Ground water-surface water interactions sensor technology, Savannah, Georgia, March 7-9, 2005: workshop proceedings

The Alliance for Coastal Technologies (ACT) held a Workshop on Sensor Technology for Assessing Groundwater-Surface Water Interactions in the Coastal Zone on March 7 to 9,2005 in Savannah, GA. The main goal of the workshop was to summarize the general parameters, which have been found to be useful in assessing groundwater-surface water (GW-SW) interactions in the coastal zone. The workshop participants (Appendix I) were specifically charged with identifying the types of sensor systems, if any, that have been used to obtain time-series data and to make known which parameters may be the most amenable to the development/application of sensor technology. The group consisted of researchers, industry representatives, and environmental managers. Four general recommendations were made: 1. Educate coastal managers and agencies on the importance of GW-SW interactions, keeping in mind that regulatory agencies are driven by a different set of rules than researchers: the focus is on understanding the significance of the problem and providing solutions. ACT could facilitate this process in two ways. First, given that the research literature on this subject is fairly diffuse, ACT could provide links from its web site to fact sheets or other literature. Second, ACT could organize a focused meeting for managers and/or agency groups. Encourage development of primary tools for quantifying flow. The most promising technology in this respect is flow meters designed for flux chambers, mainly because they should be simple to use and can be made relatively inexpensively. However, it should be kept in mind that they provide only point measurements and several would need to be deployed as a network in order to obtain reliable flow estimates. For evaluating system wide GW-SW interactions, tools that integrate the signal over large areas would be required. Suggestions include a user-friendly hydrogeologic models, keeping in mind that freshwater flow is not the entire story, or continuous radon monitors. Though the latter would be slightly more difficult to use in terms of background knowledge, such an instrument would be low power and easy to operate and maintain. ACT could facilitate this recommendation by identifying funding opportunities on its web site and/or performing evaluations of existing technologies that could be summarized on the web site. (pdf contains 18 pages)

Biotechnologies for cancer diagnostics : cell sorting, protein analysis and imaging of cellular metabolism

This thesis presents the development of chip-based technology for informative in vitro cancer diagnostics. In the first part of this thesis, I will present my contribution in the development of a technology called “Nucleic Acid Cell Sorting (NACS)”, based on microarrays composed of nucleic acid encoded peptide major histocompatibility complexes (p/MHC), and the experimental and theoretical methods to detect and analyze secreted proteins from single or few cells.

Secondly, a novel portable platform for imaging of cellular metabolism with radio probes is presented. A microfluidic chip, so called “Radiopharmaceutical Imaging Chip” (RIMChip), combined with a beta-particle imaging camera, is developed to visualize the uptake of radio probes in a small number of cells. Due to its sophisticated design, RIMChip allows robust and user-friendly execution of sensitive and quantitative radio assays. The performance of this platform is validated with adherent and suspension cancer cell lines. This platform is then applied to study the metabolic response of cancer cells under the treatment of drugs. Both cases of mouse lymphoma and human glioblastoma cell lines, the metabolic responses to the drug exposures are observed within a short time (~ 1 hour), and are correlated with the arrest of cell-cycle, or with changes in receptor tyrosine kinase signaling.

The last parts of this thesis present summaries of ongoing projects: development of a new agent as an in vivo imaging probe for c-MET, and quantitative monitoring of glycolytic metabolism of primary glioblastoma cells. To develop a new agent for c-MET imaging, the one-bead-one-compound combinatorial library method is used, coupled with iterative screening. The performance of the agent is quantitatively validated with cell-based fluorescent assays. In the case of monitoring the metabolism of primary glioblastoma cell, by RIMChip, cells were sorting according to their expression levels of oncoprotein, or were treated with different kinds of drugs to study the metabolic heterogeneity of cancer cells or metabolic response of glioblastoma cells to drug treatments, respectively.

A new adaptive marine policy toolbox to support ecosystem-based approach to management

4 p.

Modelling algal blooms

This is the final report on the research project to develop predictive models to quantify algal blooms in relation to environmental variables. The project's objectives were to develop models simulating the impact of vertical structure and mass transfer upon the dynamics of planktonic algae, including cyanobacteria, in lakes and reservoirs, to assess the potential of sedimentary phosphorus to sustain algal growth following reduction in external loading and to expand and enhance formulations to predict behaviour of blue-green algal populations and to incorporate these into a model software package. As part of the project a strategy for the production of a user-friendly packaging for the modelling software PROTEC-2 adaptable to particular sites was developed.

