PropBase QueryLayer : a single portal to UK physical property databases (extended abstract)

As the host institution of the National Geoscience Data Centre (NGDC), the British Geological Survey (BGS) holds significant volumes of subsurface data on behalf of the UK. These are derived both from the BGS�fs own data collection for research programmes, collected over many decades, and also as the national repository of data collected for other, often commercial, purposes deposited in the NGDC as a place of national deposit under statutory and other obligations. With the changing environment ensuring the security of the most basic requirements for human life, including the availability of potable groundwater, requires successful utilisation of finite resources from the subsurface, which in turn requires an ever greater understanding of the physical properties of the subsurface of the UK landmass. BGS has already moved from a mapping to a modelling paradigm, where the �gfundamental product�h of all of BGS�fs outputs is no longer represented as a two dimensional (2D) paper map but as a computer visualised three�]dimensional (3D) framework model. (Figure 1: an example 3D geological framework model). These show the geometric location of the subsurface information, realistically represented with shells or volumes representing geologically defined units. The next phase of this continuing process is to populate these geometric volumes with physical properties information that describe the heterogeneity of the subsurface. Understanding the physical properties data is vital for the undertaking of the behaviour of the subsurface, and is directly relevant to understanding the composition and behaviour of the rocks and fluids underground. This is of enormous vast societal and economic importance, and of increase. Understanding of the subsurface heterogeneity of the UK, in particular the changes in attributes such as porosity and rock �gstrength�h are of increasing importance in understanding the opportunities and threats represented by our subsurface. Once incorporated into the framework model this will be voxelated to demonstrate variation of property within the geometry (Figure 2). BGS has for many years stored all digital scientific analysis and records in relational databases to ensure the long�]term continuity of this information. However the structure of these databases is, by necessity, complex; each database, as well as containing positional reference data and model information, also contained metadata such as sample identification information and attributes that define the source and sample processing. Such metadata is critical to detailed assessment of the value of these analyses. It is however also hugely complicating for a simple understanding of variation of the physical property under assessment. Given that the UK�es populated areas are mostly underlain by clastic sedimentary rocks, understanding the variability of porosity is fundamental to understanding the nature of these rocks. However porosity data has been measured in a significant variety of ways, for a significant variety of end�]uses over a long period of time. This means that the extraction of physical properties from these databases for a first look at understanding porosity is difficult; therefore the PropBase Query Layer has been created to allow a simplified aggregation of and extraction of all related data. The concept of the Query Layer is the presentation of complex data in simple, often denormalized, tables. The PropBase Query Layer brings together property information from various databases (each with its own database structure that reflects the nature of the data) into a single system. This means that data from all of the BGS�fs subsurface data holdings can be viewed together in simple interfaces. Technical descriptions of the Query Layer (denormalized layer) The PropBase data architecture is based around the concept of a query layer to present complex data in a simple but often denormalized set of tables and other programmable units within a relational database system. The query layer brings together property information from various databases each with their own relational structure into a generalised structure, so that there's a single consistent point of access of the data for any applications that may require the data. The query layer is implemented within an Oracle relational database system where the source databases also reside or are re�]engineered into to facilitate easy loading of the data. The denormalization techniques used to build the query layer are not unique to Oracle and can be implemented on other RDBMS (Relational database management system). The query layer structure comprises a set of tables, procedures, functions, triggers, views and possibly materialised views. The structure contains a main table PRB_DATA which contains all of the data with the following attribution: . a unique identifier for each record . the source of the data . the corresponding unique identifier of the record from its parent database for traceability. . the geographic co�]ordinates of the record . the depth values . the type of property . the value of the property . the units of measure . the appropriate qualifiers . precision values and a full audit trail for the record The data source, property type and units of measure are constrained by a series of dictionaries collated from the values used in the different databases from which data is extracted to populate the query layer. The property dictionary is a key component of the structure as this defines what properties and inherit hierarchies are to be coded and also guides the process as to what and how these are extracted from the structure. The data model (Figure 3) shows that the structure also contains a child table PRB_DATA_COORD that holds secondary geographic co�]ordinates in different projections from the primary record in the PRB_DATA table for a given record. This allows for the presentation of a property with its location in the primary projection and any others as maybe recorded in the database. The structure incorporates a level of flexibility because of the it's simplistic structure that enables us to add on any extra tables required linked off the main PRB_DATA table to capture extra attribution with a 1�]to�]many relationship or even a 1�]to�]1 if adding any extra attributes to the main table comprises the simplicity of the structure. In a similar vein to adding the capability to hold primary and secondary co�]ordinates references for a record at different projections, the structure also incorporates a GROUND_REFERENCE table that allows secondary ground reference information at different surface level data to be recorded in a separate table to the primary record held in the main table. The surface level datum attribute in this extra table is constrained by a dictionary of such surface level datum types. Given the size of the denormalized structure and the many property types and their values from various data sources, it's important that there's a co�]ordinated technical approach to keep the layer synchronised. The query layer therefore makes use of oracle procedures written in PL/SQL containing the logic to carry out the data manipulation (inserts, updates, deletes) to keep the layer synchronised with the underlying databases. These procedures and/or packages are run as scheduled jobs at regular intervals (weekly, monthly etc.) or can be invoked on demand. Implications for need to improve BGS database structures Several databases have been in operation for 10�]15 years without review. Work on PropBase has further identified redundancy within the data structures, data quality issues and opportunities for where improvement to the database structure that will not only allow delivery of information more effectively but also improve data quality at little cost. Conclusions The implementation of the PropBase QueryLayer has enabled BGS to find display and interpret more dataset with greater ease, massively simplifying the process of populating 3D framework models volumes with physical properties for parameterisation and study of geological intra�]unit heterogeneity. This has enabled more rapid data discovery and population of 3D models with data held in our databases, enabling different datasets to be easily compared improving the data verification process. This technology will assist BGS is continuing to be one of the world leading national geological surveys

