In-situ fines migration and grains redistribution induced by mineral reactions – Implications for clogging during water injection in carbonate aquifers

Water injection into an aquifer is generally motivated by one of three objectives: disposal, managed aquifer recharge (MAR), or aquifer storage and recovery (ASR). Any of these would be undermined if an injection well were to become clogged. This paper investigates whether mineral reactions can cause mobilization of fines and rock grains, and if so, how this would affect clogging. Injection experiments are performed on Edwards Brown (dolomite) and Indiana limestone core samples. X-ray Powder Diffraction analysis of the rocks shows that no clays are present. Filtered-deaired deionized water and pure salts are used to prepare the injection fluids. The core samples are subjected to four sequential injections of fluids: at salinities 44,580 mg/L (referred to as “seawater”), 14,860 mg/L, 7,430 mg/L, and 0 mg/L (deionized water). These salinities are selected to represent disposal, and less saline fluids to represent MAR and ASR projects. Pressure difference is recorded across the core sample at each stage and is used to calculate permeability. The effluent samples are collected to characterize produced fines and elements. The increase in the pH of the effluent samples suggest mineral reactions, which is supported by an increase in the concentration of chemical elements in the effluent samples. Scanning Electron Microscopy (SEM) images show pore enlargement due to dissolution and depict pore blockage due to fines migration, grains redistribution, and mineral precipitation. Mineral reactions dissolved the grain's surface and intergranular cement, releasing silicate fines and rock grains, which in turn reduce the permeability of the rock by 68 % to 99.9 %

Vertical hydraulic conductivity of a clayey-silt aquitard: accelerated fluid flow in a centrifuge permeameter compared with in situ conditions

This discussion paper is a preprint. It has been under review for the journal Hydrology and Earth System Sciences (HESS). The revised manuscript was not accepted.Evaluating the possibility of leakage through low permeability geological strata is critically important for sustainable water supplies, extraction of fuels from strata such as coal beds, and confinement of waste within the earth. Characterizing low or negligible flow rates and transport of solutes can require impractically long periods of field or laboratory testing, but is necessary for evaluations over regional areas and over multi-decadal timescales. The current work reports a custom designed centrifuge permeameter (CP) system, which can provide relatively rapid and reliable hydraulic conductivity (K) measurement compared to column permeameter tests at standard gravity (1g). Linear fluid velocity through a low K porous sample is linearly related to g-level during a CP flight unless consolidation or geochemical reactions occur. The CP module is designed to fit within a standard 2 m diameter, geotechnical centrifuge with a capacity for sample dimensions of 30 to 100 mm diameter and 30 to 200 mm in length. At maximum RPM the resultant centrifugal force is equivalent to 550g at base of sample or a total stress of ~2 MPa. K is calculated by measuring influent and effluent volumes. A custom designed mounting system allows minimal disturbance of drill core samples and a centrifugal force that represents realistic in situ stress conditions is applied. Formation fluids were used as influent to limit any shrink-swell phenomena which may alter the resultant K value. Vertical hydraulic conductivity (Kv) results from CP testing of core from the sites in the same clayey silt formation varied (10−7 to 10−9 m s−1, n = 14) but higher than 1g column permeameter tests of adjacent core using deionized water (10−9 to 10−11 m s−1, n = 7). Results at one site were similar to in situ Kv values (3 × 10−9 m s−1) from pore pressure responses within a 30 m clayey sequence in a homogenous area of the formation. Kv sensitivity to sample heterogeneity was observed, and anomalous flow via preferential pathways could be readily identified. Results demonstrate the utility of centrifuge testing for measuring minimum K values that can contribute to assessments of geological formations at large scale. The importance of using realistic stress conditions and influent geochemistry during hydraulic testing is also demonstrated.Australian Research CouncilNational Water Commissio

High resolution synteny maps allowing direct comparisons between the coffee and tomato genomes

Tomato (Solanum lycopersicum) and coffee (Coffea canephora) belong to the sister families Solanaceae and Rubiaceae, respectively. We report herein the mapping of a common set of 257 Conserved Ortholog Set II genes in the genomes of both species. The mapped markers are well distributed across both genomes allowing the first syntenic comparison between species from these two families. The majority (75%) of the synteny blocks are short (<4 cM); however, some extend up to 50 cM. In an effort to further characterize the synteny between these two genomes, we took advantage of the available sequence for the tomato genome to show that tomato chromosome 7 is syntenic to half of the two coffee linkage groups E and F with the putative break point in tomato localized to the boundary of the heterochromatin and euchromatin on the long arm. In addition to the new insight on genome conservation and evolution between the plant families Solanaceae and Rubiaceae, the comparative maps presented herein provide a translational tool by which coffee researchers may take benefit of DNA sequence and genetic information from tomato and vice versa. It is thus expected that these comparative genome information will help to facilitate and expedite genetic and genomic research in coffee

Soil and aquifer salinization: toward an integrated approach for salinity management of groundwater

