K-Surfer: a KNIME extension for the management and analysis of Human brain MRI FreeSurfer/FSL data

Human brain imaging techniques, such as Magnetic Resonance Imaging (MRI) or Diffusion Tensor Imaging (DTI), have been established as scientific and diagnostic tools and their adoption is growing in popularity. Statistical methods, machine learning and data mining algorithms have successfully been adopted to extract predictive and descriptive models from neuroimage data. However, the knowledge discovery process typically requires also the adoption of pre-processing, post-processing and visualisation techniques in complex data workflows. Currently, a main problem for the integrated preprocessing and mining of MRI data is the lack of comprehensive platforms able to avoid the manual invocation of preprocessing and mining tools, that yields to an error-prone and inefficient process. In this work we present K-Surfer, a novel plug-in of the Konstanz Information Miner (KNIME) workbench, that automatizes the preprocessing of brain images and leverages the mining capabilities of KNIME in an integrated way. K-Surfer supports the importing, filtering, merging and pre-processing of neuroimage data from FreeSurfer, a tool for human brain MRI feature extraction and interpretation. K-Surfer automatizes the steps for importing FreeSurfer data, reducing time costs, eliminating human errors and enabling the design of complex analytics workflow for neuroimage data by leveraging the rich functionalities available in the KNIME workbench.

Soil, food security and human health: a review

Direct effects of soil or its constituents on human health are through its ingestion, inhalation or absorption. The soil contains many infectious organisms that may enter the human body through these pathways, but it also provides organisms on which our earliest antibiotics are based. Indirect effects of soil arise from the quantity and quality of food that humans consume. Trace elements can have both beneficial and toxic effects on humans, especially where the range for optimal intake is narrow. We focus on four trace elements (iodine, iron, selenium and zinc) whose deficiencies have substantial effects on human health. As the world’s population increases issues of food security become more pressing, as does the need to sustain soil fertility and minimize its degradation. Lack of adequate food and food of poor nutritional quality lead to differing degrees of under-nutrition, which in turn causes ill health. Soil and land are finite resources and agricultural land is under severe competition from other uses. Relationships between soil and health are often difficult to extricate because of the many confounding factors present. Nevertheless, recent scientific understanding of soil processes and factors that affect human health are enabling greater insight into the effects of soil on our health. Multidisciplinary research that includes soil science, agronomy, agricultural sustainability, toxicology, epidemiology and the medical sciences will facilitate the discovery of new antibiotics, a greater understanding of how materials added to soil used for food production affect health and deciphering of the complex relationships between soil and human health.

Genomic signals of migration and continuity in Britain before the Anglo-Saxons

The purported migrations that have formed the peoples of Britain have been the focus of generations of scholarly controversy. However, this has not benefited from direct analyses of ancient genomes. Here we report nine ancient genomes (~1 x) of individuals from northern Britain: seven from a Roman era York cemetery, bookended by earlier Iron-Age and later Anglo-Saxon burials. Six of the Roman genomes show affinity with modern British Celtic populations, particularly Welsh, but significantly diverge from populations from Yorkshire and other eastern English samples. They also show similarity with the earlier Iron-Age genome, suggesting population continuity, but differ from the later Anglo-Saxon genome. This pattern concords with profound impact of migrations in the Anglo-Saxon period. Strikingly, one Roman skeleton shows a clear signal of exogenous origin, with affinities pointing towards the Middle East, confirming the cosmopolitan character of the Empire, even at its northernmost fringes.

Thermo luminescence of natural and synthetic diopside

Diopside, a natural silicate mineral of formula CaMgSi2O6, has been investigated concerning its thermoluminescence (TL) and electron paramagnetic resonance (EPR) properties. Glow curves and TL vs. gamma-dose were obtained irradiating natural samples to additional dose varying from 50 to 10,000Gy. Except for a 410 degrees C peak found in the Al-doped artificial diopside, all the other peaks grow linearly with radiation dose, but saturate beyond -1 kGy. To investigate high-temperature effect before irradiation, measurements of TL intensity in samples annealed at 500-900 degrees C and then irradiated to I kGy gamma-dose were carried out. Also the TL emission spectrum has been obtained. To compare with natural diopside, a synthetic pure polycrystal was produced and further those doped with iron, aluminum and manganese were also produced. (c) 2007 Elsevier B.V. All rights reserved.

