Big brands impact small islands: Sources of plastic pollution in a remote and protected archipelago.

Remote islands are disproportionately affected by plastic pollution, often originating from elsewhere, so it is important to understand its origins, to stop debris entering the ocean at their source. We investigated the origins of beached plastic drink bottles in the Chagos Archipelago, a large remote Marine Protected Area (MPA) in the Indian Ocean. We recorded the brands, countries of manufacture, types of drink, and ages of plastic bottles and their lids. The prevalent type of drink was water, with items mostly manufactured in Indonesia, China, and the Maldives. The main brands were Danone and the Coca-Cola Company. We deduced that 10 % of the items originated from ships passing the archipelago, including all the items manufactured in China. The identification of the brands creating plastic pollution in remote MPAs with high biodiversity supports extended producer responsibility, one of the proposed policy development areas of the Global Plastics Treaty.

Development of a prototype modeling system to estimate the GHG mitigation potential of forest and wildfire management.

Having recently experienced the three worst wildfire seasons in British Columbia's history in 2017, 2018 and 2021, and anticipating more severe impacts in the future, a key Carbon (C) research priority is to develop reliable models to explore options and identify a portfolio of regionally differentiated solutions for wildfire and forest management. We contribute to this effort by developing a prototype integrated C modeling framework which includes future wildfires that respond to forest stand characteristics and wildfire history. Model validation evaluated net GHG emissions relative to a 'do-nothing' baseline for several management scenarios and included emissions from forest ecosystems, harvested wood products and substitution benefits from avoided fossil fuel burning and avoided emissions-intensive materials. Data improvements are needed to accurately quantify the baseline and scenario GHG emissions, and to identify trade-offs and uncertainties. • A Fire Tolerant scenario included post-fire restoration with planting of climatically suitable fire-resistant species and salvage harvest in place of clearcut harvest.

Cumulative effects of natural and anthropogenic disturbances on the forest carbon balance in the oil sands region of Alberta, Canada; a pilot study (1985-2012).

BACKGROUND: Assessing cumulative effects of anthropogenic and natural disturbances on forest carbon (C) stocks and fluxes, because of their relevance to climate change, is a requirement of environmental impact assessments (EIAs) in Canada. However, tools have not been developed specifically for these purposes, and in particular for the boreal forest of Canada, so current forest C assessments in EIAs take relatively simple approaches. Here, we demonstrate how an existing tool, the Generic Carbon Budget Model (GCBM), developed for national and international forest C reporting, was used for an assessment of the cumulative effects of anthropogenic and natural disturbances to support EIA requirements. We applied the GCBM to approximately 1.3 million ha of upland forest in a pilot study area of the oil sands region of Alberta that has experienced a large number of anthropogenic (forestry, energy sector) and natural (wildfire, insect) disturbances. RESULTS: Over the 28 years, 25% of the pilot study area was disturbed. Increasing disturbance emissions, combined with declining net primary productivity and reductions in forest area, changed the study area from a net C sink to a net C source. Forest C stocks changed from 332.2 Mt to 327.5 Mt, declining by 4.7 Mt at an average rate of 0.128 tC ha-1 yr-1. The largest cumulative areas of disturbance were caused by wildfire (139,000 ha), followed by the energy sector (110,000 ha), insects (33,000 ha) and harvesting (31,000 ha) but the largest cumulative disturbance emissions were caused by the energy sector (9.5 Mt C), followed by wildfire (5.5 Mt C), and then harvesting (1.3 Mt C). CONCLUSION: An existing forest C model was used successfully to provide a rigorous regional cumulative assessment of anthropogenic and natural disturbances on forest C, which meets requirements of EIAs in Canada. The assessment showed the relative importance of disturbances on C emissions in the pilot study area, but their relative importance is expected to change in other parts of the oil sands region because of its diversity in disturbance types, patterns and intensity. Future assessments should include peatland C stocks and fluxes, which could be addressed by using the Canadian Model for Peatlands.

Analysis of historical negative control group data from the rat in vivo micronucleus assay.

A database of micronuclei counts for historical negative control data from rat in vivo micronuclei tests performed in 10 different laboratories was established. Data were available from over 4000 negative control rats from 10 laboratories. The mean frequency of micronucleated cells (MN)/1000 cells ranged from 0.44 to 2.22, a 5-fold range. Overall there were no major sex or strain differences in frequency, although there were some small but statistically significant differences within laboratories. There was appreciable variability between experiments compared with variability within experiments in some laboratories. No specific factor was identified which could explain this variability although it was noted that many different vehicles were used in the experiments. It is hoped that these data will help laboratories beginning studies with the rat micronucleus assay and those involved in the assessment of micronucleus assay results.

Standardized cell sources and recommendations for good cell culture practices in genotoxicity testing.

