Anisotropic diffusion at the field scale in a 4-year multi-tracer diffusion and retention experiment – I: Insights from the experimental data

Abstract Claystones are considered worldwide as barrier materials for nuclear waste repositories. In the Mont Terri underground research laboratory (URL), a nearly 4-year diffusion and retention (DR) experiment has been performed in Opalinus Clay. It aimed at (1) obtaining data at larger space and time scales than in laboratory experiments and (2) under relevant in situ conditions with respect to pore water chemistry and mechanical stress, (3) quantifying the anisotropy of in situ diffusion, and (4) exploring possible effects of a borehole-disturbed zone. The experiment included two tracer injection intervals in a borehole perpendicular to bedding, through which traced artificial pore water (APW) was circulated, and a pressure monitoring interval. The APW was spiked with neutral tracers (HTO, HDO, H2O-18), anions (Br, I, SeO4), and cations (Na-22, Ba-133, Sr-85, Cs-137, Co-60, Eu-152, stable Cs, and stable Eu). Most tracers were added at the beginning, some were added at a later stage. The hydraulic pressure in the injection intervals was adjusted according to the measured value in the pressure monitoring interval to ensure transport by diffusion only. Concentration time-series in the APW within the borehole intervals were obtained, as well as 2D concentration distributions in the rock at the end of the experiment after overcoring and subsampling which resulted in �250 samples and �1300 analyses. As expected, HTO diffused the furthest into the rock, followed by the anions (Br, I, SeO4) and by the cationic sorbing tracers (Na-22, Ba-133, Cs, Cs-137, Co-60, Eu-152). The diffusion of SeO4 was slower than that of Br or I, approximately proportional to the ratio of their diffusion coefficients in water. Ba-133 diffused only into �0.1 m during the �4 a. Stable Cs, added at a higher concentration than Cs-137, diffused further into the rock than Cs-137, consistent with a non-linear sorption behavior. The rock properties (e.g., water contents) were rather homogeneous at the centimeter scale, with no evidence of a borehole-disturbed zone. In situ anisotropy ratios for diffusion, derived for the first time directly from field data, are larger for HTO and Na-22 (�5) than for anions (�3�4 for Br and I). The lower ionic strength of the pore water at this location (�0.22 M) as compared to locations of earlier experiments in the Mont Terri URL (�0.39 M) had no notable effect on the anion accessible pore fraction for Cl, Br, and I: the value of 0.55 is within the range of earlier data. Detailed transport simulations involving different codes will be presented in a companion paper.

5-HT and GABA modulate intrinsic excitability of type I interneurons in Hermissenda.

The sensory neurons (photoreceptors) in the visual system of Hermissenda are one site of plasticity produced by Pavlovian conditioning. A second site of plasticity produced by conditioning is the type I interneurons in the cerebropleural ganglia. Both photoreceptors and statocyst hair cells of the graviceptive system form monosynaptic connections with identified type I interneurons. Two proposed neurotransmitters in the graviceptive system, serotonin (5-HT) and gamma-aminobutyric acid (GABA), have been shown to modify synaptic strength and intrinsic neuronal excitability in identified photoreceptors. However, the potential role of 5-HT and GABA in plasticity of type I interneurons has not been investigated. Here we show that 5-HT increased the peak amplitude of light-evoked complex excitatory postsynaptic potentials (EPSPs), enhanced intrinsic excitability, and increased spike activity of identified type I(e(A)) interneurons. In contrast, 5-HT decreased spike activity and intrinsic excitability of type I(e(B)) interneurons. The classification of two categories of type I(e) interneurons was also supported by the observation that 5-HT produced opposite effects on whole cell steady-state outward currents in type I(e) interneurons. Serotonin produced a reduction in the amplitude of light-evoked complex inhibitory PSPs (IPSPs), increased spontaneous spike activity, decreased intrinsic excitability, and depolarized the resting membrane potential of identified type I(i) interneurons. In contrast to the effects of 5-HT, GABA produced inhibition in both types of I(e) interneurons and type I(i) interneurons. These results show that 5-HT and GABA can modulate the intrinsic excitability of type I interneurons independent of the presynaptic effects of the same transmitters on excitability and synaptic efficacy of photoreceptors.

