synthesis and properties of heterobifunctional photoaffinity reagents for the identification and isolation of receptors

A method employing isotopically- and photoaffinity-labeled probes and polyclonal and monoclonal antibody to the probes for the identification, isolation and recovery of protein receptors is described. Antibody was raised against N-(3-(p-azido-m-($\sp{125}$I) -iodophenyl)) propionate (AIPP) coupled to and photolyzed to BSA. The antibodies specifically bound AIPP-derivatized proteins. An isolation system was developed utilizing this probe and two antigenically identical reversible analogues. N-(3-((p-azido-m-($\sp{125}$I) -iodo-phenyl)propionyl)amidoethyl-1,3-dithiopropionyl) succinimide (Reversible $\sp{125}$I-AIPPS) reacts with primary amines and N-(((3-p-azido-m-($\sp{125}$I) -iodophenyl)propionyl)amidoethyl)dithiopyridine ($\sp{125}$I-AIPP-PDA) reacts with reduced thiols. The applicability of the system was established by derivatizing known ligands (Transferrin and Interferon-alpha) with one of the probes. The ligand-probe was then allowed to interact with its receptor by incubation with SS5 lymphoma cells and cross-linked by photolysis at 300 nm. The photolyzed ligand/probe/receptor preparation was then recovered with AIPP antibody. Utilization of N-(3-((p-azido-m-($\sp{125}$I) -iodo-phenyl-propionyl)-amidoethyl-1,3-dithiopropionyl) succinimide (Reversible $\sp{125}$I-AIPPS) allowed the components of the photolyzed complex to be separated by treatment with 2-mercaptoethanol in the SDS-PAGE solubilization buffer. Ligand and receptor labeling were then assessed by Coomassie staining and autoradiography. Results of receptor assays suggest that $\sp{125}$I-AIPP was, indeed, transferred to moieties that represent the receptors for both Transferrin and Interferon-alpha. ^

Studies on the adhesion properties of the liver-metastatic murine RAW117 large-cell lymphoma cells: Roles of $\beta\sb3$ integrin

Metastasis is the major cause of death in cancer patients. Since many cancers show organ-preference of metastasis, elucidation of the underlying mechanisms of metastasis will benefit diagnosis or treatment of metastatic diseases. Adhesion mechanisms are thought to be involved in organ-preference of metastasis, because metastatic cells show organ preference in adhering to organ-derived microvascular endothelial cells. The adhesion molecules in this process remain largely unidentified. I have examined a series of murine RAW117 large-cell lymphoma cells variants selected in vivo for liver-colonizing properties ($\rm{H10{>>}L17>P}$). The highly liver-metastatic H10 cells were found to differentially express much higher levels of integrin $\alpha\rm\sb{v}\beta\sb3$ than L17 or P cells. H10 cells also adhered at higher rates to vitronectin and fibronectin than to fibrinogen, fibrin, laminin and type I collagen, and adhered at significantly higher rates to (GRGDS)$\sb4$ than to monomeric RGD-peptides. In contrast, P and L17 cells did not adhere well to the above substrates. H10 cells also spread well on vitronectin and migrated toward vitronectin concentration gradients. Pretreament of H10 cells with anti-$\beta\sb3$ monoclonal antibodies resulted in significant decreases in adhesion of H10 cells to vitronectin and immobilized (GRGDS)$\sb4$, and reduced the formation of experimental liver metastases in syngeneic Balb/c mice.^ Adhesion of RAW117 cells under hydrodynamic shear stresses was also studied because tumor cell adhesion occurs under fluid shear stresses in target organ microvessels. Similar to their properties found with static adhesion assays, H10 cells stabilized their hydrodynamic adhesion to vitronectin, fibronectin and (GRGDS)$\sb4$ much more quickly than P or L17 cells. Unlike their static adhesion properties, RAW117 cells showed differential adhesion stabilization to liver-sinusoidal endothelial cell-derived extracellular matrix ($\rm{H10{>>}L17>P}$). Although not supporting static adhesion of RAW117 cells, monomeric RGD-peptides mediated adhesion stabilization of H10 cells but not L17 or P cells. Integrin $\rm\alpha\sb{v}\beta\sb3$ was found to be involved in stabilizing H10 cell adhesion to vitronectin, (GRGDS)$\sb4$, monomeric RGD-peptide R1, and liver sinusoidal endothelial cell-derived extracellular matrix.^ This study is the first to provide evidence that integrin $\rm\alpha\sb{v}\beta\sb3$ is differentially expressed in liver-metastatic lymphoma cells and involved in differential adhesion of these cells. The results indicate that strong static adhesion and especially the unique hydrodynamic adhesion of RAW117 cells to the RGD-containing substrates correlate with liver-metastatic potentials. Thus, integrin $\rm\alpha\sb{v}\beta\sb3$ may play an important role in liver-preferential metastasis of RAW117 large-cell lymphoma cells. ^

