Tracking NSZD mass removal rates over decades: Site-wide and local scale assessment of mass removal at a legacy petroleum site.

Long-term estimates of natural source zone depletion (NSZD) rates for petroleum LNAPL (light non-aqueous phase liquid) sites are not available. One-off measurements are often thought valid over the lifetime of LNAPL sites. In the context of site-wide LNAPL mass estimates, we report site-specific gasoline and diesel NSZD rates spanning 21-26 years. Using depth profiles of soil gases (oxygen, carbon dioxide, methane, volatiles) above LNAPL, NSZD rates were estimated in 1994, 2006 and 2020 for diesel and 1999, 2009 and 2020 for gasoline. Each date also had soil-core mass estimates, which together with NSZD rates allow estimation of the longevity for LNAPL presence. Site-wide coring (in 1992, 2002, 2007) estimated LNAPL mass reductions of 12,000 t. For diesel NSZD, the ratio of NSZD rates for 2006 (16,000-49,000 L/ha/y) to those in 2020 (2600-14,000 L/ha/y) was ~3-6. By 2020, the 1994 diesel NSZD rates would have predicted the entire removal of measured mass (16-42 kg/m2). For gasoline, NSZD rates in 1999 were extremely high (50,000-270,000 L/ha/y) but 9-27 times lower (5800-10,000 L/ha/y) a decade later. The gasoline NSZD rates in 1999 predicted near complete mass removal in 2-12 years, but 10-11 kg/m2 was measured 10 and 21 years later which is 26% of the initial mass in 1999. The outcomes substantiate the need to understand NSZD rate changes over the lifetime of LNAPL-impacted sites.

Novel polymorphisms in TICAM2 and NOD1 associated with tuberculosis progression phenotypes in Ethiopian populations.

BACKGROUND: Infection by Mycobacterium tuberculosis (Mtb) is a necessary but not sufficient cause for tuberculosis (TB). Although numerous studies suggest human genetic variation may influence TB pathogenesis, there is a conspicuous lack of replication, likely due to imprecise phenotype definition. We aimed to replicate novel findings from a Ugandan cohort in Ethiopian populations. METHOD: We ascertained TB cases and household controls (n = 292) from three different ethnic groups. Latent Mtb infection was determined using Quantiferon to develop reliable TB progression phenotypes. We sequenced exonic regions of TICAM2 and NOD1. RESULT: Significant novel associations were observed between two variants in NOD1 and TB: rs751770147 [unadjusted p = 7.28 × 10-5] and chr7:30477156(T), a novel variant, [unadjusted p = 1.04 × 10-4]. Two SNPs in TICAM2 were nominally associated with TB, including rs2288384 [unadjusted p = 0.003]. Haplotype-based association tests supported the SNP-based results. CONCLUSION: We replicated the association of TICAM2 and NOD1 with TB and identified novel genetic associations with TB in Ethiopian populations.

Design of a Virtual Reality System for Affect Analysis in Facial Expressions (VR-SAAFE); Application to Schizophrenia.

Schizophrenia is a life-long, debilitating psychotic disorder with poor outcome that affects about 1% of the population. Although pharmacotherapy can alleviate some of the acute psychotic symptoms, residual social impairments present a significant barrier that prevents successful rehabilitation. With limited resources and access to social skills training opportunities, innovative technology has emerged as a potentially powerful tool for intervention. In this paper, we present a novel virtual reality (VR)-based system for understanding facial emotion processing impairments that may lead to poor social outcome in schizophrenia. We henceforth call it a VR System for Affect Analysis in Facial Expressions (VR-SAAFE). This system integrates a VR-based task presentation platform that can minutely control facial expressions of an avatar with or without accompanying verbal interaction, with an eye-tracker to quantitatively measure a participants real-time gaze and a set of physiological sensors to infer his/her affective states to allow in-depth understanding of the emotion recognition mechanism of patients with schizophrenia based on quantitative metrics. A usability study with 12 patients with schizophrenia and 12 healthy controls was conducted to examine processing of the emotional faces. Preliminary results indicated that there were significant differences in the way patients with schizophrenia processed and responded towards the emotional faces presented in the VR environment compared with healthy control participants. The preliminary results underscore the utility of such a VR-based system that enables precise and quantitative assessment of social skill deficits in patients with schizophrenia.