Senescence-related gene expression profiles of rosette leaves of Arabidopsis thaliana: Leaf age versus plant age

Senescence is a form of programmed cell death (PCD) which leads to the death of whole organs, e.g., leaves or flowers, and eventually to the death of entire plants. Like all forms of PCD, senescence is a highly regulated and energy consuming process. Senescence parameters, like protein content, chlorophyll content, expression of photosynthesis-associated genes or senescence-associated genes (SAGs), reveal that senescence occurs in old leaves derived from young plants (6 week old) as well as in young leaves derived from older plants (8 week old), indicating that it is governed by the actual age of the leaves. in order to analyse the differential gene expression profiles during leaf senescence, hybridizations of high-density genome arrays were performed with: i) individual leaves within the rosette of a 6-week-old plant and ii) leaves of the same position within the rosette but harvested from plants of different ages, ranging from 5 to 8 weeks. Cluster and genetree analyses, according to the expression pattern revealed that genes which are up-regulated with respect to the age of the entire plant, showed completely different expression profiles with respect to the age of the individual leaves within one rosette. This was observed even though the actual difference in leaf age was approximately the same. This indicates that gene expression appears to be governed by different parameters: i) the age of the individual leaf and ii) the age and developmental stage of the entire plant.

Distortion-free enhancement of terahertz signals measured by electro-optic sampling. I. Theory

We present three methods for the distortion-free enhancement of THz signals measured by electro-optic sampling in zinc blende-type detector crystals, e.g., ZnTe or GaP. A technique commonly used in optically heterodyne-detected optical Kerr effect spectroscopy is introduced, which is based on two measurements at opposite optical biases near the zero transmission point in a crossed polarizer detection geometry. In contrast to other techniques for an undistorted THz signal enhancement, it also works in a balanced detection scheme and does not require an elaborate procedure for the reconstruction of the true signal as the two measured waveforms are simply subtracted to remove distortions. We study three different approaches for setting an optical bias using the Jones matrix formalism and discuss them also in the framework of optical heterodyne detection. We show that there is an optimal bias point in realistic situations where a small fraction of the probe light is scattered by optical components. The experimental demonstration will be given in the second part of this two-paper series [J. Opt. Soc. Am. B, doc. ID 204877 (2014, posted online)].

Pollen-based quantitative reconstructions of Holocene regional vegetation cover (plant-functional types and land-cover types) in Europe suitable for climate modelling

We present quantitative reconstructions of regional vegetation cover in north-western Europe, western Europe north of the Alps, and eastern Europe for five time windows in the Holocene around 6k, 3k, 0.5k, 0.2k, and 0.05k calendar years before present (bp)] at a 1 degrees x1 degrees spatial scale with the objective of producing vegetation descriptions suitable for climate modelling. The REVEALS model was applied on 636 pollen records from lakes and bogs to reconstruct the past cover of 25 plant taxa grouped into 10 plant-functional types and three land-cover types evergreen trees, summer-green (deciduous) trees, and open land]. The model corrects for some of the biases in pollen percentages by using pollen productivity estimates and fall speeds of pollen, and by applying simple but robust models of pollen dispersal and deposition. The emerging patterns of tree migration and deforestation between 6k bp and modern time in the REVEALS estimates agree with our general understanding of the vegetation history of Europe based on pollen percentages. However, the degree of anthropogenic deforestation (i.e. cover of cultivated and grazing land) at 3k, 0.5k, and 0.2k bp is significantly higher than deduced from pollen percentages. This is also the case at 6k in some parts of Europe, in particular Britain and Ireland. Furthermore, the relationship between summer-green and evergreen trees, and between individual tree taxa, differs significantly when expressed as pollen percentages or as REVEALS estimates of tree cover. For instance, when Pinus is dominant over Picea as pollen percentages, Picea is dominant over Pinus as REVEALS estimates. These differences play a major role in the reconstruction of European landscapes and for the study of land cover-climate interactions, biodiversity and human resources.

Penetrability of the inner mucus layer: who is out there?