Dirichlet multinomial mixtures: generative models for microbial metagenomics

We introduce Dirichlet multinomial mixtures (DMM) for the probabilistic modelling of microbial metagenomics data. This data can be represented as a frequency matrix giving the number of times each taxa is observed in each sample. The samples have different size, and the matrix is sparse, as communities are diverse and skewed to rare taxa. Most methods used previously to classify or cluster samples have ignored these features. We describe each community by a vector of taxa probabilities. These vectors are generated from one of a finite number of Dirichlet mixture components each with different hyperparameters. Observed samples are generated through multinomial sampling. The mixture components cluster communities into distinct ‘metacommunities’, and, hence, determine envirotypes or enterotypes, groups of communities with a similar composition. The model can also deduce the impact of a treatment and be used for classification. We wrote software for the fitting of DMM models using the ‘evidence framework’ (http://code.google.com/p/microbedmm/). This includes the Laplace approximation of the model evidence. We applied the DMM model to human gut microbe genera frequencies from Obese and Lean twins. From the model evidence four clusters fit this data best. Two clusters were dominated by Bacteroides and were homogenous; two had a more variable community composition. We could not find a significant impact of body mass on community structure. However, Obese twins were more likely to derive from the high variance clusters. We propose that obesity is not associated with a distinct microbiota but increases the chance that an individual derives from a disturbed enterotype. This is an example of the ‘Anna Karenina principle (AKP)’ applied to microbial communities: disturbed states having many more configurations than undisturbed. We verify this by showing that in a study of inflammatory bowel disease (IBD) phenotypes, ileal Crohn's disease (ICD) is associated with a more variable community

The Role of Agricultural Colleges and Universities in Rural Development and Lifelong Learning in Asia

