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Sample records for small-scale dna sample

  1. STATISTICAL EVALUATION OF SMALL SCALE MIXING DEMONSTRATION SAMPLING AND BATCH TRANSFER PERFORMANCE - 12093

    Energy Technology Data Exchange (ETDEWEB)

    GREER DA; THIEN MG

    2012-01-12

    The ability to effectively mix, sample, certify, and deliver consistent batches of High Level Waste (HLW) feed from the Hanford Double Shell Tanks (DST) to the Waste Treatment and Immobilization Plant (WTP) presents a significant mission risk with potential to impact mission length and the quantity of HLW glass produced. DOE's Tank Operations Contractor, Washington River Protection Solutions (WRPS) has previously presented the results of mixing performance in two different sizes of small scale DSTs to support scale up estimates of full scale DST mixing performance. Currently, sufficient sampling of DSTs is one of the largest programmatic risks that could prevent timely delivery of high level waste to the WTP. WRPS has performed small scale mixing and sampling demonstrations to study the ability to sufficiently sample the tanks. The statistical evaluation of the demonstration results which lead to the conclusion that the two scales of small DST are behaving similarly and that full scale performance is predictable will be presented. This work is essential to reduce the risk of requiring a new dedicated feed sampling facility and will guide future optimization work to ensure the waste feed delivery mission will be accomplished successfully. This paper will focus on the analytical data collected from mixing, sampling, and batch transfer testing from the small scale mixing demonstration tanks and how those data are being interpreted to begin to understand the relationship between samples taken prior to transfer and samples from the subsequent batches transferred. An overview of the types of data collected and examples of typical raw data will be provided. The paper will then discuss the processing and manipulation of the data which is necessary to begin evaluating sampling and batch transfer performance. This discussion will also include the evaluation of the analytical measurement capability with regard to the simulant material used in the demonstration tests. The

  2. Small Scale Mixing Demonstration Batch Transfer and Sampling Performance of Simulated HLW - 12307

    Energy Technology Data Exchange (ETDEWEB)

    Jensen, Jesse; Townson, Paul; Vanatta, Matt [EnergySolutions, Engineering and Technology Group, Richland, WA, 99354 (United States)

    2012-07-01

    The ability to effectively mix, sample, certify, and deliver consistent batches of High Level Waste (HLW) feed from the Hanford Double Shell Tanks (DST) to the Waste treatment Plant (WTP) has been recognized as a significant mission risk with potential to impact mission length and the quantity of HLW glass produced. At the end of 2009 DOE's Tank Operations Contractor, Washington River Protection Solutions (WRPS), awarded a contract to EnergySolutions to design, fabricate and operate a demonstration platform called the Small Scale Mixing Demonstration (SSMD) to establish pre-transfer sampling capacity, and batch transfer performance data at two different scales. This data will be used to examine the baseline capacity for a tank mixed via rotational jet mixers to transfer consistent or bounding batches, and provide scale up information to predict full scale operational performance. This information will then in turn be used to define the baseline capacity of such a system to transfer and sample batches sent to WTP. The Small Scale Mixing Demonstration (SSMD) platform consists of 43'' and 120'' diameter clear acrylic test vessels, each equipped with two scaled jet mixer pump assemblies, and all supporting vessels, controls, services, and simulant make up facilities. All tank internals have been modeled including the air lift circulators (ALCs), the steam heating coil, and the radius between the wall and floor. The test vessels are set up to simulate the transfer of HLW out of a mixed tank, and collect a pre-transfer sample in a manner similar to the proposed baseline configuration. The collected material is submitted to an NQA-1 laboratory for chemical analysis. Previous work has been done to assess tank mixing performance at both scales. This work involved a combination of unique instruments to understand the three dimensional distribution of solids using a combination of Coriolis meter measurements, in situ chord length distribution

  3. Development and small-scale validation of a novel pigeon-associated mitochondrial DNA source tracking marker for the detection of fecal contamination in harvested rainwater.

    Science.gov (United States)

    Waso, M; Khan, S; Khan, W

    2018-02-15

    The current study was aimed at designing and validating (on a small-scale) a novel pigeon mitochondrial DNA (mtDNA) microbial source tracking (MST) marker for the detection of pigeon fecal matter in harvested rainwater. The pigeon mtDNA MST marker was designed to target the mtDNA Cytochrome b gene by employing mismatch amplification mutation assay kinetics. The pigeon marker was validated by screening 69 non-pigeon and 9 pigeon fecal samples. The host-sensitivity of the assay was determined as 1.00 while the host-specificity of the assay was 0.96. Harvested rainwater samples (n=60) were screened for the prevalence of the marker with the mtDNA Cytochrome b marker detected in 78% of the samples. Bayes' theorem was applied to calculate the conditional probability of the marker detecting true pigeon contamination and the marker subsequently displayed a 99% probability of detecting true pigeon contamination in the harvested rainwater samples. In addition, the mtDNA Cytochrome b marker displayed high concurrence frequencies versus heterotrophic bacteria (78.3%), E. coli (73.3%), total coliforms (71.1%) and fecal coliforms (66.7%). This study thus validates that targeting mtDNA for the design of source tracking markers may be a valuable tool to detect avian fecal contamination in environmental waters. Copyright © 2017 Elsevier B.V. All rights reserved.

  4. Antibiotic Resistance in Animal and Environmental Samples Associated with Small-Scale Poultry Farming in Northwestern Ecuador.

    Science.gov (United States)

    Braykov, Nikolay P; Eisenberg, Joseph N S; Grossman, Marissa; Zhang, Lixin; Vasco, Karla; Cevallos, William; Muñoz, Diana; Acevedo, Andrés; Moser, Kara A; Marrs, Carl F; Foxman, Betsy; Trostle, James; Trueba, Gabriel; Levy, Karen

    2016-01-01

    The effects of animal agriculture on the spread of antibiotic resistance (AR) are cross-cutting and thus require a multidisciplinary perspective. Here we use ecological, epidemiological, and ethnographic methods to examine populations of Escherichia coli circulating in the production poultry farming environment versus the domestic environment in rural Ecuador, where small-scale poultry production employing nontherapeutic antibiotics is increasingly common. We sampled 262 "production birds" (commercially raised broiler chickens and laying hens) and 455 "household birds" (raised for domestic use) and household and coop environmental samples from 17 villages between 2010 and 2013. We analyzed data on zones of inhibition from Kirby-Bauer tests, rather than established clinical breakpoints for AR, to distinguish between populations of organisms. We saw significantly higher levels of AR in bacteria from production versus household birds; resistance to either amoxicillin-clavulanate, cephalothin, cefotaxime, and gentamicin was found in 52.8% of production bird isolates and 16% of household ones. A strain jointly resistant to the 4 drugs was exclusive to a subset of isolates from production birds (7.6%) and coop surfaces (6.5%) and was associated with a particular purchase site. The prevalence of AR in production birds declined with bird age (P resistance (AR) in E. coli isolates from small-scale poultry production environments versus domestic environments in rural Ecuador, where such backyard poultry operations have become established over the past decade. Our previous research in the region suggests that introduction of AR bacteria through travel and commerce may be an important source of AR in villages of this region. This report extends the prior analysis by examining small-scale production chicken farming as a potential source of resistant strains. Our results suggest that AR strains associated with poultry production likely originate from sources outside the study

  5. Sampling large landscapes with small-scale stratification-User's Manual

    Science.gov (United States)

    Bart, Jonathan

    2011-01-01

    This manual explains procedures for partitioning a large landscape into plots, assigning the plots to strata, and selecting plots in each stratum to be surveyed. These steps are referred to as the "sampling large landscapes (SLL) process." We assume that users of the manual have a moderate knowledge of ArcGIS and Microsoft ® Excel. The manual is written for a single user but in many cases, some steps will be carried out by a biologist designing the survey and some steps will be carried out by a quantitative assistant. Thus, the manual essentially may be passed back and forth between these users. The SLL process primarily has been used to survey birds, and we refer to birds as subjects of the counts. The process, however, could be used to count any objects. ®

  6. Differential representation of sunflower ESTs in enriched organ-specific cDNA libraries in a small scale sequencing project

    Directory of Open Access Journals (Sweden)

    Heinz Ruth A

    2003-09-01

    Full Text Available Abstract Background Subtractive hybridization methods are valuable tools for identifying differentially regulated genes in a given tissue avoiding redundant sequencing of clones representing the same expressed genes, maximizing detection of low abundant transcripts and thus, affecting the efficiency and cost effectiveness of small scale cDNA sequencing projects aimed to the specific identification of useful genes for breeding purposes. The objective of this work is to evaluate alternative strategies to high-throughput sequencing projects for the identification of novel genes differentially expressed in sunflower as a source of organ-specific genetic markers that can be functionally associated to important traits. Results Differential organ-specific ESTs were generated from leaf, stem, root and flower bud at two developmental stages (R1 and R4. The use of different sources of RNA as tester and driver cDNA for the construction of differential libraries was evaluated as a tool for detection of rare or low abundant transcripts. Organ-specificity ranged from 75 to 100% of non-redundant sequences in the different cDNA libraries. Sequence redundancy varied according to the target and driver cDNA used in each case. The R4 flower cDNA library was the less redundant library with 62% of unique sequences. Out of a total of 919 sequences that were edited and annotated, 318 were non-redundant sequences. Comparison against sequences in public databases showed that 60% of non-redundant sequences showed significant similarity to known sequences. The number of predicted novel genes varied among the different cDNA libraries, ranging from 56% in the R4 flower to 16 % in the R1 flower bud library. Comparison with sunflower ESTs on public databases showed that 197 of non-redundant sequences (60% did not exhibit significant similarity to previously reported sunflower ESTs. This approach helped to successfully isolate a significant number of new reported sequences

  7. DNA Sampling Hook

    Data.gov (United States)

    National Oceanic and Atmospheric Administration, Department of Commerce — The DNA Sampling Hook is a significant improvement on a method of obtaining a tissue sample from a live fish in situ from an aquatic environment. A tissue sample...

  8. Small scale optics

    CERN Document Server

    Yupapin, Preecha

    2013-01-01

    The behavior of light in small scale optics or nano/micro optical devices has shown promising results, which can be used for basic and applied research, especially in nanoelectronics. Small Scale Optics presents the use of optical nonlinear behaviors for spins, antennae, and whispering gallery modes within micro/nano devices and circuits, which can be used in many applications. This book proposes a new design for a small scale optical device-a microring resonator device. Most chapters are based on the proposed device, which uses a configuration know as a PANDA ring resonator. Analytical and nu

  9. Triacylglycerol Analysis in Human Milk and Other Mammalian Species: Small-Scale Sample Preparation, Characterization, and Statistical Classification Using HPLC-ELSD Profiles.

    Science.gov (United States)

    Ten-Doménech, Isabel; Beltrán-Iturat, Eduardo; Herrero-Martínez, José Manuel; Sancho-Llopis, Juan Vicente; Simó-Alfonso, Ernesto Francisco

    2015-06-24

    In this work, a method for the separation of triacylglycerols (TAGs) present in human milk and from other mammalian species by reversed-phase high-performance liquid chromatography using a core-shell particle packed column with UV and evaporative light-scattering detectors is described. Under optimal conditions, a mobile phase containing acetonitrile/n-pentanol at 10 °C gave an excellent resolution among more than 50 TAG peaks. A small-scale method for fat extraction in these milks (particularly of interest for human milk samples) using minimal amounts of sample and reagents was also developed. The proposed extraction protocol and the traditional method were compared, giving similar results, with respect to the total fat and relative TAG contents. Finally, a statistical study based on linear discriminant analysis on the TAG composition of different types of milks (human, cow, sheep, and goat) was carried out to differentiate the samples according to their mammalian origin.

  10. Authentication of forensic DNA samples.

    Science.gov (United States)

    Frumkin, Dan; Wasserstrom, Adam; Davidson, Ariane; Grafit, Arnon

    2010-02-01

    Over the past twenty years, DNA analysis has revolutionized forensic science, and has become a dominant tool in law enforcement. Today, DNA evidence is key to the conviction or exoneration of suspects of various types of crime, from theft to rape and murder. However, the disturbing possibility that DNA evidence can be faked has been overlooked. It turns out that standard molecular biology techniques such as PCR, molecular cloning, and recently developed whole genome amplification (WGA), enable anyone with basic equipment and know-how to produce practically unlimited amounts of in vitro synthesized (artificial) DNA with any desired genetic profile. This artificial DNA can then be applied to surfaces of objects or incorporated into genuine human tissues and planted in crime scenes. Here we show that the current forensic procedure fails to distinguish between such samples of blood, saliva, and touched surfaces with artificial DNA, and corresponding samples with in vivo generated (natural) DNA. Furthermore, genotyping of both artificial and natural samples with Profiler Plus((R)) yielded full profiles with no anomalies. In order to effectively deal with this problem, we developed an authentication assay, which distinguishes between natural and artificial DNA based on methylation analysis of a set of genomic loci: in natural DNA, some loci are methylated and others are unmethylated, while in artificial DNA all loci are unmethylated. The assay was tested on natural and artificial samples of blood, saliva, and touched surfaces, with complete success. Adopting an authentication assay for casework samples as part of the forensic procedure is necessary for maintaining the high credibility of DNA evidence in the judiciary system.

  11. Rolling at small scales

    DEFF Research Database (Denmark)

    Nielsen, Kim L.; Niordson, Christian F.; Hutchinson, John W.

    2016-01-01

    The rolling process is widely used in the metal forming industry and has been so for many years. However, the process has attracted renewed interest as it recently has been adapted to very small scales where conventional plasticity theory cannot accurately predict the material response. It is well....... Metals are known to be stronger when large strain gradients appear over a few microns; hence, the forces involved in the rolling process are expected to increase relatively at these smaller scales. In the present numerical analysis, a steady-state modeling technique that enables convergence without...

  12. Potassium hydroxide-ethylene diamine tetraacetic acid method for the rapid preparation of small-scale PCR template DNA from actinobacteria.

    Science.gov (United States)

    Sun, Zhibin; Huang, Yan; Wang, Yanzhuo; Zhao, Yuguo; Cui, Zhongli

    2014-01-01

    Genomic DNA extraction from Gram-positive bacteria is a laborious and time-consuming process. A rapid and convenient method was established to extract genomic DNA from a single colony as a PCR template. KOH-EDTA is used as a lysis buffer to disrupt the cell envelope, releasing genomic DNA, and Tris-HCl (pH = 4) is then added to neutralize the lysate. The lysate can be used directly as a template for PCR amplification. 16S rDNA was successfully amplified from Gram-positive bacteria from the genera of Bacillus, Streptomyces, Micromonospora, Nonomuraea, Microbispora, and Staphylococcus. Amplification of the trpB gene indicated that this method could also be applied to the amplification of functional genes. Compared to colony PCR methods without KOH-EDTA, this method is extremely fast and efficient, and it is applicable to high-throughput PCR amplifications.

  13. Morocco - Small-Scale Fisheries

    Data.gov (United States)

    Millennium Challenge Corporation — The final performance evaluation roadmap for the Small-Scale Fisheries Project (PPA-MCC) is developed using a grid constructed around indicators relating to Project...

  14. Using Web2.0 social network technology for sampling framework identification and respondent recruitment: experiences with a small-scale experiment

    NARCIS (Netherlands)

    Grigolon, A.B.; Kemperman, A.D.A.M.; Timmermans, H.J.P.

    2011-01-01

    In this paper, we report the results of a small–scale experiment to explore the potential of using social network technology for respondent recruitment. Of particular interest are the following questions (i) can social media be used for the identification of sampling frames, (ii) what response rates

  15. Small-scale classification schemes

    DEFF Research Database (Denmark)

    Hertzum, Morten

    2004-01-01

    Small-scale classification schemes are used extensively in the coordination of cooperative work. This study investigates the creation and use of a classification scheme for handling the system requirements during the redevelopment of a nation-wide information system. This requirements...... classification inherited a lot of its structure from the existing system and rendered requirements that transcended the framework laid out by the existing system almost invisible. As a result, the requirements classification became a defining element of the requirements-engineering process, though its main...... effects remained largely implicit. The requirements classification contributed to constraining the requirements-engineering process by supporting the software engineers in maintaining some level of control over the process. This way, the requirements classification provided the software engineers...

  16. Assessment of Small-scale Buffalo Milk Dairy Production-A Premise for a Durable Development

    Directory of Open Access Journals (Sweden)

    Marian MIHAIU

    2012-05-01

    Full Text Available Buffalo husbandry is an important source of income for a number of small-scale producers in Romania that is why an assessment of its products quality is much needed for improvement and evaluation of their vulnerability to international competition. In order to ascertain possible developments in the buffalo dairy sector and to broadly identify areas of intervention that favor small-scale dairy producers, the study examined the potential to improve buffalo milk production by evaluating its authenticity and hygienic quality. The methods used involved the molecular testing (PCR-technique for identifying cow, sheep or goat DNA in the dairy products samples collected from the small-scale producers market. The hygienic quality of these samples was determined through classical microbiology methods, highly developed techniques (Trek System and PCR for bacterial species confirmation. The results showed that a high percent (65%, from the products found were adulterated with other species milk, mostly cow milk. The most commonly falsified buffalo dairy products were the cheese and the traditional product telemea. The prevalence of the bacterial species identified belonged to Listeria innocua and Listeria welshmeri. The conclusion of this study is the need of a durable development system in this particular dairy chain to improve and assure the authenticity and quality of the small-scale producers products and their reliability for the consumers.

  17. Assessment of Small-scale Buffalo Milk Dairy Production-A Premise for a Durable Development

    Directory of Open Access Journals (Sweden)

    Marian MIHAIU

    2012-05-01

    Full Text Available Buffalo husbandry is an important source of income for a number of small-scale producers in Romania that is why an assessment of its� product�s quality is much needed for improvement and evaluation of their vulnerability to international competition. In order to ascertain possible developments in the buffalo dairy sector and to broadly identify areas of intervention that favor small-scale dairy producers, the study examined the potential to improve buffalo milk production by evaluating its authenticity and hygienic quality. The methods used involved the molecular testing (PCR-technique for identifying cow, sheep or goat DNA in the dairy products� samples collected from the small-scale producers market. The hygienic quality of these samples was determined through classical microbiology methods, highly developed techniques (Trek System and PCR for bacterial species confirmation. The results showed that a high percent (65%, from the products found were adulterated with other species milk, mostly cow milk. The most commonly falsified buffalo dairy products were the cheese and the traditional product �telemea�. The prevalence of the bacterial species identified belonged to Listeria innocua and Listeria welshmeri. The conclusion of this study is the need of a durable development system in this particular dairy chain to improve and assure the authenticity and quality of the small-scale producers� products and their reliability for the consumers.

  18. 28 CFR 28.12 - Collection of DNA samples.

    Science.gov (United States)

    2010-07-01

    ... Homeland Security, collecting DNA samples from: (1) Aliens lawfully in, or being processed for lawful... 28 Judicial Administration 1 2010-07-01 2010-07-01 false Collection of DNA samples. 28.12 Section 28.12 Judicial Administration DEPARTMENT OF JUSTICE DNA IDENTIFICATION SYSTEM DNA Sample Collection...

