Determination of histopathological tumor grade in neuroepithelial brain tumors by using spectral pattern analysis of in vivo spectroscopic data

OBJECT: In this study, 1H magnetic resonance (MR) spectroscopy was prospectively tested as a reliable method for presurgical grading of neuroepithelial brain tumors. METHODS: Using a database of tumor spectra obtained in patients with histologically confirmed diagnoses, 94 consecutive untreated patients were studied using single-voxel 1H spectroscopy (point-resolved spectroscopy; TE 135 msec, TE 135 msec, TR 1500 msec). A total of 90 tumor spectra obtained in patients with diagnostic 1H MR spectroscopy examinations were analyzed using commercially available software (MRUI/VARPRO) and classified using linear discriminant analysis as World Health Organization (WHO) Grade I/II, WHO Grade III, or WHO Grade IV lesions. In all cases, the classification results were matched with histopathological diagnoses that were made according to the WHO classification criteria after serial stereotactic biopsy procedures or open surgery. Histopathological studies revealed 30 Grade I/II tumors, 29 Grade III tumors, and 31 Grade IV tumors. The reliability of the histological diagnoses was validated considering a minimum postsurgical follow-up period of 12 months (range 12-37 months). Classifications based on spectroscopic data yielded 31 tumors in Grade I/II, 32 in Grade III, and 27 in Grade IV. Incorrect classifications included two Grade II tumors, one of which was identified as Grade III and one as Grade IV; two Grade III tumors identified as Grade II; two Grade III lesions identified as Grade IV; and six Grade IV tumors identified as Grade III. Furthermore, one glioblastoma (WHO Grade IV) was classified as WHO Grade I/II. This represents an overall success rate of 86%, and a 95% success rate in differentiating low-grade from high-grade tumors. CONCLUSIONS: The authors conclude that in vivo 1H MR spectroscopy is a reliable technique for grading neuroepithelial brain tumors.

Change in pain severity with open label venlafaxine use in patients with a depressive symptomatology: an observational study in primary care

PURPOSE: Venlafaxine has shown benefit in the treatment of depression and pain. Worldwide data are extensively lacking investigating the outcome of chronic pain patients with depressive symptoms treated by venlafaxine in the primary care setting. This observational study aimed to elucidate the efficacy of venlafaxine and its prescription by Swiss primary care physicians and psychiatrists in patients with chronic pain and depressive symptomatology. SUBJECTS AND METHODS: We studied 505 patients with depressive symptoms suffering from chronic pain in a prospective naturalistic Swiss community based observational trial with venlafaxine in primary care. These patients have been treated with venlafaxine by 122 physicians, namely psychiatrists, general practitioners, and internists. RESULTS: On average, patients were treated with 143+/-75 mg (0-450 mg) venlafaxine daily for a follow-up of three months. Venlafaxine proved to be beneficial in the treatment of both depressive symptoms and chronic pain. DISCUSSION: Although side effects were absent in most patients, physicians might have frequently omitted satisfactory response rate of depression by underdosing venlafaxine. Our results reflect the complexity in the treatment of chronic pain in patients with depressive symptoms in primary care. CONCLUSION: Further randomized dose-finding studies are needed to learn more about the appropriate dosage in treating depression and comorbid pain with venlafaxine.

Estimation of scots pine defoliation by the common pine sawfly (Diprion pini L.) using multi-temporal radar data

In 1998-2001 Finland suffered the most severe insect outbreak ever recorded, over 500,000 hectares. The outbreak was caused by the common pine sawfly (Diprion pini L.). The outbreak has continued in the study area, Palokangas, ever since. To find a good method to monitor this type of outbreaks, the purpose of this study was to examine the efficacy of multi-temporal ERS-2 and ENVISAT SAR imagery for estimating Scots pine (Pinus sylvestris L.) defoliation. Three methods were tested: unsupervised k-means clustering, supervised linear discriminant analysis (LDA) and logistic regression. In addition, I assessed if harvested areas could be differentiated from the defoliated forest using the same methods. Two different speckle filters were used to determine the effect of filtering on the SAR imagery and subsequent results. The logistic regression performed best, producing a classification accuracy of 81.6% (kappa 0.62) with two classes (no defoliation, >20% defoliation). LDA accuracy was with two classes at best 77.7% (kappa 0.54) and k-means 72.8 (0.46). In general, the largest speckle filter, 5 x 5 image window, performed best. When additional classes were added the accuracy was usually degraded on a step-by-step basis. The results were good, but because of the restrictions in the study they should be confirmed with independent data, before full conclusions can be made that results are reliable. The restrictions include the small size field data and, thus, the problems with accuracy assessment (no separate testing data) as well as the lack of meteorological data from the imaging dates.