Lipid hydroperoxide-induced and hemoglobin-enhanced oxidative damage to colon cancer cells

Epidemiological studies have indicated that Western diets are related to an increase in a series of malignancies. Among the compounds that are credited for this toxic effect are heme and lipid peroxides. We evaluated the effects of hemoglobin (Hb) and linoleic acid hydroperoxides (LAOOH) on a series of toxicological endpoints, such as cytotoxicity, redox status, lipid peroxidation, and DNA damage. We demonstrated that the preincubation of SW480 cells with Hb and its subsequent exposure to LAOOH (Hb + LAOOH) led to an increase in cell death, DCFH oxidation, malonaldehyde formation, and DNA fragmentation and that these effects were related to the peroxide group and the heme present in Hb. Furthermore, Hb and LAOOH alone exerted a toxic effect on the endpoints assayed only at concentrations higher than 100 mu M. We were also able to show that SW480 cells presented a higher level of the modified DNA bases 8-oxo-7,8-dihydro-2`-deoxyguanosine and 1,N(2)-etheno-2`-deoxyguanosine compared to the control. Furthermore, incubations with Hb led to an increase in intracellular iron levels, and this high level of iron correlated with DNA oxidation, as measured as EndoIII- and Fpg-sensitive sites. Thus, Hb from either red meat or bowel bleeding could act as an enhancer of fatty acid hydroperoxide genotoxicity, which contributes to the accumulation of DNA lesions in colon cancer cells. (C) 2011 Elsevier Inc. All rights reserved.

Occupational airborne contamination in south Brazil: 1. Oxidative stress detected in the blood of coal miners

Reactive oxygen species and nitrogen species have been implicated in the pathogenesis of coal dust-induced toxicity. The present study investigated several oxidative stress biomarkers (Contents of lipoperoxidation = TBARS, reduced = GSH, oxidized = GSSG and total glutathione = TG, alpha-tocopherol, and the activities of glutathione S-transferase = GST, glutathione reductase = GR, glutathione peroxidase = GPx, catalase = CAT and superoxide dismutase = SOD), in the blood of three different groups (n = 20 each) exposed to airborne contamination associated with coal mining activities: underground workers directly exposed, surface workers indirectly exposed, residents indirectly exposed (subjects living near the mines), and controls (non-exposed subjects). Plasma TBARS were increased and whole blood TG and GSH levels were decreased in all groups compared to controls. Plasma alpha-tocopherol contents showed approximately half the values in underground workers compared to controls. GST activity was induced in workers and also in residents at the vicinity of the mining plant, whilst CAT activity was induced only in mine workers. SOD activity was decreased in all groups examined, while GPx activity showed decreased values only in underground miners, and GR did not show any differences among the groups. The results showed that subjects directly and indirectly exposed to coal dusts face an oxidative stress condition. They also indicate that people living in the vicinity of the mine plant are in health risk regarding coal mining-related diseases.

Electrochemical studies of the interface Fe/0.5 mol L(-1) H(2)SO(4) in the presence of benzotriazole and tolytriazole

The effect of benzotriazole (BTAH) and tolytriazole (TTAH) on the electrochemical behaviour of the Fe/0.5 mol L(-1) H(2)SO(4) interface at 25 degrees C was studied using cronopotentiometry, anodic and cathodic polarization curves and electrochemical impedance spectroscopy. BTAH and TTAH are inhibitors of anodic iron dissolution and the subsequent hydrogen evolution in 0.5 mol L(-1) H(2)SO(4) medium. Mass transport is an important step in the anodic process of inhibitive film formation. Electrochemical impedance spectroscopy was used to investigate the iron dissolution mechanism in the presence of the inhibitors and showed that BTAH and TTAH are adsorbed on the iron surface, thereby changing its dissolution mechanism in sulfate media. Starting from an iron dissolution model, it was possible to suggest two different mechanisms for iron dissolution in 0.5 mol L(-1) H(2)SO(4) containing BTAH or TTAH that involve a complex Fe(II)-inhibitor. (C) 2009 Elsevier B.V. All rights reserved

