Sediment Quality Triad assessment in Kachemak Bay: characterization of soft bottom benthic habitats and contaminant bioeffects assessment

A baseline environmental characterization of the inner Kachemak Bay, Alaska was conducted using the sediment quality triad approach based on sediment chemistry, sediment toxicity, and benthic invertebrate community structure. The study area was subdivided into 5 strata based on geophysical and hydrodynamic patterns in the bay (eastern and western intertidal mud flats, eastern and western subtidal, and Homer Harbor). Three to seven locations were synoptically sampled within each stratum using a stratified random statistical design approach. Three sites near the village of Port Graham and two sites in the footprint of a proposed Homer Harbor expansion were also collected for comparison. Concentrations of over 120 organic and metallic contaminants were analyzed. Ambient toxicity was assessed using two amphipod bioassays. A detailed benthic community condition assessment was performed. Habitat parameters (depth, salinity, temperature, dissolved oxygen, sediment grain size, and organic carbon content) that influence species and contaminant distribution were also measured at each sampling site. Sediments were mostly mixed silt and sand; characteristic of high energy habitats, with pockets of muddy zones. Organic compounds (PAHs, DDTs, PCBs, cyclodienes, cyclohexanes) were detected throughout the bay but at relatively low concentrations. Tributyltin was elevated in Homer Harbor relative to the other strata. With a few exceptions, metals concentrations were relatively low and probably reflect the input of glacial runoff. Relative to other sites, Homer Harbor sites were shown to have elevated concentrations of metallic and organic contaminants. The Homer Harbor stratum however, is a deep, low energy depositional environment with fine grained sediment. Concentrations of organic contaminants measured were five to ten times higher in the harbor sites than in the open bay sites. Concentration of PAHs is of a particular interest because of the legacy of oil spills in the region. There was no evidence of residual PAHs attributable to oil spills, outside of local input, beyond the confines of the harbor. Concentrations were one to ten times below NOAA sediment quality guidelines. Selected metal concentrations were found to be relatively elevated compared to other data collected in the region. However, levels are still very low in the scale of NOAA’s sediment quality guidelines, and therefore appear to pose little or no ecotoxicity threat to biota. Infaunal assessment showed a diverse assemblage with more than 240 taxa recorded and abundances greater than 3,000 animals m-22 in all but a few locations. Annelid worms, crustaceans, snails, and clams were the dominant taxa accounting for 63 %, 19%, 5%, and 7 % respectively of total individuals. Specific benthic community assemblages were identified that were distributed based on depth and water clarity. Species richness and diversity was lower in the eastern end of the bay in the vicinity of the Fox River input. Abundance was also generally lower in the eastern portion of the study area, and in the intertidal areas near Homer. The eastern portions of the bay are stressed by the sediment load from glacial meltwater. Significant toxicity was virtually absent. Conditions at the sites immediately outside the existing Homer Harbor facility did not differ significantly from other subtidal locations in the open Kachemak Bay. The benthic fauna at Port Graham contained a significant number of species not found in Kachemak Bay. Contaminant conditions were variable depending on specific location. Selected metal concentrations were elevated at Port Graham and some were lower relative to Kachemak Bay, probably due to local geology. Some organic contaminants were accumulating at a depositional site

Sediment quality triad assessment in Kachemak Bay: characterization of soft bottom benthic habitats and contaminant bioeffects assessment condensed. A NOAA/NOS/NCCOS/CCMA Special Report