Framework for the assessment of interaction between CO2 geological storage and other sedimentary basin resources.

Sedimentary basins around the world considered suitable for carbon storage usually contain other natural resources such as petroleum, coal, geothermal energy and groundwater. Storing carbon dioxide in geological formations in the basins adds to the competition for access to the subsurface and the use of pore space where other resource-based industries also operate. Managing potential impacts that industrial-scale injection of carbon dioxide may have on other resource development must be focused to prevent potential conflicts and enhance synergies where possible. Such a sustainable coexistence of various resource developments can be accomplished by implementing a Framework for Basin Resource Management strategy (FBRM). The FBRM strategy utilizes the concept of an Area of Review (AOR) for guiding development and regulation of CO2 geological storage projects and for assessing their potential impact on other resources. The AOR is determined by the expected physical distribution of the CO2 plume in the subsurface and the modelled extent of reservoir pressure increase resulting from the injection of the CO2. This information is used to define the region to be characterised and monitored for a CO2 injection project. The geological characterisation and risk- and performance-based monitoring will be most comprehensive within the region of the reservoir containing the carbon dioxide plume and should consider geological features and wells continuously above the plume through to its surface projection; this region defines where increases in reservoir pressure will be greatest and where potential for unplanned migration of carbon dioxide is highest. Beyond the expanse of the carbon dioxide plume, geological characterisation and monitoring should focus only on identified features that could be a potential migration conduit for either formation water or carbon dioxide.

Behaviour and fate of nine recycled water trace organics during managed aquifer recharge in an aerobic aquifer.

The fate of nine trace organic compounds was evaluated during a 12month large-scale laboratory column experiment. The columns were packed with aquifer sediment and evaluated under natural aerobic and artificial anaerobic geochemical conditions, to assess the potential for natural attenuation of these compounds during aquifer passage associated with managed aquifer recharge (MAR). The nine trace organic compounds were bisphenol A (BPA), 17ß-estradiol (E2), 17α-ethynylestradiol (EE2), N-nitrosodimethylamine (NDMA), N-nitrosomorpholine (NMOR), carbamazepine, oxazepam, iohexol and iodipamide. In the low organic carbon content Spearwood sediment, all trace organics were non-retarded with retardation coefficients between 1.0 and 1.2, indicating that these compounds would travel at near groundwater velocities within the aquifer. The natural aerobic geochemical conditions provided a suitable environment for the rapid degradation for BPA, E2, iohexol (half life <1day). Lag-times for the start of degradation of these compounds ranged from <15 to 30days. While iodipamide was persistent under aerobic conditions, artificial reductive geochemical conditions promoted via the addition of ethanol, resulted in rapid degradation (half life <1days). Pharmaceuticals (carbamazepine and oxazepam) and disinfection by-products (NDMA and NMOR) did not degrade under either aerobic or anaerobic aquifer geochemical conditions (half life >50days). Field-based validation experiments with carbamazepine and oxazepam also showed no degradation. If persistent trace organics are present in recycled waters at concentrations in excess of their intended use, natural attenuation during aquifer passage alone may not result in extracted water meeting regulatory requirements. Additional pre treatment of the recycled water would therefore be required.

Managed aquifer recharge: rediscovering nature as a leading edge technology.