The paper expounds on the challenges confronting institutions of higher agricultural education (HAE) in the context of the significant role of education in alleviating poverty, especially in rural areas, and in light of the changing needs of rural areas and economies. Specifically, HAE institutions are called upon to initiate and lead in articulating a vision for the future that serves the needs not only of agriculture but also of all who inhabit the rural areas. They can step beyond their traditional role by merging forces with other stakeholders to enrich and support other levels of education with critical knowledge and information on agriculture and natural resources management (NRM), the latter being crucial in the pursuit of rural development, poverty education, and food security. To perform an active and constructive role in rural development, agricultural universities need to adjust their programs to accommodate new topics, as well as teaching and learning models; forge new partnerships with schools, academia and rural space stakeholders; expand its representation in governance; and hold continuous dialogue with policymakers. Their extension services could include support to education for rural people that encompasses primary, secondary, vocational, and adult education. University-school linkages are perceived to be illustrative of a decentralized, democratic, and community-based response to rural development problems. It is noted that universities can potentially become showcases of local traditions and knowledge, reflecting the regional, cultural, and ethical traditions of their society, as well as global movements and forces. In reinforcing their roles as contributors to a culture of learning and rural development, it is emphasized that HAE institutions need to engage more directly and more effectively in partnerships and dialogue with other local educational institutions and their surrounding communities. Findings of the ongoing IIEP-UNESCO/FAO program of research on HAE institutions in Asia are expected to provide information on how higher education institutions contribute to learning and rural development, and insights on how their strategic role in this field could be strengthened and further developed.higher agricultural education, rural development, Asia, lifelong learning

Hyperglycaemia does not increase perfusion deficits after focal cerebral ischaemia in male Wistar rats

Background: Hyperglycaemia is associated with a worse outcome in acute ischaemic stroke patients; yet the pathophysiological mechanisms of hyperglycaemia-induced damage are poorly understood. We hypothesised that hyperglycaemia at the time of stroke onset exacerbates ischaemic brain damage by increasing the severity of the blood flow deficit. Methods: Adult, male Wistar rats were randomly assigned to receive vehicle or glucose solutions prior to permanent middle cerebral artery occlusion. Cerebral blood flow was assessed semi-quantitatively either 1 h after middle cerebral artery occlusion using 99mTc-D, L-hexamethylpropyleneamine oxime (99mTc-HMPAO) autoradiography or, in a separate study, using quantitative pseudo-continuous arterial spin labelling for 4 h after middle cerebral artery occlusion. Diffusion weighted imaging was performed alongside pseudo-continuous arterial spin labelling and acute lesion volumes calculated from apparent diffusion coefficient maps. Infarct volume was measured at 24 h using rapid acquisition with refocused echoes T2-weighted magnetic resonance imaging. Results: Glucose administration had no effect on the severity of ischaemia when assessed by either 99mTc-HMPAO autoradiography or pseudo-continuous arterial spin labelling perfusion imaging. In comparison to the vehicle group, apparent diffusion coefficient–derived lesion volume 2–4 h post-middle cerebral artery occlusion and infarct volume 24 h post-middle cerebral artery occlusion were significantly greater in the glucose group. Conclusions: Hyperglycaemia increased acute lesion and infarct volumes but there was no evidence that the acute blood flow deficit was exacerbated. The data reinforce the conclusion that the detrimental effects of hyperglycaemia are rapid, and that treatment of post-stroke hyperglycaemia in the acute period is essential but the mechanisms of hyperglycaemia-induced harm remain unclear

Stroke penumbra defined by an MRI-based oxygen challenge technique: 1. validation using [14C]2-deoxyglucose autoradiography