A baseline environmental characterization of the inner Kachemak Bay, Alaska was conducted using standardized National Status and Trends Bioeffects Program methods. Three sites near the village of Port Graham were also sampled for comparison. Concentrations of over 120 organic and metallic contaminants were analyzed. Ambient toxicity was assessed using two bioassays. A detailed benthic community condition assessment was performed. Habitat parameters (e.g. depth, salinity, temperature, dissolved oxygen, sediment grain size, and organic carbon content) that influence species and contaminant distribution were also measured at each sampling site. The following is the synopsis of findings • Sediments were mostly mixed silt and sand with pockets of muddy zones. Organic compounds (PAHs, DDTs, PCBs, chlorinated pesticides) were detected throughout the bay but at relatively low concentrations. With some exceptions, metals concentrations were relatively low and probably reflect the input of glacial runoff. • Homer Harbor had elevated concentrations of metallic and organic contaminants. Concentrations of organic contaminants measured were five to ten times higher in the harbor sites than in the open bay sites. Tributyltin was elevated in Homer Harbor relative to the other areas. • There was no evidence of residual PAHs attributable to oil spills, outside of local input in the confines of the harbor. • The benthic community is very diverse. Specific community assemblages were distributed based on depth and water clarity. Species richness and diversity was lower in the eastern end of the bay in the vicinity of the Fox River input. Abundance was also generally lower in the eastern portion of the study area, and in the intertidal areas near Homer. The eastern portions of the bay are stressed by the sediment load from glacial meltwater. • Significant toxicity was virtually absent. • The benthic fauna at Port Graham contained a significant number of species not found in Kachemak Bay. • Selected metal concentrations were elevated at Port Graham relative to Kachemak Bay, probably due to local geology. Organic contaminants were elevated at a site south of the village

The quaternary structure of the amidase from Geobacillus pallidus RAPc8 is revealed by its crystal packing

The amidase from Geobacillus pallidus RAPc8, a moderate thermophile, is a member of the nitrilase enzyme superfamily. It converts amides to the corresponding acids and ammonia and has application as an industrial catalyst. RAPc8 amidase has been cloned and functionally expressed in Escherichia coli and has been purified by heat treatment and a number of chromatographic steps. The enzyme was crystallized using the hanging-drop vapour-diffusion method. Crystals produced in the presence of 1.2 M sodium citrate, 400 mM NaCl, 100 mM sodium acetate pH 5.6 were selected for X-ray diffraction studies. A data set having acceptable statistics to 1.96 Å resolution was collected under cryoconditions using an in-house X-ray source. The space group was determined to be primitive cubic P4232, with unit-cell parameter a = 130.49 (±0.05) Å. The structure was solved by molecular replacement using the backbone of the hypothetical protein PH0642 from Pyrococcus horikoshii (PDB code 1j31 ) with all non-identical side chains substituted with alanine as a probe. There is one subunit per asymmetric unit. The subunits are packed as trimers of dimers with D3 point-group symmetry around the threefold axis in such a way that the dimer interface seen in the homologues is preserved

Parental experiences of childcare in an informal urban settlement: qualitative interview findings from the Nairobi Early Childcare in Slums (NECS) project

OBJECTIVES: To gain an in-depth understanding of parent/carers' perspectives on, and decision-making about, early childhood care in general, and paid childcare specifically, in informal settlements in Nairobi. DESIGN: In-depth telephone interviews, conducted using a topic guide, were analysed through a combination of deductive and inductive thematic analysis and regular reflexivity meetings. We explored parents' childcare needs and experiences over time, and their perspectives on the provision of paid childcare in the slums. SETTING: Three informal settlements or slums in Nairobi: Kibera; Kawangware; and Mukuru-Viwandani. PARTICIPANTS: A purposively selected sample of 21 parental and non-parental carers of children aged under 5 years who were currently living in three Nairobi slums, including men and women, and users and non-users of paid childcare. RESULTS: Childcare is complex, with a plurality of approaches being used. Common strategies include family member provided care (often but not exclusively by mothers, at home or at a place of work), paid childcare and informal or ad hoc arrangements with neighbours. Childcare decision-making in these settings is constrained by economics and the broader context of living in the slum. Paid childcare is frequently used, but is widely understood to be lacking in quality, especially for the poorest. Quality of childcare is understood to comprise a combination of structural factors, such as the physical space, play and learning resources and processes such as interactions between the care provider and children or parents. CONCLUSIONS: These findings suggest a need, and opportunity, to improve early childhood care in slums. Understanding parental perspectives on both the deficiencies and valued features of childcare is likely to be vital to informing efforts to improve childcare in these settings