  19. Risk management strategies utilized by small scale poultry farmers ...

    African Journals Online (AJOL)

    Birds can only tolerate narrow temperature changes; therefore, poultry flocks are vulnerable to climate induced risk. This study investigated risk management strategies utilized by small scale poultry farmers in Oyo state. A total of 118 respondents were sampled using multi stage sampling procedure. Interview schedule was ...

  20. The importance of sound methodology in environmental DNA sampling

    Science.gov (United States)

    T. M. Wilcox; K. J. Carim; M. K. Young; K. S. McKelvey; T. W. Franklin; M. K. Schwartz

    2018-01-01

    Environmental DNA (eDNA) sampling - which enables inferences of species’ presence from genetic material in the environment - is a powerful tool for sampling rare fishes. Numerous studies have demonstrated that eDNA sampling generally provides greater probabilities of detection than traditional techniques (e.g., Thomsen et al. 2012; McKelvey et al. 2016; Valentini et al...

  1. KONTAMINASI MERKURI PADA SAMPEL LINGKUNGAN DAN FAKTOR RISIKO PADA MASYARAKAT DARI KEGIATAN PENAMBANGAN EMAS SKALA KECIL KRUENG SABEE PROVINSI ACEH (Mercury Contamination in the Environmental Samples and Risk Factors in Inhabitants of the Small Scale Gold

    Directory of Open Access Journals (Sweden)

    Sofia Sofia

    2016-09-01

    Full Text Available ABSTRAK Kegiatan penambangan emas skala kecil dengan teknik amalgamasi dapat memberikan peluang introduksi merkuri (Hg ke lingkungan dan manusia. Penelitian kontaminasi Hg pada air minum, ikan, rambut kepala manusia, dan faktor risiko pada manusia telah dilakukan di wilayah Krueng Sabee, Provinsi Aceh. Metode pengambilan dan pengujian sampel yang mengandung Hg dilakukan dengan prosedur SNI, EPA dan WHO. Rancangan cross sectional survey dilakukan pada empat desa dengan 72 responden yang dipilih secara acak. Wawancara dilakukan menggunakan kuesioner terstruktur untuk mendapatkan informasi terkait faktor risiko kesehatan. Pengukuran konsentrasi Hg untuk sampel air dan ikan dilakukan dengan Cold Vapor Atomic Absorption Spectrophotometer dan untuk sampel rambut kepala menggunakan Inductively Coupled Plasma Mass Spectrometry. Analisis data dilakukan dengan analisis varian, uji t sampel bebas, dan uji t satu sampel. Model prediksi dihasilkan menggunakan analisis regresi linier berganda. Hasil penelitian ini menunjukkan konsentrasi Hg pada sampel air sumur sebesar 0,24 ± 0,25 µg/L; sampel ikan: Rastrellinger kanagurta,149,46 ± 2,00 µg/g, Selaroides sp, 58,6 ± 3,01 µg/g, Euthynnus affinis, 46,3 ± 2,98 µg/g; dan pada rambut kepala mulai dari 11,2 ± 4,02 µg/g hingga 48,3 ± 22,29 µg/g. Faktor-faktor risiko yang berpengaruh terhadap konsentrasi Hg pada responden adalah status bekerja di Krueng Sabee, lokasi, lama tinggal, status pekerja tambang dan lama penggunaan pembakar amalgam. Faktor-faktor risiko ini memberi peran sebesar 45,8% terhadap akumulasi Hg di dalam rambut kepala responden.   ABSTRACT Small-scale gold mining activities with amalgamation process can contribute the entry of mercury (Hg into environment and humans. Research on Hg contamination in drinking water, fish, human head hair, and risk factors has been conducted in the area of Krueng Sabee, Aceh Province. Methods of samples collection and Hg concentrations testing conducted

  2. Biomass for energy - small scale technologies

    Energy Technology Data Exchange (ETDEWEB)

    Salvesen, F.; Joergensen, P.F. [KanEnergi, Rud (Norway)

    1997-12-31

    The bioenergy markets and potential in EU region, the different types of biofuels, the energy technology, and the relevant applications of these for small-scale energy production are reviewed in this presentation

  3. Small scale structure on cosmic strings

    International Nuclear Information System (INIS)

    Albrecht, A.

    1989-01-01

    I discuss our current understanding of cosmic string evolution, and focus on the question of small scale structure on strings, where most of the disagreements lie. I present a physical picture designed to put the role of the small scale structure into more intuitive terms. In this picture one can see how the small scale structure can feed back in a major way on the overall scaling solution. I also argue that it is easy for small scale numerical errors to feed back in just such a way. The intuitive discussion presented here may form the basis for an analytic treatment of the small structure, which I argue in any case would be extremely valuable in filling the gaps in our resent understanding of cosmic string evolution. 24 refs., 8 figs

  4. Chemical Transfer (Single Small-Scale) Facility

    Data.gov (United States)

    Federal Laboratory Consortium — Description/History: Chemistry laboratoryThe Chemical Transfer Facility (CTF)  is the only U.S. single small-scale  facility, a single repository for the Army’s...

  5. Biomass for energy - small scale technologies

    Energy Technology Data Exchange (ETDEWEB)

    Salvesen, F; Joergensen, P F [KanEnergi, Rud (Norway)

    1998-12-31

    The bioenergy markets and potential in EU region, the different types of biofuels, the energy technology, and the relevant applications of these for small-scale energy production are reviewed in this presentation

  6. Characteristics of small-scale palm oil production enterprise in ...

    African Journals Online (AJOL)

    The study examined characteristics of small-scale palm oil production enterprise in Anambra State, Nigeria. All the palm oil producers in Anambra State formed the population of the study. Multi-stage sampling technique was used to select 120 respondents for the study. Data were collected from primary source through ...

  7. Economic Analysis of Small Scale Egg Production in Gombe Local ...

    African Journals Online (AJOL)

    This study was conducted to determine the economic profitability of small-scale egg production in Gombe L.G.A. Gombe State. Data were collected from 36 famers using simple random sampling technique. The data collected were analyzed using descriptive statistics, gross margin and farm financial ratio analysis. The study ...

  8. A non-destructive DNA sampling technique for herbarium specimens.

    Science.gov (United States)

    Shepherd, Lara D

    2017-01-01

    Herbarium specimens are an important source of DNA for plant research but current sampling methods require the removal of material for DNA extraction. This is undesirable for irreplaceable specimens such as rare species or type material. Here I present the first non-destructive sampling method for extracting DNA from herbarium specimens. DNA was successfully retrieved from robust leaves and/or stems of herbarium specimens up to 73 years old.

  9. [Quality of DNA from archival pathological samples of gallbladder cancer].

    Science.gov (United States)

    Roa, Iván; de Toro, Gonzalo; Sánchez, Tamara; Slater, Jeannie; Ziegler, Anne Marie; Game, Anakaren; Arellano, Leonardo; Schalper, Kurt; de Aretxabala, Xabier

    2013-12-01

    The quality of the archival samples stored at pathology services could be a limiting factor for molecular biology studies. To determine the quality of DNA extracted from gallbladder cancer samples at different institutions. One hundred ninety four samples coming from five medical centers in Chile, were analyzed. DNA extraction was quantified determining genomic DNA concentration. The integrity of DNA was determined by polymerase chain reaction amplification of different length fragments of a constitutive gene (β-globin products of 110, 268 and 501 base pairs). The mean DNA concentration obtained in 194 gallbladder cancer samples was 48 ± 43.1 ng/µl. In 22% of samples, no amplification was achieved despite obtaining a mean DNA concentration of 58.3 ng/ul. In 81, 67 and 22% of samples, a DNA amplification of at least 110, 268 or 501 base pairs was obtained, respectively. No differences in DNA concentration according to the source of the samples were demonstrated. However, there were marked differences in DNA integrity among participating centers. Samples from public hospitals were of lower quality than those from private clinics. Despite some limitations, in 80% of cases, the integrity of DNA in archival samples from pathology services in our country would allow the use of molecular biology techniques.

  10. Microbial diversity in fecal samples depends on DNA extraction method

    DEFF Research Database (Denmark)

    Mirsepasi, Hengameh; Persson, Søren; Struve, Carsten

    2014-01-01

    was to evaluate two different DNA extraction methods in order to choose the most efficient method for studying intestinal bacterial diversity using Denaturing Gradient Gel Electrophoresis (DGGE). FINDINGS: In this study, a semi-automatic DNA extraction system (easyMag®, BioMérieux, Marcy I'Etoile, France......BACKGROUND: There are challenges, when extracting bacterial DNA from specimens for molecular diagnostics, since fecal samples also contain DNA from human cells and many different substances derived from food, cell residues and medication that can inhibit downstream PCR. The purpose of the study...... by easyMag® from the same fecal samples. Furthermore, DNA extracts obtained using easyMag® seemed to contain inhibitory compounds, since in order to perform a successful PCR-analysis, the sample should be diluted at least 10 times. DGGE performed on PCR from DNA extracted by QIAamp DNA Stool Mini Kit DNA...

  11. The Phenomenology of Small-Scale Turbulence

    Science.gov (United States)

    Sreenivasan, K. R.; Antonia, R. A.

    I have sometimes thought that what makes a man's work classic is often just this multiplicity [of interpretations], which invites and at the same time resists our craving for a clear understanding. Wright (1982, p. 34), on Wittgenstein's philosophy Small-scale turbulence has been an area of especially active research in the recent past, and several useful research directions have been pursued. Here, we selectively review this work. The emphasis is on scaling phenomenology and kinematics of small-scale structure. After providing a brief introduction to the classical notions of universality due to Kolmogorov and others, we survey the existing work on intermittency, refined similarity hypotheses, anomalous scaling exponents, derivative statistics, intermittency models, and the structure and kinematics of small-scale structure - the latter aspect coming largely from the direct numerical simulation of homogeneous turbulence in a periodic box.

  12. Small scale smugglers in Tamaulipas, Mexico

    Directory of Open Access Journals (Sweden)

    Simón Pedro Izcara Palacios

    2013-07-01

    Full Text Available Small-scale part-time smugglers are embedded in the migrant community itself. They work in the United States for several months before returning to their place of origin to organize, with the help of several assistants, a small group of migrants, who are transported where the coyotes themselves are going. This article analyses small-scale smuggling carried out by Tamaulipas' polleros, who transport to the United States, one or a few times per year, migrants from their hometowns or other neighboring areas in order to be employed in the farming sector.

  13. DNA methylation analysis from saliva samples for epidemiological studies.

    Science.gov (United States)

    Nishitani, Shota; Parets, Sasha E; Haas, Brian W; Smith, Alicia K

    2018-06-18

    Saliva is a non-invasive, easily accessible tissue, which is regularly collected in large epidemiological studies to examine genetic questions. Recently, it is becoming more common to use saliva to assess DNA methylation. However, DNA extracted from saliva is a mixture of both bacterial and human DNA derived from epithelial and immune cells in the mouth. Thus, there are unique challenges to using salivary DNA in methylation studies that can influence data quality. This study assesses: (1) quantification of human DNA after extraction; (2) delineation of human and bacterial DNA; (3) bisulfite conversion (BSC); (4) quantification of BSC DNA; (5) PCR amplification of BSC DNA from saliva and; (6) quantitation of DNA methylation with a targeted assay. The framework proposed will allow saliva samples to be more widely used in targeted epigenetic studies.

  14. Microcredit Loan Repayment Default among Small Scale ...

    African Journals Online (AJOL)

    The model is applied to primary data from a survey of 200 small scale entrepreneurs in the Upper West Region of Ghana. Results show that enterprise size, interest rate, loan duration, level of profit and loan amount are the simultaneous determinants of probability and rate of default. The study recommends that the National ...

  15. Small Scale Regenerative Desulfurization of Biogas

    NARCIS (Netherlands)

    Linders, M.J.G.; Stille, L.C.; Miedema, M.C.; Groenestijn, J.W. van; Goetheer, E.L.V.

    2016-01-01

    The application of small scale biogas digesters to supply biogas to households in developing countries is well established. The biogas is used for different applications, amongst other cooking. Generally, no further treatment of the biogas is applied. Hydrogen Sulfide (H2S) is present in varying

  16. [DNA quantification of blood samples pre-treated with pyramidon].

    Science.gov (United States)

    Zhu, Chuan-Hong; Zheng, Dao-Li; Ni, Rao-Zhi; Wang, Hai-Sheng; Ning, Ping; Fang, Hui; Liu, Yan

    2014-06-01

    To study DNA quantification and STR typing of samples pre-treated with pyramidon. The blood samples of ten unrelated individuals were anticoagulated in EDTA. The blood stains were made on the filter paper. The experimental groups were divided into six groups in accordance with the storage time, 30 min, 1 h, 3 h, 6 h, 12 h and 24h after pre-treated with pyramidon. DNA was extracted by three methods: magnetic bead-based extraction, QIAcube DNA purification method and Chelex-100 method. The quantification of DNA was made by fluorescent quantitative PCR. STR typing was detected by PCR-STR fluorescent technology. In the same DNA extraction method, the sample DNA decreased gradually with times after pre-treatment with pyramidon. In the same storage time, the DNA quantification in different extraction methods had significant differences. Sixteen loci DNA typing were detected in 90.56% of samples. Pyramidon pre-treatment could cause DNA degradation, but effective STR typing can be achieved within 24 h. The magnetic bead-based extraction is the best method for STR profiling and DNA extraction.

  17. Degradation mechanisms of small scale piping systems

    International Nuclear Information System (INIS)

    Bartonicek, J.; Koenig, G.; Blind, D.

    1996-01-01

    Operational experience shows that many degradation mechanisms can have an effect on small-scale piping systems. We can see from the analyses carried out that the degradation which has occurred is primarily linked with the fact that these piping systems were classified as being of low safety relevance. This is mainly due to such components being classified into low safety relevance category at the design stage, as well as to the low level of operational monitoring. Since in spite of the variety of designs and operational modes the degradation mechanisms detected may be attributed to the piping systems, we can make decisive statements on how to avoid such degradation mechanisms. Even small-scale piping systems may achieve guaranteed integrity in such cases by taking the appropriate action. (orig.) [de

  18. Small-scale household biogas digesters

    DEFF Research Database (Denmark)

    Bruun, Sander; Jensen, Lars Stoumann; Khanh Vu, Van Thi

    2014-01-01

    There are a number of advantages to small-scale biogas production on farms, including savings on firewood or fossil fuels and reductions in odour and greenhouse gas emissions. For these reasons, governments and development aid agencies have supported the installation of biogas digesters. However......, biogas digesters are often poorly managed and there is a lack of proper distribution systems for biogas. This results in methane being released inadvertently through leaks in digesters and tubing, and intentionally when production exceeds demand. As methane has a global warming potential 25 times greater......% of the produced biogas is released, depending on the type of fuel that has been replaced. The limited information available as regards methane leaking from small-scale biogas digesters in developing countries indicates that emissions may be as high as 40%. With the best estimates of global numbers of small...

  19. Small-scale tearing mode in tokamaks

    International Nuclear Information System (INIS)

    Ivanov, N.V.

    1983-01-01

    Considerations are given on the possible effect of small-scale tearing mode with m >> 1 on the plasma electron thermal conductivity in a tokamak. The estimate of the electron thermal conductivity coefficient is obtained. Calculation results are compared with experimental data. The calculated dependence of radial distribution of electron temperature is shown to vary weakly with the tn(m 2 /m 1 ) alteration everywhere, except for the vicinity of point r approximately 0

  20. Extraction of DNA from Forensic Biological Samples for Genotyping.

    Science.gov (United States)

    Stray, J E; Liu, J Y; Brevnov, M G; Shewale, J G

    2010-07-01

    Biological forensic samples constitute evidence with probative organic matter. Evidence believed to contain DNA is typically processed for extraction and purification of its nucleic acid content. Forensic DNA samples are composed of two things, a tissue and the substrate it resides on. Compositionally, a sample may contain almost anything and for each, the type, integrity, and content of both tissue and substrate will vary, as will the contaminant levels. This fact makes the success of extraction one of the most unpredictable steps in genotypic analysis. The development of robust genotyping systems and analysis platforms for short tandem repeat (STR) and mitochondrial DNA sequencing and the acceptance of results generated by these methods in the court system, resulted in a high demand for DNA testing. The increasing variety of sample submissions created a need to isolate DNA from forensic samples that may be compromised or contain low levels of biological material. In the past decade, several robust chemistries and isolation methods have been developed to safely and reliably recover DNA from a wide array of sample types in high yield and free of PCR inhibitors. In addition, high-throughput automated workflows have been developed to meet the demand for processing increasing numbers of samples. This review summarizes a number of the most widely adopted methods and the best practices for DNA isolation from forensic biological samples, including manual, semiautomated, and fully automated platforms. Copyright © 2010 Central Police University.

  1. Methods to maximise recovery of environmental DNA from water samples.

    Directory of Open Access Journals (Sweden)

    Rheyda Hinlo

    Full Text Available The environmental DNA (eDNA method is a detection technique that is rapidly gaining credibility as a sensitive tool useful in the surveillance and monitoring of invasive and threatened species. Because eDNA analysis often deals with small quantities of short and degraded DNA fragments, methods that maximize eDNA recovery are required to increase detectability. In this study, we performed experiments at different stages of the eDNA analysis to show which combinations of methods give the best recovery rate for eDNA. Using Oriental weatherloach (Misgurnus anguillicaudatus as a study species, we show that various combinations of DNA capture, preservation and extraction methods can significantly affect DNA yield. Filtration using cellulose nitrate filter paper preserved in ethanol or stored in a -20°C freezer and extracted with the Qiagen DNeasy kit outperformed other combinations in terms of cost and efficiency of DNA recovery. Our results support the recommendation to filter water samples within 24hours but if this is not possible, our results suggest that refrigeration may be a better option than freezing for short-term storage (i.e., 3-5 days. This information is useful in designing eDNA detection of low-density invasive or threatened species, where small variations in DNA recovery can signify the difference between detection success or failure.

  2. Non-destructive sampling of ancient insect DNA

    DEFF Research Database (Denmark)

    Thomsen, Philip Francis; Elias, Scott; Gilbert, Tom

    2009-01-01

    BACKGROUND: A major challenge for ancient DNA (aDNA) studies on insect remains is that sampling procedures involve at least partial destruction of the specimens. A recent extraction protocol reveals the possibility of obtaining DNA from past insect remains without causing visual morphological...... of 77-204 base pairs (-bp) in size using species-specific and general insect primers. CONCLUSION/SIGNIFICANCE: The applied non-destructive DNA extraction method shows promising potential on insect museum specimens of historical age as far back as AD 1820, but less so on the ancient permafrost......-preserved insect fossil remains tested, where DNA was obtained from samples up to ca. 26,000 years old. The non-frozen sediment DNA approach appears to have great potential for recording the former presence of insect taxa not normally preserved as macrofossils and opens new frontiers in research on ancient...