A computer software package for assessing and managing risks posed by experiments with genetically modified fish and shellfish

Assessment and management of risk is needed for sustainable use of genetically modified aquatic organisms (aquatic GMOs). A computer software package for safely conducting research with genetically modified fish and shellfish is described. By answering a series of questions about the organism and the accessible aquatic ecosystem, a researcher or oversight authority can either identify specific risks or conclude that there is a specific reason for safety of the experiment. Risk assessment protocols with examples involving transgenic coho salmon, triploid grass carp and hybrid tilapia are described. In case a specific risk is identified, the user is led to consider risk management measures, involving culture methods, facilities design and operations management, to minimize the risk. Key features of the software are its user-friendly organization; easy access to explanatory text, literature citations and glossary; and automated completion of a worksheet. Documented completion of the Performance Standards can facilitate approval of a well designed experiment by oversight authorities.

Invasionsoft: a web-enabled tool for invasive species colonization predictions

Predicting and averting the spread of invasive species is a core focus of resource managers in all ecosystems. Patterns of invasion are difficult to forecast, compounded by a lack of user-friendly species distribution model (SDM) tools to help managers focus control efforts. This paper presents a web-based cellular automata hybrid modeling tool developed to study the invasion pattern of lionfish (Pterois volitans/miles) in the western Atlantic and is a natural extension our previous lionfish study. Our goal is to make publically available this hybrid SDM tool and demonstrate both a test case (P. volitans/miles) and a use case (Caulerpa taxifolia). The software derived from the model, titled Invasionsoft, is unique in its ability to examine multiple default or user-defined parameters, their relation to invasion patterns, and is presented in a rich web browser-based GUI with integrated results viewer. The beta version is not species-specific and includes a default parameter set that is tailored to the marine habitat. Invasionsoft is provided as copyright protected freeware at http://www.invasionsoft.com.

Health and disease status of Thai pangas, Pangasius hypophthalmus cultured in rural ponds of Mymensingh, Bangladesh

Thai pangas, Pangasius hypophthalmus is one of the important aquaculture species in Bangladesh. Over the last few years spectacular development has been taking place in Thai pangas farming in Mymensingh district. Due to availability of easy breeding and culture techniques as well as quick return, more and more people are converting their rice fields into pangas farms overnight. The present study was carried out to examine health and disease status of Thai pangas mainly through clinical, histopathological and bacteriological techniques. In addition, for collecting primary data on disease and health status of Thai pangas and the resultant socioeconomic impacts on rural households, questionnaire interview and participatory rural appraisal tools were used with selected farming households in three upazilas of Mymensingh district. The most prevalent diseases as reported by the farmers were red spot, followed by anal protrusion, tail and fin rot, pop eye, dropsy and gill rot. Other conditions like cotton wool type lesion, ulceration and white spot were reported but with lower incidence. Four isolates of Aeromonas hydrophila were recovered from kidney and lesion of diseased fish. Hemorrhage over the body especially near mouth and caudal region was noticed in the fishes associated with aeromonad infection. Internally, kidney, liver and spleen became swollen and enlarged. The isolates varied with their pathogenicity. All the four isolates were sensitive to Nitrofurantoin, Cotrimoxazole and Tetracycline but were resistant to Amoxycilline. An attempt was made to treat diseased fish with extracts from neem leaf, garlic and turmeric. Recovery of infection was monitored through mortality and histopathology. General histopathological changes of different organs were also studied. Extract from neem (Azadirachta indica) leaf gave better result. Telangiectasis, lamellar hypertrophy and hyperplasia hemorrhage, lamellar fusion, necrosis of lamellar epithelial cells, presence of parasites and their cysts were the major pathology of gills. Hemorrhagic lesion, pyknotic nuclei and melanomacrophage centers (MMC) were found in the liver of fish. Major pathologies in kidney of fish included presence of MMC, necrotic and ruptured kidney tubules, severe haemopoietic necrosis, and hemorrhage. The economic loss due to disease in Thai pangas farming was estimated from the difference between expected production and actual production. On an average, Thai pangas farmers of Mymensingh incur a loss of Tk. 23,104/ha/cycle due to fish disease (3.6% of expected total production). The loss, however, varied with location and size of farms, type of farmers and management practices. The study also highlighted fish health management related problems and recommended further work for the development of user-friendly farmer-oriented fish health management packages.