Large numbers of microorganisms colonise the skin and mucous membranes of animals, with their highest density in the lower gastrointestinal tract. The impact of these microbes on the host can be demonstrated by comparing animals (usually mice) housed under germ-free conditions, or colonised with different compositions of microbes. Inbreeding and embryo manipulation programs have generated a wide variety of mouse strains with a fixed germ-line (isogenic) and hygiene comparisons robustly show remarkably strong interactions between the microbiota and the host, which can be summarised in three axioms. (I) Live microbes are largely confined to their spaces at body surfaces, provided the animal is not suffering from an infection. (II) There is promiscuous molecular exchange throughout the host and its microbiota in both directions [1]. (III) Every host organ system is profoundly shaped by the presence of body surface microbes. It follows that one must draw a line between live microbial and host “spaces” (I) to understand the crosstalk (II and III) at this interesting interface of the host-microbial superorganism. Of course, since microbes can adapt to very different niches, there has to be more than one line. In this issue of EMBO Reports, Johansson and colleagues have studied mucus, which is the main physical frontier for most microbes in the intestinal tract: they report how different non-pathogenic microbiota compositions affect its permeability and the functional protection of the epithelial surface [2].

First thoughts on surface tonal patterns in Amawaka, a Panoan language of Peru and Brazil

Amawaka ([ɑmɨ̃ˈwɐkɑ]) is a highly endangered and underdocumented tonal language of the Headwaters (Fleck 2011) subgroup of the Panoan family in the Southwest Amazon Basin, spoken by approximately 200 people. Undocumented phonetic and phonological phenomena of Amawaka include its tonal structure, both in terms of surface realizations and the patterns underlying these realizations. Original audiovisual data from the author’s fieldwork in various Amawaka communities at the Peru-Brazil border will illuminate the as-yet obscure tonal systematicity of the language. Unlike other elements, monosyllabic bimoraic phonological nominal words with long vowels display variation in their surface realization. All the words with the open back unrounded /ɑ/, like /ˈkɑ̀:/ (patarashca, a traditional Amazonian dish), /ˈnɑ̀:/ “mestizo” etc. [with the exception of /ˈtɑ:/ “reed”, which surfaces with either a H or L tone] bear a low tone in isolation. This realization contrasts with all the encountered nominal monosyllables with vowels from the close and close-mid front and central spectrum /i, ɘ, ɨ, ɨ̃/, which clearly surface as high tone words in isolation, for example /ˈmɨ̃́:/ (a clay-lick for animals), /ˈwí:/ “Anopheles, spp. mosquito”. Monosyllables with close-mid back rounded /o/ have a less restrictive pitch that varies among speakers from low to high realizations, and sometimes even across the speech tokens from an individual speaker, e.g. /wó:/ or /wō:/ “hair”, /ɧō:/ or /ɧò:/ (a type of tarantula). Phrasal tonal phonology is more complex, when these three kinds of monosyllables appear in larger noun phrases. Some retain the same surface tones as their isolation form, while others seem to vary freely in their surface realization, e.g. /ˈtɘ́:.nɑ̀:/ or /ˈtɘ́:.nɑ́:/ ‘one mestizo’. Yet other monosyllables, e.g. /mɑ̀:/, exhibit a falling tone when preceded by a H syllable, suggesting probably latent tone sandhi phenomena, e.g /ˈtɘ́:.mɑ̂:/ (one clay-lick for parrots). In disyllabic, trisyllabic and quadrisyllabic nouns, tonal and stress patterns generally seem to be more consistent and tend to be retained both in isolation and in larger intonational phrases. Disyllabic nouns, for instance, surface as L-H or L-L when a glottal stop is in coda position. The association of L with a glottal stop is a feature that occurs in other Panoan languages as well, like Capanahua (Loos 1969), and more generally it is an areal feature, found in other parts of Amazonia (Hyman 2010). So, tone has significant interactions with the glottal stop and glottalization, which generally co-occurs with L. The data above suggest that the underlying tonal system of Amawaka is much more complex than the privative one-tone analysis (/H/ vs. Ø, i.e. lack of tone) that was proposed by Russell and Russell (1959). Evidence from field data suggests either an equipollent (Hyman 2010) two-tone opposition between /H/ and /L/, or a hybrid system, with both equipollent and privative features; that is, /H/ vs. /L/ vs. either Ø or /M/. This first systematic description of Amawaka tone, in conjunction with ongoing research, is poised to address broader questions concerning interrelationships between surface/underlying tone and other suprasegmental features, such as nasality, metrical stress, and intonation. References Fleck, David W. 2011. Panoan languages and linguistics. In Javier Ruedas and David W. Fleck (Eds.), Panoan Histories and Interethnic Identities, To appear. Hyman, Larry. 2010. Amazonia and the typology of tone systems. Presented at the conference Amazonicas III: The structure of the Amazonian languages. Bogotá. Loos, Eugene E. 1969. The phonology of Capanahua and its grammatical basis. Norman: SIL and U. Oklahoma. Russell, Robert & Dolores. 1959. Syntactotonemics in Amahuaca (Pano). Série Lingüistica Especial, 128-167. Publicaçoes do Museu Nacional, Rio de Janeiro, Brasil.