Investigation of the effect of using data collection technology on students' attitudes to science instruction

The purpose of this project was to investigate the effect of using of data collection technology on student attitudes towards science instruction. The study was conducted over the course of two years at Madison High School in Adrian, Michigan, primarily in college preparatory physics classes, but also in one college preparatory chemistry class and one environmental science class. A preliminary study was conducted at a Lenawee County Intermediate Schools student summer environmental science day camp. The data collection technology used was a combination of Texas Instruments TI-84 Silver Plus graphing calculators and Vernier LabPro data collection sleds with various probeware attachments, including motion sensors, pH probes and accelerometers. Students were given written procedures for most laboratory activities and were provided with data tables and analysis questions to answer about the activities. The first year of the study included a pretest and posttest measuring student attitudes towards the class they were enrolled in. Pre-test and post-test data were analyzed to determine effect size, which was found to be very small (Coe, 2002). The second year of the study focused only on a physics class and used Keller’s ARCS model for measuring student motivation based on the four aspects of motivation: Attention, Relevance, Confidence and Satisfaction (Keller, 2010). According to this model, it was found that there were two distinct groups in the class, one of which was motivated to learn and the other that was not. The data suggest that the use of data collection technology in science classes should be started early in a student’s career, possibly in early middle school or late elementary. This would build familiarity with the equipment and allow for greater exploration by the student as they progress through high school and into upper level science courses.

Modeling and classifying variable width riparian zones utilizing digital elevation models, flood height data, digital soil data and national wetlands inventory : a new approach for riparian zone delineation

Riparian zones are dynamic, transitional ecosystems between aquatic and terrestrial ecosystems with well defined vegetation and soil characteristics. Development of an all-encompassing definition for riparian ecotones, because of their high variability, is challenging. However, there are two primary factors that all riparian ecotones are dependent on: the watercourse and its associated floodplain. Previous approaches to riparian boundary delineation have utilized fixed width buffers, but this methodology has proven to be inadequate as it only takes the watercourse into consideration and ignores critical geomorphology, associated vegetation and soil characteristics. Our approach offers advantages over other previously used methods by utilizing: the geospatial modeling capabilities of ArcMap GIS; a better sampling technique along the water course that can distinguish the 50-year flood plain, which is the optimal hydrologic descriptor of riparian ecotones; the Soil Survey Database (SSURGO) and National Wetland Inventory (NWI) databases to distinguish contiguous areas beyond the 50-year plain; and land use/cover characteristics associated with the delineated riparian zones. The model utilizes spatial data readily available from Federal and State agencies and geospatial clearinghouses. An accuracy assessment was performed to assess the impact of varying the 50-year flood height, changing the DEM spatial resolution (1, 3, 5 and 10m), and positional inaccuracies with the National Hydrography Dataset (NHD) streams layer on the boundary placement of the delineated variable width riparian ecotones area. The result of this study is a robust and automated GIS based model attached to ESRI ArcMap software to delineate and classify variable-width riparian ecotones.

Quantifying the ecological benefits of lakeshore restoration in northern Wisconsin