  3. DNA Qualification Workflow for Next Generation Sequencing of Histopathological Samples

    Science.gov (United States)

    Simbolo, Michele; Gottardi, Marisa; Corbo, Vincenzo; Fassan, Matteo; Mafficini, Andrea; Malpeli, Giorgio; Lawlor, Rita T.; Scarpa, Aldo

    2013-01-01

    Histopathological samples are a treasure-trove of DNA for clinical research. However, the quality of DNA can vary depending on the source or extraction method applied. Thus a standardized and cost-effective workflow for the qualification of DNA preparations is essential to guarantee interlaboratory reproducible results. The qualification process consists of the quantification of double strand DNA (dsDNA) and the assessment of its suitability for downstream applications, such as high-throughput next-generation sequencing. We tested the two most frequently used instrumentations to define their role in this process: NanoDrop, based on UV spectroscopy, and Qubit 2.0, which uses fluorochromes specifically binding dsDNA. Quantitative PCR (qPCR) was used as the reference technique as it simultaneously assesses DNA concentration and suitability for PCR amplification. We used 17 genomic DNAs from 6 fresh-frozen (FF) tissues, 6 formalin-fixed paraffin-embedded (FFPE) tissues, 3 cell lines, and 2 commercial preparations. Intra- and inter-operator variability was negligible, and intra-methodology variability was minimal, while consistent inter-methodology divergences were observed. In fact, NanoDrop measured DNA concentrations higher than Qubit and its consistency with dsDNA quantification by qPCR was limited to high molecular weight DNA from FF samples and cell lines, where total DNA and dsDNA quantity virtually coincide. In partially degraded DNA from FFPE samples, only Qubit proved highly reproducible and consistent with qPCR measurements. Multiplex PCR amplifying 191 regions of 46 cancer-related genes was designated the downstream application, using 40 ng dsDNA from FFPE samples calculated by Qubit. All but one sample produced amplicon libraries suitable for next-generation sequencing. NanoDrop UV-spectrum verified contamination of the unsuccessful sample. In conclusion, as qPCR has high costs and is labor intensive, an alternative effective standard workflow for

  4. DNA qualification workflow for next generation sequencing of histopathological samples.

    Directory of Open Access Journals (Sweden)

    Michele Simbolo

    Full Text Available Histopathological samples are a treasure-trove of DNA for clinical research. However, the quality of DNA can vary depending on the source or extraction method applied. Thus a standardized and cost-effective workflow for the qualification of DNA preparations is essential to guarantee interlaboratory reproducible results. The qualification process consists of the quantification of double strand DNA (dsDNA and the assessment of its suitability for downstream applications, such as high-throughput next-generation sequencing. We tested the two most frequently used instrumentations to define their role in this process: NanoDrop, based on UV spectroscopy, and Qubit 2.0, which uses fluorochromes specifically binding dsDNA. Quantitative PCR (qPCR was used as the reference technique as it simultaneously assesses DNA concentration and suitability for PCR amplification. We used 17 genomic DNAs from 6 fresh-frozen (FF tissues, 6 formalin-fixed paraffin-embedded (FFPE tissues, 3 cell lines, and 2 commercial preparations. Intra- and inter-operator variability was negligible, and intra-methodology variability was minimal, while consistent inter-methodology divergences were observed. In fact, NanoDrop measured DNA concentrations higher than Qubit and its consistency with dsDNA quantification by qPCR was limited to high molecular weight DNA from FF samples and cell lines, where total DNA and dsDNA quantity virtually coincide. In partially degraded DNA from FFPE samples, only Qubit proved highly reproducible and consistent with qPCR measurements. Multiplex PCR amplifying 191 regions of 46 cancer-related genes was designated the downstream application, using 40 ng dsDNA from FFPE samples calculated by Qubit. All but one sample produced amplicon libraries suitable for next-generation sequencing. NanoDrop UV-spectrum verified contamination of the unsuccessful sample. In conclusion, as qPCR has high costs and is labor intensive, an alternative effective standard

  5. Using long ssDNA polynucleotides to amplify STRs loci in degraded DNA samples

    Science.gov (United States)

    Pérez Santángelo, Agustín; Corti Bielsa, Rodrigo M.; Sala, Andrea; Ginart, Santiago; Corach, Daniel

    2017-01-01

    Obtaining informative short tandem repeat (STR) profiles from degraded DNA samples is a challenging task usually undermined by locus or allele dropouts and peak-high imbalances observed in capillary electrophoresis (CE) electropherograms, especially for those markers with large amplicon sizes. We hereby show that the current STR assays may be greatly improved for the detection of genetic markers in degraded DNA samples by using long single stranded DNA polynucleotides (ssDNA polynucleotides) as surrogates for PCR primers. These long primers allow a closer annealing to the repeat sequences, thereby reducing the length of the template required for the amplification in fragmented DNA samples, while at the same time rendering amplicons of larger sizes suitable for multiplex assays. We also demonstrate that the annealing of long ssDNA polynucleotides does not need to be fully complementary in the 5’ region of the primers, thus allowing for the design of practically any long primer sequence for developing new multiplex assays. Furthermore, genotyping of intact DNA samples could also benefit from utilizing long primers since their close annealing to the target STR sequences may overcome wrong profiling generated by insertions/deletions present between the STR region and the annealing site of the primers. Additionally, long ssDNA polynucleotides might be utilized in multiplex PCR assays for other types of degraded or fragmented DNA, e.g. circulating, cell-free DNA (ccfDNA). PMID:29099837

  6. Current developments in forensic interpretation of mixed DNA samples (Review)

    Science.gov (United States)

    HU, NA; CONG, BIN; LI, SHUJIN; MA, CHUNLING; FU, LIHONG; ZHANG, XIAOJING

    2014-01-01

    A number of recent improvements have provided contemporary forensic investigations with a variety of tools to improve the analysis of mixed DNA samples in criminal investigations, producing notable improvements in the analysis of complex trace samples in cases of sexual assult and homicide. Mixed DNA contains DNA from two or more contributors, compounding DNA analysis by combining DNA from one or more major contributors with small amounts of DNA from potentially numerous minor contributors. These samples are characterized by a high probability of drop-out or drop-in combined with elevated stutter, significantly increasing analysis complexity. At some loci, minor contributor alleles may be completely obscured due to amplification bias or over-amplification, creating the illusion of additional contributors. Thus, estimating the number of contributors and separating contributor genotypes at a given locus is significantly more difficult in mixed DNA samples, requiring the application of specialized protocols that have only recently been widely commercialized and standardized. Over the last decade, the accuracy and repeatability of mixed DNA analyses available to conventional forensic laboratories has greatly advanced in terms of laboratory technology, mathematical models and biostatistical software, generating more accurate, rapid and readily available data for legal proceedings and criminal cases. PMID:24748965

  7. Fast Ordered Sampling of DNA Sequence Variants

    Directory of Open Access Journals (Sweden)

    Anthony J. Greenberg

    2018-05-01

    Full Text Available Explosive growth in the amount of genomic data is matched by increasing power of consumer-grade computers. Even applications that require powerful servers can be quickly tested on desktop or laptop machines if we can generate representative samples from large data sets. I describe a fast and memory-efficient implementation of an on-line sampling method developed for tape drives 30 years ago. Focusing on genotype files, I test the performance of this technique on modern solid-state and spinning hard drives, and show that it performs well compared to a simple sampling scheme. I illustrate its utility by developing a method to quickly estimate genome-wide patterns of linkage disequilibrium (LD decay with distance. I provide open-source software that samples loci from several variant format files, a separate program that performs LD decay estimates, and a C++ library that lets developers incorporate these methods into their own projects.

  8. Fast Ordered Sampling of DNA Sequence Variants.

    Science.gov (United States)

    Greenberg, Anthony J

    2018-05-04

    Explosive growth in the amount of genomic data is matched by increasing power of consumer-grade computers. Even applications that require powerful servers can be quickly tested on desktop or laptop machines if we can generate representative samples from large data sets. I describe a fast and memory-efficient implementation of an on-line sampling method developed for tape drives 30 years ago. Focusing on genotype files, I test the performance of this technique on modern solid-state and spinning hard drives, and show that it performs well compared to a simple sampling scheme. I illustrate its utility by developing a method to quickly estimate genome-wide patterns of linkage disequilibrium (LD) decay with distance. I provide open-source software that samples loci from several variant format files, a separate program that performs LD decay estimates, and a C++ library that lets developers incorporate these methods into their own projects. Copyright © 2018 Greenberg.

  9. A DNA based method to detect the grapevine root-rotting fungus Roesleria subterranea in soil and root samples

    Directory of Open Access Journals (Sweden)

    S. Neuhauser

    2009-05-01

    Full Text Available Roesleria subterranea causes root rot in grapevine and fruit trees. The fungus has long been underestimated as a weak parasite, but during the last years it has been reported to cause severe damages in German vineyards. Direct, observation-based detection of the parasite is time consuming and destructive, as large parts of the rootstocks have to be uprooted and screened for the tiny, stipitate, hypogeous ascomata of R. subterranea. To facilitate rapid detection in vineyards, protocols to extract DNA from soil samples and grapevine roots, and R.-subterranea-specific PCR primers were designed. Twelve DNA-extraction protocols for soil samples were tested in small-scale experiments, and selected parameters were optimised. A protocol based on ball-mill homogenization, DNA extraction with SDS, skim milk, chloroform, and isopropanol, and subsequent purifi cation of the raw extracts with PVPP-spin-columns was most effective. This DNA extraction protocol was found to be suitable for a wide range of soil-types including clay, loam and humic-rich soils. For DNA extraction from grapevine roots a CTAB-based protocol was more reliable for various grapevine rootstock varieties. Roesleria-subterranea-specific primers for the ITS1-5.8S-ITS2 rDNA region were developed and tested for their specifi city to DNA extracts from eleven R. subterranea strains isolated from grapevine and fruit trees. No cross reactions were detected with DNA extracts from 44 different species of fungi isolated from vineyard soils. The sensitivity of the species-specifi c primers in combination with the DNA extraction method for soil was high: as little as 100 fg μl-1 R.-subterranea-DNA was suffi cient for a detection in soil samples and plant material. Given that specifi c primers are available, the presented method will also allow quick and large-scale testing for other root pathogens.

  10. Small-scale rural bakery; Maaseudun pienleipomo

    Energy Technology Data Exchange (ETDEWEB)

    Alkula, R.; Malin, A.; Reisbacka, A.; Rytkoenen, A.

    1997-12-31

    The purpose of the study was to clarify how running a small-scale bakery can provide a farming enterprise with its primary or secondary source of livelihood. A questionnaire and interviews were conducted to clarify the current situation concerning small-scale rural bakeries. The experimental part of the study looked into different manners of production, devices used in preparing and processing of doughs, and baking of different kinds of pastries in different types of ovens in laboratory conditions. Based on the results obtained, solutions serving as examples were formulated for small-scale bakeries run with various modes and methods of production. Additionally, market reviews were conducted concerning appropriate equipment for small-scale bakeries. Baking for commercial purposes on the farm is still something new as ca. 80 % of the enterprises covered by the study had operated for no more than five years. Many entrepreneurs (ca. 70 %) expressed a need for supplementary knowledge from some field related to baking. Rural bakeries are small-scale operations with one-person enterprises amounting to 69 % and two-person enterprises to 29 %. Women are primarily responsible for baking. On average, the enterprises baked seven different products, but the amounts baked were usually small. In the experimental part of the study, loaves of rye bread were baked using five different types and sizes of oven accommodating 5-22 loaves of rye bread at the one time. The oven type was found not to affect bread structure. The energy consumption for one ovenful varied between 2.4 and 7.0 kWh, i.e. 0.25-0.43 kWh per kilo. When baking rolls (30-140 rolls at a time), the power consumption varied between 1.2 and 3.5 kWh, i.e. 0.32-0.53 kWh per kilo. The other devices included in the comparative study were an upright deep-freezer, a multi-temperature cabinet and a fermenting cabinet. Furthermore, making rolls by hand was compared to using a machine for the same job, and likewise manual

  11. Philippines: Small-scale renewable energy update

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1997-12-01

    This paper gives an overview of the application of small scale renewable energy sources in the Philippines. Sources looked at include solar, biomass, micro-hydroelectric, mini-hydroelectric, wind, mini-geothermal, and hybrid. A small power utilities group is being spun off the major utility, to provide a structure for developing rural electrification programs. In some instances, private companies have stepped forward, avoiding what is perceived as overwhelming beaurocracy, and installed systems with private financing. The paper provides information on survey work which has been done on resources, and the status of cooperative programs to develop renewable systems in the nation.

  12. Getting DNA copy numbers without control samples

    Directory of Open Access Journals (Sweden)

    Ortiz-Estevez Maria

    2012-08-01

    Full Text Available Abstract Background The selection of the reference to scale the data in a copy number analysis has paramount importance to achieve accurate estimates. Usually this reference is generated using control samples included in the study. However, these control samples are not always available and in these cases, an artificial reference must be created. A proper generation of this signal is crucial in terms of both noise and bias. We propose NSA (Normality Search Algorithm, a scaling method that works with and without control samples. It is based on the assumption that genomic regions enriched in SNPs with identical copy numbers in both alleles are likely to be normal. These normal regions are predicted for each sample individually and used to calculate the final reference signal. NSA can be applied to any CN data regardless the microarray technology and preprocessing method. It also finds an optimal weighting of the samples minimizing possible batch effects. Results Five human datasets (a subset of HapMap samples, Glioblastoma Multiforme (GBM, Ovarian, Prostate and Lung Cancer experiments have been analyzed. It is shown that using only tumoral samples, NSA is able to remove the bias in the copy number estimation, to reduce the noise and therefore, to increase the ability to detect copy number aberrations (CNAs. These improvements allow NSA to also detect recurrent aberrations more accurately than other state of the art methods. Conclusions NSA provides a robust and accurate reference for scaling probe signals data to CN values without the need of control samples. It minimizes the problems of bias, noise and batch effects in the estimation of CNs. Therefore, NSA scaling approach helps to better detect recurrent CNAs than current methods. The automatic selection of references makes it useful to perform bulk analysis of many GEO or ArrayExpress experiments without the need of developing a parser to find the normal samples or possible batches within the

  13. Getting DNA copy numbers without control samples.

    Science.gov (United States)

    Ortiz-Estevez, Maria; Aramburu, Ander; Rubio, Angel

    2012-08-16

    The selection of the reference to scale the data in a copy number analysis has paramount importance to achieve accurate estimates. Usually this reference is generated using control samples included in the study. However, these control samples are not always available and in these cases, an artificial reference must be created. A proper generation of this signal is crucial in terms of both noise and bias.We propose NSA (Normality Search Algorithm), a scaling method that works with and without control samples. It is based on the assumption that genomic regions enriched in SNPs with identical copy numbers in both alleles are likely to be normal. These normal regions are predicted for each sample individually and used to calculate the final reference signal. NSA can be applied to any CN data regardless the microarray technology and preprocessing method. It also finds an optimal weighting of the samples minimizing possible batch effects. Five human datasets (a subset of HapMap samples, Glioblastoma Multiforme (GBM), Ovarian, Prostate and Lung Cancer experiments) have been analyzed. It is shown that using only tumoral samples, NSA is able to remove the bias in the copy number estimation, to reduce the noise and therefore, to increase the ability to detect copy number aberrations (CNAs). These improvements allow NSA to also detect recurrent aberrations more accurately than other state of the art methods. NSA provides a robust and accurate reference for scaling probe signals data to CN values without the need of control samples. It minimizes the problems of bias, noise and batch effects in the estimation of CNs. Therefore, NSA scaling approach helps to better detect recurrent CNAs than current methods. The automatic selection of references makes it useful to perform bulk analysis of many GEO or ArrayExpress experiments without the need of developing a parser to find the normal samples or possible batches within the data. The method is available in the open-source R package

  14. Adopting small-scale production of electricity

    Energy Technology Data Exchange (ETDEWEB)

    Tengvard, Maria; Palm, Jenny (Linkoeping Univ., Dept. of Technology and Social Change, Linkoeping (Sweden)). e-mail: maria.tengvard@liu.se

    2009-07-01

    In Sweden in 2008, a 'new' concept for small-scale electricity production attracted massive media attention. This was mainly due to the efforts of Swedish company Egen El, which is marketing small-scale photovoltaics (PVs) and wind turbines to households, both homeowners and tenants. Their main selling point is simplicity: their products are so easy to install that everyone can do it. Autumn 2008 also saw IKEA announce that within three years it would market solar panels. How, then, do households perceive these products? Why would households choose to buy them? How do households think about producing their own electricity? Analysis of material based on in-depth interviews with members of 20 households reveals that environmental concerns supply the main motive for adopting PVs or micro wind power generation. In some cases, the adopting households have an extensively ecological lifestyle and such adoption represents a way to take action in the energy area. For some, this investment is symbolic: a way of displaying environmental consciousness or setting an example to others. For still others, the adoption is a protest against 'the system' with its large dominant actors or is a way to become self-sufficient. These microgeneration installations are rejected mainly on economic grounds; other motives are respect for neighbours and difficulties finding a place to install a wind turbine.

  15. Small-scale topography modulates elevational α-, β- and γ-diversity of Andean leaf beetles.

    Science.gov (United States)

    Thormann, Birthe; Ahrens, Dirk; Espinosa, Carlos Iván; Armijos, Diego Marín; Wagner, Thomas; Wägele, Johann W; Peters, Marcell K

    2018-03-09

    Elevational diversity gradients are typically studied without considering the complex small-scale topography of large mountains, which generates habitats of strongly different environmental conditions within the same elevational zones. Here we analyzed the importance of small-scale topography for elevational diversity patterns of hyperdiverse tropical leaf beetles (Coleoptera: Chrysomelidae). We compared patterns of elevational diversity and species composition of beetles in two types of forests (on mountain ridges and in valleys) and analyzed whether differences in the rate of species turnover among forest habitats lead to shifts in patterns of elevational diversity when scaling up from the local study site to the elevational belt level. We sampled beetle assemblages at 36 sites in the Podocarpus National Park, Ecuador, which were equally distributed over two forest habitats and three elevational levels. DNA barcoding and Poisson tree processes modelling were used to delimitate putative species. On average, local leaf beetle diversity showed a clear hump-shaped pattern. However, only diversity in forests on mountain ridges peaked at mid-elevation, while beetle diversity in valleys was similarly high at low- and mid-elevation and only declined at highest elevations. A higher turnover of species assemblages at lower than at mid-elevations caused a shift from a hump-shaped diversity pattern found at the local level to a low-elevation plateau pattern (with similar species numbers at low and mid-elevation) at the elevational belt level. Our study reveals an important role of small-scale topography and spatial scale for the inference on gradients of elevational species diversity.

  16. Mercury use in small scale gold mining in Ghana: an assessment of its impact on miners

    International Nuclear Information System (INIS)

    Biagya, Robert Yakubu

    2002-12-01

    Small scale gold mining is responsible for about 5% of Ghana’s annual gold production. It is estimated that between 80,000 and 100,000 people are engaged in small scale gold mining either on part-time or permanent basis. Amalgamation is the preferred method used by small scale gold miners for extracting free gold from its ores. The rate at which mercury, an important input in this method, is discharged into the atmosphere and water bodies is alarming. This research describes the various mining and processing methods in small scale gold mining and the extent of mercury use and releases to the environment. It discusses mercury and its human and environmental effects. It defines the various forms of mercury, routes of exposure, toxic effects. The levels of exposure to mercury by all groups of small scale gold miners are determined, and the impacts on the miners and the environment are assessed. It concludes that: • Mercury is mainly released into the environment as a result of small scale gold mining through spillage of elemental mercury and evaporation of mercury from the amalgam and sponge gold when they are heated on open fire. • Mercury in environmental samples from small scale gold mining areas is well above standard limit values. • Mercury released into the environment through small scale gold mining impacts negatively on the miners themselves and the general environment. Finally, it recommends the need for the adoption of mercury emission reduction strategies for dealing with the mercury problem. (au)

  17. Small scale structure formation in chameleon cosmology

    International Nuclear Information System (INIS)

    Brax, Ph.; Bruck, C. van de; Davis, A.C.; Green, A.M.