Towards an analysis of tonal patterns in Amawaka, a Panoan language of Peru and Brazil

Amawaka ([ɑmɨ̃ˈwɐkɑ]) is a highly endangered and underdocumented tonal language of the Headwaters (Fleck 2011) subgroup of the Panoan family in the Southwest Amazon Basin, spoken by approximately 200 people. Undocumented phonetic and phonological phenomena of Amawaka include its tonal structure, both in terms of surface realizations and the patterns underlying these realizations. Original audiovisual data from the author’s fieldwork in various Amawaka communities at the Peru-Brazil border will illuminate the as-yet obscure tonal systematicity of the language. Unlike other elements, monosyllabic bimoraic phonological nominal words with long vowels display variation in their surface realization. All the words with the open back unrounded /ɑ/, like /ˈkɑ̀:/ (a traditional Amazonian dish), /ˈnɑ̀:/ “mestizo” etc. [with the exception of /ˈtɑ:/ “reed”, which surfaces with either a H or L tone] bear a low tone in isolation. This realization contrasts with all the encountered nominal monosyllables with vowels from the close and close-mid front and central spectrum /i, ɘ, ɨ, ɨ̃/, which clearly surface as high tone words in isolation, for example /ˈmɨ̃́:/ (a clay-lick for animals), /ˈwí:/ “Anopheles, spp. mosquito”. Monosyllables with close-mid back rounded /o/ have a less restrictive pitch that varies among speakers from low to high realizations, and sometimes even across the speech tokens from an individual speaker, e.g. /wó:/ or /wō:/ “hair”, /ɧō:/ or /ɧò:/ (a type of tarantula). Phrasal tonal phonology is more complex, when these three kinds of monosyllables appear in larger noun phrases. Some retain the same surface tones as their isolation form, while others seem to vary freely in their surface realization, e.g. /ˈtɘ́:.nɑ̀:/ or /ˈtɘ́:.nɑ́:/ ‘one mestizo’. Yet other monosyllables, e.g. /mɑ̀:/, exhibit a falling tone when preceded by a H syllable, suggesting probably latent tone sandhi phenomena, e.g /ˈtɘ́:.mɑ̂:/ (one clay-lick for parrots). In disyllabic, trisyllabic and quadrisyllabic nouns, tonal and stress patterns generally seem to be more consistent and tend to be retained both in isolation and in larger intonational phrases. Disyllabic nouns, for instance, surface as L-H or L-L when a glottal stop is in coda position. The association of L with a glottal stop is a feature that occurs in other Panoan languages as well, like Capanahua (Loos 1969), and more generally it is an areal feature, found in other parts of Amazonia (Hyman 2010). So, tone has significant interactions with the glottal stop and glottalization, which generally co-occurs with L. The data above suggest that the underlying tonal system of Amawaka is much more complex than the privative one-tone analysis (/H/ vs. Ø, i.e. lack of tone) that was proposed by Russell and Russell (1959). Evidence from field data suggests either an equipollent (Hyman 2010) two-tone opposition between /H/ and /L/, or a hybrid system, with both equipollent and privative features; that is, /H/ vs. /L/ vs. either Ø or /M/. This first systematic description of Amawaka tone, in conjunction with ongoing research, is poised to address broader questions concerning interrelationships between surface/underlying tone and other suprasegmental features, such as nasality, metrical stress, and intonation. References Fleck, David W. 2011. Panoan languages and linguistics. In Javier Ruedas and David W. Fleck (Eds.), Panoan Histories and Interethnic Identities, To appear. Hyman, Larry. 2010. Amazonia and the typology of tone systems. Presented at the conference Amazonicas III: The structure of the Amazonian languages. Bogotá. Loos, Eugene E. 1969. The phonology of Capanahua and its grammatical basis. Norman: SIL and U. Oklahoma. Russell, Robert & Dolores. 1959. Syntactotonemics in Amahuaca (Pano). Série Lingüistica Especial, 128-167. Publicaçoes do Museu Nacional, Rio de Janeiro, Brasil.