Use of Managed Aquifer Recharge (MAR) has rapidly increased in Australia, USA, and Europe in recent years as an efficient means of recycling stormwater or treated sewage effluent for non-potable and indirect potable reuse in urban and rural areas. Yet aquifers have been relied on knowingly for water storage and unwittingly for water treatment for millennia. Hence if 'leading edge' is defined as 'the foremost part of a trend; a vanguard', it would be misleading to claim managed aquifer recharge as a leading edge technology. However it has taken a significant investment in scientific research in recent years to demonstrate the effectiveness of aquifers as sustainable treatment systems to enable managed aquifer recharge to be recognised along side engineered treatment systems in water recycling. It is a 'cross-over' technology that is applicable to water and wastewater treatment and makes use of passive low energy processes to spectacularly reduce the energy requirements for water supply. It is robust within limits, has low cost, is suitable from village to city scale supplies, and offers as yet almost untapped opportunities for producing safe drinking water supplies where they do not yet exist. It will have an increasingly valued role in securing water supplies to sustain cities affected by climate change and population growth. However it is not a universal panacea and relies on the presence of suitable aquifers and sources of water together with effective governance to ensure human health and environment protection and water resources planning and management. This paper describes managed aquifer recharge, illustrates its use in Australia, outlining economics, guidelines and policies, and presents some of the knowledge about aquifer treatment processes that are revealing the latent value of aquifers as urban water infrastructure and provide a driver to improving our understanding of urban hydrogeology.

Using treated wastewater to save wetlands impacted by climate change and pumping.

Wetlands occur where the watertable which underlies much of Perth intersects the land surface. Regional groundwater levels have been falling since the 1970s as a result of lower rainfall and increased extraction causing a loss of environmental and social values. This paper examines a scheme to add almost 2 GL/yr of treated wastewater to infiltration galleries immediately down-gradient of Perry Lakes so that the wetlands may be restored. Modelling suggest that groundwater levels would be raised up-gradient of the galleries, increasing both lake levels and groundwater supplies in the vicinity. It is not envisaged that wastewater will enter the lakes. Adding treated wastewater to nearby trial galleries has shown that phosphorus, pathogens and organic carbon are greatly reduced within 5 to 50 m. Nitrogen levels are less reduced but are similar to those in the lakes and nearby aquifer. It is estimated that the wetlands add about $54 m to land prices near the lakes and would add more than $24M to the sale price of proposed nearby land if they contain water. If successful, the proposal could be a test case for the use of treated wastewater to create hydraulic barriers against salt water intrusion into coastal areas.

A critical evaluation of combined engineered and aquifer treatment systems in water recycling.

Australian experience at five research sites where stormwater and reclaimed water have been stored in aquifers prior to reuse, have yielded valuable information about water treatment processes in anaerobic and aerobic aquifers. One of these sites is the stormwater to potable water ASTR project at the City of Salisbury, a demonstration project within the broader EC project 'RECLAIM WATER'. A framework for characterising the effectiveness of such treatment for selected organic chemicals, natural organic matter, and pathogens is being developed for inclusion in new Australian Guidelines for Management of Aquifer Recharge. The combination of pre-treatments (including passive systems such as reed beds) and aquifer treatment effectiveness in relation to source waters and intended uses of recovered water will be described. Advantages and disadvantages of various types of pre-treatments in relation to effectiveness and sustainability of managed aquifer recharge will be discussed taking account of aquifer characteristics. These observations will be consolidated into a draft set of principles to assist in selection of engineered treatments compatible with passive treatment in aquifers.

Population genetic structure of Anopheles arabiensis mosquitoes in Ethiopia and Eritrea.

This study examined the population genetic structure of the major malaria vector, Anopheles arabiensis mosquitoes, in Ethiopia and Eritrea. Ethiopia and Eritrea have great geographical diversity, with high mountains, rugged plateaus, deep gorges, and rolling plains. The plateau is bisected diagonally by the Great Rift Valley into the Northwestern Highlands and the Southeastern Highlands. Five A. arabiensis populations from the Northwestern Highlands region and two populations from high-altitude sites in the Great Rift Valley were genotyped using six microsatellite markers to estimate the genetic diversity and population genetic structure of A. arabiensis. We found that A. arabiensis populations from the Northwestern Highlands and the Great Rift Valley region showed a similar level of genetic diversity. The genetic differentiation (F(ST)) of the five mosquito populations within the Northwestern Highlands region was 0.038 (P <.001), while the two populations within the Great Rift Valley showed little genetic differentiation (F(ST) = 0.007, P <.01). The degree of genetic differentiation between the Northwestern Highlands region and the Great Rift Valley region was small but statistically significant (F(ST) = 0.017, P <.001). The population genetic structure of A. arabiensis in the study area did not follow the isolation-by-distance model (r(2) = 0.014, P >.05). The low F(ST) estimates for A. arabiensis populations in Ethiopia and Eritrea are consistent with the general population genetic structure of this species in East Africa based on other molecular markers.