Degradation of the quality of groundwater due to salinization processes is one of the key issues limiting the global dependence on groundwater in aquifers. As the salinization of shallow aquifers is closely related to root-zone salinization, the two must be considered together. This chapter initially describes the physical and chemical processes causing salinization of the root-zone and shallow aquifers, highlighting the dynamics of these processes and how they can be influenced by irrigation and drainage practices, thus illustrating the connectivity between soil and groundwater salinization. The processes leading to aquifer salinization in both inland and coastal areas are discussed. The roles of extractive resource industries, such as mining and coal bed methane operations, in causing aquifer salinization are also outlined. Hydrogeochemical changes occurring during salinization of aquifers are examined with the aid of Piper and Mixing Diagrams. The chapter then illustrates the extent of the problem of groundwater salinization as influenced by management and policy using two case studies. The first is representative of a developing country and explores management of salt-affected soils in the Indus Valley, Pakistan, while the second looks at a developed country, and illustrates how through monitoring we can deducecauses of shallow aquifer salinity in the Namoi Catchment of NSW, Australia. Finally, there is a section on integration and conclusions where we illustrate how management to mitigate salinization needs to be integrated with policy to diminish the threat to productivity that occurs with groundwater degradation

Burden of mental disorders and unmet needs among street homeless people in Addis Ababa, Ethiopia

BACKGROUND: The impact of mental disorders among homeless people is likely to be substantial in low income countries because of underdeveloped social welfare and health systems. As a first step towards advocacy and provision of care, we conducted a study to determine the burden of psychotic disorders and associated unmet needs, as well as the prevalence of mental distress, suicidality, and alcohol use disorder among homeless people in Addis Ababa, the capital of Ethiopia. METHODS: A cross-sectional survey was conducted among street homeless adults. Trained community nurses screened for potential psychosis and administered standardized measures of mental distress, alcohol use disorder and suicidality. Psychiatric nurses then carried out confirmatory diagnostic interviews of psychosis and administered a locally adapted version of the Camberwell Assessment of Needs Short Appraisal Schedule. RESULTS: We assessed 217 street homeless adults, about 90% of whom had experienced some form of mental or alcohol use disorder: 41.0% had psychosis, 60.0% had hazardous or dependent alcohol use, and 14.8% reported attempting suicide in the previous month. Homeless people with psychosis had extensive unmet needs with 80% to 100% reporting unmet needs across 26 domains. Nearly 30% had physical disability (visual and sensory impairment and impaired mobility). Only 10.0% of those with psychosis had ever received treatment for their illness. Most had lived on the streets for over 2 years, and alcohol use disorder was positively associated with chronicity of homelessness. CONCLUSION: Psychoses and other mental and behavioural disorders affect most people who are street homeless in Addis Ababa. Any programme to improve the condition of homeless people should include treatment for mental and alcohol use disorders. The findings have significant implications for advocacy and intervention programmes, particularly in similar low income settings. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12916-014-0138-x) contains supplementary material, which is available to authorized users

Neuroendocrine–immune disequilibrium and endometriosis: an interdisciplinary approach

Endometriosis, a chronic disease characterized by endometrial tissue located outside the uterine cavity, affects one fourth of young women and is associated with chronic pelvic pain and infertility. However, an in-depth understanding of the pathophysiology and effective treatment strategies of endometriosis is still largely elusive. Inadequate immune and neuroendocrine responses are significantly involved in the pathophysiology of endometriosis, and key findings are summarized in the present review. We discuss here the role of different immune mechanisms particularly adhesion molecules, protein–glycan interactions, and pro-angiogenic mediators in the development and progression of the disease. Finally, we introduce the concept of endometrial dissemination as result of a neuroendocrine-immune disequilibrium in response to high levels of perceived stress caused by cardinal clinical symptoms of endometriosis

Pan-cancer analysis of whole genomes

Cancer is driven by genetic change, and the advent of massively parallel sequencing has enabled systematic documentation of this variation at the whole-genome scale(1-3). Here we report the integrative analysis of 2,658 whole-cancer genomes and their matching normal tissues across 38 tumour types from the Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium of the International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA). We describe the generation of the PCAWG resource, facilitated by international data sharing using compute clouds. On average, cancer genomes contained 4-5 driver mutations when combining coding and non-coding genomic elements; however, in around 5% of cases no drivers were identified, suggesting that cancer driver discovery is not yet complete. Chromothripsis, in which many clustered structural variants arise in a single catastrophic event, is frequently an early event in tumour evolution; in acral melanoma, for example, these events precede most somatic point mutations and affect several cancer-associated genes simultaneously. Cancers with abnormal telomere maintenance often originate from tissues with low replicative activity and show several mechanisms of preventing telomere attrition to critical levels. Common and rare germline variants affect patterns of somatic mutation, including point mutations, structural variants and somatic retrotransposition. A collection of papers from the PCAWG Consortium describes non-coding mutations that drive cancer beyond those in the TERT promoter(4); identifies new signatures of mutational processes that cause base substitutions, small insertions and deletions and structural variation(5,6); analyses timings and patterns of tumour evolution(7); describes the diverse transcriptional consequences of somatic mutation on splicing, expression levels, fusion genes and promoter activity(8,9); and evaluates a range of more-specialized features of cancer genomes(8,10-18).Peer reviewe

Addressing food and nutrition insecurity in the Caribbean through domestic smallholder farming system innovation

Structural conditions underlying the development of CARICOM’s two-tiered agricultural innovation system depict diverse drivers of change over time, versus institutional inertia of export-oriented formal institutions and the neglect of informal domestic markets. Key principles of taking an agroecological approach would include: supporting diversity and redundancy, building connectivity, managing slow variables and feedbacks, improving understanding of socioecological systems as complex adaptive systems, and encouraging polycentric governance systems. In this paper, we review the conditions that have been undermining sustainable food and nutrition security in the Caribbean, focusing on issues of history, economy, and innovation