Good cell culture practice and characterization of the cell lines used are of critical importance in in vitro genotoxicity testing. The objective of this initiative was to make continuously available stocks of the characterized isolates of the most frequently used mammalian cell lines in genotoxicity testing anywhere in the world ('IVGT' cell lines). This project was organized under the auspices of the International Life Sciences Institute (ILSI) Health and Environmental Sciences Institute (HESI) Project Committee on the Relevance and Follow-up of Positive Results in In Vitro Genetic Toxicity (IVGT) Testing. First, cell isolates were identified that are as close as possible to the isolate described in the initial publications reporting their use in genotoxicity testing. The depositors of these cell lines managed their characterization and their expansion for preparing continuously available stocks of these cells that are stored at the European Collection of Cell Cultures (ECACC, UK) and the Japanese Collection of Research Bioresources (JCRB, Japan). This publication describes how the four 'IVGT' cell lines, i.e. L5178Y TK+/- 3.7.2C, TK6, CHO-WBL and CHL/IU, were prepared for deposit at the ECACC and JCRB cell banks. Recommendations for handling these cell lines and monitoring their characteristics are also described. The growth characteristics of these cell lines (growth rates and cell cycles), their identity (karyotypes and genetic status) and ranges of background frequencies of select endpoints are also reported to help in the routine practice of genotoxicity testing using these cell lines.

Automatic spike sorting for neural decoding.

While various automated spike sorting techniques have been developed, their impact on neural decoding has not been investigated. In this paper we extend previous Gaussian mixture models and expectation maximization (EM) techniques for automatic spike sorting. We suggest that good initialization of EM is critical and can be achieved via spectral clustering. To account for noise we extend the mixture model to include a uniform outlier process. Automatically determining the number of neurons recorded per electrode is a challenging problem which we solve using a greedy optimization algorithm that selects models with different numbers of neurons according to their decoding accuracy. We focus on data recorded from motor cortex and evaluate performance with respect to the decoding of hand kinematics from firing rates. We found that spike trains obtained by our automated technique result in more accurate neural decoding than those obtained by human experts.

Reconstruction of hand movement trajectories from a dynamic ensemble of spiking motor cortical neurons.

One of the many challenges in long-term decoding from chronically implanted electrodes involves tracking changes in the firing properties of the neural ensemble while simultaneously reconstructing the desired signal. We provide an approach to this problem based on adaptive point process filtering. In particular, we construct a lock-step adaptive filter built upon stochastic models for: a) the receptive field parameters of individual neurons within the ensemble, b) the biological signal to be reconstructed, and c) the instantaneous likelihood of firing in each neuron given the current state of a) and b). We assessed the ability of this filter to maintain a good representation of movement information in a dynamic ensemble of primary motor neurons tuned to hand kinematics. We simulated a recording scenario for this ensemble, where neurons were continuously becoming lost to the recording device while recordings from other, previously unobserved neurons became available. We found that this adaptive decoding algorithm was able to maintain accurate estimates of hand direction, even after the entire neural population had been replaced multiple times, but that the hand velocity signal tended to degrade over long periods.

The neglect of response bias in mental health research.

A number of researchers have observed that response biases, defined as when subjects respond to items in research instruments in ways that do not coincide with the intent or content of the instrument, suffuse measurements and assessments of mental disorders. They cautioned that the response bias problem has been neglected in mental health research at the price of substantial error. Have the cautions been heeded? Or does the neglect of response bias continue? Articles published in 1998 in three major psychiatric journals were examined: Archives of General Psychiatry, American Journal of Psychiatry, and the Journal of Nervous and Mental Disease. The articles were examined to determine whether response biases were mentioned and whether systematic efforts were made to attend to their influence on the findings of the study. Each article was assessed twice by independent raters. The examination indicates that a very small minority of the articles reviewed mentioned response bias and that among those mentioning it, a minority attempted to control for bias effects. Cautions offered about response bias have not been heeded. Accordingly, the issue is one of how to incorporate concerns about response bias into the institutional structures that influence the culture of mental health research.

Ames assays and unscheduled DNA synthesis assays on 2, 4-dichlorophenoxyacetic acid and its derivatives.

2,4-dichlorophenoxyacetic acid and several of its derivatives (collectively known as 2,4-D) are herbicides used to control a wide variety of broadleaf and woody plants. The genetic toxicity in vitro of 2,4-D and seven of its salts and esters were examined by employing gene mutation in bacteria (Ames test) and induction of DNA damage and repair in rat hepatocytes. In addition, an in vivo unscheduled DNA synthesis (UDS) assay was performed on 2,4-D. There were no indications of genotoxic potential for 2,4-D acid, or any of its derivatives, in these assays. These results are consistent with the reported lack of carcinogenic potential for 2,4-D in both mice and rats.

Approaches to detection of distantly related proteins by database searches.

The searching of protein databases as a method of identifying newly sequenced genes is commonplace in molecular biology laboratories. However, it is a procedure that is not usually formally taught to students, and method cookbooks discuss it only briefly. This article uses a single family of highly diverged uracil-DNA glycosylases, which fall into two distinct groups, to highlight some of the difficulties associated with identification of such proteins by database searching.