    2006-01-01

    Chameleon fields are scalar fields whose mass depends on the ambient matter density. We investigate the effects of these fields on the growth of density perturbations on sub-galactic scales and the formation of the first dark matter halos. Density perturbations on comoving scales R<1 pc go non-linear and collapse to form structure much earlier than in standard ΛCDM cosmology. The resulting mini-halos are hence more dense and resilient to disruption. We therefore expect (provided that the density perturbations on these scales have not been erased by damping processes) that the dark matter distribution on small scales would be more clumpy in chameleon cosmology than in the ΛCDM model

  18. Appendix - A small scale research review

    DEFF Research Database (Denmark)

    Larsen, Lea Lund

    over two questions asked in the abstract concerning workshop C - Effects of teacher training in lifelong learning - at the current ASEM conference. At first it is asked what do we already know about teacher training effects in relation to adult learners? This will be identified by a search...... for systematic reviews in the international This will be identified by a search for systematic reviews in the international clearinghouses and afterwards by a small scale mapping done in the pedagogic databaseERIC. The second question sounds: which methods can be used to measure the effects of teacher...... training? This will be illustrated by describing a research design in progress at the National Centre of Competence Development, DK, regarding a program where teachers are taught Cooperative Learning as a pedagogical and didactical method. This appendix concerns the first question. In search for empiric results concerning: What do...

  19. New markets for small-scale hydro

    International Nuclear Information System (INIS)

    Maurer, E.A.

    1997-01-01

    The market for small and medium sized hydro-electric power plant is more attractive than ever. The boom in Europe has increasingly spread to the emerging countries, and here too small hydro plays an important ecological role. In addition to new plant rehabilitation of 'historical' plant is now a major factor. The last few years have seen a market shift from single machine components to complete plant and systems, requiring a strategy re-think on the part of larger companies. Following the influx of private capital into the power industry, business conditions have also undergone a thorough transformation. In place of 'fast money', hydro power offers the prospect of earning longer-term, sustainable money'. The term small-scale hydro-electric power (or simply 'small hydro') is used slightly differently depending on the country and market. Here, it is used to denote plant with turbines up to 10 MW. (Author)

  20. Small scale soft x-ray lasers

    International Nuclear Information System (INIS)

    Skinner, C.H.; DiCicco, D.S.; Kim, D.; Voorhees, D.; Suckewer, S.

    1990-01-01

    The widespread application of soft x-ray laser technology is contingent on the development of small scale soft x-ray lasers that do not require large laser facilities. Progress in the development of soft x-ray lasers pumped by a Nd laser of energy 6-12J is reported below. Application of an existing soft x-ray laser to x-ray microscopy has begun. A soft x-ray laser of output energy 1-3 mJ at 18,2 nm has been used to record high resolution images of biological specimens. The contact images were recorded on photoresist which was later viewed in a scanning electron microscope. The authors present a composite optical x-ray laser microscope design

  1. Cold dark matter: Controversies on small scales.

    Science.gov (United States)

    Weinberg, David H; Bullock, James S; Governato, Fabio; Kuzio de Naray, Rachel; Peter, Annika H G

    2015-10-06

    The cold dark matter (CDM) cosmological model has been remarkably successful in explaining cosmic structure over an enormous span of redshift, but it has faced persistent challenges from observations that probe the innermost regions of dark matter halos and the properties of the Milky Way's dwarf galaxy satellites. We review the current observational and theoretical status of these "small-scale controversies." Cosmological simulations that incorporate only gravity and collisionless CDM predict halos with abundant substructure and central densities that are too high to match constraints from galaxy dynamics. The solution could lie in baryonic physics: Recent numerical simulations and analytical models suggest that gravitational potential fluctuations tied to efficient supernova feedback can flatten the central cusps of halos in massive galaxies, and a combination of feedback and low star formation efficiency could explain why most of the dark matter subhalos orbiting the Milky Way do not host visible galaxies. However, it is not clear that this solution can work in the lowest mass galaxies, where discrepancies are observed. Alternatively, the small-scale conflicts could be evidence of more complex physics in the dark sector itself. For example, elastic scattering from strong dark matter self-interactions can alter predicted halo mass profiles, leading to good agreement with observations across a wide range of galaxy mass. Gravitational lensing and dynamical perturbations of tidal streams in the stellar halo provide evidence for an abundant population of low-mass subhalos in accord with CDM predictions. These observational approaches will get more powerful over the next few years.

  2. Small Scale Hydrocarbon Fire Test Concept

    Directory of Open Access Journals (Sweden)

    Joachim Søreng Bjørge

    2017-11-01

    Full Text Available In the oil and gas industry, hydrocarbon process equipment was previously often thermally insulated by applying insulation directly to the metal surface. Fire protective insulation was applied outside the thermal insulation. In some cases, severe corrosion attacks were observed due to ingress of humidity and condensation at cold surfaces. Introducing a 25 mm air gap to prevent wet thermal insulation and metal wall contact is expected to solve the corrosion issues. This improved insulation methodology does, however, require more space that may not be available when refurbishing older process plants. Relocating structural elements would introduce much hot work, which should be minimized in live plants. It is also costly. The aim of the present study is therefore to develop a test concept for testing fire resistance of equipment protected with only air-gap and thermal insulation, i.e., without the fire-protective insulation. The present work demonstrates a conceptual methodology for small scale fire testing of mockups resembling a section of a distillation column. The mockups were exposed to a small-scale propane flame in a test configuration where the flow rate and the flame zone were optimized to give heat flux levels in the range 250–350 kW/m2. Results are presented for a mockup resembling a 16 mm thick distillation column steel wall. It is demonstrated that the modern distance insulation in combination with the heat capacity of the column wall indicates 30+ minutes fire resistance. The results show that this methodology has great potentials for low cost fire testing of other configurations, and it may serve as a set-up for product development.

  3. Comparative evaluation of serum, FTA filter-dried blood and oral fluid as sample material for PRRSV diagnostics by RT-qPCR in a small-scale experimental study.

    Science.gov (United States)

    Steinrigl, Adolf; Revilla-Fernández, Sandra; Wodak, Eveline; Schmoll, Friedrich; Sattler, Tatjana

    2014-01-01

    Recently, research into alternative sample materials, such as oral fluid or filter-dried blood has been intensified, in order to facilitate cost-effective and animal-friendly sampling of individuals or groups of pigs for diagnostic purposes. The objective of this study was to compare the sensitivity of porcine reproductive and respiratory syndrome virus (PRRSV)-RNA detection by reverse transcription quantitative real-time PCR (RT-qPCR) in serum, FTA filter-dried blood and oral fluid sampled from individual pigs. Ten PRRSV negative pigs were injected with an EU-type PRRSV live vaccine. Blood and oral fluid samples were taken from each pig before, and 4, 7, 14 and 21 days after vaccination. All samples were then analyzed by PRRSV RT-qPCR. In serum, eight often pigs tested RT-qPCR positive at different time points post infection. Absolute quantification showed low serum PRRSV-RNA loads in most samples. In comparison to serum, sensitivity of PRRSV-RNA detection was strongly reduced in matched FTA filter-dried blood and in oral fluid from the same pigs. These results indicate that with low PRRSV-RNA loads the diagnostic sensitivity of PRRSV-RNA detection by RT-qPCR achieved with serum is currently unmatched by either FTA filter-dried blood or oral fluid.

  4. Controls to validate plasma samples for cell free DNA quantification

    DEFF Research Database (Denmark)

    Pallisgaard, Niels; Spindler, Karen-Lise Garm; Andersen, Rikke Fredslund

    2015-01-01

    , are diverging due to methodological differences with lack of standardisation and definition of sensitivity. The new biological information has not yet come into routine use. The present study presents external standardisation by spiking with non-human DNA fragments to control for loss of DNA during sample...... preparation and measurement. It also suggests a method to control for admixture of DNA from normal lymphocytes by utilizing the unique immunoglobulin gene rearrangement in the B-cells. The results show that this approach improves the quality of the analysis and lowers the risk of falsely increased values...

  5. Rapid DNA analysis for automated processing and interpretation of low DNA content samples.

    Science.gov (United States)

    Turingan, Rosemary S; Vasantgadkar, Sameer; Palombo, Luke; Hogan, Catherine; Jiang, Hua; Tan, Eugene; Selden, Richard F

    2016-01-01

    Short tandem repeat (STR) analysis of casework samples with low DNA content include those resulting from the transfer of epithelial cells from the skin to an object (e.g., cells on a water bottle, or brim of a cap), blood spatter stains, and small bone and tissue fragments. Low DNA content (LDC) samples are important in a wide range of settings, including disaster response teams to assist in victim identification and family reunification, military operations to identify friend or foe, criminal forensics to identify suspects and exonerate the innocent, and medical examiner and coroner offices to identify missing persons. Processing LDC samples requires experienced laboratory personnel, isolated workstations, and sophisticated equipment, requires transport time, and involves complex procedures. We present a rapid DNA analysis system designed specifically to generate STR profiles from LDC samples in field-forward settings by non-technical operators. By performing STR in the field, close to the site of collection, rapid DNA analysis has the potential to increase throughput and to provide actionable information in real time. A Low DNA Content BioChipSet (LDC BCS) was developed and manufactured by injection molding. It was designed to function in the fully integrated Accelerated Nuclear DNA Equipment (ANDE) instrument previously designed for analysis of buccal swab and other high DNA content samples (Investigative Genet. 4(1):1-15, 2013). The LDC BCS performs efficient DNA purification followed by microfluidic ultrafiltration of the purified DNA, maximizing the quantity of DNA available for subsequent amplification and electrophoretic separation and detection of amplified fragments. The system demonstrates accuracy, precision, resolution, signal strength, and peak height ratios appropriate for casework analysis. The LDC rapid DNA analysis system is effective for the generation of STR profiles from a wide range of sample types. The technology broadens the range of sample

  6. DNA cards: determinants of DNA yield and quality in collecting genetic samples for pharmacogenetic studies.

    Science.gov (United States)

    Mas, Sergi; Crescenti, Anna; Gassó, Patricia; Vidal-Taboada, Jose M; Lafuente, Amalia

    2007-08-01

    As pharmacogenetic studies frequently require establishment of DNA banks containing large cohorts with multi-centric designs, inexpensive methods for collecting and storing high-quality DNA are needed. The aims of this study were two-fold: to compare the amount and quality of DNA obtained from two different DNA cards (IsoCode Cards or FTA Classic Cards, Whatman plc, Brentford, Middlesex, UK); and to evaluate the effects of time and storage temperature, as well as the influence of anticoagulant ethylenediaminetetraacetic acid on the DNA elution procedure. The samples were genotyped by several methods typically used in pharmacogenetic studies: multiplex PCR, PCR-restriction fragment length polymorphism, single nucleotide primer extension, and allelic discrimination assay. In addition, they were amplified by whole genome amplification to increase genomic DNA mass. Time, storage temperature and ethylenediaminetetraacetic acid had no significant effects on either DNA card. This study reveals the importance of drying blood spots prior to isolation to avoid haemoglobin interference. Moreover, our results demonstrate that re-isolation protocols could be applied to increase the amount of DNA recovered. The samples analysed were accurately genotyped with all the methods examined herein. In conclusion, our study shows that both DNA cards, IsoCode Cards and FTA Classic Cards, facilitate genetic and pharmacogenetic testing for routine clinical practice.

  7. A 'feather-trap' for collecting DNA samples from birds.

    Science.gov (United States)

    Maurer, Golo; Beck, Nadeena; Double, Michael C

    2010-01-01

    Genetic analyses of birds are usually based on DNA extracted from a blood sample. For some species, however, obtaining blood samples is difficult because they are sensitive to handling, pose a conservation or animal welfare concern, or evade capture. In such cases, feathers obtained from live birds in the wild can provide an alternative source of DNA. Here, we provide the first description and evaluation of a 'feather-trap', consisting of small strips of double-sided adhesive tape placed close to a nest with chicks, as a simple, inexpensive and minimally invasive method to collect feathers. The feather-trap was tested in tropical conditions on the Australian pheasant coucal (Centropus phasianinus). None of the 12 pairs of coucals on which the feather-trap was used abandoned the nest, and feeding rates did not differ from those of birds not exposed to a feather-trap. On average, 4.2 feathers were collected per trap over 2-5 days and, despite exposure to monsoonal rain, DNA was extracted from 71.4% of samples, albeit at low concentrations. The amount of genomic DNA extracted from each feather was sufficient to reliably genotype individuals at up to five microsatellite loci for parentage analysis. We show that a feather-trap can provide a reliable alternative for obtaining DNA in species where taking blood is difficult. It may also prove useful for collecting feather samples for other purposes, e.g. stable-isotope analysis. © 2009 Blackwell Publishing Ltd.

  8. Small scale combined woodgas power plant

    International Nuclear Information System (INIS)

    Gulbis, V.

    2003-01-01

    As a first attempt to introduce biomass gasification technology in Latvia at the Faculty of Engineering of Latvia University of Agriculture an integral small scale combined heat and power (CHP) system based on a used Russian-made diesel-alternator set with electrical output 100 kWe was developed. The diesel is converted to dual fuel gas engine, using producer gas as the main fuel and gas oil as pilot fuel. To get sufficiently clean (tar content ≤ 250 mg/m 3 ) woodgas for using in IC engine a downdraft type of gasifier was chosen designed and constructed on the IMBERT gasifier principles. The test runs of the first experimental model showed that the engine does not develop expected power because of high resistance of gasifier and gas cleaning system does not work sufficiently enough. There was rather high level of tar content in woodgas because the temperature in the reduction zone was low. Calculations were carried out and new technological scheme of gasification system was worked out, introducing innovative ideas aimed on improving the working parameters (author)

  9. Small Scale Foundries in Ghana: The challenges

    Directory of Open Access Journals (Sweden)

    Anthony ANDREWS

    2012-08-01

    Full Text Available Small Scale Foundries (SSFs have been in existence for several years in Ghana. The industry has created several jobs for the people of Ghana and has minimized the burden on government to find ways of disposing scrap metals generated within the country. While scrap metals are still being exported, the quantity exported has decreased as a result of recycling by foundrymen in producing various parts. The government of Ghana has not paid special attention to this industry. Nevertheless, individuals and private investors are heavily involved in producing several thousands of tonnes of castings annually generating revenue for the government through taxation as well as helping with metal waste disposal. Metal cast products are sold both locally and internationally to neighbouring countries. The industry is however faced with numerous challenges. These include quality issues due to lack of technical know-how, access to funding from both government and private financial institutions and foundry waste management. To promote this industry, government and private financial institutions must be encouraged to come on board. Policies must be established and proper training programme developed to improve and promote this technology. This could go a long way in reducing the high unemployment rate in Ghana.

  10. Small-scale irradiated fuel electrorefining

    International Nuclear Information System (INIS)

    Benedict, R.W.; Krsul, J.R.; Mariani, R.D.; Park, K.; Teske, G.M.

    1993-01-01

    In support of the metallic fuel cycle development for the Integral Fast Reactor (IFR), a small scale electrorefiner was built and operated in the Hot Fuel Examination Facility (HFEF) at Argonne National Laboratory-West. The initial purpose of this apparatus was to test the single segment dissolution of irradiated metallic fuel via either direct dissolution in cadmium or anodic dissolution. These tests showed that 99.95% of the uranium and 99.99% of the plutonium was dissolved and separated from the fuel cladding material. The fate of various fission products was also measured. After the dissolution experiments, the apparatus was upgraded to stady fission product behavior during uranium electrotransport. Preliminary decontamination factors were estimated for different fission products under different processing conditions. Later modifications have added the following capabilities: Dissolution of multiple fuel segments simultaneously, electrotransport to a solid cathode or liquid cathode and actinide recovery with a chemical reduction crucible. These capabilities have been tested with unirradiated uranium-zirconium fuel and will support the Fuel Cycle Demonstration program

  11. Hoopa Valley Small Scale Hydroelectric Feasibility Project

    Energy Technology Data Exchange (ETDEWEB)

    Curtis Miller

    2009-03-22

    This study considered assessing the feasibility of developing small scale hydro-electric power from seven major tributaries within the Hoopa Valley Indian Reservation of Northern California (http://www.hoopa-nsn.gov/). This study pursued the assessment of seven major tributaries of the Reservation that flow into the Trinity River. The feasibility of hydropower on the Hoopa Valley Indian Reservation has real potential for development and many alternative options for project locations, designs, operations and financing. In order to realize this opportunity further will require at least 2-3 years of intense data collection focusing on stream flow measurements at multiple locations in order to quantify real power potential. This also includes on the ground stream gradient surveys, road access planning and grid connectivity to PG&E for sale of electricity. Imperative to this effort is the need for negotiations between the Hoopa Tribal Council and PG&E to take place in order to finalize the power rate the Tribe will receive through any wholesale agreement that utilizes the alternative energy generated on the Reservation.

  12. Small-scale tunnel test for blast performance

    International Nuclear Information System (INIS)

    Felts, J E; Lee, R J

    2014-01-01

    The data reported here provide a validation of a small-scale tunnel test as a tool to guide the optimization of new explosives for blast performance in tunnels. The small-scale arrangement consisted of a 2-g booster and 10-g sample mounted at the closed end of a 127 mm diameter by 4.6-m long steel tube with pressure transducers along its length. The three performance characteristics considered were peak pressure, initial energy release, and impulse. The relative performance from five explosives was compared to that from a 1.16-m diameter by 30-m long tunnel that used 2.27-kg samples. The peak pressure values didn't correlate between the tunnels. Partial impulse for the explosives did rank similarly. The initial energy release was determined from a one-dimensional point-source analysis, which nearly tracked with impulse suggesting additional energy released further down the tunnel for some explosives. This test is a viable tool for optimizing compositional variations for blast performance in target scenarios of similar geometry.