Structure/affinity studies in the bicyclo-DNA series: Synthesis and properties of oligonucleotides containing bcen-T and iso-tricyclo-T nucleosides

We present the synthesis of the two novel nucleosides iso-tc-T and bcen-T, belonging to the bicyclo-/tricyclo-DNA molecular platform. In both modifications the torsion around C6’–C7’ within the carbocyclic ring is planarized by either the presence of a C6’–C7’ double bond or a cyclopropane ring. Structural analysis of these two nucleosides by X-ray analysis reveals a clear preference of torsion angle γ for the gauche orientation with the furanose ring in a near perfect 2’-endo conformation. Both modifications were incorporated into oligodeoxynucleotides and their thermal melting behavior with DNA and RNA as complements was assessed. We found that the iso-tc-T modification was significantly more destabilizing in duplex formation compared to the bcen-T modification. In addition, duplexes with complementary RNA were less stable as compared to duplexes with DNA as complement. A structure/affinity analysis, including the already known bc-T and tc-T modifications, does not lead to a clear correlation of the orientation of torsion angle γ with DNA or RNA affinity. There is, however, some correlation between furanose conformation (N- or S-type) and affinity in the sense that a preference for a 3’-endo like conformation is associated with a preference for RNA as complement. As a general rule it appears that Tm data of single modifications with nucleosides of the bicyclo-/tricyclo-DNA platform within deoxyoligonucleotides are not predictive for the stability of fully modified oligonucleotides.

On The Breakdown Properties of some Multivariate M-Functionals

For probability distributions on ℝq, a detailed study of the breakdown properties of some multivariate M-functionals related to Tyler's [Ann. Statist. 15 (1987) 234] ‘distribution-free’ M-functional of scatter is given. These include a symmetrized version of Tyler's M-functional of scatter, and the multivariate t M-functionals of location and scatter. It is shown that for ‘smooth’ distributions, the (contamination) breakdown point of Tyler's M-functional of scatter and of its symmetrized version are 1/q and inline image, respectively. For the multivariate t M-functional which arises from the maximum likelihood estimate for the parameters of an elliptical t distribution on ν ≥ 1 degrees of freedom the breakdown point at smooth distributions is 1/(q + ν). Breakdown points are also obtained for general distributions, including empirical distributions. Finally, the sources of breakdown are investigated. It turns out that breakdown can only be caused by contaminating distributions that are concentrated near low-dimensional subspaces.

Psychometric properties of the Trauma and Distress Scale, TADS, in an adult community sample in Finland

BACKGROUND: There is increasing evidence that a history of childhood abuse and neglect is not uncommon among individuals who experience mental disorder and that childhood trauma experiences are associated with adult psychopathology. Although several interview and self-report instruments for retrospective trauma assessment have been developed, many focus on sexual abuse (SexAb) rather than on multiple types of trauma or adversity. METHODS: Within the European Prediction of Psychosis Study, the Trauma and Distress Scale (TADS) was developed as a new self-report assessment of multiple types of childhood trauma and distressing experiences. The TADS includes 43 items and, following previous measures including the Childhood Trauma Questionnaire, focuses on five core domains: emotional neglect (EmoNeg), emotional abuse (EmoAb), physical neglect (PhyNeg), physical abuse (PhyAb), and SexAb.This study explores the psychometric properties of the TADS (internal consistency and concurrent validity) in 692 participants drawn from the general population who completed a mailed questionnaire, including the TADS, a depression self-report and questions on help-seeking for mental health problems. Inter-method reliability was examined in a random sample of 100 responders who were reassessed in telephone interviews. RESULTS: After minor revisions of PhyNeg and PhyAb, internal consistencies were good for TADS totals and the domain raw score sums. Intra-class coefficients for TADS total score and the five revised core domains were all good to excellent when compared to the interviewed TADS as a gold standard. In the concurrent validity analyses, the total TADS and its all core domains were significantly associated with depression and help-seeking for mental problems as proxy measures for traumatisation. In addition, robust cutoffs for the total TADS and its domains were calculated. CONCLUSIONS: Our results suggest the TADS as a valid, reliable, and clinically useful instrument for assessing retrospectively reported childhood traumatisation.

