Climate spectrum estimation in the presence of timescale errors

We introduce an algorithm (called REDFITmc2) for spectrum estimation in the presence of timescale errors. It is based on the Lomb-Scargle periodogram for unevenly spaced time series, in combination with the Welch's Overlapped Segment Averaging procedure, bootstrap bias correction and persistence estimation. The timescale errors are modelled parametrically and included in the simulations for determining (1) the upper levels of the spectrum of the red-noise AR(1) alternative and (2) the uncertainty of the frequency of a spectral peak. Application of REDFITmc2 to ice core and stalagmite records of palaeoclimate allowed a more realistic evaluation of spectral peaks than when ignoring this source of uncertainty. The results support qualitatively the intuition that stronger effects on the spectrum estimate (decreased detectability and increased frequency uncertainty) occur for higher frequencies. The surplus information brought by algorithm REDFITmc2 is that those effects are quantified. Regarding timescale construction, not only the fixpoints, dating errors and the functional form of the age-depth model play a role. Also the joint distribution of all time points (serial correlation, stratigraphic order) determines spectrum estimation.

Presence of UV filters in surface water and the effects of phenylbenzimidazole sulfonic acid on rainbow trout (Oncorhynchus mykiss) following a chronic toxicity test

UV filters belong to a group of compounds that are used by humans and are present in municipal waste-waters, effluents from sewage treatment plants and surface waters. Current information regarding UV filters and their effects on fish is limited. In this study, the occurrence of three commonly used UV filters - 2-phenylbenzimidazole-5-sulfonic acid (PBSA), 2-hydroxy-4-methoxybenzophenone (benzophenone-3, BP-3) and 5-benzoyl-4-hydroxy-2-methoxy-benzenesulfonic acid (benzophenone-4, BP-4) - in South Bohemia (Czech Republic) surface waters is presented. PBSA concentrations (up to 13μgL(-1)) were significantly greater than BP-3 or BP-4 concentrations (up to 620 and 390ngL(-1), respectively). On the basis of these results, PBSA was selected for use in a toxicity test utilizing the common model organism rainbow trout (Oncorhynchus mykiss). Fish were exposed to three concentrations of PBSA (1, 10 and 1000µgL(-1)) for 21 and 42 days. The PBSA concentrations in the fish plasma, liver and kidneys were elevated after 21 and 42 days of exposure. PBSA increased activity of certain P450 cytochromes. Exposure to PBSA also changed various biochemical parameters and enzyme activities in the fish plasma. However, no pathological changes were obvious in the liver or gonads.

Exploring "fringe" consciousness: the subjective experience of perceptual fluency and its objective bases

Perceptual fluency is the subjective experience of ease with which an incoming stimulus is processed. Although perceptual fluency is assessed by speed of processing, it remains unclear how objective speed is related to subjective experiences of fluency. We present evidence that speed at different stages of the perceptual process contributes to perceptual fluency. In an experiment, figure-ground contrast influenced detection of briefly presented words, but not their identification at longer exposure durations. Conversely, font in which the word was written influenced identification, but not detection. Both contrast and font influenced subjective fluency. These findings suggest that speed of processing at different stages condensed into a unified subjective experience of perceptual fluency.

