Quality evaluation of tandem mass spectral libraries

Tandem mass spectral libraries are gaining more and more importance for the identification of unknowns in different fields of research, including metabolomics, forensics, toxicology, and environmental analysis. Particularly, the recent invention of reliable, robust, and transferable libraries has increased the general acceptance of these tools. Herein, we report on results obtained from thorough evaluation of the match reliabilities of two tandem mass spectral libraries: the MSforID library established by the Oberacher group in Innsbruck and the Weinmann library established by the Weinmann group in Freiburg. Three different experiments were performed: (1) Spectra of the libraries were searched against their corresponding library after excluding either this single compound-specific spectrum or all compound-specific spectra prior to searching; (2) the libraries were searched against each other using either library as reference set or sample set; (3) spectra acquired on different mass spectrometric instruments were matched to both libraries. Almost 13,000 tandem mass spectra were included in this study. The MSforID search algorithm was used for spectral matching. Statistical evaluation of the library search results revealed that principally both libraries enable the sensitive and specific identification of compounds. Due to higher mass accuracy of the QqTOF compared with the QTrap instrument, matches to the MSforID library were more reliable when comparing spectra with both libraries. Furthermore, only the MSforID library was shown to be efficiently transferable to different kinds of tandem mass spectrometers, including "tandem-in-time" instruments; this is due to the coverage of a large range of different collision energy settings-including the very low range-which is an outstanding characteristics of the MSforID library.

Sideband-Ratio and Harmonic Response of Sub-Millimeter Wave Mixers measured with a Martin Puplett Interferometer

Heterodyne receivers at millimeter and submillimeter wavelength are widely used for radiometric spectral line observations for atmospheric remote sensing or radio astronomy. The quantitative analysis of such observations requires an accurate knowledge of the mixers's sideband ratio. In addition, its potential sensitivity to spurious harmonics needs to be well understood. In this paper, we discuss a measurement technique for these receiver characteristics, which is based on a scanning Martin Puplett Interferometer used in conjunction with a wide band digital autocorrelation spectrometer for the analysis of the intermediate frequency band. We present measurement results of different double sideband and sideband separating mixers, which were developed for the proposed 340GHz multi-beam limb sounder STEAMR.

Identifying characteristics of mentally ill homeless individuals who are successfully linked to health and social services post-incarceration via the jail inreach project

Healthcare for the Homeless—Houston (HHH) received a research grant from The Medallion Foundation, Inc. in March 2006 to pilot The Jail Inreach Project, an intensive “inreach” initiative to assess the impact of providing continuity of mental and primary health care services for homeless individuals who suffer from mental illness and/or substance abuse being released from jail. This pilot project was initiated by HHH, in collaboration with the Harris County Sheriff’s Office and the Mental Health Mental Retardation Authority of Harris County (MHMRA). Those who are flagged as “frequent flyers” and who are diagnosed with a mental illness are referred to the Jail Inreach Project. In order to maximize the effectiveness of the discharge plan, case managers offer the option of meeting the client at the time of release and bring them to the HHH clinic located four blocks from the jail. Participation in both the program and the option for direct release to the care of a case manager are voluntary.^ The purpose of this study is to determine the outcomes of the Jail Inreach Project and addresses the following objectives: (1) to evaluate the characteristics of inmates that chose to be released from jail to the direct care of an HHH case manager versus those who opt for self release and (2) to determine the number and percent of inmates that are linked to services and relationship with type of release (direct versus indirect), (3) to determine if there is a relationship between outcomes and characteristics and (4) to determine what outcomes are a function of release, controlling for characteristics. Statistical analysis, including frequencies, cross tabulations, chi-square and logistical regression, found that those who opt for self release are six times less likely to be successfully linked to services and that gender is the most significant predictor of choosing self release. Men are far more likely to opt for self release than women engaged in this program. These findings help inform policy and program design and development that addresses the difference in service utilization and successful linkage to services post-incarceration. Successful linkage to services, thus continuity of and access to care, further impact the effects of the revolving door phenomenon of mentally ill homeless individuals cycling between the streets, jails and hospital emergency centers.^

Chemical characteristics of coal pebbles and Barzas-type coals

Coal pebbles found in 1994 in the Greham Bell Island (Franz Josef Land Archipelago) are made up of Barzas-type cuticular liptobiolith. The coal belongs to the initial stage of catagenesis and is characterized by high content of cutinite (up to 70%) with very low reflectance (Ro = 0.1%). Maceration products show some tegillate elements of Arthropoda and individual Devonian spores. It is supposed that plant cuticle and Arthropoda exocuticle are present in this coal. Obtained data suggest presence of Paleozoic rocks in the sedimentary sequence, although they are not yet recovered. These data complement available information on distribution of specific Devonian coals and allow to have a new insight into zoogenic material involved in coal formation.