Hepatosplenomegaly associated with chronic malaria exposure: evidence for a pro-inflammatory mechanism exacerbated by schistosomiasis

In sub-Saharan Africa, chronic hepatosplenomegaly, with palpable firm/hard organ consistency, is common, particularly among school-aged children. This morbidity can be caused by long-term exposure to malaria, or by Schistosoma mansoni, and it is exacerbated when these two occur together. Although immunological mechanisms probably underlie the pathogenic process, these mechanisms have not been identified, nor is it known whether the two parasites augment the same mechanisms or induce unrelated processes that nonetheless have additive or synergistic effects. Kenyan primary schoolchildren, living in a malaria/schistosomiasis co-transmission area, participated in cross-sectional parasitological and clinical studies in which circulating immune modulator levels were also measured. Plasma IL-12p70, sTNF-RII, IL-10 and IL-13 levels correlated with relative exposure to malaria, and with hepatosplenomegaly. Soluble-TNF-RII and IL-10 were higher in children infected withS. mansoniHepatosplenomegaly caused by chronic exposure to malaria was clearly associated with increased circulating levels of pro-inflammatory mediators, with higher levels of regulatory modulators, and with tissue repair cytokines, perhaps being required to control the inflammatory response. The higher levels of regulatory modulators amongstS. mansoniinfected children, compared to those without detectableS. mansoni and malarial infections, but exposed to malaria, suggest thatS. mansoniinfection may augment the underlying inflammatory reaction

The Effect of Switching to Second-Line Antiretroviral Therapy on the Risk of Opportunistic Infections Among Patients Infected With Human Immunodeficiency Virus in Northern Tanzania

Background. Due to the unintended potential misclassifications of the World Health Organization (WHO) immunological failure criteria in predicting virological failure, limited availability of treatment options, poor laboratory infrastructure, and healthcare providers’ confidence in making switches, physicians delay switching patients to second-line antiretroviral therapy (ART). Evaluating whether timely switching and delayed switching are associated with the risk of opportunistic infections (OI) among patients with unrecognized treatment failure is critical to improve patient outcomes

To add or not to add a new treatment arm to a multiarm study: A decision-theoretic framework.

Multiarm clinical trials, which compare several experimental treatments against control, are frequently recommended due to their efficiency gain. In practise, all potential treatments may not be ready to be tested in a phase II/III trial at the same time. It has become appealing to allow new treatment arms to be added into on-going clinical trials using a "platform" trial approach. To the best of our knowledge, many aspects of when to add arms to an existing trial have not been explored in the literature. Most works on adding arm(s) assume that a new arm is opened whenever a new treatment becomes available. This strategy may prolong the overall duration of a study or cause reduction in marginal power for each hypothesis if the adaptation is not well accommodated. Within a two-stage trial setting, we propose a decision-theoretic framework to investigate when to add or not to add a new treatment arm based on the observed stage one treatment responses. To account for different prospect of multiarm studies, we define utility in two different ways; one for a trial that aims to maximise the number of rejected hypotheses; the other for a trial that would declare a success when at least one hypothesis is rejected from the study. Our framework shows that it is not always optimal to add a new treatment arm to an existing trial. We illustrate a case study by considering a completed trial on knee osteoarthritis

Adapting Agriculture to Climate Change: An Evaluation of Yield Potential of Maize, Sorghum, Common Bean and Pigeon Pea Varieties in a Very Cool-Wet Region of Nyandarua County, Central Kenya