Understanding and communicating the value of technology: A process perspective

Technological investment is an important driver of innovation and the evaluation of technology potential is becoming increasingly important in this context. Although there is a range of possible approaches and tools for understanding and communicating the value of technology to potential customers, not all are useful or accessible in practice, where the situation is often complex and constantly evolving. Although many companies have their own customised processes in place for securing approval for technology development, often combining several techniques, very few empirical studies have been performed to learn from these practices and provide an overall view of the process of ";selling"; technologies internally or externally. In this paper, the current literature and practice related to technology valuation is reviewed and summarised in a five step process for building a business case for technology investment that gives guidance on where and when to use specific valuation tools. The seller or proposer's perspective is taken and consultative sales techniques incorporated. This provides a flexible reference for R&D managers and adds to the body of literature on the selection and use of valuation tools. A user friendly guide has been published detailing the five step approach. © 2011 IEEE.

SNPNB: analyzing neighboring-nucleotide biases on single nucleotide polymorphisms (SNPs)

SNPNB is a user-friendly and platform-independent application for analyzing Single Nucleotide Polymorphism NeighBoring sequence context and nucleotide bias patterns, and subsequently evaluating the effective SNP size for the bias patterns observed from the whole data. It was implemented by Java and Perl. SNPNB can efficiently handle genome-wide or chromosome-wide SNP data analysis in a PC or a workstation. It provides visualizations of the bias patterns for SNPs or each type of SNPs.

Manopt, a matlab toolbox for optimization on manifolds

Optimization on manifolds is a rapidly developing branch of nonlinear optimization. Its focus is on problems where the smooth geometry of the search space can be leveraged to design effcient numerical algorithms. In particular, optimization on manifolds is well-suited to deal with rank and orthogonality constraints. Such structured constraints appear pervasively in machine learning applications, including low-rank matrix completion, sensor network localization, camera network registration, independent component analysis, metric learning, dimensionality reduction and so on. The Manopt toolbox, available at www.manopt.org, is a user-friendly, documented piece of software dedicated to simplify experimenting with state of the art Riemannian optimization algorithms. By dealing internally with most of the differential geometry, the package aims particularly at lowering the entrance barrier. © 2014 Nicolas Boumal.

Development of multi-channel gated integrator and PXI-DAQ system for nuclear detector arrays

A multi-channel gated integrator and PXI based data acquisition system have been developed for nuclear detector arrays with hundreds of detector units. The multi-channel gated integrator can be controlled by a programmable Cl controller. The PXI-DAQ system consists of NI PXI-1033 chassis with several PXI-DAQ cards. The system software has a user-friendly GUI which is written in C language using LabWindows/CVI under Windows XP operating system. The performance of the PXI-DAQ system is very reliable and capable of handling event rate up to 40 kHz. (C) 2010 Elsevier B.V. All rights reserved.

Soil microbial community analysis using terminal restriction fragment length polymorphisms

Terminal restriction fragment length polymorphism (T-RFLP) analysis is a polymerase chain reaction (PCR)-fingerprinting method that is commonly used for comparative microbial community analysis. The method can be used to analyze communities of bacteria, archaea, fungi, other phylogenetic groups or subgroups, as well as functional genes. The method is rapid, highly reproducible, and often yields a higher number of operational taxonomic units than other, commonly used PCR-fingerprinting methods. Sizing of terminal restriction fragments (T-RFs) can now be done using capillary sequencing technology allowing samples contained in 96- or 384-well plates to be sized in an overnight run. Many multivariate statistical approaches have been used to interpret and compare T-RFLP fingerprints derived from different communities. Detrended correspondence analysis and the additive main effects with multiplicative interaction model are particularly useful for revealing trends in T-RFLP data. Due to biases inherent in the method, linking the size of T-RFs derived from complex communities to existing sequence databases to infer their taxonomic position is not very robust. This approach has been used successfully, however, to identify and follow the dynamics of members within very simple or model communities. The T-RFLP approach has been used successfully to analyze the composition of microbial communities in soil, water, marine, and lacustrine sediments, biofilms, feces, in and on plant tissues, and in the digestive tracts of insects and mammals. The T-RFLP method is a user-friendly molecular approach to microbial community analysis that is adding significant information to studies of microbial populations in many environments.