  13. Environmental DNA (eDNA sampling improves occurrence and detection estimates of invasive burmese pythons.

    Directory of Open Access Journals (Sweden)

    Margaret E Hunter

    Full Text Available Environmental DNA (eDNA methods are used to detect DNA that is shed into the aquatic environment by cryptic or low density species. Applied in eDNA studies, occupancy models can be used to estimate occurrence and detection probabilities and thereby account for imperfect detection. However, occupancy terminology has been applied inconsistently in eDNA studies, and many have calculated occurrence probabilities while not considering the effects of imperfect detection. Low detection of invasive giant constrictors using visual surveys and traps has hampered the estimation of occupancy and detection estimates needed for population management in southern Florida, USA. Giant constrictor snakes pose a threat to native species and the ecological restoration of the Florida Everglades. To assist with detection, we developed species-specific eDNA assays using quantitative PCR (qPCR for the Burmese python (Python molurus bivittatus, Northern African python (P. sebae, boa constrictor (Boa constrictor, and the green (Eunectes murinus and yellow anaconda (E. notaeus. Burmese pythons, Northern African pythons, and boa constrictors are established and reproducing, while the green and yellow anaconda have the potential to become established. We validated the python and boa constrictor assays using laboratory trials and tested all species in 21 field locations distributed in eight southern Florida regions. Burmese python eDNA was detected in 37 of 63 field sampling events; however, the other species were not detected. Although eDNA was heterogeneously distributed in the environment, occupancy models were able to provide the first estimates of detection probabilities, which were greater than 91%. Burmese python eDNA was detected along the leading northern edge of the known population boundary. The development of informative detection tools and eDNA occupancy models can improve conservation efforts in southern Florida and support more extensive studies of invasive

  14. Environmental DNA (eDNA) sampling improves occurrence and detection estimates of invasive burmese pythons.

    Science.gov (United States)

    Hunter, Margaret E; Oyler-McCance, Sara J; Dorazio, Robert M; Fike, Jennifer A; Smith, Brian J; Hunter, Charles T; Reed, Robert N; Hart, Kristen M

    2015-01-01

    Environmental DNA (eDNA) methods are used to detect DNA that is shed into the aquatic environment by cryptic or low density species. Applied in eDNA studies, occupancy models can be used to estimate occurrence and detection probabilities and thereby account for imperfect detection. However, occupancy terminology has been applied inconsistently in eDNA studies, and many have calculated occurrence probabilities while not considering the effects of imperfect detection. Low detection of invasive giant constrictors using visual surveys and traps has hampered the estimation of occupancy and detection estimates needed for population management in southern Florida, USA. Giant constrictor snakes pose a threat to native species and the ecological restoration of the Florida Everglades. To assist with detection, we developed species-specific eDNA assays using quantitative PCR (qPCR) for the Burmese python (Python molurus bivittatus), Northern African python (P. sebae), boa constrictor (Boa constrictor), and the green (Eunectes murinus) and yellow anaconda (E. notaeus). Burmese pythons, Northern African pythons, and boa constrictors are established and reproducing, while the green and yellow anaconda have the potential to become established. We validated the python and boa constrictor assays using laboratory trials and tested all species in 21 field locations distributed in eight southern Florida regions. Burmese python eDNA was detected in 37 of 63 field sampling events; however, the other species were not detected. Although eDNA was heterogeneously distributed in the environment, occupancy models were able to provide the first estimates of detection probabilities, which were greater than 91%. Burmese python eDNA was detected along the leading northern edge of the known population boundary. The development of informative detection tools and eDNA occupancy models can improve conservation efforts in southern Florida and support more extensive studies of invasive constrictors

  15. Filtration recovery of extracellular DNA from environmental water samples

    Science.gov (United States)

    qPCR methods are able to analyze DNA from microbes within hours of collecting water samples, providing the promptest notification and public awareness possible when unsafe pathogenic levels are reached. Health risk, however, may be overestimated by the presence of extracellular ...

  16. Cassini RTG's -- Small scale module tests

    International Nuclear Information System (INIS)

    Kelly, C.E.; Klee, P.M.

    1994-01-01

    The Cassini spacecraft, scheduled for a 1997 launch to Saturn, will be powered by three GPHS RTGs (General Purpose Heat Source Radioisotope thermoelectric Generators). The RTGs are the same type as those powering the Galileo and Ulysses spacecraft. Three new converters (F-6, F-7, and F-8) are to be built and one converter (F-2) remaining from the GPHS program will be used. F-6 and F-7 are to be fueled and F-8 serves as a spare converter. In addition, the back-up RTG (F-5) from the Ulysses launch, which is still fueled, will serve as the Cassini back-up RTG. The new RTGs will have a lower fuel loading than in the past and will provide a minimum of 276 watts each at B.O.M. (beginning of mission). The mission length is 10.75 years, at which time these RTGs will provide a minimum of 216 watts and a possible extension to 16 years when the power will be 199 watts. This paper discusses tests performed to date to confirm the successful re-establishment of the unicouple production at Martin Marietta. This production line, shut down 10 years ago, has been restarted and over 1,500 unicouples have been produced to date. Confirmation will be primarily obtained by the performance of three small scale converters in comparison with previously tested modules from the Multi Hundred Watt (MHW) (Voyager) and GPHS (Galileo, Ulysses) programs. Test results to date have shown excellent agreement with the data base

  17. Small scale imaging using ultrasonic tomography

    International Nuclear Information System (INIS)

    Zakaria, Z.; Abdul Rahim, R.; Megat Ali, M.S.A.; Baharuddin, M.Y.; Jahidin, A.H.

    2009-01-01

    Ultrasound technology progressed through the 1960 from simple A-mode and B-mode scans to today M-mode and Doppler two dimensional (2-D) and even three dimensional (3-D) systems. Modern ultrasound imaging has its roots in sonar technology after it was first described by Lord John Rayleigh over 100 years ago on the interaction of acoustic waves with media. Tomography technique was developed as a diagnostic tool in the medical area since the early of 1970s. This research initially focused on how to retrieve a cross sectional images from living and non-living things. After a decade, the application of tomography systems span into the industrial area. However, the long exposure time of medical radiation-based method cannot tolerate the dynamic changes in industrial process two phase liquid/ gas flow system. An alternative system such as a process tomography systems, can give information on the nature of the flow regime characteristic. The overall aim of this paper is to investigate the use of a small scale ultrasonic tomography method based on ultrasonic transmission mode tomography for online monitoring of liquid/ gas flow in pipe/ vessel system through ultrasonic transceivers application. This non-invasive technique applied sixteen transceivers as the sensing elements to cover the pipe/ vessel cross section. The paper also details the transceivers selection criteria, hardware setup, the electronic measurement circuit and also the image reconstruction algorithm applied. The system was found capable of visualizing the internal characteristics and provides the concentration profile for the corresponding liquid and gas phases. (author)

  18. Exposure of Small-Scale Gold Miners in Prestea to Mercury, Ghana, 2012.

    Science.gov (United States)

    Mensah, Ebenezer Kofi; Afari, Edwin; Wurapa, Frederick; Sackey, Samuel; Quainoo, Albert; Kenu, Ernest; Nyarko, Kofi Mensah

    2016-01-01

    Small-scale gold miners in Ghana have been using mercury to amalgamate gold for many years. Mercury is toxic even at low concentration. We assessed occupational exposure of small-scale gold miners to mercury in Prestea, a gold mining town in Ghana . We conducted a cross-sectional study in which we collected morning urine samples from 343 small-scale gold miners and tested for elemental mercury. Data on small-scale gold miner's socio-demographics, adverse health effects and occupational factors for mercury exposure were obtained and analyzed using SPSS Version 16 to determine frequency and percentage. Bivariate analysis was used to determine occupational factors associated with mercury exposure at 95% confidence level. The mean age of the small-scale gold miners was 29.5 ±9.6 years, and 323(94.20%) were males. One hundred and sixty (46.65%) of the small-scale gold miners had urine mercury above the recommended exposure limit (mercury exposure among those who have previously worked at other small-scale gold mines (χ 2 =4.96, p=0.03). The use of personal protective equipment among the small-scale gold miners was low. Retorts, which are globally recommended for burning amalgam, were not found at mining sites. A large proportion of small-scale gold miners in Prestea were having mercury exposure in excess of occupational exposure limits, and are at risk of experiencing adverse health related complications. Ghana Environmental Protection Agency should organize training for the miners.

  19. Searching for the Optimal Sampling Solution: Variation in Invertebrate Communities, Sample Condition and DNA Quality.

    Directory of Open Access Journals (Sweden)

    Martin M Gossner

    Full Text Available There is a great demand for standardising biodiversity assessments in order to allow optimal comparison across research groups. For invertebrates, pitfall or flight-interception traps are commonly used, but sampling solution differs widely between studies, which could influence the communities collected and affect sample processing (morphological or genetic. We assessed arthropod communities with flight-interception traps using three commonly used sampling solutions across two forest types and two vertical strata. We first considered the effect of sampling solution and its interaction with forest type, vertical stratum, and position of sampling jar at the trap on sample condition and community composition. We found that samples collected in copper sulphate were more mouldy and fragmented relative to other solutions which might impair morphological identification, but condition depended on forest type, trap type and the position of the jar. Community composition, based on order-level identification, did not differ across sampling solutions and only varied with forest type and vertical stratum. Species richness and species-level community composition, however, differed greatly among sampling solutions. Renner solution was highly attractant for beetles and repellent for true bugs. Secondly, we tested whether sampling solution affects subsequent molecular analyses and found that DNA barcoding success was species-specific. Samples from copper sulphate produced the fewest successful DNA sequences for genetic identification, and since DNA yield or quality was not particularly reduced in these samples additional interactions between the solution and DNA must also be occurring. Our results show that the choice of sampling solution should be an important consideration in biodiversity studies. Due to the potential bias towards or against certain species by Ethanol-containing sampling solution we suggest ethylene glycol as a suitable sampling solution when

  20. Producing standard damaged DNA samples by heating: pitfalls and suggestions.

    Science.gov (United States)

    Fattorini, Paolo; Marrubini, Giorgio; Bonin, Serena; Bertoglio, Barbara; Grignani, Pierangela; Recchia, Elisa; Pitacco, Paola; Procopio, Francesca; Cantoni, Carolina; Pajnič, Irena Zupanič; Sorçaburu-Cigliero, Solange; Previderè, Carlo

    2018-05-15

    Heat-mediated hydrolysis of DNA is a simple and inexpensive method for producing damaged samples in vitro. Despite heat-mediated DNA hydrolysis is being widely used in forensic and clinical validation procedures, the lack of standardized procedures makes it impossible to compare the intra and inter-laboratory outcomes of the damaging treatments. In this work, a systematic approach to heat induced DNA hydrolysis was performed at 70 °C for 0-18 h to test the role both of the hydrolysis buffer and of the experimental conditions. Specifically, a trial DNA sample, resuspended in three different media (ultrapure water, 0.1% DEPC-water and, respectively, TE) was treated both in Eppendorf tubes ("Protocol P") and in Eppendorf tubes provided with screwcaps ("Protocol S"). The results of these comparative tests were assessed by normalization of the qPCR results. DEPC-water increased the degradation of the samples up to about 100 times when compared to the ultrapure water. Conversely, the TE protected the DNA from degradation whose level was about 1700 times lower than in samples treated in ultrapure water. Even the employment of the "Protocol S" affected the level of degradation, by consistently increasing it (up to about 180 times in DEPC-water). Thus, this comparative approach showed that even seemingly apparently trivial and often underestimated parameters modify the degradation level up to 2-3 orders of magnitude. The chemical-physical reasons of these findings are discussed together with the role of potential factors such as enhanced reactivity of CO 2 , ROS, NO x and pressure, which are likely to be involved. Since the intra and inter-laboratory comparison of the outcomes of the hydrolytic procedure is the first step toward its standardization, the normalization of the qPCR data by the UV/qPCR ratio seems to be the simplest and most reliable way to allow this. Finally, the supplying (provided with the commercial qPCR kits) of a DNA sample whose degree of

  1. The development for small scale soft X-ray spectrometer

    International Nuclear Information System (INIS)

    Sun Kexu; Jiang Shaoen; Yi Rongqing; Cui Yanli

    2004-12-01

    For the development of small-scale soft X-ray spectrometer, first, some small-scale soft X-ray detection elements are developed, it is included GaAs irradiated with neutron, GaAs irradiated with proton, multi-layer mirror, plane mirror and small scale X-ray diode et al. Soft X-ray spectrometers built of multi-layer mirror-GaAs (with neutron irradiation), and plane mirror-small-scale XRD, and plane mirror-GaAs (with proton irradiation) are prepared. These spectrometers are examined in Shen Guang-II laser facility, and some external estimation are given. (authors)

  2. Small-Scale Shock Testing of Propellants and Ingredients

    National Research Council Canada - National Science Library

    Dawley, S

    2004-01-01

    .... The use of small-scale gap testing to evaluate the shock sensitivity of individual propellant ingredients and propellant formulations is a valuable method for experimentally establishing shock...

  3. Effect of sample storage time on detection of hybridization signals in Checkerboard DNA-DNA hybridization.

    Science.gov (United States)

    do Nascimento, Cássio; Muller, Katia; Sato, Sandra; Albuquerque Junior, Rubens Ferreira

    2012-04-01

    Long-term sample storage can affect the intensity of the hybridization signals provided by molecular diagnostic methods that use chemiluminescent detection. The aim of this study was to evaluate the effect of different storage times on the hybridization signals of 13 bacterial species detected by the Checkerboard DNA-DNA hybridization method using whole-genomic DNA probes. Ninety-six subgingival biofilm samples were collected from 36 healthy subjects, and the intensity of hybridization signals was evaluated at 4 different time periods: (1) immediately after collecting (n = 24) and (2) after storage at -20 °C for 6 months (n = 24), (3) for 12 months (n = 24), and (4) for 24 months (n = 24). The intensity of hybridization signals obtained from groups 1 and 2 were significantly higher than in the other groups (p  0.05). The Checkerboard DNA-DNA hybridization method was suitable to detect hybridization signals from all groups evaluated, and the intensity of signals decreased significantly after long periods of sample storage.

  4. Validated methodology for quantifying infestation levels of dreissenid mussels in environmental DNA (eDNA) samples.

    Science.gov (United States)

    Peñarrubia, Luis; Alcaraz, Carles; Vaate, Abraham Bij de; Sanz, Nuria; Pla, Carles; Vidal, Oriol; Viñas, Jordi

    2016-12-14

    The zebra mussel (Dreissena polymorpha Pallas, 1771) and the quagga mussel (D. rostriformis Deshayes, 1838) are successful invasive bivalves with substantial ecological and economic impacts in freshwater systems once they become established. Since their eradication is extremely difficult, their detection at an early stage is crucial to prevent spread. In this study, we optimized and validated a qPCR detection method based on the histone H2B gene to quantify combined infestation levels of zebra and quagga mussels in environmental DNA samples. Our results show specific dreissenid DNA present in filtered water samples for which microscopic diagnostic identification for larvae failed. Monitoring a large number of locations for invasive dreissenid species based on a highly specific environmental DNA qPCR assay may prove to be an essential tool for management and control plans focused on prevention of establishment of dreissenid mussels in new locations.

  5. Technical efficiency of small-scale fishing households in Tanzanian ...

    African Journals Online (AJOL)

    This paper examines the technical efficiency of Tanzanian small-scale fishing households, based on data from two coastal villages located near Bagamoyo and Zanzibar, using a stochastic frontier model with technical inefficiency. The estimated mean technical efficiency of small-scale fishing households was 52%, showing ...

  6. Economic Analysis of Small Scale Fish Pond Production in Oguta ...

    African Journals Online (AJOL)

    What are the costs and returns of small-scale fishpond enterprises? What problems hinder the development of small-scale fishpond production? Data were collected with the aid of structured questionnaires and interviews. Descriptive statistics, gross margin and likert scale were employed in data analysis. Gross margin ...

  7. Transaction Cost Of Borrowing Among Small Scale Farmers In ...

    African Journals Online (AJOL)

    The study examined transaction cost of borrowing among small scale farmers in Rivers State, Nigeria. Data was collected with the aid of structured questionnaire from 109 randomly selected small scale farmers in the study area. Data analysis was by frequency, percentage and mean. It was found that farmers mostly ...

  8. Economic efficiency among small scale poultry farmers in Imo State ...

    African Journals Online (AJOL)

    ... household size and extension, were found to be the significant factors that account for the observed variation in efficiency among the small scale poultry farmers. Keywords: economic efficiency, small scale poultry farmers, stochastic frontier production model. International Journal of Agriculture and Rural Development Vol.

  9. Undermining the myths about small-scale mining

    NARCIS (Netherlands)

    Verbrugge, B.L.P.; Besmanos, B.

    2015-01-01

    Along with many other countries, in recent decades the Philippines –have witnessed a dramatic expansion of small-scale mining (SSM), mostly (but not exclusively)in the form of small-scale gold mining. As can be seen in the graph below (figure 1), official gold production fromSSM has

  10. Small Scale Biodiversity of an Alkaline Hot Spring in Yellowstone National Park

    Science.gov (United States)

    Walther, K.; Oiler, J.; Meyer-Dombard, D. R.

    2012-12-01

    To date, many phylogenetic diversity studies have been conducted in Yellowstone National Park (YNP) [1-7] focusing on the amplification of the 16S rRNA gene and "metagenomic" datasets. However, few reports focus on diversity at small scales. Here, we report on a small scale biodiversity study of sediment and biofilm communities within a confined area of a YNP hot spring, compare and contrast these communities to other sediment and biofilm communities from previous studies [1-7], and with other sediment and biofilm communities in the same system. Sediment and biofilm samples were collected, using a 30 x 50 cm sampling grid divided in 5 x 5 cm squares, which was placed in the outflow channel of "Bat Pool", an alkaline (pH 7.9) hot spring in YNP. Accompanying geochemical data included a full range of spectrophotometry measurements along with major ions, trace elements, and DIC/DOC. In addition, in situ temperature and conductivity arrays were placed within the grid location. The temperature array closest to the source varied between 83-88°C, while the temperature array 40 cm downstream varied between ~83.5-86.5°C. The two conductivity arrays yielded measurements of 5632 μS and 5710 μS showing little variation within the sampling area. Within the grid space, DO ranged from 0.5-1.33 mg/L, with relatively similar, but slightly lower values down the outflow channel. Sulfide values within the grid ranged from 1020-1671 μg/L, while sulfide values outside of the grid region fluctuated, but generally followed the trend of decreasing from source down the outflow. Despite the relative heterogeneity of chemical and physical parameters in the grid space, there was biological diversity in sediments and biofilms at the 5 cm scale. Small scale biodiversity was analyzed by selecting a representative number of samples from within the grid. DNA was extracted and variable regions V3 and V6 (Archaea and Bacteria, respectively) were sequenced with 454 pyrosequencing. The datasets

  11. Application of DNA-DNA colony hybridization to the detection of catabolic genotypes in environmental samples

    International Nuclear Information System (INIS)

    Sayler, G.S.; Shields, M.S.; Tedford, E.T.; Breen, A.; Hooper, S.W.; Sirotkin, K.M.; Davis, J.W.