Accurate identification of ischemic penumbra will improve stroke patient selection for reperfusion therapies and clinical trials. Current magnetic resonance imaging (MRI) techniques have limitations and lack validation. Oxygen challenge T2* MRI (T2* OC) uses oxygen as a biotracer to detect tissue metabolism, with penumbra displaying the greatest T2* signal change during OC. [14C]2-deoxyglucose (2-DG) autoradiography was combined with T2* OC to determine metabolic status of T2*-defined penumbra. Permanent middle cerebral artery occlusion was induced in anesthetized male Sprague-Dawley rats (n=6). Ischemic injury and perfusion deficit were determined by diffusion- and perfusion-weighted imaging, respectively. At 147±32 minutes after stroke, T2* signal change was measured during a 5-minute 100% OC, immediately followed by 125 μCi/kg 2-DG, intravenously. Magnetic resonance images were coregistered with the corresponding autoradiograms. Regions of interest were located within ischemic core, T2*-defined penumbra, equivalent contralateral structures, and a region of hyperglycolysis. A T2* signal increase of 9.22%±3.9% (mean±s.d.) was recorded in presumed penumbra, which displayed local cerebral glucose utilization values equivalent to contralateral cortex. T2* signal change was negligible in ischemic core, 3.2%±0.78% in contralateral regions, and 1.41%±0.62% in hyperglycolytic tissue, located outside OC-defined penumbra and within the diffusion abnormality. The results support the utility of OC-MRI to detect viable penumbral tissue follow

Diameter-controlled solid-phase seeding of germanium nanowires: structural characterization and electrical transport properties

Despite the huge progress recently made in understanding the phenomena of metal-promoted growth of one-dimensional (1D) semiconductors, the controlled formation of small diameter semiconductor nanowires is still challenging. Liquid growth promoters, such as the low melting Au/Ge eutectic, allow control of the aspect ratio, diameter, and structure of 1D crystals via external parameters, such as precursor feedstock, temperature, and operating pressure. However, the incorporation of metal atoms during the growth process, size variations of the nanowires due to agglomeration of the nucleating metal seeds, and surface diffusion of Au via the vapor–liquid–solid route have been reported. Here, we detail the influence of solid growth seeds, such as NiGe2 formed from Ni nanoparticles, on the lateral dimensions of Ge nanowires grown using a supercritical fluid growth process. Beneficial control over the mean nanowire diameter, in the sub-20 nm regime, with a predominantly ⟨110⟩ growth direction and low structural defect concentration was obtained using Ni seeds. In addition, the effect of prealloying of Ni–Fe films for the growth of Ge nanowires was investigated, which leads to a bimodal nanowire distribution. Electrical characterization performed on single nanowire devices showed p-type behavior for Ge nanowires grown from Ni and Ni/Fe seeds. Determination of resistivities, majority carrier concentrations, and mobilities suggest significant doping of the Ge nanowires by Ni when grown via a supercritical fluid–solid–solid (SFSS) mechanism

Misdiagnosis, Mistreatment, and Harm - When Medical Care Ignores Social Forces.

The Case Studies in Social Medicine demonstrate that when physicians use only biologic or individual behavioral interventions to treat diseases that stem from or are exacerbated by social factors, we risk harming the patients we seek to serve

Potential use of oxygen as a metabolic biosensor in combination with T2*-weighted MRI to define the ischemic penumbra

We describe a novel magnetic resonance imaging technique for detecting metabolism indirectly through changes in oxyhemoglobin:deoxyhemoglobin ratios and T2* signal change during ‘oxygen challenge’ (OC, 5 mins 100% O2). During OC, T2* increase reflects O2 binding to deoxyhemoglobin, which is formed when metabolizing tissues take up oxygen. Here OC has been applied to identify tissue metabolism within the ischemic brain. Permanent middle cerebral artery occlusion was induced in rats. In series 1 scanning (n=5), diffusion-weighted imaging (DWI) was performed, followed by echo-planar T2* acquired during OC and perfusion-weighted imaging (PWI, arterial spin labeling). Oxygen challenge induced a T2* signal increase of 1.8%, 3.7%, and 0.24% in the contralateral cortex, ipsilateral cortex within the PWI/DWI mismatch zone, and ischemic core, respectively. T2* and apparent diffusion coefficient (ADC) map coregistration revealed that the T2* signal increase extended into the ADC lesion (3.4%). In series 2 (n=5), FLASH T2* and ADC maps coregistered with histology revealed a T2* signal increase of 4.9% in the histologically defined border zone (55% normal neuronal morphology, located within the ADC lesion boundary) compared with a 0.7% increase in the cortical ischemic core (92% neuronal ischemic cell change, core ADC lesion). Oxygen challenge has potential clinical utility and, by distinguishing metabolically active and inactive tissues within hypoperfused regions, could provide a more precise assessment of penumbra