Multiple imputation for missing continuous and dichotomous data: The effects of patterns of missingness and variable correlations on type I error with small samples

The purpose of this study is to investigate the effects of predictor variable correlations and patterns of missingness with dichotomous and/or continuous data in small samples when missing data is multiply imputed. Missing data of predictor variables is multiply imputed under three different multivariate models: the multivariate normal model for continuous data, the multinomial model for dichotomous data and the general location model for mixed dichotomous and continuous data. Subsequent to the multiple imputation process, Type I error rates of the regression coefficients obtained with logistic regression analysis are estimated under various conditions of correlation structure, sample size, type of data and patterns of missing data. The distributional properties of average mean, variance and correlations among the predictor variables are assessed after the multiple imputation process. ^ For continuous predictor data under the multivariate normal model, Type I error rates are generally within the nominal values with samples of size n = 100. Smaller samples of size n = 50 resulted in more conservative estimates (i.e., lower than the nominal value). Correlation and variance estimates of the original data are retained after multiple imputation with less than 50% missing continuous predictor data. For dichotomous predictor data under the multinomial model, Type I error rates are generally conservative, which in part is due to the sparseness of the data. The correlation structure for the predictor variables is not well retained on multiply-imputed data from small samples with more than 50% missing data with this model. For mixed continuous and dichotomous predictor data, the results are similar to those found under the multivariate normal model for continuous data and under the multinomial model for dichotomous data. With all data types, a fully-observed variable included with variables subject to missingness in the multiple imputation process and subsequent statistical analysis provided liberal (larger than nominal values) Type I error rates under a specific pattern of missing data. It is suggested that future studies focus on the effects of multiple imputation in multivariate settings with more realistic data characteristics and a variety of multivariate analyses, assessing both Type I error and power. ^

Age and chemical composition of apatites from five DSDP and ODP Sites in the Pacific, Atlantic and Indian Oceans

Since studies on deep-sea cores were carried out in the early 1990s it has been known that ambient temperature may have a marked affect on apatite fission track annealing. Due to sluggish annealing kinetics, this effect cannot be quantified by laboratory annealing experiments. The unknown amount of low-temperature annealing remains one of the main uncertainties for extracting thermal histories from fission track data, particularly for samples which experienced slow cooling in shallow crustal levels. To further elucidate these uncertainties, we studied volcanogenic sediments from five deep-sea drill cores, that were exposed to maximum temperatures between ~10° and 70°C over geological time scales of ~15-120 Ma. Mean track lengths (MTL) and etch pit diameters (Dpar) of all samples were measured, and the chemical composition of each grain analyzed for age and track length measurements was determined by electron microprobe analysis. Thermal histories of the sampled sites were independently reconstructed, based on vitrinite reflectance measurements and/or 1D numerical modelling. These reconstructions were used to test the most widely used annealing models for their ability to predict low-temperature annealing. Our results show that long-term exposure to temperatures below the temperature range of the nominal apatite fission track partial annealing zone results in track shortening ranging between 4 and 11%. Both chlorine content and Dpar values explain the downhole annealing patterns equally well. Low chlorine apatite from one drill core revealed a systematic relation between Si-content and Dpar value. The question whether Si-substitution in apatite has direct and systematic effects on annealing properties however, cannot be addressed by our data. For samples, which remained at temperatures <30°C, and which are low in chlorine, the Laslett et al. [Laslett G., Green P., Duddy I. and Gleadow A. (1987) Thermal annealing of fission tracks in apatite. Chem. Geol. 65, 1-13] annealing model predicts MTL up to 0.6 µm longer than those actually measured, whereas for apatites with intermediate to high chlorine content, which experienced temperatures >30°C, the predictions of the Laslett et al. (1987) model agree with the measured MTL data within error levels. With few exceptions, predictions by the Ketcham et al. [Ketcham R., Donelick R. and Carlson W. (1999) Variability of apatite fission-track annealing kinetics. III: Extrapolation to geological time scales. Am. Mineral. 84/9, 1235-1255] annealing model are consistent with the measured data for samples which remained at temperatures below ~30°C. For samples which experienced maximum temperatures between ~30 and 70°C, and which are rich in chlorine, the Ketcham et al. (1999) model overestimates track annealing.