    1985-01-01

    The application of preexisting DNA hybridization techniques was investigated for potential in determining populations of specific gene sequences in environmental samples. Cross-hybridizations among two degradative plasmids, TOL and NAH, and two cloning vehicles, pLAFR1 and RSF1010, were determined. The detection limits for the TOL plasmid against a nonhomologous plasmid-bearing bacterial background was ascertained. The colony hybridization technique allowed detection of one colony containing TOL plasmid among 10(6) Escherichia coli colonies of nonhomologous DNA. Comparisons between population estimates derived from growth on selective substrates and from hybridizations were examined. Findings indicated that standard sole carbon source enumeration procedures for degradative populations lead to overestimations due to nonspecific growth of other bacteria on the microcontaminant carbon sources present in the media. Population estimates based on the selective growth of a microcosm population on two aromatic substrates (toluene and naphthalene) and estimates derived from DNA-DNA colony hybridizations, using the TOL or NAH plasmid as a probe, corresponded with estimates of substrate mineralization rates and past exposure to environmental contaminants. The applications of such techniques are hoped to eventually allow enumeration of any specific gene sequences in the environment, including both anabolic and catabolic genes. In addition, this procedure should prove useful in monitoring recombinant DNA clones released into environmental situations

  12. Comparison of DNA preservation methods for environmental bacterial community samples.

    Science.gov (United States)

    Gray, Michael A; Pratte, Zoe A; Kellogg, Christina A

    2013-02-01

    Field collections of environmental samples, for example corals, for molecular microbial analyses present distinct challenges. The lack of laboratory facilities in remote locations is common, and preservation of microbial community DNA for later study is critical. A particular challenge is keeping samples frozen in transit. Five nucleic acid preservation methods that do not require cold storage were compared for effectiveness over time and ease of use. Mixed microbial communities of known composition were created and preserved by DNAgard(™), RNAlater(®), DMSO-EDTA-salt (DESS), FTA(®) cards, and FTA Elute(®) cards. Automated ribosomal intergenic spacer analysis and clone libraries were used to detect specific changes in the faux communities over weeks and months of storage. A previously known bias in FTA(®) cards that results in lower recovery of pure cultures of Gram-positive bacteria was also detected in mixed community samples. There appears to be a uniform bias across all five preservation methods against microorganisms with high G + C DNA. Overall, the liquid-based preservatives (DNAgard(™), RNAlater(®), and DESS) outperformed the card-based methods. No single liquid method clearly outperformed the others, leaving method choice to be based on experimental design, field facilities, shipping constraints, and allowable cost. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  13. Optimal purification and sensitive quantification of DNA from fecal samples

    DEFF Research Database (Denmark)

    Jensen, Annette Nygaard; Hoorfar, Jeffrey

    2002-01-01

    Application of reliable, rapid and sensitive methods to laboratory diagnosis of zoonotic infections continues to challenge microbiological laboratories. The recovery of DNA from a swine fecal sample and a bacterial culture extracted by a conventional phenol-chloroform extraction method was compared...... = 0.99 and R-2 = 1.00). In conclusion, silica-membrane, columns can provide a more convenient and less hazardous alternative to the conventional phenol-based method. The results have implication for further improvement of sensitive amplification methods for laboratory diagnosis....

  14. Small-scale and reconnaissance surveys

    Science.gov (United States)

    Bart, Jonathan; Andres, Brad A.; Elliott, Kyle; Francis, Charles M.; Johnston, Victoria; Morrison, R.I.G.; Pierce, Elin P.; Rausch, Jennie; Bart, Jonathan; Johnston, Victoria

    2012-01-01

    This brief chapter addresses two related issues: how effort should be allocated to different parts of the sampling plan and, given optimal allocation, how large a sample will be required to achieve the PRISM accuracy target. Simulations based on data collected to date showed that 2 plots per cluster on rapid surveys, 2 intensive camps per field crew-year, 2-4 intensive plots per intensive camp, and 2-3 rapid surveys per intensive plot is the most efficient allocation of resources. Using this design, we investigated how crew-years should be allocated to each region in order to meet the PRISM accuracy target most efficiently. The analysis indicated that 40-50 crew-years would achieve the accuracy target for 18-24 of the 26 species breeding widely in the Arctic. This analysis was based on assuming that two rounds of surveys were conducted and that a 50% decline occurred between them. We discuss the complexity of making these estimates and why they should be viewed as first approximations.

  15. A Guide to Bundling Small-scale CDM Projects

    International Nuclear Information System (INIS)

    Mariyappan, J.; Bhardwaj, N.; De Coninck, H.; Van der Linden, N.

    2005-07-01

    Small-scale renewable energy and energy efficiency projects that fit the development needs of many developing countries, can potentially be supported via the Clean Development Mechanism (CDM), one of the Kyoto Protocol's flexible mechanisms for tackling climate change. However, there is concern that due to high transaction costs, as well as many existing barriers, very few investments will be made in small-scale projects, which are often the most suitable development option in countries such as India. In view of this, the 'bundling' together of appropriate small-scale projects on a regional basis has been proposed as a way in which funding can be leveraged from international sources and transaction costs reduced. IT Power, IT Power India and the Energy research Centre of the Netherlands (ECN) are carrying out a 2-year project to establish the capacity within India to enable individual small scale projects to be bundled as a single CDM project. Overall objectives are to develop the necessary institutional capabilities to formulate and implement small scale CDM projects in India; to provide a guide on how to bundle small scale projects under the CDM in developing countries; and to raise the awareness of the potential for investment in small scale energy projects which can gain funding through the CDM

  16. Small-scale fisheries bycatch jeopardizes endangered Pacific loggerhead turtles.

    Directory of Open Access Journals (Sweden)

    S Hoyt Peckham

    2007-10-01

    Full Text Available Although bycatch of industrial-scale fisheries can cause declines in migratory megafauna including seabirds, marine mammals, and sea turtles, the impacts of small-scale fisheries have been largely overlooked. Small-scale fisheries occur in coastal waters worldwide, employing over 99% of the world's 51 million fishers. New telemetry data reveal that migratory megafauna frequent coastal habitats well within the range of small-scale fisheries, potentially producing high bycatch. These fisheries occur primarily in developing nations, and their documentation and management are limited or non-existent, precluding evaluation of their impacts on non-target megafauna.30 North Pacific loggerhead turtles that we satellite-tracked from 1996-2005 ranged oceanwide, but juveniles spent 70% of their time at a high use area coincident with small-scale fisheries in Baja California Sur, Mexico (BCS. We assessed loggerhead bycatch mortality in this area by partnering with local fishers to 1 observe two small-scale fleets that operated closest to the high use area and 2 through shoreline surveys for discarded carcasses. Minimum annual bycatch mortality in just these two fleets at the high use area exceeded 1000 loggerheads year(-1, rivaling that of oceanwide industrial-scale fisheries, and threatening the persistence of this critically endangered population. As a result of fisher participation in this study and a bycatch awareness campaign, a consortium of local fishers and other citizens are working to eliminate their bycatch and to establish a national loggerhead refuge.Because of the overlap of ubiquitous small-scale fisheries with newly documented high-use areas in coastal waters worldwide, our case study suggests that small-scale fisheries may be among the greatest current threats to non-target megafauna. Future research is urgently needed to quantify small-scale fisheries bycatch worldwide. Localizing coastal high use areas and mitigating bycatch in

  17. Small-scale fisheries bycatch jeopardizes endangered Pacific loggerhead turtles.

    Science.gov (United States)

    Peckham, S Hoyt; Maldonado Diaz, David; Walli, Andreas; Ruiz, Georgita; Crowder, Larry B; Nichols, Wallace J

    2007-10-17

    Although bycatch of industrial-scale fisheries can cause declines in migratory megafauna including seabirds, marine mammals, and sea turtles, the impacts of small-scale fisheries have been largely overlooked. Small-scale fisheries occur in coastal waters worldwide, employing over 99% of the world's 51 million fishers. New telemetry data reveal that migratory megafauna frequent coastal habitats well within the range of small-scale fisheries, potentially producing high bycatch. These fisheries occur primarily in developing nations, and their documentation and management are limited or non-existent, precluding evaluation of their impacts on non-target megafauna. 30 North Pacific loggerhead turtles that we satellite-tracked from 1996-2005 ranged oceanwide, but juveniles spent 70% of their time at a high use area coincident with small-scale fisheries in Baja California Sur, Mexico (BCS). We assessed loggerhead bycatch mortality in this area by partnering with local fishers to 1) observe two small-scale fleets that operated closest to the high use area and 2) through shoreline surveys for discarded carcasses. Minimum annual bycatch mortality in just these two fleets at the high use area exceeded 1000 loggerheads year(-1), rivaling that of oceanwide industrial-scale fisheries, and threatening the persistence of this critically endangered population. As a result of fisher participation in this study and a bycatch awareness campaign, a consortium of local fishers and other citizens are working to eliminate their bycatch and to establish a national loggerhead refuge. Because of the overlap of ubiquitous small-scale fisheries with newly documented high-use areas in coastal waters worldwide, our case study suggests that small-scale fisheries may be among the greatest current threats to non-target megafauna. Future research is urgently needed to quantify small-scale fisheries bycatch worldwide. Localizing coastal high use areas and mitigating bycatch in partnership with small-scale

  18. Quantification of damage in DNA recovered from highly degraded samples – a case study on DNA in faeces

    Directory of Open Access Journals (Sweden)

    Eveson J Paige

    2006-08-01

    Full Text Available Abstract Background Poorly preserved biological tissues have become an important source of DNA for a wide range of zoological studies. Measuring the quality of DNA obtained from these samples is often desired; however, there are no widely used techniques available for quantifying damage in highly degraded DNA samples. We present a general method that can be used to determine the frequency of polymerase blocking DNA damage in specific gene-regions in such samples. The approach uses quantitative PCR to measure the amount of DNA present at several fragment sizes within a sample. According to a model of random degradation the amount of available template will decline exponentially with increasing fragment size in damaged samples, and the frequency of DNA damage (λ can be estimated by determining the rate of decline. Results The method is illustrated through the analysis of DNA extracted from sea lion faecal samples. Faeces contain a complex mixture of DNA from several sources and different components are expected to be differentially degraded. We estimated the frequency of DNA damage in both predator and prey DNA within individual faecal samples. The distribution of fragment lengths for each target fit well with the assumption of a random degradation process and, in keeping with our expectations, the estimated frequency of damage was always less in predator DNA than in prey DNA within the same sample (mean λpredator = 0.0106 per nucleotide; mean λprey = 0.0176 per nucleotide. This study is the first to explicitly define the amount of template damage in any DNA extracted from faeces and the first to quantify the amount of predator and prey DNA present within individual faecal samples. Conclusion We present an approach for characterizing mixed, highly degraded PCR templates such as those often encountered in ecological studies using non-invasive samples as a source of DNA, wildlife forensics investigations and ancient DNA research. This method will

  19. A Small-Scale Low-Cost Gas Chromatograph

    Science.gov (United States)

    Gros, Natasa; Vrtacnik, Margareta

    2005-01-01

    The design and application of a small-scale portable gas chromatograph for learning of the basic concepts of chromatography is described. The apparatus consists of two basic separable units, which includes a chromatographic unit and an electronic unit.

  20. management and growth paradox of rural small-scale industrial

    African Journals Online (AJOL)

    User

    Keywords: Rural Small-Scale Industries, firm growth, management, proprietors, workforce ... veloping countries as a solution to the problem of scarcity .... In the analysis logistic regression sta- ..... of imported raw materials such as high cost and.

  1. Resource-Use Efficiency in Rice Production Under Small Scale ...

    African Journals Online (AJOL)

    acer

    specific objectives of the study were to determine resource use efficiency, describe ... economic level. ... this key variable with a view to stepping ... focused on small-scale irrigation systems for ... farmers were assumed to be operating under.

  2. Contributions of Small-Scale Community-Owned Infrastructure (SCI ...

    African Journals Online (AJOL)

    Contributions of Small-Scale Community-Owned Infrastructure (SCI) and Asset ... Descriptive analysis was employed to explain access to productive rural ... for asset maintenance and replacement; support targeted value chains given the ...

  3. Strengthening industry-research linkage for small scale industrial ...

    African Journals Online (AJOL)

    Strengthening industry-research linkage for small scale industrial development in Ghana - the relevance of scientific and technological information. ... Journal of Applied Science and Technology. Journal Home · ABOUT · Advanced Search ...

  4. Financing small scale wind energy projects in the UK

    International Nuclear Information System (INIS)

    Mitchell, Catherine

    1993-01-01

    This paper shows how wind energy projects in the UK have obtained finance. It attempts to list the financing options open to small scale developments and to note any likely problems which may occur. (UK)

  5. The hazardous nature of small scale underground mining in Ghana

    Directory of Open Access Journals (Sweden)

    K.J. Bansah

    2016-01-01

    Full Text Available Small scale mining continues to contribute significantly to the growth of Ghana's economy. However, the sector poses serious dangers to human health and the environment. Ground failures resulting from poorly supported stopes have led to injuries and fatalities in recent times. Dust and fumes from drilling and blasting of ore present health threats due to poor ventilation. Four prominent small scale underground mines were studied to identify the safety issues associated with small scale underground mining in Ghana. It is recognized that small scale underground mining in Ghana is inundated with unsafe acts and conditions including stope collapse, improper choice of working tools, absence of personal protective equipment and land degradation. Inadequate monitoring of the operations and lack of regulatory enforcement by the Minerals Commission of Ghana are major contributing factors to the environmental, safety and national security issues of the operations.

  6. Ancient DNA and Forensics Mutual Benefits a Practical Sampling and Laboratory Guide Through a Virtual Ancient DNA Study

    Directory of Open Access Journals (Sweden)

    Jan Cemper-Kiesslich

    2014-09-01

    In this review the authors give a general overview on the field of ancient DNA analysis focussing of the potentials and limits, fields of application, requirements for samples, laboratory setup, reaction design and equipment as well as a brief outlook on current developments, future perspectives and potential cross links with associated scientific disciplines. Key words: Human DNA, Ancient DNA, Forensic DNA typing, Molecular archaeology, Application.

  7. Small-scale eruptive filaments on the quiet sun

    International Nuclear Information System (INIS)

    Hermans, L.M.; Martin, S.F.

    1986-01-01

    A study of a little known class of eruptive events on the quiet sun was conducted. All of 61 small-scale eruptive filamentary structures were identified in a systematic survey of 32 days of H alpha time-lapse films of the quiet sun acquired at Big Bear Solar Observatory. When fully developed, these structures have an average length of 15 arc seconds before eruption. They appear to be the small-scale analog of large-scale eruptive filaments observed against the disk. At the observed rate of 1.9 small-scale eruptive features per field of view per average 7.0 hour day, the rate of occurence of these events on the sun were estimated to be greater than 600 per 24 hour day.. The average duration of the eruptive phase was 26 minutes while the average lifetime from formation through eruption was 70 minutes. A majority of the small-scale filamentary sturctures were spatially related to cancelling magnetic features in line-of-sight photospheric magnetograms. Similar to large-scale filaments, the small-scale filamentary structures sometimes divided opposite polarity cancelling fragments but often had one or both ends terminating at a cancellation site. Their high numbers appear to reflect the much greater flux on the quiet sun. From their characteristics, evolution, and relationship to photospheric magnetic flux, it was concluded that the structures described are small-scale eruptive filaments and are a subset of all filaments

  8. Solution-based targeted genomic enrichment for precious DNA samples

    Directory of Open Access Journals (Sweden)

    Shearer Aiden

    2012-05-01

    Full Text Available Abstract Background Solution-based targeted genomic enrichment (TGE protocols permit selective sequencing of genomic regions of interest on a massively parallel scale. These protocols could be improved by: 1 modifying or eliminating time consuming steps; 2 increasing yield to reduce input DNA and excessive PCR cycling; and 3 enhancing reproducible. Results We developed a solution-based TGE method for downstream Illumina sequencing in a non-automated workflow, adding standard Illumina barcode indexes during the post-hybridization amplification to allow for sample pooling prior to sequencing. The method utilizes Agilent SureSelect baits, primers and hybridization reagents for the capture, off-the-shelf reagents for the library preparation steps, and adaptor oligonucleotides for Illumina paired-end sequencing purchased directly from an oligonucleotide manufacturing company. Conclusions This solution-based TGE method for Illumina sequencing is optimized for small- or medium-sized laboratories and addresses the weaknesses of standard protocols by reducing the amount of input DNA required, increasing capture yield, optimizing efficiency, and improving reproducibility.

  9. Learning Business Practices from Peers : Experimental Evidence from Small-scale Retailers in an Emerging Market

    NARCIS (Netherlands)

    Dalton, Patricio; Rüschenpöhler, Julius; Uras, Burak; Zia, Bilal

    This paper studies whether small-scale businesses can learn and adopt protable practices of their successful peers. We identify such practices through a detailed business survey in urban Indonesia and disseminate the information to a randomly selected sample of small retailers through a

  10. Aspirations of Small-scale Entrepreneurs : Evidence from Urban Retailers in Indonesia

    NARCIS (Netherlands)

    Dalton, Patricio; Rüschenpöhler, Julius; Zia, Bilal

    Small-scale entrepreneurs are ubiquitous in developing countries, yet very few graduate to become larger businesses. We ask whether such entrepreneurs even aspire to grow, and if so on which dimensions of the business? Among a representative sample of retail shop owners in Jakarta, we find that the

  11. Development of small-scale peat production; Pienturvetuotannon kehittaeminen

    Energy Technology Data Exchange (ETDEWEB)

    Erkkilae, A.; Kallio, E. [VTT Energy, Jyvaeskylae (Finland)

    1997-12-01

    The aim of the project is to develop production conditions, methods and technology of small-scale peat production to such a level that the productivity is improved and competitivity maintained. The aim in 1996 was to survey the present status of small-scale peat production, and research and development needs and to prepare a development plan for small-scale peat production for a continued project in 1997 and for the longer term. A questionnaire was sent to producers by mail, and its results were completed by phone interviews. Response was obtained from 164 producers, i.e. from about 75 - 85 % of small-scale peat producers. The quantity of energy peat produced by these amounted to 3.3 TWh and that of other peat to 265 000 m{sup 3}. The total production of energy peat (large- scale producers Vapo Oy and Turveruukki Oy included) amounted to 25.0 TWh in 1996 in Finland, of which 91 % (22.8 TWh) was milled peat and 9 % (2.2 TWh) of sod peat. The total production of peat other than energy peat amounted to 1.4 million m{sup 3}. The proportion of small-scale peat production was 13 % of energy peat, 11 % of milled peat and 38 % of sod peat. The proportion of small-scale producers was 18 % of other peat production. The results deviate clearly from those obtained in a study of small-scale production in the 1980s. The amount of small-scale production is clearly larger than generally assessed. Small-scale production focuses more on milled peat than on sod peat. The work will be continued in 1997. Based on development needs appeared in the questionnaire, the aim is to reduce environmental impacts and runoff effluents from small- scale production, to increase the efficiency of peat deliveries and to reduce peat production costs by improving the service value of machines by increasing co-operative use. (orig.)

  12. Study on a hidden protein-DNA binding in salmon sperm DNA sample by dynamic kinetic capillary isoelectric focusing

    International Nuclear Information System (INIS)

    Liang Liang; Dou Peng; Dong Mingming; Ke Xiaokang; Bian Ningsheng; Liu Zhen

    2009-01-01

    Nuclease P1 is an important enzyme that hydrolyzes RNA or single-stranded DNA into nucleotides, and complete digestion is an essential basis for assays based on this enzyme. To digest a doubled-stranded DNA, the enzyme is usually combined with heat denaturing, which breaks doubled-stranded DNA into single strands. This paper presents an un-expected phenomenon that nuclease P1, in combination with heat denaturing, fails to completely digest a DNA sample extracted from salmon sperm. Under the experimental conditions used, at which nuclease P1 can completely digest calf thymus DNA, the digestion yield of salmon sperm DNA was only 89.5%. Spectrometric measurement indicated that a total protein of 4.7% is present in the DNA sample. To explain the reason for this phenomenon, the dynamic kinetic capillary isoelectric focusing (DK-CIEF) approach proposed previously, which allows for the discrimination of different types of protein-DNA interactions and the measurement of the individual dissociation rate constants, was modified and applied to examine possible protein-DNA interactions involved. It was found that a non-specific DNA-protein binding occurs in the sample, the dissociation rate constant for which was measured to be 7.05 ± 0.83 x 10 -3 s -1 . The formation of DNA-protein complex was suggested to be the main reason for the incomplete digestion of the DNA sample. The modified DK-CIEF approach can be applied as general DNA samples, with the advantages of fast speed and low sample consumption.