Geographic and altitudinal allozyme variation in sorghum (Sorghum bicolor (L.) Moench) landraces from Ethiopia and Eritrea.

The amount and distribution of genetic variation was investigated in 48 sorghum landrace accessions, representing 13 regions of origin and three adaptation zones (lowland, intermediate and highland elevation) in Ethiopia and Eritrea. Assaying 11 enzymes systems, 23 putative loci were scored for a total of 27 alleles. Nineteen loci were monomorphic and fixed for the same allele, while the remaining 4 loci, each with 2 alleles, were polymorphic across the 48 accessions. The results show significant differences in allele frequencies among the accessions, regions of origin and the adaptation zones. However, all measures of genetic variation used show that the accessions maintained much lower levels of variation than the corresponding mean values for self-pollinating crop plants, confirming previous conclusions that sorghum is depauperated in allozymic variation. The total gene diversity was 0.25, which partitioned 59% within and 41% among accessions. The latter was largely due to variation among accessions within the adaptation zones (38%), while only 3% was due to variation among accessions between the adaptation zones. Similarly, most of the total gene diversity was found within the regions of origin (80%) and within the adaptation zones (97%). Both the dendrogram constructed from NEI's unbiased genetic distance and the plot of the first two principal components distinguished three groups of regions. The level of gene flow was low among accessions, regions of origin and among accessions within adaptation zones, but high among adaptation zones. The results are discussed with emphasis on genetic resources conservation and utilization.

A molecular genetic analysis of Eragrostis tef (Zucc.) Trotter: non-coding regions of chloroplast DNA, 18S rDNA and the transcription factor VP1.

The non-coding chloroplast DNA sequences of the trnL (UAA) intron and the trnL-trnF (GAA) intergeneric spacer (IGS), the coding sequences of nuclear 18S rDNA, and the transcription factor Vp1 of the cereal tef (Eragrostis tef (Zucc.) Trotter) were studied. No intraspecific variation was found among the 6 studied tef varieties. However, the study displayed that Eragrostis tef has a number of unique traits compared to other grasses. Phylogenetic analysis of the chloroplast DNA gave three grass clades, joining Eragrostis with sorghum and maize in one. In the analysis of the 18S rDNA sequences, the three grass species were joined in a monophyletic trichotomy in the cladogram, in which maize is the most divergent, rice the least and tef intermediate. The Vp1 is highly conserved. The Vp1 phylogeny showed that the tef Vp1-sequence is the hitherto most divergent Vp1-sequence reported from a grass.

Genetic variation in wild sorghum (Sorghum bicolor ssp. verticilliflorum (L.) Moench) germplasm from Ethiopia assessed by random amplified polymorphic DNA (RAPD).

The extent and distribution of genetic variation in wild sorghum (Sorghum bicolor ssp. verticilliflorum (L.) Moench) collected from five different geographical regions in Ethiopia were analyzed using random amplified polymorphic DNA (RAPD) markers for 93 individuals representing 11 populations. Nine decamer primers generated a total of 83 polymorphic bands with 8-12 bands per primer and a mean of 9 bands across the 93 individuals. The amount of genetic variation among the populations (H = 0.37) and among the geographical region (H = 0.44) was low to moderate, despite the high degree of polymorphic bands per primer. Similarly, the mean genetic distance (0.08) among populations as well as among regions of origin (0.04) of the population was found to be low. The low genetic variation may be due to the reduced population size of the wild sorghum in Ethiopia because of habitat change. Partitioning of the genetic variation into between and within the population as well as between and within the regions of origin revealed that 75% and 88% of the variation was found within the populations and within the regions, respectively. Cluster analysis of genetic distance estimates further confirmed low level of differentiation of wild sorghum populations both on population and regional bases. The implications of the results for genetic conservation purposes are discussed.