Surface modelling of soil pH

In addition to classical methods, namely kriging, Inverse Distance Weighting (IDW) and splines, which have been frequently used for interpolating the spatial patterns of soil properties, a relatively more accurate surface modelling technique is being developed in recent years, namely high accuracy surface modelling (HASM). It has been used in the numerical tests, DEM construction and the interpolation of climate and ecosystem changes. In this paper, HASM was applied to interpolate soil pH for assessing its feasibility of soil property interpolation in a red soil region of Jiangxi Province, China. Soil pH was measured on 150 samples of topsoil (0-20 cm) for the interpolation and comparing the performance of HASM, kriging. IDW and splines. The mean errors (MEs) of interpolations indicate little bias of interpolation for soil pH by the four techniques. HASM has less mean absolute error (MAE) and root mean square error (RMSE) than kriging, IDW and splines. HASM is still the most accurate one when we use the mean rank and the standard deviation of the ranks to avoid the outlier effects in assessing the prediction performance of the four methods. Therefore, HASM can be considered as an alternative and accurate method for interpolating soil properties. Further researches of HASM are needed to combine HASM with ancillary variables to improve the interpolation performance and develop a user-friendly algorithm that can be implemented in a GIS package. (C) 2009 Elsevier B.V. All rights reserved.

Determination of total calcium in plasma by flow injection analysis with tris(2,2 '-bipyridyl)ruthenium(II) electrochemiluminescent detection

We described here a new method for the determination of total calcium in plasma. The method is based on the precipitation of calcium with excess oxalate and the measurement of residual oxalate by flow injection analysis with Ru(bpy)(3)(2+) electrochemiluminescent detection. It has the advantages of extremely stable reagent, user-friendly instrument, high selectivity, good analytical recovery, wide dynamic range, and nice correlation with atomic absorption spectroscopy. The calibration plot for calcium is linear over a concentration range from 0.5 mmol L-1 to 4.8 mmol L-1, which is wider than those obtained by most other methods. The analytical recoveries for plasma calcium are 98.4-101.2% with coefficients of variation (CVs) of 1.96-2.52%. The within-day CVs range from 0.76% to 0.95%, and between-day CVs were from 1.12% to 1.46%. The time for each injection is one minute. Because the proposed method can be readily carried out on increasingly popular instruments for Ru(bpy)(3)(2+) ECL immunoassays and DNA probe assays, Ru(bpy)32+ ECL method is suitable for routine clinical analysis of calcium.

Biblioteka Uniwersytecka w Poznaniu w Web 2.0 - rozwój przyjaznej komunikacji cyfrowej i wynikające z niej korzyści

Poster pokazuje metody komunikacji z czytelnikiem stosowane w Bibliotece Uniwersyteckiej w Poznaniu w technologii mediów cyfrowych. Cyfrowe narzędzia komunikacji stały się bardzo pomocne, niemal niezbędne w pozyskiwaniu nowych czytelników, podtrzymywaniu i rozwijaniu współpracy w społeczności w sieci Web.2.0, zarówno tej globalnej, jak i lokalnej akademickiej. Strona WWW jako statyczna komunikacyjnie jest wspierana przez fora dyskusyjne, chaty, wideokonferencje, warsztaty informacyjne, które są prowadzone w czasie rzeczywistym. Twórczą siłę relacji społecznych z biblioteką rozwinęły interaktywne serwisy społecznościowe (Facebook) oraz komunikatory internetowe integrowane na platformie Ask a Librarian. Biblioteka stała się Biblioteką 2.0 ukierunkowaną na komunikację z czytelnikiem. Aktywne uczestnictwo i udział czytelników przy tworzeniu zasobów naukowych wdrożyliśmy w projekcie instytucjonalnego repozytorium - Adam Mickiewicz Repository (AMUR). Biblioteka zmienia się dla czytelników i z czytelnikami. Wykorzystywane platformy i serwisy społecznościowe dostarczają unikatowych danych o nowych potrzebach informacyjnych i oczekiwaniach docelowego Patrona 2.0, co skutkuje doskonaleniu usług istniejących i tworzeniu nowych. Biblioteka monitoruje usługi i potrzeby czytelników przez prowadzone badania społeczne. Technologie cyfrowe stosowane w komunikacji sprawiają, iż biblioteka staje się bliższa, bardziej dostępna, aby stać się w rezultacie partnerem dla stałych i nowych czytelników. Biblioteka Uniwersytecka w Poznaniu bierze udział w programach europejskich w zakresie katalogowania i digitalizacji zasobu biblioteki cyfrowej WBC, w zakresie wdrożenia nowych technologii i rozwiązań podnoszących jakość usług bibliotecznych, działalności kulturotwórczej (Poznańska Dyskusyjna Akademia Kominksu, deBiUty) i edukacji informacyjnej. Biblioteka Uniwersytecka w Poznaniu jest członkiem organizacji międzynarodowych: LIBER (Liga Europejskich Bibliotek Naukowych), IAML (Stowarzyszenie Bibliotek Muzycznych, Archiwów i Ośrodków Dokumentacji), CERL - Europejskie Konsorcjum Bibliotek Naukowych.