(Table T1) Magnetic properties of MORB from ODP Leg 187 sites

The core samples of mid-ocean-ridge basalts (including Indian and Pacific type) recovered from the Southeast Indian Ridge (SEIR) area near the Australian Antarctic Discordance during Ocean Drilling Program Leg 187 were studied using rock magnetism, mineralogy, and petrography methods. On the basis of thermomagnetic analyses and low-temperature magnetometry, the dominant magnetic carrier in most of the basalt samples (pillow basalts) is characterized as titanomaghemite, which presumably formed by low-temperature oxidation of primary titanomagnetite. Some samples from unaltered massive basalts contain nearly unoxidized titanomagnetite as the main magnetic mineral. A metadiabase sample showing greenschist facies metamorphism contains magnetic minerals dominated by magnetite. The pillow basalts contain titanomaghemite ranging from stable single-domain to pseudosingle-domain (PSD) grains, and the majority are characterized by a single stable component of remanence. The massive basalts show hysteresis features of larger PSD grains and contain a very low coercivity remanence. The values of natural remanent magnetization (NRM) of the samples in this SEIR area are on the same order as those of other oceanic ridge basalts. They show a general decreasing trend of NRM with increasing crust age. However, the values of NRM show no correlation either with the tectonic zonations (Zone A vs. Zone B) or with the mantle provinces (Pacific vs. Indian types).

Seismic properties of sheeted dikes from ODP Hole 111-504B

Seismic velocities have been measured at confining pressures to 600 MPa for eight samples of sheeted dike rock obtained from Hole 504B during Leg ODP 111. The compressional- and shear-wave velocities are, in general, higher than the velocities measured in overlying dike rocks obtained from the hole during DSDP Leg 83. The velocity gradients observed in Layer 2C result from decreasing porosity with depth and increasing metamorphic grade. The laboratory-measured velocities of the Leg 111 dike rocks are similar to those of dike rocks reported for the Bay of Islands, Samail, and Troodos ophiolites.

Mineralogy and diagenesis: Their effect on acoustic and electrical properties of pelagic clays at DSDP Leg 86 Holes

Analysis of pelagic clay samples from Sites 576, 578, and 581 shows that physical, acoustic, and electrical trends with increasing burial depth are related to mineralogical and diagenetic changes. The properties of interest are bulk density (roo), porosity (phi), compressional-wave velocity (Vp) and velocity anisotropy (Ap), and electrical resistivity (Ro) and resistivity anisotropy (Ar). In general, as demonstrated in particular for the brown pelagic clay, the increase in roo, Vp, Ro, and to a lesser extent Ap and Ar with increasing depth is primarily caused by decreasing phi (and water content) as a result of compaction. The mineralogy and chemistry of the pelagic clays vary as a function of burial depth at all three sites. These variations are interpreted to reflect changes in the relative importance of detrital and diagenetic components. Mineralogical and chemical variations, however, play minor roles in determining variations in acoustic and electrical properties of the clays with increasing burial depth.

Composition and properties of rocks and sediments from the Cape Verde fracture zone

The book presents results of comprehensive geological and geophysical studies, carried out in the Cape Verde fault zone in the 3-rd cruise of R/V Akademik Nikolaj Strakhov (1986). Detailed characterization of bottom relief, thickness and structure of the sedimentary cover, magnetic field, crust structure, lithology and stratigraphy of sediments, petrography and geochemistry of magmatic rocks. Conclusions about tectonic layering of the crust and upper mantle in the fault zone, and about a concurrent structural section of large mantle inhomogeneities have been done. The book is the first monographic description of a major fault structure of the ocean floor.