A view of modern human origins from Y chromosome microsatellite variation.

The idea that all modern humans share a recent (within the last 150, 000 years) African origin has been proposed and supported on the basis of three observations. Most genetic loci examined to date have (1) shown greater diversity in African populations than in others, (2) placed the first branch between African and all non-African populations in phylogenetic trees, and (3) indicated recent dates for either the molecular coalescence (with the exception of some autosomal and X-chromosomal loci) or for the time of separation between African and non-African populations. We analyze variation at 10 Y chromosome microsatellite loci that were typed in 506 males representing 49 populations and every inhabited continent and find significantly greater Y chromosome diversity in Africa than elsewhere, find the first branch in phylogenetic trees of the continental populations to fall between African and all non-African populations, and date this branching with the (deltamu)2 distance measure to 5800-17,400 or 12,800-36,800 years BP depending on the mutation rate used. The magnitude of the excess Y chromosome diversity in African populations appears to result from a greater antiquity of African populations rather than a greater long-term effective population size. These observations are most consistent with a recent African origin for all modern humans.

Cw*1701 defines a divergent african HLA-C allelic lineage.

The complete sequence of a new HLA-C allele, Cw*1701, was determined from a South African Zulu individual. Unique features that distinguish Cw*1701 from other HLA-C alleles include multiple point substitutions and an 18 nucleotide insertion in exon 5, which encodes the transmembrane domain. In a phylogenetic analysis of HLA-C sequences, Cw*1701 forms a third, distinct allelic lineage. A comparison of the transmembrane domain of Cw*1701 with other HLA-B and -C alleles reveals that duplications and deletions have been common in the evolution of these loci. A polymerase chain reaction based typing method was used to determine the distribution of this unusual allele in human populations. In contrast to the other two lineages of HLA-C alleles, the Cw*17 lineage is found at high frequencies only in populations of African descent. In addition, the HLA-B/Cw*17 haplotype diversity is higher in Africa.

Two new modified trichothecenes from Fusarium sporotrichioides.

Two new modified trichothecenes, 2-deoxy-11-epi-3 alpha-hydroxysambucoin [1] and 2-deoxy-11-epi-12-acetyl-3 alpha-hydroxysambucoin [2], were isolated from Fusarium sporotrichioides culture. This is the first report of modified trichothecenes where the two six-membered rings are cis-fused. Structures were elucidated using gc-ms, nmr, X-ray crystallography, and other spectroscopic techniques. Compounds 1 and 2 were screened for relative cytotoxicity in cultured baby hamster kidney (BHK-21) cells and found to be non-toxic.

Two new trichothecenes from Fusarium sporotrichioides.

Two new trichothecenes, 8-n-pentanoylneosolaniol and 8-n-hexanoylneosolaniol, were isolated from corn grits cultured with Fusarium sporotrichioides. The structures of these compounds were elucidated using gc-ms, nmr, X-ray crystallography, and other spectroscopic techniques. Seven known trichothecenes were also isolated, and the relative cytotoxicity of these nine trichothecenes in cultured baby hamster kidney (BHK-21) cells was determined.

Indigenous livestock disease problems and slaughter cattle infections in the Ada district of the Ethiopian highlands.

In the farming enterprises of the Ada district, sheep and goats were most commonly diseased by pneumonia and helminthiasis among all farming animals, which led to severe losses of lambs and sheep. In cattle, helminthiasis and malnutrition conditioned considerable losses of calves. Faecal investigations showed that 72% of the cattle were infected with internal parasites, with nematodes more frequent in calves and fascioliasis among adult cattle. Pathological malformations of organs were encountered in 65% of the cattle slaughtered at the Debre Zeit abbatoir. Economically and hygienically most important are fascioliasis, hydatidosis, and cysticercosis.