Housing development has increased dramatically in the Midwest with a high concentration around lakes. This development plays an important role in the economy of Northwoods communities. However, poorly planned development has the potential to alter a lake’s ecological processes and integrity. Studies have documented the impacts of housing developments and reported dramatic, negative changes to the flora and fauna in Vilas County, Wisconsin. One component of my research included examining the previously unstudied effects of residential development on the abundance and diversity of medium to large-bodied mammals using lakeshore ecosystems. The results suggest that a higher diversity of mammals were detected on low-development lakes. Coyotes were the most numerous species detected with the majority encountered on low-development lakes. White-tailed deer and red fox were more abundant on high-development lakes as compared to low-development lakes. I concluded that high-development lakes are having a negative affect on the mammal community in this area. Recently, lakeshore restoration has occurred on privately owned property in Vilas County and elsewhere in the Northwoods, but little is known about the benefit, if any, from these restoration efforts. A partnership between government agencies and academia has launched a long-term research project investigating the ecological benefits of lakeshore restoration. I investigated the impacts of using down woody material (DWM) to increase the success of restoration projects. Specifically, I tested the hypothesis that down woody material would reduce the variation in soil temperature, retain soil moisture, and improve plant survival and growth rates. I randomly assigned three DWM coverage treatments (0%, 25%, and 50%) on 3 m × 3 m experimental plots (n = 10 per treatment). The mean maximum soil temperature, temperature variation, and change in soil moisture content were significantly lower in the 25% and 50% DWM plots. I found no difference in survival, but snowberry (Symphoricarpos albus) and Barren strawberry (Waldstenia fragaroides) growth was significant greater in the 25% and 50% DWM plots. DWM addition can be considered a useful technique to physically manipulate soil properties and improve plant growth. Finally, I provided baseline data on vegetation structure, bird and small mammal community diversity and abundance for three lakes targeted for restoration efforts and their paired reference lakes. This study is one of the first of it kind in the area and continuing to document the degree of change in subsequent years will provide insight into the way the local ecosystem functions and how ecological communities are structured.

Simulating dioxane transport in a heterogeneous glacial aquifer system (Washtenaw County, Michigan) using publicly available models and data

The primary challenge in groundwater and contaminant transport modeling is obtaining the data needed for constructing, calibrating and testing the models. Large amounts of data are necessary for describing the hydrostratigraphy in areas with complex geology. Increasingly states are making spatial data available that can be used for input to groundwater flow models. The appropriateness of this data for large-scale flow systems has not been tested. This study focuses on modeling a plume of 1,4-dioxane in a heterogeneous aquifer system in Scio Township, Washtenaw County, Michigan. The analysis consisted of: (1) characterization of hydrogeology of the area and construction of a conceptual model based on publicly available spatial data, (2) development and calibration of a regional flow model for the site, (3) conversion of the regional model to a more highly resolved local model, (4) simulation of the dioxane plume, and (5) evaluation of the model's ability to simulate field data and estimation of the possible dioxane sources and subsequent migration until maximum concentrations are at or below the Michigan Department of Environmental Quality's residential cleanup standard for groundwater (85 ppb). MODFLOW-2000 and MT3D programs were utilized to simulate the groundwater flow and the development and movement of the 1, 4-dioxane plume, respectively. MODFLOW simulates transient groundwater flow in a quasi-3-dimensional sense, subject to a variety of boundary conditions that can simulate recharge, pumping, and surface-/groundwater interactions. MT3D simulates solute advection with groundwater flow (using the flow solution from MODFLOW), dispersion, source/sink mixing, and chemical reaction of contaminants. This modeling approach was successful at simulating the groundwater flows by calibrating recharge and hydraulic conductivities. The plume transport was adequately simulated using literature dispersivity and sorption coefficients, although the plume geometries were not well constrained.

Community managed rural water supply systems in the Dominican Republic : assessment of sustainability of systems built by the National Institute of Potable Water and Peace Corps, Dominican Republic