Paleomagnetic and rock magnetic properties of IODP Expedition 318 cores

The Integrated Ocean Drilling Program Expedition 318 to the Wilkes Land margin of Antarctica recovered a sedimentary succession ranging in age from lower Eocene to the Holocene. Excellent stratigraphic control is key to understanding the timing of paleoceanographic events through critical climate intervals. Drill sites recovered the lower and middle Eocene, nearly the entire Oligocene, the Miocene from about 17 Ma, the entire Pliocene and much of the Pleistocene. The paleomagnetic properties are generally suitable for magnetostratigraphic interpretation, with well-behaved demagnetization diagrams, uniform distribution of declinations, and a clear separation into two inclination modes. Although the sequences were discontinuously recovered with many gaps due to coring, and there are hiatuses from sedimentary and tectonic processes, the magnetostratigraphic patterns are in general readily interpretable. Our interpretations are integrated with the diatom, radiolarian, calcareous nannofossils and dinoflagellate cyst (dinocyst) biostratigraphy. The magnetostratigraphy significantly improves the resolution of the chronostratigraphy, particularly in intervals with poor biostratigraphic control. However, Southern Ocean records with reliable magnetostratigraphies are notably scarce, and the data reported here provide an opportunity for improved calibration of the biostratigraphic records. In particular, we provide a rare magnetostratigraphic calibration for dinocyst biostratigraphy in the Paleogene and a substantially improved diatom calibration for the Pliocene. This paper presents the stratigraphic framework for future paleoceanographic proxy records which are being developed for the Wilkes Land margin cores. It further provides tight constraints on the duration of regional hiatuses inferred from seismic surveys of the region.

Remanent and intrinsic properties of basalts at DSDP Leg 82 Holes

The magnetic properties of 56 samples of basalt from DSDP Leg 82 were studied in order to examine regional variations as well as the general question of the origin or remanence. Magnetization was carried, for the most part, by typical low temperature oxidized titanomagnetites, although two samples did show anomalous thermomagnetic curves. The natural remanence is distinctly different from an anhysteretic remanent magnetization and is hypothesized (by inference) to also be different from a thermoremanent magnetization (TRM) also. This suggests that alteration not only reduces the initial TRM but also changes it to chemical remanent magnetization with a significantly different magnetic character. An examination of thermomagnetic data tentatively suggests that the ulvospinel content of the titanomagnetites may be more variable than is commonly assumed. With the exception of a slight increase in saturation magnetization with decreasing latitude, no significant regional variations were evident.

(Table 1) Properties of grab sampled sediments from the Nha Trang Bay

General characteristics of macrobenthos of muddy sediments of the subtidal (19-24 m) zone in the Nha Trang Bay (South Vietnam) were described based on the survey performed in April-May 2002. The mean abundance of organisms was 637 ind/m**2 and the mean biomass was 2.3 g/m**2. Sixty-seven macrobenthic species were found during the study. The main structural features of the macrobenthos were high species diversity, low species recurrence, and high evenness of species structure with the absence of clearly manifested dominants. The number of species encountered regularly increased with the increase in the total area sampled from 210 to 5000 cm**2, though the relation did not reach saturation. Similarities and differences between the macrobenthos structures in the Nha Trang Bay and those in some tropical and boreal soft-bottom communities are discussed.

Physical, geochemical and magnetic properties of several ODP Leg 192 sites, Ontong Java Plateau

In this manuscript, we present the results of a physical properties investigation carried out on basaltic cores recovered from the four Leg 192 basement sites, focusing on the relationship between physical properties and alteration in basalts. Variations in physical properties in the Leg 192 basement sites closely resemble each other and reflect the amount of alteration and vein formation in the basement basalts. P-wave velocities, magnetic susceptibilities, and densities for the dense massive basalts are higher than those of more altered and heavily veined basalts. Porosity-dependent alteration is observed at Leg 192 basement sites: P-wave velocity displays a general decrease with increasing loss on ignition and potassium content. These trends are consistent with trends documented for typical alteration of oceanic crust and suggest that basalt alteration is largely responsible for the variation of the physical properties exhibited by rocks at Leg 192 basement sites. Our physical property data support the conclusion that only low-temperature seawater-mediated alteration occurred in the lava flows of the Ontong Java Plateau (OJP). This lack of higher-temperature hydrothermal alteration is consistent with the idea that the OJP basement sites are far from their eruptive vents.