Presence of the Gpr179(nob5) allele in a C3H-derived transgenic mouse

PURPOSE To identify the mutation responsible for an abnormal electroretinogram (ERG) in a transgenic mouse line (tg21) overexpressing erythropoietin (Epo). The tg21 line was generated on a mixed (C3H; C57BL/6) background and lacked the b-wave component of the ERG. This no-b-wave (nob) ERG is seen in other mouse models with depolarizing bipolar cell (DBC) dysfunction and in patients with the complete form of congenital stationary night blindness (cCSNB). We determined the basis for the nob ERG phenotype and screened C3H mice for the mutation to evaluate whether this finding is important for the vision research community. METHODS ERGs were used to examine retinal function. The retinal structure of the transgenic mice was investigated using histology and immunohistochemistry. Inverse PCR was performed to identify the insertion site of the Epo transgene in the mouse genome. Affected mice were backcrossed to follow the inheritance pattern of the nob ERG phenotype. Quantitative real-time PCR (qRT PCR), Sanger sequencing, and immunohistochemistry were used to identify the mutation causing the defect. Additional C3H sublines were screened for the detected mutation. RESULTS Retinal histology and blood vessel structure were not disturbed, and no loss of DBCs was observed in the tg21 nob mice. The mutation causing the nob ERG phenotype is inherited independently of the tg21 transgene. The qRT PCR experiments revealed that the nob ERG phenotype reflected a mutation in Gpr179, a gene involved in DBC signal transduction. PCR analysis confirmed the presence of the Gpr179(nob5) insertional mutation in intron 1 of Gpr179. Screening for mutations in other C3H-derived lines revealed that C3H.Pde6b(+) mice carry the Gpr179 (nob5) allele whereas C3H/HeH mice do not. CONCLUSIONS We identified the presence of the Gpr179(nob5) mutation causing DBC dysfunction in a C3H-derived transgenic mouse line. The nob phenotype is not related to the presence of the transgene. The Gpr179(nob5) allele can be added to the list of background alleles that impact retinal function in commonly used mouse lines. By providing primers to distinguish between Gpr179 mutant and wild-type alleles, this study allows investigators to monitor for the presence of the Gpr179(nob5) mutation in other mouse lines derived from C3H.

Integrating Events Across Levels of Consciousness

Our knowledge grows as we integrate events experienced at different points in time. We may or may not become aware of events, their integration, and their impact on our knowledge and decisions. But can we mentally integrate two events, if they are experienced at different time points and at different levels of consciousness? In this study, an event consisted of the presentation of two unrelated words. In the stream of events, half of events shared one component ("tree desk" … "desk fish") to facilitate event integration. We manipulated the amount of time and trials that separated two corresponding events. The contents of one event were presented subliminally (invisible) and the contents of the corresponding overlapping event supraliminally (visible). Hence, event integration required the binding of contents between consciousness levels and between time points. At the final test of integration, participants judged whether two supraliminal test words ("tree fish") fit together semantically or not. Unbeknown to participants, half of test words were episodically related through an overlap ("desk"; experimental condition) and half were not (control condition). Participants judged episodically related test words to be closer semantically than unrelated test words. This subjective decrease in the semantic distance between test words was both independent of whether the invisible event was encoded first or second in order and independent of the number of trials and the time that separated two corresponding events. Hence, conscious and unconscious memories were mentally integrated into a linked mnemonic representation.

Intratumoural budding (ITB) in preoperative biopsies predicts the presence of lymph node and distant metastases in colon and rectal cancer patients

Background:In colorectal cancer (CRC), tumour budding at the invasion front is associated with lymph node (LN) and distant metastasis. Interestingly, tumour budding can also be detected in biopsies (intratumoural budding; ITB) and may have similar clinical importance. Here we investigate whether ITB in preoperative CRC biopsies can be translated into daily diagnostic practice.Methods:Preoperative biopsies from 133 CRC patients (no neoadjuvant therapy) underwent immunohistochemistry for pan-cytokeratin marker AE1/AE3. Across all biopsies for each patient, the densest region of buds at × 40 (high-power field; HPF) was identified and buds were counted.Results:A greater number of tumour buds in the biopsy was associated with pT stage (P=0.0143), LN metastasis (P=0.0007), lymphatic (P=0.0065) and venous vessel invasion (P=0.0318) and distant metastasis (cM1) (P=0.0013). Using logistic regression, a 'scale' was developed to estimate the probability of LN and distant metastasis using the number of tumour buds (e.g. 10 buds per HPF: 64% chance of LN metastasis; 30 buds per HPF: 86% chance). Inter-observer agreement for ITB was excellent (intraclass correlation coefficient: 0.813).Conclusion:Tumour budding can be assessed in the preoperative biopsy of CRC patients. It is practical, reproducible and predictive of LN and distant metastasis. Intratumoural budding qualifies for further investigation in the prospective setting.