In the Dominican Republic economic growth in the past twenty years has not yielded sufficient improvement in access to drinking water services, especially in rural areas where 1.5 million people do not have access to an improved water source (WHO, 2006). Worldwide, strategic development planning in the rural water sector has focused on participatory processes and the use of demand filters to ensure that service levels match community commitment to post-project operation and maintenance. However studies have concluded that an alarmingly high percentage of drinking water systems (20-50%) do not provide service at the design levels and/or fail altogether (up to 90%): BNWP (2009), Annis (2006), and Reents (2003). World Bank, USAID, NGOs, and private consultants have invested significant resources in an effort to determine what components make up an “enabling environment” for sustainable community management of rural water systems (RWS). Research has identified an array of critical factors, internal and external to the community, which affect long term sustainability of water services. Different frameworks have been proposed in order to better understand the linkages between individual factors and sustainability of service. This research proposes a Sustainability Analysis Tool to evaluate the sustainability of RWS, adapted from previous relevant work in the field to reflect the realities in the Dominican Republic. It can be used as a diagnostic tool for government entities and development organizations to characterize the needs of specific communities and identify weaknesses in existing training regimes or support mechanisms. The framework utilizes eight indicators in three categories (Organization/Management, Financial Administration, and Technical Service). Nineteen independent variables are measured resulting in a score of sustainability likely (SL), possible (SP), or unlikely (SU) for each of the eight indicators. Thresholds are based upon benchmarks from the DR and around the world, primary data collected during the research, and the author’s 32 months of field experience. A final sustainability score is calculated using weighting factors for each indicator, derived from Lockwood (2003). The framework was tested using a statistically representative geographically stratified random sample of 61 water systems built in the DR by initiatives of the National Institute of Potable Water (INAPA) and Peace Corps. The results concluded that 23% of sample systems are likely to be sustainable in the long term, 59% are possibly sustainable, and for 18% it is unlikely that the community will be able to overcome any significant challenge. Communities that were scored as unlikely sustainable perform poorly in participation, financial durability, and governance while the highest scores were for system function and repair service. The Sustainability Analysis Tool results are verified by INAPA and PC reports, evaluations, and database information, as well as, field observations and primary data collected during the surveys. Future research will analyze the nature and magnitude of relationships between key factors and the sustainability score defined by the tool. Factors include: gender participation, legal status of water committees, plumber/operator remuneration, demand responsiveness, post construction support methodologies, and project design criteria.

Peer influence in NIPF landowner decision making in the western Upper Peninsula, Michigan

Non-industrial private forest (NIPF) owners hold the largest amount of privately owned forest in the United States. Activities undertaken by NIPF owners have the potential to drastically impact the forested landscape of the United States, along with its associated biodiversity and ecological services. Many government sanctioned programs are in place to discourage the conversion of forest to other uses as well as to ensure sustainable management and a continuous supply of timber. Reaching NIPF owners with information about these programs and other management information is therefore important to the forests of the United States. This thesis presents research on how the NIPF owners of the western Upper Peninsula of Michigan communicate about forest management with neighboring NIPF owners. The data were obtained from 34 telephone interviews with owners of NIPF properties in the western Upper Peninsula. The goal of this research was to understand the way information moves through NIPF owner dominated landscapes in order to provide recommendations to policy implementers on how to best reach NIPF owners with information. Understanding where NIPF owners get information about management and landowner assistance programs is vital to ensuring a sustainably managed forest landscape in the western Upper Peninsula of Michigan.

Comparisons between OMI SO2 data and ground-based SO2 measurements at Turrialba volcano

Turrialba is one of the largest and most active stratovolcanoes in the Central Cordillera of Costa Rica and an excellent target for validation of satellite data using ground based measurements due to its high elevation, relative ease of access, and persistent elevated SO2 degassing. The Ozone Monitoring Instrument (OMI) aboard the Aura satellite makes daily global observations of atmospheric trace gases and it is used in this investigation to obtain volcanic SO2 retrievals in the Turrialba volcanic plume. We present and evaluate the relative accuracy of two OMI SO2 data analysis procedures, the automatic Band Residual Index (BRI) technique and the manual Normalized Cloud-mass (NCM) method. We find a linear correlation and good quantitative agreement between SO2 burdens derived from the BRI and NCM techniques, with an improved correlation when wet season data are excluded. We also present the first comparisons between volcanic SO2 emission rates obtained from ground-based mini-DOAS measurements at Turrialba and three new OMI SO2 data analysis techniques: the MODIS smoke estimation, OMI SO2 lifetime, and OMI SO2 transect techniques. A robust validation of OMI SO2 retrievals was made, with both qualitative and quantitative agreements under specific atmospheric conditions, proving the utility of satellite measurements for estimating accurate SO2 emission rates and monitoring passively degassing volcanoes.