Stroke penumbra defined by an MRI-based oxygen challenge technique: 2. Validation based on the consequences of reperfusion

Magnetic resonance imaging (MRI) with oxygen challenge (T2* OC) uses oxygen as a metabolic biotracer to define penumbral tissue based on CMRO2 and oxygen extraction fraction. Penumbra displays a greater T2* signal change during OC than surrounding tissue. Since timely restoration of cerebral blood flow (CBF) should salvage penumbra, T2* OC was tested by examining the consequences of reperfusion on T2* OC-defined penumbra. Transient ischemia (109±20 minutes) was induced in male Sprague-Dawley rats (n=8). Penumbra was identified on T2*-weighted MRI during OC. Ischemia and ischemic injury were identified on CBF and apparent diffusion coefficient maps, respectively. Reperfusion was induced and scans repeated. T2 for final infarct and T2* OC were run on day 7. T2* signal increase to OC was 3.4% in contralateral cortex and caudate nucleus and was unaffected by reperfusion. In OC-defined penumbra, T2* signal increased by 8.4%±4.1% during ischemia and returned to 3.25%±0.8% following reperfusion. Ischemic core T2* signal increase was 0.39%±0.47% during ischemia and 0.84%±1.8% on reperfusion. Penumbral CBF increased from 41.94±13 to 116.5±25 mL per 100 g per minute on reperfusion. On day 7, OC-defined penumbra gave a normal OC response and was located outside the infarct. T2* OC-defined penumbra recovered when CBF was restored, providing further validation of the utility of T2* OC for acute stroke management

School-age effects of the newborn individualized developmental care and assessment program for preterm infants with intrauterine growth restriction: preliminary findings

Background: The experience in the newborn intensive care nursery results in premature infants’ neurobehavioral and neurophysiological dysfunction and poorer brain structure. Preterms with severe intrauterine growth restriction are doubly jeopardized given their compromised brains. The Newborn Individualized Developmental Care and Assessment Program improved outcome at early school-age for preterms with appropriate intrauterine growth. It also showed effectiveness to nine months for preterms with intrauterine growth restriction. The current study tested effectiveness into school-age for preterms with intrauterine growth restriction regarding executive function (EF), electrophysiology (EEG) and neurostructure (MRI). Methods: Twenty-three 9-year-old former growth-restricted preterms, randomized at birth to standard care (14 controls) or to the Newborn Individualized Developmental Care and Assessment Program (9 experimentals) were assessed with standardized measures of cognition, achievement, executive function, electroencephalography, and magnetic resonance imaging. The participating children were comparable to those lost to follow-up, and the controls to the experimentals, in terms of newborn background health and demographics. All outcome measures were corrected for mother’s intelligence. Analysis techniques included two-group analysis of variance and stepwise discriminate analysis for the outcome measures, Wilks’ lambda and jackknifed classification to ascertain two-group classification success per and across domains; canonical correlation analysis to explore relationships among neuropsychological, electrophysiological and neurostructural domains at school-age, and from the newborn period to school-age. Results: Controls and experimentals were comparable in age at testing, anthropometric and health parameters, and in cognitive and achievement scores. Experimentals scored better in executive function, spectral coherence, and cerebellar volumes. Furthermore, executive function, spectral coherence and brain structural measures discriminated controls from experimentals. Executive function correlated with coherence and brain structure measures, and with newborn-period neurobehavioral assessment. Conclusion: The intervention in the intensive care nursery improved executive function as well as spectral coherence between occipital and frontal as well as parietal regions. The experimentals’ cerebella were significantly larger than the controls’. These results, while preliminary, point to the possibility of long-term brain improvement even of intrauterine growth compromised preterms if individualized intervention begins with admission to the NICU and extends throughout transition home. Larger sample replications are required in order to confirm these results