The effect of hydrophobic and hydrophilic fumed silica on the rheology of magnetorheological suspensions

We investigate magnetorheological fluids (MRFs) prepared with carbonyl iron powder and different types of hydrophobic and hydrophilic fumed silica. The rheological properties of the MRF suspensions were investigated with and without an applied magnetic field. The MRF samples prepared with hydrophobic silicas presented a more pronounced thixotropic effect and a higher recovery rate than those prepared with hydrophilic silicas. The application of a magnetic field to all the MRFs samples investigated leads to an increase in the viscosity and the thixotropic effect. MRF prepared with hydrophobic silicas presented smaller values of the viscosity than those prepared with hydrophilic silicas. At low applied magnetic fields, the type of the silica used to prepare the MRF leads to noticeable differences in the shear stress. However, these differences disappear at high magnetic fields. The results obtained showed that MRF samples prepared with the hydrophobic silica with the biggest particle diameter presented better characteristics for magnetorheological fluids, with higher values of yield stress, recovery rate, and elastic modulus. (C) 2009 The Society of Rheology. [DOI: 10.1122/1.3086870]

Guides of the Falu Mine : Perceptions of Differences and Similarities onDomestic and International Visitors

Industrial heritage tourism has been in focus for many academic studies and tourism is an alternative developmental tool for mines and contributes to their economic success. This thesis is about the Falu Mine in Dalarna, Sweden, which has World Heritage status since 2001 and is one of the biggest attractions in the region. Its history and cultural importance are reasons for the importance of preserving the heritage. The Falu Mine is under the management of the Great Copper Mountain Trust and one of their ambitions is to ensure the continuous popularity among domestic and international visitors. In order to gain a better understanding of the visitors and to find strategies to improve performance, a visitor survey has been conducted in the summer of 2011. It is the authors believe that the guides of the Falu Mine have the best available insight and that their perceptions help to add to the understanding about the visitors. Therefore, this thesis aims to explore the perceptions of the guides about their visitors, to investigate how the perceptions correspond to the statistical results and to study if there are any differences between domestic and international visitors. The mixed methods approach will increase the depth and accuracy of the results, by linking qualitative with quantitative data. The results show that differences between domestic and international visitors exist, both proven by interviews with the guides and the visitor survey. These differences occur in the factors, such as level of education of the visitors, group size and number of children in the group, knowledge of the visitors prior to and after the visit, sources of information and the fulfillment of the visitor expectations. The perceptions emphasize how these differences impact the guided tours. The guides of the Falu Mine have to be aware of those differences in order to adjust the tour accordingly, as well as the management of the Falu Mine can use this knowledge in order to identify strategies for improving performance.

The right to convert exploration licences to mining leases in Australia: a proposed national uniform model

In this article, the authors raise an important proposal for reform to Australia's mining legislation: a nationally-consistent model providing exploration licence holders with a legislative right to be granted a mining lease. This proposed national model will be designed to reflect the present Western Australian system - Western Australia being the only jurisdiction to provide exploration licence holders with the express right to be granted a mining lease on application. The authors believe that the Western Australian system should provide the basis for a national legislative model, given that it is designed to balance appropriately the interests of companies wanting a right to mine to recoup the costs involved in exploring for minerals, and the interests of the public in ensuring that exploration and mining is conducted
reasonably.