  13. Specific amplification of bacterial DNA by optimized so-called universal bacterial primers in samples rich of plant DNA.

    Science.gov (United States)

    Dorn-In, Samart; Bassitta, Rupert; Schwaiger, Karin; Bauer, Johann; Hölzel, Christina S

    2015-06-01

    Universal primers targeting the bacterial 16S-rRNA-gene allow quantification of the total bacterial load in variable sample types by qPCR. However, many universal primer pairs also amplify DNA of plants or even of archaea and other eukaryotic cells. By using these primers, the total bacterial load might be misevaluated, whenever samples contain high amounts of non-target DNA. Thus, this study aimed to provide primer pairs which are suitable for quantification and identification of bacterial DNA in samples such as feed, spices and sample material from digesters. For 42 primers, mismatches to the sequence of chloroplasts and mitochondria of plants were evaluated. Six primer pairs were further analyzed with regard to the question whether they anneal to DNA of archaea, animal tissue and fungi. Subsequently they were tested with sample matrix such as plants, feed, feces, soil and environmental samples. To this purpose, the target DNA in the samples was quantified by qPCR. The PCR products of plant and feed samples were further processed for the Single Strand Conformation Polymorphism method followed by sequence analysis. The sequencing results revealed that primer pair 335F/769R amplified only bacterial DNA in samples such as plants and animal feed, in which the DNA of plants prevailed. Copyright © 2015 Elsevier B.V. All rights reserved.

  14. Detection of transgenes in local maize varieties of small-scale farmers in eastern cape, South Africa.

    Directory of Open Access Journals (Sweden)

    Marianne Iversen

    Full Text Available Small-scale subsistence farmers in South Africa have been introduced to genetically modified (GM crops for more than a decade. Little is known about i the extent of transgene introgression into locally recycled seed, ii what short and long-term ecological and socioeconomic impacts such mixing of seeds might have, iii how the farmers perceive GM crops, and iv to what degree approval conditions are followed and controlled. This study conducted in the Eastern Cape, South Africa, aims primarily at addressing the first of these issues. We analysed for transgenes in 796 individual maize plants (leaves and 20 seed batches collected in a village where GM insect resistant maize was previously promoted and grown as part of an governmental agricultural development program over a seven year period (2001-2008. Additionally, we surveyed the varieties of maize grown and the farmers' practices of recycling and sharing of seed in the same community (26 farmers were interviewed. Recycling and sharing of seeds were common in the community and may contribute to spread and persistence of transgenes in maize on a local or regional level. By analysing DNA we found that the commonly used transgene promoter p35s occurred in one of the 796 leaf samples (0.0013% and in five of the 20 seed samples (25%. Three of the 20 seed samples (15% included herbicide tolerant maize (NK603 intentionally grown by the farmers from seed bought from local seed retailers or acquired through a currently running agricultural development program. The two remaining positive seed samples (10% included genes for insect resistance (from MON810. In both cases the farmers were unaware of the transgenes present. In conclusion, we demonstrate that transgenes are mixed into seed storages of small-scale farming communities where recycling and sharing of seeds are common, i.e. spread beyond the control of the formal seed system.

  15. Impact of Deficient Electricity Supply on the Operations of Small Scale Businesses in North East Nigeria

    Directory of Open Access Journals (Sweden)

    Ahmed Ado

    2015-03-01

    Full Text Available Electricity supply in Nigeria is often erratic. Consumers of electricity (residential, commercial and industrial consumers suffer untold hardships as the State Owned Enterprise; the Power Holding Company of Nigeria (PHCN has been unable to supply reliable power. This is despite massive injections of funds by the Federal Government into the operations of the company over recent years. The failure has significantly impacted negatively on the operations of the business sector especially the small scale subsector that operates with little capital and are thus in most cases unable to afford a back-up facility to ensure un-interrupted power supply for their operations. The study examined the impact of deficient electric power supply on the operations of small scale businesses operating in north east of Nigeria. From the population of small scale businesses, a sample was selected through the use of stratified random sampling to ensure the effective representation of the population of small scale businesses in north east Nigeria. Results from data analysis indicates the severity of electricity supply outages and the costs imposed by power supply outages on the operation of this class of businesses in the region. The paper therefore recommends the need for policy attention towards revitalizing the electricity sector of Nigeria for enhanced supply of electricity to the national economy. When this is achieved, the small business sub-sector will be in a position to effectively lead in the drive towards industrializing the Nigerian economy.

  16. Statistical model for degraded DNA samples and adjusted probabilities for allelic drop-out

    DEFF Research Database (Denmark)

    Tvedebrink, Torben; Eriksen, Poul Svante; Mogensen, Helle Smidt

    2012-01-01

    Abstract DNA samples found at a scene of crime or obtained from the debris of a mass disaster accident are often subject to degradation. When using the STR DNA technology, the DNA profile is observed via a so-called electropherogram (EPG), where the alleles are identified as signal peaks above...... data from degraded DNA, where cases with varying amounts of DNA and levels of degradation are investigated....

  17. Statistical model for degraded DNA samples and adjusted probabilities for allelic drop-out

    DEFF Research Database (Denmark)

    Tvedebrink, Torben; Eriksen, Poul Svante; Mogensen, Helle Smidt

    2012-01-01

    DNA samples found at a scene of crime or obtained from the debris of a mass disaster accident are often subject to degradation. When using the STR DNA technology, the DNA profile is observed via a so-called electropherogram (EPG), where the alleles are identified as signal peaks above a certain...... data from degraded DNA, where cases with varying amounts of DNA and levels of degradation are investigated....

  18. Engineering development for a small-scale recirculator experiment

    International Nuclear Information System (INIS)

    Newton, M.A.; Deadrick, F.J.; Hanks, R.L.; Hawkins, S.A.; Holm, K.A.; Kirbie, H.C.; Karpenko, V.P.; Nattrass, L.A.; Longinotti, D.B.

    1995-01-01

    Lawrence Livermore National Laboratory (LLNL) is evaluating the physics and technology of recirculating induction accelerators for heavy-ion inertial-fusion drivers. As part of this evaluation, the authors are building a small-scale recirculator to demonstrate the concept and to use as a test bed for the development of recirculator technologies. System designs have been completed and components are presently being designed and developed for the small-scale recirculator. This paper discusses results of the design and development activities that are presently being conducted to implement the small-scale recirculator experiments. An, overview of the system design is presented along with a discussion of the implications of this design on the mechanical and electrical hardware. The paper focuses primarily on discussions of the development and design of the half-lattice period hardware and the advanced solid-state modulator

  19. Airfoil optimization for noise emission problem on small scale turbines

    Energy Technology Data Exchange (ETDEWEB)

    Gocmen, Tuhfe; Ozerdem, Baris [Mechanical Engineering Department, Yzmir Institute of Technology (Turkey)

    2011-07-01

    Wind power is a preferred natural resource and has had benefits for the energy industry and for the environment all over the world. However, noise emission from wind turbines is becoming a major concern today. This study paid close attention to small scale wind turbines close to urban areas and proposes an optimum number of six airfoils to address noise emission concerns and performance criteria. The optimization process aimed to decrease the noise emission levels and enhance the aerodynamic performance of a small scale wind turbine. This study determined the sources and the operating conditions of broadband noise emissions. A new design is presented which enhances aerodynamic performance and at the same time reduces airfoil self noise. It used popular aerodynamic functions and codes based on aero-acoustic empirical models. Through numerical computations and analyses, it is possible to derive useful improvements that can be made to commercial airfoils for small scale wind turbines.

  20. CO2-impacts of a small-scale consumers levy

    International Nuclear Information System (INIS)

    1995-02-01

    Because of a number of developments (altered budgets of Dutch ministries and implementation of environmental policy plans of energy distribution companies in the Netherlands) the 1993 analyses of the effects of a small-scale consumer levy on the emission of CO 2 are updated. First, attention is paid to the conservation impetus as a result of an increase of the energy price for small-scale consumers. Next, the effects that can occur as a consequence of the presently suggested form of the levy (in particular, the exemption of renewable energy and waste heat) are discussed. Subsequently, the alterations of other policy tools, that are necessary in case a higher effectiveness of conservation measures is realized, are dealt with. The direct effect of a higher energy price on the saving behavior of the small-scale consumers is calculated by means of the CENECA-model. 4 tabs., 1 appendix, 8 refs

  1. An Optimized DNA Analysis Workflow for the Sampling, Extraction, and Concentration of DNA obtained from Archived Latent Fingerprints.

    Science.gov (United States)

    Solomon, April D; Hytinen, Madison E; McClain, Aryn M; Miller, Marilyn T; Dawson Cruz, Tracey

    2018-01-01

    DNA profiles have been obtained from fingerprints, but there is limited knowledge regarding DNA analysis from archived latent fingerprints-touch DNA "sandwiched" between adhesive and paper. Thus, this study sought to comparatively analyze a variety of collection and analytical methods in an effort to seek an optimized workflow for this specific sample type. Untreated and treated archived latent fingerprints were utilized to compare different biological sampling techniques, swab diluents, DNA extraction systems, DNA concentration practices, and post-amplification purification methods. Archived latent fingerprints disassembled and sampled via direct cutting, followed by DNA extracted using the QIAamp® DNA Investigator Kit, and concentration with Centri-Sep™ columns increased the odds of obtaining an STR profile. Using the recommended DNA workflow, 9 of the 10 samples provided STR profiles, which included 7-100% of the expected STR alleles and two full profiles. Thus, with carefully selected procedures, archived latent fingerprints can be a viable DNA source for criminal investigations including cold/postconviction cases. © 2017 American Academy of Forensic Sciences.

  2. Small scale wood combustion in Germany. Recent research and trends

    Energy Technology Data Exchange (ETDEWEB)

    Maier, H.; Unterberger, S.; Hein, K.R.G. [Institute of Process Engineering and Power Plant Technology, University of Stuttgart (Germany)

    1998-12-31

    To reduce Europe`s greenhouse gas emission CO{sub 2} it is a challenging task utilising biomass fuels as there are wood or wood residues from the forest industry. The utilisation can be done either in commercially operated medium (> 50 kWth) or full scale (> 1 MWth) decentralised heat and power stations or in small scale (< 50 kWth) domestic heating systems. In small scale heating systems untreated wood logs, wood briquette or wood pellets and in few cases wood chips are used. The present market in Germany is focused on the use of wood logs. Presently, the use of wood pellets in small scale automatically operated boilers < 15 kW especially for low energy houses is discussed more and more. Since 1980 the installation of new wood fired small scale domestic heating systems reached a significant size due to the interest of the customers to have a alternative inhouse heating system and to increase the living comfort. In 1994 the amount of sold small scale heaters in Germany were in total about 133.258 units. The thermal power of in 1994 sold units is estimated of about 1350 MW which is a significant size in total with regard to domestic heating purposes. Since few years there is a clear market trend in Germany towards the installation of open fire stoves. Due to this trend in Germany and the design characteristic of open fire stoves using huge glass doors of glass windows it is very difficult to achieve a further reduction of emissions like CO and unburned volatile hydrocarbons (VOC). In the text the requirements for modern small scale wood fired stoves in Germany as well as the actual stage and trend of research and development (R and D) are discussed 4 refs.

  3. Small-scale dynamo at low magnetic Prandtl numbers

    Science.gov (United States)

    Schober, Jennifer; Schleicher, Dominik; Bovino, Stefano; Klessen, Ralf S.

    2012-12-01

    The present-day Universe is highly magnetized, even though the first magnetic seed fields were most probably extremely weak. To explain the growth of the magnetic field strength over many orders of magnitude, fast amplification processes need to operate. The most efficient mechanism known today is the small-scale dynamo, which converts turbulent kinetic energy into magnetic energy leading to an exponential growth of the magnetic field. The efficiency of the dynamo depends on the type of turbulence indicated by the slope of the turbulence spectrum v(ℓ)∝ℓϑ, where v(ℓ) is the eddy velocity at a scale ℓ. We explore turbulent spectra ranging from incompressible Kolmogorov turbulence with ϑ=1/3 to highly compressible Burgers turbulence with ϑ=1/2. In this work, we analyze the properties of the small-scale dynamo for low magnetic Prandtl numbers Pm, which denotes the ratio of the magnetic Reynolds number, Rm, to the hydrodynamical one, Re. We solve the Kazantsev equation, which describes the evolution of the small-scale magnetic field, using the WKB approximation. In the limit of low magnetic Prandtl numbers, the growth rate is proportional to Rm(1-ϑ)/(1+ϑ). We furthermore discuss the critical magnetic Reynolds number Rmcrit, which is required for small-scale dynamo action. The value of Rmcrit is roughly 100 for Kolmogorov turbulence and 2700 for Burgers. Furthermore, we discuss that Rmcrit provides a stronger constraint in the limit of low Pm than it does for large Pm. We conclude that the small-scale dynamo can operate in the regime of low magnetic Prandtl numbers if the magnetic Reynolds number is large enough. Thus, the magnetic field amplification on small scales can take place in a broad range of physical environments and amplify week magnetic seed fields on short time scales.

  4. Small-scale dynamo at low magnetic Prandtl numbers.

    Science.gov (United States)

    Schober, Jennifer; Schleicher, Dominik; Bovino, Stefano; Klessen, Ralf S

    2012-12-01

    The present-day Universe is highly magnetized, even though the first magnetic seed fields were most probably extremely weak. To explain the growth of the magnetic field strength over many orders of magnitude, fast amplification processes need to operate. The most efficient mechanism known today is the small-scale dynamo, which converts turbulent kinetic energy into magnetic energy leading to an exponential growth of the magnetic field. The efficiency of the dynamo depends on the type of turbulence indicated by the slope of the turbulence spectrum v(ℓ)∝ℓ^{ϑ}, where v(ℓ) is the eddy velocity at a scale ℓ. We explore turbulent spectra ranging from incompressible Kolmogorov turbulence with ϑ=1/3 to highly compressible Burgers turbulence with ϑ=1/2. In this work, we analyze the properties of the small-scale dynamo for low magnetic Prandtl numbers Pm, which denotes the ratio of the magnetic Reynolds number, Rm, to the hydrodynamical one, Re. We solve the Kazantsev equation, which describes the evolution of the small-scale magnetic field, using the WKB approximation. In the limit of low magnetic Prandtl numbers, the growth rate is proportional to Rm^{(1-ϑ)/(1+ϑ)}. We furthermore discuss the critical magnetic Reynolds number Rm_{crit}, which is required for small-scale dynamo action. The value of Rm_{crit} is roughly 100 for Kolmogorov turbulence and 2700 for Burgers. Furthermore, we discuss that Rm_{crit} provides a stronger constraint in the limit of low Pm than it does for large Pm. We conclude that the small-scale dynamo can operate in the regime of low magnetic Prandtl numbers if the magnetic Reynolds number is large enough. Thus, the magnetic field amplification on small scales can take place in a broad range of physical environments and amplify week magnetic seed fields on short time scales.

  5. Still Another Book of Small-Scale Motets

    OpenAIRE

    Rodríguez-Garcia, Esperanza

    2016-01-01

    UID/EAT/00693/2013 PTDC/CPC-MMU/0314/2014 ‘Still another book of small-scale motets: Sebastián Raval’s Motecta (1600)’ Lodovico Viadana’s Cento concerti ecclesiastici (Venice: Giacomo Vincenti, 1602), a collection of small-scale motets with basso continuo, is still considered ‘chronologically the first publication to include a basso continuo with sacred vocal music’. It has become the epitome of the advent of the Baroque in Italian sacred music. But, as has been argued in recent times, ...

  6. Design and Modelling of Small Scale Low Temperature Power Cycles

    DEFF Research Database (Denmark)

    Wronski, Jorrit

    he work presented in this report contributes to the state of the art within design and modelling of small scale low temperature power cycles. The study is divided into three main parts: (i) fluid property evaluation, (ii) expansion device investigations and (iii) heat exchanger performance......-oriented Modelica code and was included in the thermo Cycle framework for small scale ORC systems. Special attention was paid to the valve system and a control method for variable expansion ratios was introduced based on a cogeneration scenario. Admission control based on evaporator and condenser conditions...

  7. Y-STR analysis on DNA mixture samples--results of a collaborative project of the ENFSI DNA Working Group

    DEFF Research Database (Denmark)

    Parson, Walther; Niederstätter, Harald; Lindinger, Alexandra

    2008-01-01

    The ENFSI (European Network of Forensic Science Institutes) DNA Working Group undertook a collaborative project on Y-STR typing of DNA mixture samples that were centrally prepared and thoroughly tested prior to the shipment. Four commercial Y-STR typing kits (Y-Filer, Applied Biosystems, Foster C...... a laboratory-specific optimization process is indicated to reach a comparable sensitivity for the analysis of minute amounts of DNA....

  8. Environmental DNA from seawater samples correlate with trawl catches of Subarctic, deepwater fishes

    DEFF Research Database (Denmark)

    Thomsen, Philip Francis; Møller, Peter Rask; Sigsgaard, Eva Egelyng

    2016-01-01

    such as bottom trawling, and on official reporting of global catches, which can be unreliable. Thus, there is need for alternative and non-invasive techniques for qualitative and quantitative oceanic fish surveys. Here we report environmental DNA (eDNA) metabarcoding of seawater samples from continental slope...... depths in Southwest Greenland. We collected seawater samples at depths of 188-918 m and compared seawater eDNA to catch data from trawling. We used Illumina sequencing of PCR products to demonstrate that eDNA reads show equivalence to fishing catch data obtained from trawling. Twenty-six families were...... found with both trawling and eDNA, while three families were found only with eDNA and two families were found only with trawling. Key commercial fish species for Greenland were the most abundant species in both eDNA reads and biomass catch, and interpolation of eDNA abundances between sampling sites...

  9. Human DNA quantification and sample quality assessment: Developmental validation of the PowerQuant(®) system.

    Science.gov (United States)

    Ewing, Margaret M; Thompson, Jonelle M; McLaren, Robert S; Purpero, Vincent M; Thomas, Kelli J; Dobrowski, Patricia A; DeGroot, Gretchen A; Romsos, Erica L; Storts, Douglas R

    2016-07-01

    Quantification of the total amount of human DNA isolated from a forensic evidence item is crucial for DNA normalization prior to short tandem repeat (STR) DNA analysis and a federal quality assurance standard requirement. Previous commercial quantification methods determine the total human DNA and total human male DNA concentrations, but provide limited information about the condition of the DNA sample. The PowerQuant(®) System includes targets for quantification of total human and total human male DNA as well as targets for evaluating whether the human DNA is degraded and/or PCR inhibitors are present in the sample. A developmental validation of the PowerQuant(®) System was completed, following SWGDAM Validation Guidelines, to evaluate the assay's specificity, sensitivity, precision and accuracy, as well as the ability to detect degraded DNA or PCR inhibitors. In addition to the total human DNA and total human male DNA concentrations in a sample, data from the degradation target and internal PCR control (IPC) provide a forensic DNA analyst meaningful information about the quality of the isolated human DNA and the presence of PCR inhibitors in the sample that can be used to determine the most effective workflow and assist downstream interpretation. Copyright © 2016 The Author(s). Published by Elsevier Ireland Ltd.. All rights reserved.

  10. Why small-scale cannabis growers stay small: five mechanisms that prevent small-scale growers from going large scale.