Parameterized complexity analysis in computational biology.

Many computational problems in biology involve parameters for which a small range of values cover important applications. We argue that for many problems in this setting, parameterized computational complexity rather than NP-completeness is the appropriate tool for studying apparent intractability. At issue in the theory of parameterized complexity is whether a problem can be solved in time O(n alpha) for each fixed parameter value, where alpha is a constant independent of the parameter. In addition to surveying this complexity framework, we describe a new result for the Longest Common Subsequence problem. In particular, we show that the problem is hard for W[t] for all t when parameterized by the number of strings and the size of the alphabet. Lower bounds on the complexity of this basic combinatorial problem imply lower bounds on more general sequence alignment and consensus discovery problems. We also describe a number of open problems pertaining to the parameterized complexity of problems in computational biology where small parameter values are important.

Differential mineralocorticoid (type 1) and glucocorticoid (type 2) receptor expression in Lewis and Fischer rats.

Lewis (LEW/N) and Fischer (F344/N) rats represent two extremes of the spectrum of corticosterone responses to stressful stimuli, from the chronical hyporesponsiveness of LEW/N to the chronical hyperresponsiveness of F344/N. It might be expected that the amount of mineralocorticoid receptor (MR) and glucocorticoid receptor (GR) binding, and the levels of their corresponding mRNAs in various tissues in LEW/N and F344/N rats might reflect the overall integrated levels of corticosterone to which these receptors have been exposed. We have found that while the binding affinity (Kd) of MR and GR varies between tissues, there was no strain difference in any tissue. Receptor binding number (Bmax), however, varied not only between tissues, but also between strains. MR Bmax in the hippocampus and pituitary was lower in LEW/N than in F344/N, whereas the GR Bmax in the LEW/N thymus was greater than that found in F344/N rats. The hippocampal levels of MR mRNAs in Adx LEW/N and F344/N rats were in good agreement with, and paralleled, the functional levels of these receptors as determined by binding assays. On the other hand, the number of hippocampal GR binding sites and the level of GR nRNA while similar were not identical in the two strains: the hippocampal GR Bmax did not differ between strains, while the hippocampal GR mRNA level was slightly, but significantly, lower in Adx LEW/N compared to F344/N rats.

Fluorescent measurement of desmin intermediate filament assembly.

Intermediate filaments (IF) are cytoskeletal elements that are believed to play a major role in the specification and maintenance of cell form. Although previously thought to be stable and static because of their relative insolubility in physiological solvents, IF have recently been shown to have dynamic properties not unlike those of other cytoskeletal elements. The methodology for measuring this dynamic behavior, however, has been mostly borrowed from studies of other filament proteins and are poorly suited to IF because of their unusual physicochemical properties. In this report we introduce a fluorescence assay for quantifying in vitro IF assembly. Desmin subunits labeled with iodoacetamidofluorescein (IAF) to approximately 0.4 mol/mol retain the ability to polymerize into filaments indistinguishable from unlabeled IF in the electron microscope. By spectrophotometry, however, up to 90% of the starting fluorescence is quenched upon maximal IF assembly from IAF-desmin subunits. This quench is proportional to the total concentration of desmin subunits and is a sensitive measure of the assembly process. The critical concentration of assembly, measured at 170 mM NaCl, 1 mM MgCl2, 10 mM Tris-HCl, pH 7.0, is 0.2 microM. This indicates that a significant level of unpolymerized desmin exists in steady-state equilibrium with polymerized filaments under these conditions and suggests that IF subunit-filament equilibria may play a role in cytoskeletal dynamics.

A new procedure to analyze free fatty acids. Application to 20-mg brain tissue samples.

Fatty acids were analyzed by a new method which involved their isolation from hexane extracts of serum or brain tissue in aqueous potassium hydroxide (10 microliter) and methylation directly in this solution with methyl iodide. The resulting fatty acid methyl esters were partitioned into ethylene chloride (25 microliter) and were quantitated by gas-liquid chromatography. The procedure was documented by comparison with conventional methylation reactions on serum fatty acids. This method, which avoids thin-layer chromatography and which measures individual free fatty acid concentrations in 20-mg brain tissue samples, should be of particular value for examining regional free fatty acids in brain following ischemia and trauma.

Stomatal movement in Zea mays: Shuttle of potassium and chloride between guard cells and subsidiary cells.

When stomates of Zea mays open K and Cl migrate from the subsidiary cells into the guard cells; when the stomates close both elements return to the subsidiary cells. Subsidiary cells function as reservoirs for K and Cl. Import of K and Cl into the guard cells and loss of both elements from the guard cells become observable 1 or 2 min after light is turned on or off, both when histochemical methods and the electron-probe microanalyzer are used for detection. Each stomatal complex of maize contains on the average 10±3×10(-13) gram equivalents (eq) of K and 4±1×10(-13) eq of Cl. Guard cells accumulate K in the light and CO2-free air at an average rate of 10×10(-15) eq K per minute, and Cl at approximately half that rate.