Heavy metal concentrations in wild and cultured blacklip abalone (haliotis rubra Leach) from southern Australian waters

The concentrations of 12 trace metals were assessed in wild and cultured specimens of blacklip abalone, Haliotis rubra, from each of two sites, Geelong and Port Fairy, in Victoria, Australia. Cadmium, copper, iron and zinc were quantified in the foot muscle of specimens from all four populations but the concentrations of aluminium, arsenic, beryllium, chromium, lead, manganese, nickel and vanadium were below the detection limits of the instrumental techniques employed. When similar sized specimens from each population were compared, the concentrations of each of the quantifiable metals varied according to location. The Geelong wild population had the highest or equal highest concentrations of each metal. Metal concentrations in the wild populations were usually greater than or equal to the concentrations in the corresponding cultured population. The concentrations of the regulated essential elements, copper and zinc, decreased with an increase in abalone length whereas the concentrations of iron, manganese and cadmium were independent of length. Metal concentrations in H. rubra from all sites complied with the Australian Food Code and other standards of food safety.

Coastal state fisheries management : a review of Australian enforcement action in the Heard and McDonald Islands Australian Fishing Zone

In 1953 the Heard and McDonald Islands Act, which formalised the transfer of sovereignty over the two named sub-Antarctic islands from the United Kingdom, was passed by the Australian Government. For the ensuing 40 years, Australian management of the Islands was uneventful. The first subAntarctic scientific station was established at Atlas Cove, on Heard Island, in December 1947 following the initial indication by Britain of a willingness to transfer rights to the Islands. In 1987 the Islands, together with their 12 mile territorial sea, were proclaimed a wilderness reserve with a number of activities including fishing and mining prohibited. The same area was included on the WorId Heritage List in 1997. In 1979 a 200 nautical mile Australian Fishing Zone (AFZ) was proclaimed around all Australian territories. In 1994 new terminology was embraced and the Exclusive Economic Zone was declared.

Photochemical degradation of 2,4-D and atrazine in well-defined media

Atrazine and 2,4-D are common herbicides used for crop, lawn, and rangeland management. Photochemical degradation has been proposed as one safe and efficient remediation strategy for both 2,4-D and Atrazine. In the presence of iron(llI) and hydrogen peroxide these herbicides decay by both thermal and light induced oxidation. Past studies have focused primarily on sun light as an energy source. This work provides a mechanistic description of herbicide degradation incorporating intermediate degradation products produced in the dark and under well-defined light conditions.

'Iron-saturated' lactoferrin is a potent natural adjuvant for augmenting cancer chemotherapy

Bovine lactoferrin (bLf), an iron-containing natural defence protein found in bodily secretions, has been reported to inhibit carcinogenesis and the growth of tumours. Here, we investigated whether natural bLf and iron-saturated forms of bLf differ in their ability to augment cancer chemotherapy. bLf was supplemented into the diet of C57BL/6 mice that were subsequently challenged subcutaneously with tumour cells, and treated by chemotherapy. Chemotherapy eradicated large (0.6 cm diameter) EL-4 lymphomas in mice that had been fed iron-saturated bLf (here designated Lf(+)) for 6 weeks prior to chemotherapy, but surprisingly not in mice that were fed lesser iron-saturated forms of bLf, including apo-bLf (4% iron saturated), natural bLf (approximately 15% iron saturated) and 50% iron-saturated bLf. Lf(+)-fed mice bearing either EL-4, Lewis lung carcinoma or B16 melanoma tumours completely rejected their tumours within 3 weeks following a single injection of either paclitaxel, doxorubicin, epirubicin or fluorouracil, whereas mice fed the control diet were resistant to chemotherapy. Lf(+) had to be fed to mice for more than 2 weeks prior to chemotherapy to be wholly effective in eradicating tumours from all mice, suggesting that it acts as a competence factor. It significantly reduced tumour vascularity and blood flow, and increased antitumour cytotoxicity, tumour apoptosis and the infiltration of tumours by leukocytes. Lf(+) bound to the intestinal epithelium and was preferentially taken up within Peyer's patches. It increased the production of Th1 and Th2 cytokines within the intestine and tumour, including TNF, IFN-gamma, as well as nitric oxide that have been reported to sensitize tumours to chemotherapy. Importantly, it restored both red and white peripheral blood cell numbers depleted by chemotherapy, potentially fortifying the mice against cancer. In summary, bLf is a potent natural adjuvant and fortifying agent for augmenting cancer chemotherapy, but needs to be saturated with iron to be effective.