(Table 1) Characteristics of Klebsormidium (filamentous green algae) strains from the Antarctic, Arctic and Slovakia

The freezing and desiccation tolerance of 12 Klebsormidium strains, isolated from various habitats (aero-terrestrial, terrestrial, and hydro-terrestrial) from distinct geographical regions (Antarctic - South Shetlands, King George Island, Arctic - Ellesmere Island, Svalbard, Central Europe - Slovakia) were studied. Each strain was exposed to several freezing (-4°C, -40°C, -196°C) and desiccation (+4°C and +20°C) regimes, simulating both natural and semi-natural freeze-thaw and desiccation cycles. The level of resistance (or the survival capacity) was evaluated by chlorophyll a content, viability, and chlorophyll fluorescence evaluations. No statistical differences (Kruskal-Wallis tests) between strains originating from different regions were observed. All strains tested were highly resistant to both freezing and desiccation injuries. Freezing down to -196°C was the most harmful regime for all studied strains. Freezing at -4°C did not influence the survival of studied strains. Further, freezing down to -40°C (at a speed of 4°C/min) was not fatal for most of the strains. RDA analysis showed that certain Antarctic and Arctic strains did not survive desiccation at +4°C; however, freezing at -40°C, as well as desiccation at +20 °C was not fatal to them. On the other hand, other strains from the Antarctic, the Arctic, and Central Europe (Slovakia) survived desiccation at temperatures of +4°C, and freezing down to -40°C. It appears that species of Klebsormidium which occupy an environment where both seasonal and diurnal variations of water availability prevail, are well adapted to freezing and desiccation injuries. Freezing and desiccation tolerance is not species-specific nor is the resilience only found in polar strains as it is also a feature of temperate strains.

Stable oxygen isotope record of epibenthic foraminifera and water samples of the Arctic Ocean

We determined d18OCib values of live (Rose Bengal stained) and dead epibenthic foraminifera Cibicidoides wuellerstorfi, Cibicides lobatulus, and Cibicides refulgens in surface sediment samples from the Arctic Ocean and the Greenland, Iceland, and Norwegian seas (Nordic Sea). This is the first time that a comprehensive d18OCib data set is generated and compiled from the Arctic Ocean. For comparison, we defined Atlantic Water (AW), upper Arctic Bottom Water (uABW), and Arctic Bottom Water (ABW) by their temperature/salinity characteristics and calculated mean equilibrium calcite d18Oequ from summer sea-water d18Ow and in situ temperatures. As a result, in the Arctic environment we compensate for Cibicidoides- and Cibicides-specific offsets from equilibrium calcite of -0.35 and -0.55 per mil, respectively. After this taxon-specific adjustment, mean d18OCib values plausibly reflect the density stratification of principle water masses in the Nordic Sea and Arctic Ocean. In addition, mean d18OCib from AW not only significantly differs from mean d18OCib from ABW, but also d18OCib from within AW differentiates in function of provenience and water mass age. Furthermore, in shallow waters brine-derived low d18Ow can significantly lower the d18OCib of Cibicides spp. and thus d18OCib may serve as a paleobrine indicator. There is no statistically significant difference, however, between deeper water masses mean d18OCib of the Nordic Sea, and of the Eurasian and Amerasian basins, and no influence of low-d18Ow brines is recorded in Recent uABW and ABW d18OCib of C. wuellerstorfi. This may be due to dilution of a low-d18Ow brine signal in the deep sea, and/or to preferential incorporation of relatively high-d18Ow brines from high-salinity shelves. Although our data encompass environments with seasonal sea-ice and brine formation supposed to ultimately ventilate the deep Arctic Ocean, d18OCib from uABW and ABW do not indicate negative excursions. This may challenge hypotheses that call for enhanced Arctic brine release to explain negative benthic d18O spikes in deep-sea sediments from the late Pleistocene North Atlantic Ocean.

(Table 2) Characteristics of influence of cyclonic and anticyclonic activity of water masses on hydrophysical, hydrochemical, and hydrobiological parameters in the southern part of the Black Sea in September 1996

Characteristics of the spatial structure of vertical synoptic currents were calculated from data of the density field surveys in order to estimate their influence on distribution of chlorophyll a concentration. Comparisons of chlorophyll concentration and vertical currents were implemented for two multidisciplinary surveys in the Black Sea carried out in summer, 1991 and in winter, 1994. The results showed qualitative and quantitative indications of coincidence of characteristics cited and, in particular, significant positive values of the correlation coefficient (0.65 for the summer survey and 0.83 for the winter one).