Lava discharge rate estimates from thermal infrared satellite data at Pacaya Volcano, Guatemala

Time-averaged discharge rates (TADR) were calculated for five lava flows at Pacaya Volcano (Guatemala), using an adapted version of a previously developed satellite-based model. Imagery acquired during periods of effusive activity between the years 2000 and 2010 were obtained from two sensors of differing temporal and spatial resolutions; the Moderate Resolution Imaging Spectroradiometer (MODIS), and the Geostationary Operational Environmental Satellites (GOES) Imager. A total of 2873 MODIS and 2642 GOES images were searched manually for volcanic “hot spots”. It was found that MODIS imagery, with superior spatial resolution, produced better results than GOES imagery, so only MODIS data were used for quantitative analyses. Spectral radiances were transformed into TADR via two methods; first, by best-fitting some of the parameters (i.e. density, vesicularity, crystal content, temperature change) of the TADR estimation model to match flow volumes previously estimated from ground surveys and aerial photographs, and second by measuring those parameters from lava samples to make independent estimates. A relatively stable relationship was defined using the second method, which suggests the possibility of estimating lava discharge rates in near-real-time during future volcanic crises at Pacaya.

Digital processing and data compilation approach for using remotely sensed imagery to identify geological lineaments in hard-rock terrains : an application for groundwater explorations in Nicaragua

Sustainable yields from water wells in hard-rock aquifers are achieved when the well bore intersects fracture networks. Fracture networks are often not readily discernable at the surface. Lineament analysis using remotely sensed satellite imagery has been employed to identify surface expressions of fracturing, and a variety of image-analysis techniques have been successfully applied in “ideal” settings. An ideal setting for lineament detection is where the influences of human development, vegetation, and climatic situations are minimal and hydrogeological conditions and geologic structure are known. There is not yet a well-accepted protocol for mapping lineaments nor have different approaches been compared in non-ideal settings. A new approach for image-processing/synthesis was developed to identify successful satellite imagery types for lineament analysis in non-ideal terrain. Four satellite sensors (ASTER, Landsat7 ETM+, QuickBird, RADARSAT-1) and a digital elevation model were evaluated for lineament analysis in Boaco, Nicaragua, where the landscape is subject to varied vegetative cover, a plethora of anthropogenic features, and frequent cloud cover that limit the availability of optical satellite data. A variety of digital image processing techniques were employed and lineament interpretations were performed to obtain 12 complementary image products that were evaluated subjectively to identify lineaments. The 12 lineament interpretations were synthesized to create a raster image of lineament zone coincidence that shows the level of agreement among the 12 interpretations. A composite lineament interpretation was made using the coincidence raster to restrict lineament observations to areas where multiple interpretations (at least 4) agree. Nine of the 11 previously mapped faults were identified from the coincidence raster. An additional 26 lineaments were identified from the coincidence raster, and the locations of 10 were confirmed by field observation. Four manual pumping tests suggest that well productivity is higher for wells proximal to lineament features. Interpretations from RADARSAT-1 products were superior to interpretations from other sensor products, suggesting that quality lineament interpretation in this region requires anthropogenic features to be minimized and topographic expressions to be maximized. The approach developed in this study has the potential to improve siting wells in non-ideal regions.

MARVIN: a medical research application framework based on open source software

This paper describes the open source framework MARVIN for rapid application development in the field of biomedical and clinical research. MARVIN applications consist of modules that can be plugged together in order to provide the functionality required for a specific experimental scenario. Application modules work on a common patient database that is used to store and organize medical data as well as derived data. MARVIN provides a flexible input/output system with support for many file formats including DICOM, various 2D image formats and surface mesh data. Furthermore, it implements an advanced visualization system and interfaces to a wide range of 3D tracking hardware. Since it uses only highly portable libraries, MARVIN applications run on Unix/Linux, Mac OS X and Microsoft Windows.

DIMENSION REDUCTION FOR POWER SYSTEM MODELING USING PCA METHODS CONSIDERING INCOMPLETE DATA READINGS

Principal Component Analysis (PCA) is a popular method for dimension reduction that can be used in many fields including data compression, image processing, exploratory data analysis, etc. However, traditional PCA method has several drawbacks, since the traditional PCA method is not efficient for dealing with high dimensional data and cannot be effectively applied to compute accurate enough principal components when handling relatively large portion of missing data. In this report, we propose to use EM-PCA method for dimension reduction of power system measurement with missing data, and provide a comparative study of traditional PCA and EM-PCA methods. Our extensive experimental results show that EM-PCA method is more effective and more accurate for dimension reduction of power system measurement data than traditional PCA method when dealing with large portion of missing data set.