(Table 2) Production characteristics of phytoplankton and selected related factors at bottle sampling stations in the subtropical and tropical Atlantic Ocean

In October and November 2002, high and relatively high values of chlorophyll a concentration at the sea surface (Cchl) were observed in the English Channel (0.47 mg/m**3), in waters of the North Atlantic Current (0.25 mg/m**3 ), in the tropical and subtropical anticyclonic gyres (0.07-0.42 mg/m**3), and also in the southwestern region of the southern subtropical anticyclonic gyre (usually 0.11-0.23 mg/m**3). The central regions of the southern subtropical anticyclonic gyre (SATG) and the North Atlantic tropical gyre (NATR) were characterized by lower values of Cchl (0.02-0.08 mg/m**3 for the SATG and 0.07-0.14 mg/m**3 for the NATR). At most of the SATG stations, values of surface primary production (Cphs) varied from 2.5 to 5.5 mg C/m**3 per day and were mainly defined by fluctuations of Cchl (r = +0.78) rather than by those of the assimilation number (r = +0.54). Low assimilation activity of phytoplankton in these waters (1.3-4.6 mg chl a per hour) pointed to a lack of nutrients. Analysis of variability of their concentration and composition of photosynthetic pigments showed that, in waters north of 30°N, the growth of phytoplankton was mostly restricted by deficiency of nitrogen, while, in more southern areas, at the majority of stations (about 60%), phosphorus concentrations were minimal. At low concentrations of nitrates and nitrites, ammonium represented itself as a buffer that prevented planktonic algae from extreme degrees of nitric starvation. In tropical waters and in waters of the SATG, primary production throughout the water column varied from 240 to 380 mg C/m**2 30° per day. This level of productivity at stations with low values of C chl (<0.08 mg/m**3) was provided by a well-developed deep chlorophyll maximum and high transparency of water. Light curves of photosynthesis based on in situ measurements point to high efficiency of utilizing penetrating solar radiation by phytoplankton on cloudy days.

(Table 2) Abundance and biomass of zooplankton in the eastern Black Sea in the beginning of September 1996

On the basis of analyses of samples collected in the eastern Black Sea in September 1996 trends of increase in surface zooplankton biomass and general decrease in Mnemiopsis biomass were revealed.

Concentration of total organic carbon in waters of the Atlantic Ocean

In pursuance of previous studies water samples were taken in the Atlantic and Mediterranean during the 12th, 14th and 15th cruises of RV Mikhail Lomonosov in 1962-1964 to determine total and particulate organic carbon and permanganate oxidizability. Preliminary processing of the water samples was carried out in the normal manner in the on-board laboratory immediately after they had been taken: destruction of bicarbonates and carbonates by precise addition of acid (by alkalinity) and evaporation to dryness at 50-60°C. It is quite probable that the corresponding volatile fraction of organic matter is lost under these conditions. In discussion it was demonstrated that it may now be assumed that the carbon of the volatile fraction averages approximately 15% of total carbon, i.e., 15% of the sum of organic carbon of the volatile and nonvolatile fractions. Oxidizability was determined in all samples in the on-board laboratory.