Physico-chemical characteristics and ikaite content of brine and ice samples taken during SIPEX and DDU campaigns in East Antarctica, 2007

Calcium carbonate precipitation in sea ice is thought to potentially drive significant CO2 uptake by the ocean. However, little is known about the quantitative spatial and temporal distribution of CaCO3 within sea ice, although it is hypothesized that high quantities of dissolved organic matter and/or phosphate (common in sea ice) may inhibit its formation. In this quantitative study of hydrous calcium carbonate as ikaite, sea ice cores and brine samples were collected from pack and land fast sea ice between September and December 2007 during two expeditions, one in the East Antarctic sector and the other off Terre Adélie. Samples were analysed for CaCO3, salinity, dissolved organic carbon/nitrogen, inorganic phosphate, and total alkalinity. No relationship between these parameters and CaCO3 precipitation was evident. Ikaite was found mostly in the uppermost layers of sea ice with maximum concentrations of up to 126 mg ikaite per litre melted sea ice being measured, although both the temporal and horizontal spatial distributions of ikaite were highly heterogeneous. The precipitate was also found in the snow on top of the sea ice at some of the sampling locations.

Production characteristics and water parameters of the Kola Bay in 2004-2005

Data on chlorophyll a concentration and phytoplankton primary production in the south Kola Bay in 2004-2005 are given.

(Table 1) Bulk and grain density, porosity, and p- and s-wave velocity characteristics of ODP Hole 163-990A sediments

Seismic velocities in rocks are influenced by the properties of the solid, the pore fluid, and the pore space. Cracks dramatically affect seismic velocities in rocks; their influence on the effective elastic moduli of rocks depends on their shape and concentration. Thin cracks (or fractures) substantially lower the moduli of a rock relative to the effect of spherical voids (or vesicles), and lower moduli are reflected by lower P- and S-wave velocities. The objective of this research is to determine the types and concentrations of cracks and their influence on the seismic properties of subaerially erupted basalts drilled from Hole 990A on the Southeast Greenland margin during Ocean Drilling Program Leg 163. Ellipsoidal cracks are used to model the voids in the rocks. The elastic moduli of the solid (grains) are also free parameters in the inverse modeling procedure. The apparent grain moduli reflect a weighted average of the moduli of the constituent minerals (e.g., plagioclase, augite, and clay minerals). The results indicate that (1) there is a strong relationship between P-wave velocity and porosity, suggesting a similarity of pore shape distributions, (2) the distribution of crack types within the massive, central region of aa flows from Hole 990A is independent of total porosity, (3) thin cracks are the first to be effectively sealed by alteration products, and (4) grain densities (an alteration index) and apparent grain moduli of the basalt samples are directly related.

Characteristics of introduced Aphididae species, an endemic fly (Anatalanta aptera) and an introduced ground beetle (Merizodus soledadinus) on the Kerguelen Islands

The suite of environments and anthropogenic modifications of sub-Antarctic islands provide key opportunities to improve our understanding of the potential consequences of climate change and biological species invasions on terrestrial ecosystems. The profound impact of human introduced invasive species on indigenous biota, and the facilitation of establishment as a result of changing thermal conditions, has been well documented on the French sub-Antarctic Kerguelen Islands (South Indian Ocean). The present study provides an overview of the vulnerability of sub-Antarctic terrestrial communities with respect to two interacting factors, namely climate change and alien insects. We present datasets assimilated by our teams on the Kerguelen Islands since 1974, coupled with a review of the literature, to evaluate the mechanism and impact of biological invasions in this region. First, we consider recent climatic trends of the Antarctic region, and its potential influence on the establishment, distribution and abundance of alien insects, using as examples one fly and one beetle species. Second, we consider to what extent limited gene pools may restrict alien species' colonisations. Finally, we consider the vulnerability of native communities to aliens using the examples of one beetle, one fly, and five aphid species taking into consideration their additional impact as plant virus vectors. We conclude that the evidence assimilated from the sub-Antarctic islands can be applied to more complex temperate continental systems as well as further developing international guidelines to minimise the impact of alien species.

Chemical composition of surficial bottom sediments from the Chukchi Sea and adjacent part of the Arctic Ocean

This paper presents data on chemical composition of bottom sediments from the Chukchi Sea and the adjacent Arctic Ocean. Multivariate statistical techniques were used for analysis of the data set and revealed that grain size fractionation of the original terrigenous component during sedimentation was the major factor of clustering of the samples in study. Secondary factors include accumulation of biogenic siliceous and carbonate material and chemogenic or biochemical accumulation of iron, manganese, and some trace elements. The latter factor was significant in areas of tectonic activity within the graben-rift system of the Chukchi Sea.