Presence of three pesticides in rural drinking water sources in Kenya

A cross-sectional study on the use of three pesticides and their presence in drinking water sources was conducted in Githunguri/Kiaria community between January 1994-March 1995. The main objective of the study was to determine the extent to which some of the pesticides used by the Githunguri/Kiaria agricultural community were polluting their drinking water sources. Due to monetary and physical limitations, only DDT, its isomers and metabolites, carbofuran and carbaryl pesticides were identified and used as surrogates of pollution for the other pesticides.^ The study area was divided into high and low lying geographic surface areas. Thirty-four and 38 water sampling sites were randomly selected respectively. During wet and dry seasons, a total of 144 water samples were collected and analyzed at the Kenya Bureau of Standards Laboratory in Nairobi. Gas chromatography was used to analyze samples for possible presence of DDT, its isomers and metabolites, while high pressure liquid chromatography was used to analyze samples for carbofuran and carbaryl pesticides.^ Six sites testing positively for DDT, its isomers and metabolites represented 19.4% of the total sampled sites, with a mean concentration of 0.00310 ppb in the dry season and 0.0130 ppb in the wet season. All the six sites testing positively for the same pesticide exceeded the European maximum contaminant limit (MCL) in the wet season, and only one site exceeded the European MCL in the dry season.^ Those sites testing positively for carbofuran and carbaryl represented 5.6% of the total sampled sites. The mean concentration for the carbofuran at the sites was 2.500 ppb and 1.590 ppb in the dry and wet seasons respectively. Similarly, the mean concentration for carbaryl at the sites was 0.281 ppb in the dry season and 0.326 ppb in the wet season.^ One site testing positively for carbofuran exceeded the European MCL and WHO set limit in the wet season, while one site testing positively for the same pesticide exceeded the USA, Canada, European and WHO MCLs in the dry season. Similarly, one site which tested positively for carbaryl pesticide exceeded the European MCL in both seasons.^ Out of the 2,587 community members in the study area, 333 (13%) were exposed through their drinking water sources to the three pesticides investigated by this study. As a public health measure, integrated pest management approaches (IPM), protection of the wells and education of the community is necessary to minimize the pollution of the environment and safeguard the drinking water sources from pollution by the pesticides. ^

The potential of stomata analysis in conifers to estimate presence of conifer trees: examples from the Alps

To estimate whether or not a plant taxon found in the fossil record was locally present may be difficult if only pollen is analyzed. Plant macrofossils, in contrast, provide a clear indication of a taxon's local presence, although in some lake sediments or peats, macrofossils may be rare or degraded. For conifers, the stomata found on pollen slides are derived from needles and thus provide a valuable proxy for local presence and they can be identified to genus level. From previously published studies, a transect across the Alps based on 13 sites is presented. For basal samples in sandy silt above the till with high pollen values of Pinus, for example, we may distinguish pine pollen from distant sources (samples with no stomata), from reworked pollen (samples with stomata present). The first apparent local presence of most conifer genera based on stomata often but not always occurs together with the phase of rapid pollen increase (rational limit). An exception is Larix, with its annual deposition of needles and heavy poorly dispersed pollen, for it often shows the first stomata earlier, at the empirical pollen limit. The decline and potential local extinction of a conifer can sometimes be shown in the stomata record. The decline may have been caused by climatic change, competition, or human impact. In situations where conifers form the timberline, the stomata record may indicate timberline fluctuations. In the discussion of immigration or migration of taxa we advocate the use of the cautious term ``apparent local presence'' to include some uncertainties. Absence of a taxon is impossible to prove.