Three experiments were conducted to evaluate the performance of maize, sorghum, common bean and pigeon pea varieties under different water management in a cool and wet region of Central Kenya, as a part of the studies at analogue sites. The first experiment evaluated the growth and performance of three varieties (early maturing: EM, medium maturing: MM and late maturing: LM) of maize (Zea mays L), sorghum (Sorghum bicolor L.), pigeon pea (Cajanus cajan) and common bean (Phaseolus vulgaris L.). The second experiment evaluated maize and sorghum response to water conservation and three fertiliser rates (0, 20 and 40 kg N/ha). The third experiment assessed the effect of water conservation measures on crop yields of common bean and pigeon pea grown under three plant densities (low, medium and high). Tied ridge tillage was used as the water conservation measure and disc plough as the control in the second and third experiments. Maize, sorghum, pigeon pea and common bean took more than 180, 245, 217 and 95 days respectively, to reach physiological maturity. The MM maize variety (DK8031), EM pigeon pea variety (ICPL 84091) and LM common bean variety (GLP 24) yielded the greatest grain of 4,938, 881 and 620 kg/ha respectively, among the respective crop varieties. The sorghum varieties were attacked by fungal and rust diseases leading to yield losses in all seasons. Soil water conservation in general did not have a significant effect on crop yield though there were yield improvements. In the plant density trial, the medium plant densities of pigeon pea (33,333 pl/ha) and common bean (148,148 pl/ha) resulted in the greatest grain yields. The highest grain yield of maize (4,184 kg/ha) and sorghum (47 kg/ha) was obtained in plots with 20 kg/ha of nitrogen fertilizer. Based on the results of this study, pigeon pea and common bean can be introduced in the farming systems to improve crop diversity. The production of the tested sorghum varieties should be discouraged in this region because they are prone to fungal and rust diseases due to the cold and wet weather conditions

Adapting agriculture to climate change - An evaluation of yield potential of maize, sorghum, common bean and pigeon pea varieties in a very cool-wet region of Nayandarua County

Soil and water conservation, use of more adaptive crop genotypes and crop diversification are widely accepted as some of the management practices that can help reduce agriculture vulnerability to impacts of climate change. A study was conducted to evaluate the yield potential of maize, sorghum, common bean and pigeon pea varieties under different water management, plant densities and fertility levels in Nyahururu, Central Kenya. The study involved three experiments. The first experiment evaluated the growth and performance of three varieties (early maturing, medium maturing and late maturing) of maize, sorghum, pigeon pea and common bean. The experimental design was a completely randomized block design (RCBD) replicated three times. The second experiment evaluated maize and sorghum yield response to water conservation and three fertiliser rates (0, 20 and 40 kg N/ha). The third experiment assessed the effect of water conservation measures on crop yields of common bean and pigeon pea grown under three plant densities (low, medium and high). Tied ridge tillage was used as the water conservation measure and disc plough as the control in the second and third experiments. Results showed that water conservation in general did not have a significant effect on crop yield though they were improved. The medium density pigeon pea gave the highest grain (719 kg/ha) followed by low (688 kg/ha) and high plant density (687 kg/ha), though not significant at 0.95 confidence level. Similar trends were observed with common bean grain and dry matter yield. Tied ridges tended to lower maize yield compared to flat tillage while it increased sorghum yields but the difference was insignificant. When average across the tillage systems, the highest maize grain (5553 kg/ha) and dry matter (14298 kg/ha) yield was obtained in plots without N fertilizer. Sorghum dry matter was highest (11333 kg/ha) in plots with 40 kg N/ha and lowest (7903 kg/ha) in plots with 20 kg/ha N. In the variety experiment, the EM pigeon pea variety (ICPL 84091) yielded the greatest grain (881 kg/ha) while the late maturing variety (ICEAP 00040) gave the least (565 kg/ha). The LM maize variety (DK8031) yielded the highest grain (5701 kg/ha) and dry matter (18843 kg/ha). The LM sorghum variety (Macia) had 47% and 49% dry matter yield advantage over MM (Kari Mtama 1) and EM (Gadam) varieties, respectively. The yields for common bean varieties tended to vary with seasons. So what are the conclusions