    Science.gov (United States)

    Hammersvik, Eirik; Sandberg, Sveinung; Pedersen, Willy

    2012-11-01

    Over the past 15-20 years, domestic cultivation of cannabis has been established in a number of European countries. New techniques have made such cultivation easier; however, the bulk of growers remain small-scale. In this study, we explore the factors that prevent small-scale growers from increasing their production. The study is based on 1 year of ethnographic fieldwork and qualitative interviews conducted with 45 Norwegian cannabis growers, 10 of whom were growing on a large-scale and 35 on a small-scale. The study identifies five mechanisms that prevent small-scale indoor growers from going large-scale. First, large-scale operations involve a number of people, large sums of money, a high work-load and a high risk of detection, and thus demand a higher level of organizational skills than for small growing operations. Second, financial assets are needed to start a large 'grow-site'. Housing rent, electricity, equipment and nutrients are expensive. Third, to be able to sell large quantities of cannabis, growers need access to an illegal distribution network and knowledge of how to act according to black market norms and structures. Fourth, large-scale operations require advanced horticultural skills to maximize yield and quality, which demands greater skills and knowledge than does small-scale cultivation. Fifth, small-scale growers are often embedded in the 'cannabis culture', which emphasizes anti-commercialism, anti-violence and ecological and community values. Hence, starting up large-scale production will imply having to renegotiate or abandon these values. Going from small- to large-scale cannabis production is a demanding task-ideologically, technically, economically and personally. The many obstacles that small-scale growers face and the lack of interest and motivation for going large-scale suggest that the risk of a 'slippery slope' from small-scale to large-scale growing is limited. Possible political implications of the findings are discussed. Copyright

  11. Small-Scale Helicopter Automatic Autorotation : Modeling, Guidance, and Control

    NARCIS (Netherlands)

    Taamallah, S.

    2015-01-01

    Our research objective consists in developing a, model-based, automatic safety recovery system, for a small-scale helicopter Unmanned Aerial Vehicle (UAV) in autorotation, i.e. an engine OFF flight condition, that safely flies and lands the helicopter to a pre-specified ground location. In pursuit

  12. Nitrate-nitrogen removal with small-scale reverse osmosis ...

    African Journals Online (AJOL)

    The nitrate-nitrogen concentration in water supplied to clinics in Limpopo Province is too high to be fit for human consumption (35 to 75 mg/ℓ NO3-N). Therefore, small-scale technologies (reverse osmosis, ion-exchange and electrodialysis) were evaluated for nitrate-nitrogen removal to make the water potable (< 10 mg/ℓ ...

  13. Effects of artisanal small-scale gold mining on fisheries ...

    African Journals Online (AJOL)

    Artisanal Small-scale Gold Mining (ASGM) has direct and indirect impacts on fisheries management. These impacts are mainly about the quality of the water where fish lives, ownership of the surrounding waters, land and human health. This study was carried out in two landing sites of Wagusu and Riskis Kogwari in ...

  14. Climate change adaptation strategies by small-scale farmers in ...

    African Journals Online (AJOL)

    Mburu

    SPSS) ... were financial constraints (93.4%), lack of relevant skills (74.5%) and lack of ... Key words: Climate change, small-scale farmers, adaptation strategies. ... investment in irrigation infrastructure, high post-harvest ..... 72.0 School drop out.

  15. Productivity and production efficiency among small scale irrigated ...

    African Journals Online (AJOL)

    The study examined productivity and production efficiency among small scale irrigated sugarcane farmers in Niger State, Nigeria using a stochastic translog frontier function. Data for the study were obtained using structured questionnaires administered to 100 randomly selected sugarcane farmers from Paiko and Gurara ...

  16. Productive Efficiency of Small Scale Sawmilling Industries in Mufindi ...

    African Journals Online (AJOL)

    A structured questionnaire was used to collect data from 80 small-scale sawmills in Mufindi District. Data were analysed using descriptive as well as quantitative methods. Technical, scale and allocative efficiency score of sawmills were computed using data envelopment analysis programme developed by Coelli. Censored ...

  17. Small-scale Aquaculture to Strengthen Food Security in Cambodia ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Small-scale Aquaculture to Strengthen Food Security in Cambodia (CIFSRF) ... for their families' consumption in the same ponds as large fish, which can be sold for income. ... The project also studies opportunities to scale up the model for broader use ... Assessing improvements in nutrition outcomes following agricultural ...

  18. New perspectives in small-scale fisheries management: challenges ...

    African Journals Online (AJOL)

    This is in response to the recognition that conventional fisheries management is not equipped to deal with the complexities, uncertainties and challenges prevalent in small-scale fishery systems. Consequently, a new fisheries paradigm is emerging based on the principles and ideas underpinning systems thinking, ...

  19. Development and utilization of spring water in small scale supply ...

    African Journals Online (AJOL)

    Development and utilization of spring water in small scale supply scheme for the Kogi State Polytechnic, Lokoja, central Nigeria. Joseph Omada. Abstract. No Abstract. Journal of Mining and Geology 2005, Vol. 41(1): 131-135. Full Text: EMAIL FULL TEXT EMAIL FULL TEXT · DOWNLOAD FULL TEXT DOWNLOAD FULL ...

  20. Agricultural Credit Utilization among Small Scale Women Farmers in ...

    African Journals Online (AJOL)

    ... monitor regularly the disbursement of agricultural loan to women farmers at the appropriate planning season with reasonable interest charge and that extension agents should ensure that the loan is utilized for only agricultural purposes. Key words: Credit utilization, small-scale farmer's income generation, Niger State.

  1. Responsible and Sustainable Tourism : Strengthening Small-Scale ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    Responsible and Sustainable Tourism : Strengthening Small-Scale ... to work with the Costa Rican association of small and medium tourism enterprises of the ... as the hub of a network of small service providers operating within the model. ... marketing and outreach, distance learning, and the integration of services that are ...

  2. Training needs of small scale poultry farmers on improved ...

    African Journals Online (AJOL)

    Poultry business is a job opportunity for numerous for earning income and ... needs of the small scale commercial poultry farmers to improve poultry production ... strategies (88%) while only 24.1% of the respondents need training on types of ...

  3. A Success Story of Organizing Small Scale Farmers in Kenya

    DEFF Research Database (Denmark)

    Buch-Hansen, Mogens

    2012-01-01

    , but not least to be used in PES schemes. The article emphasizes vertical integration and production diversification, enabling market conditions, and democratization as the main factors in KTDA’s success that could possibly be replicated in promoting small scale farmers participating in the post-Kyoto carbon...

  4. Lessons from Small-scale Standardised Testing of English Reading ...

    African Journals Online (AJOL)

    The superior performance by the public school can partly be explained by teachers teaching experience, most of them have been teaching for more than ten years and greater community support for the school. It is recommended that data produced through small-scale standardised testing should be used by school ...

  5. Designing of network planning system for small-scale manufacturing

    Science.gov (United States)

    Kapulin, D. V.; Russkikh, P. A.; Vinnichenko, M. V.

    2018-05-01

    The paper presents features of network planning in small-scale discrete production. The procedure of explosion of the production order, considering multilevel representation, is developed. The software architecture is offered. Approbation of the network planning system is carried out. This system allows carrying out dynamic updating of the production plan.

  6. Work related injuries and associated factors among small scale ...

    African Journals Online (AJOL)

    Objective: This study aims to assess the magnitude of work related injury and associated factors among small scale industrial workers in Mizan-Aman town, Bench Maji Zone, Southwest Ethiopia. Method: A cross-sectional study design was conducted from February to May, 2016. Data was collected using a structured face to ...

  7. Development of small-scale fisheries in Yemen: An exploration

    NARCIS (Netherlands)

    Wagenaar, A.; Haese, D' M.F.C.

    2007-01-01

    Yemen is one of the poorest countries in the world. The development of its fishery sector is increasingly being mentioned as a source of livelihood creation. The aims of this paper are to: (a) provide an overview of the institutional environment in which small-scale fishermen in Yemen operate; (b)

  8. Smoke emissions in small-scale burning of wood

    International Nuclear Information System (INIS)

    Tuomi, S.

    1993-01-01

    The article is based on research carried out in Finland and Sweden on the subject of emissions of smoke in the small-scale burning of wood and the factors affecting it. Due to incomplete combustion, small-scale burning of wood is particularly typified by its emissions of solid particles, carbon monoxide, hydrocarbons and PAH compounds. Included among factors influencing the volume of emissions are the load imposed on the heating device, the manner in which the fuel is fed into the firebox, fuel quality, and heating device structure. Emissions have been found to be at their minimum in connection with heating systems based on accumulators. Emissions can be significantly reduced by employing state-of-the-art technology, appropriate ways of heating and by dry fuel. A six-year bioenergy research programme was launched early in 1993 in Finland. All leading research institutions and enterprises participate in this programme. Reduction of emissions has been set as the central goal in the part dealing with small-scale burning of wood. Application of catalytic combustion in Finnish-made heating devices is one of the programmes development targets. Up to this date, the emissions produced in the small-scale burning of wood are not mentioned in official regulations pertaining to approved heating devices. In Sweden tar emissions are applied as a measure of the environmental impact imposed by heating devices

  9. Small-scale soft-bodied robot with multimodal locomotion

    Science.gov (United States)

    Hu, Wenqi; Lum, Guo Zhan; Mastrangeli, Massimo; Sitti, Metin

    2018-02-01

    Untethered small-scale (from several millimetres down to a few micrometres in all dimensions) robots that can non-invasively access confined, enclosed spaces may enable applications in microfactories such as the construction of tissue scaffolds by robotic assembly, in bioengineering such as single-cell manipulation and biosensing, and in healthcare such as targeted drug delivery and minimally invasive surgery. Existing small-scale robots, however, have very limited mobility because they are unable to negotiate obstacles and changes in texture or material in unstructured environments. Of these small-scale robots, soft robots have greater potential to realize high mobility via multimodal locomotion, because such machines have higher degrees of freedom than their rigid counterparts. Here we demonstrate magneto-elastic soft millimetre-scale robots that can swim inside and on the surface of liquids, climb liquid menisci, roll and walk on solid surfaces, jump over obstacles, and crawl within narrow tunnels. These robots can transit reversibly between different liquid and solid terrains, as well as switch between locomotive modes. They can additionally execute pick-and-place and cargo-release tasks. We also present theoretical models to explain how the robots move. Like the large-scale robots that can be used to study locomotion, these soft small-scale robots could be used to study soft-bodied locomotion produced by small organisms.

  10. A feasibility and implementation model of small-scale hydropower ...

    African Journals Online (AJOL)

    Large numbers of households and communities will not be connected to the national electricity grid for the foreseeable future due to high cost of transmission and distribution systems to remote communities and the relatively low electricity demand within rural communities. Small-scale hydropower used to play a very ...

  11. 2010 Thin Film & Small Scale Mechanical Behavior Gordon Research Conference

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Thomas Balk

    2010-07-30

    Over the past decades, it has been well established that the mechanical behavior of materials changes when they are confined geometrically at least in one dimension to small scale. It is the aim of the 2010 Gordon Conference on 'Thin Film and Small Scale Mechanical Behavior' to discuss cutting-edge research on elastic, plastic and time-dependent deformation as well as degradation mechanisms like fracture, fatigue and wear at small scales. As in the past, the conference will benefit from contributions from fundamental studies of physical mechanisms linked to material science and engineering reaching towards application in modern applications ranging from optical and microelectronic devices and nano- or micro-electrical mechanical systems to devices for energy production and storage. The conference will feature entirely new testing methodologies and in situ measurements as well as recent progress in atomistic and micromechanical modeling. Particularly, emerging topics in the area of energy conversion and storage, such as material for batteries will be highlighted. The study of small-scale mechanical phenomena in systems related to energy production, conversion or storage offer an enticing opportunity to materials scientists, who can provide new insight and investigate these phenomena with methods that have not previously been exploited.

  12. Process improvement of knives production in a small scale industry

    Science.gov (United States)

    Ananto, Gamawan; Muktasim, Irfan

    2017-06-01

    Small scale industry that produces several kinds of knive should increase its capacity due to the demand from the market. Qualitatively, this case study consisted of formulating the problems, collecting and analyzing the necessary data, and determining the possible recommendations for the improvement. While the current capacity is only 9 (nine), it is expected that 20 units of knife will produced per month. The processes sequence are: profiling (a), truing (b), beveling (c), heat treatment (d), polishing (e), assembly (f), sharpening (g) and finishing (h). The first process (a) is held by out-house vendor company while other steps from (b) to (g) are executed by in-house vendor. However, there is a high dependency upon the high skilled operator who executes the in -house processes that are mostly held manually with several unbalance successive tasks, where the processing time of one or two tasks require longer duration than others since the operation is merely relied on the operator's skill. The idea is the improvement or change of the profiling and beveling process. Due to the poor surface quality and suboptimal hardness resulted from the laser cut machine for profiling, it is considered to subst itute this kind of process with wire cut that is capable to obtain good surface quality with certain range levels of roughness. Through simple cutting experiments on the samples, it is expected that the generated surface quality is adequate to omit the truing process (b). In addition, the cutting experiments on one, two, and four test samples resulted the shortest time that was obtained through four pieces in one cut. The technical parameters were set according to the recommendation of machine standard as referred to samples condition such as thickness and path length that affect ed the rate of wear. Meanwhile, in order to guarantee the uniformity of knife angles that are formed through beveling process (c), a grinding fixture was created. This kind of tool diminishes the

  13. Pengujian Kartu Fta Sebagai Alat Sampling Dna Jamur Patogen Dariberbagi Bagian Tanaman Yang Terinfeksi

    OpenAIRE

    Sulistyawati, Purnamila

    2011-01-01

    FTA card offers a simple and fast method for retrieval of DNA samples at room temperature and storage of DNA in the short and long term. This will fasiliate the detection and identification of plant pathogens rapidly; increasing the number of samples can be collected, stored and transported in the field, especially from remote locations. The purpose of this study is to investigate the suitability of FTA cards as a new method for sampling DNA from multiple infected of plant tissues such as ...

  14. The effects of storage temperature and duration of blood samples on DNA and RNA qualities.

    Science.gov (United States)

    Huang, Lien-Hung; Lin, Pei-Hsien; Tsai, Kuo-Wang; Wang, Liang-Jen; Huang, Ying-Hsien; Kuo, Ho-Chang; Li, Sung-Chou

    2017-01-01

    DNA and RNA samples from blood are the common examination target for non-invasive physical tests and/or biomedical studies. Since high-quality DNA and RNA samples guarantee the correctness of these tests and/or studies, we investigated the effects of storage temperature and storage duration of whole blood on DNA and RNA qualities. Subjects were enrolled to donate blood samples which were stored for different durations and at different temperatures, followed by the examinations on RNA quality, qPCR, DNA quality and DNA methylation. For RNA, we observed obvious quality decline with storage duration longer than 24 hours. Storage at low temperature does not keep RNA samples from degradation. And, storing whole blood samples in freezer dramatically damage RNA. For DNA, quality decline was not observed even with storage duration for 15 days. However, DNA methylation significantly altered with storage duration longer than three days. Storage duration within 24 hours is critical for collecting high-quality RNA samples for next-generation sequencing (NGS) assays (RIN≧8). If microarray assays are expected (RIN≧7), storage duration within 32 hours is acceptable. Although DNA is resistant within 15 days when kept in whole blood, DNA quantity dramatically decreases owing to WBC lysis. In addition, duration for more than three days significantly alter DNA methylation status, globally and locally. Our result provides a reference for dealing with blood samples.

  15. DNA Profiling of Convicted Offender Samples for the Combined DNA Index System

    Science.gov (United States)

    Millard, Julie T

    2011-01-01

    The cornerstone of forensic chemistry is that a perpetrator inevitably leaves trace evidence at a crime scene. One important type of evidence is DNA, which has been instrumental in both the implication and exoneration of thousands of suspects in a wide range of crimes. The Combined DNA Index System (CODIS), a network of DNA databases, provides…

  16. Determination of DNA profiling of siwak and toothbrush samples ...

    African Journals Online (AJOL)

    Nagy Alfadaly

    2016-06-01

    Jun 1, 2016 ... b Department of Forensic Biology, College of Forensic Sciences, Naif University, AlRiadh, Saudi ... tool in criminal investigation, disaster victim identification and ... with the forensic evidence, or a degraded DNA template due.

  17. Occupational health issues in small-scale industries in Sri Lanka: An underreported burden.

    Science.gov (United States)

    Suraweera, Inoka K; Wijesinghe, Supun D; Senanayake, Sameera J; Herath, Hema D B; Jayalal, T B Ananda

    2016-10-17

    Work-related diseases and occupational accidents affect a significant number of workers globally. The majority of these diseases and accidents are reported from developing countries; and a large percentage of the workforce in developing countries is estimated to be employed in small-scale industries. Sri Lanka is no exception. These workers are exposed to occupational hazards and are at a great risk of developing work- related diseases and injuries. To identify occupational health issues faced by small-scale industry workers in Sri Lanka. A cross sectional study was conducted among workers in four selected small-scale industry categories in two districts of Sri Lanka. A small-scale industry was defined as a work setting with less than 20 workers. Cluster sampling using probability proportionate to size of workers was used. Eighty clusters with a cluster size of eight from each district were selected. Data was collected using a pre-tested interviewer administered questionnaire. Our study surveyed 198 industries. Headache (2.2%, 95% CI 1.5-3.1) and eye problems (2.1%, 95% CI 1.4-2.9) were the commonest general health issues detected. Back pain (4.8%, 95% CI 3.8-6.1) was the most prevalent work-related musculoskeletal pain reported. Knee pain was the second highest (4.4%, 95% CI 3.4-5.6). Most of the work-related musculoskeletal pain was either of short duration or long lasting. Work-related musculoskeletal pain was much more common than the general health issues reported. Health promotional programs at workplaces focusing ergonomics will benefit the workers at small-scale industries inSri Lanka.

  18. Reactive flow modeling of small scale detonation failure experiments for a baseline non-ideal explosive

    Energy Technology Data Exchange (ETDEWEB)

    Kittell, David E.; Cummock, Nick R.; Son, Steven F. [School of Mechanical Engineering, Purdue University, West Lafayette, Indiana 47907 (United States)

    2016-08-14

    Small scale characterization experiments using only 1–5 g of a baseline ammonium nitrate plus fuel oil (ANFO) explosive are discussed and simulated using an ignition and growth reactive flow model. There exists a strong need for the small scale characterization of non-ideal explosives in order to adequately survey the wide parameter space in sample composition, density, and microstructure of these materials. However, it is largely unknown in the scientific community whether any useful or meaningful result may be obtained from detonation failure, and whether a minimum sample size or level of confinement exists for the experiments. In this work, it is shown that the parameters of an ignition and growth rate law may be calibrated using the small scale data, which is obtained from a 35 GHz microwave interferometer. Calibration is feasible when the samples are heavily confined and overdriven; this conclusion is supported with detailed simulation output, including pressure and reaction contours inside the ANFO samples. The resulting shock wave velocity is most likely a combined chemical-mechanical response, and simulations of these experiments require an accurate unreacted equation of state (EOS) in addition to the calibrated reaction rate. Other experiments are proposed to gain further insight into the detonation failure data, as well as to help discriminate between the role of the EOS and reaction rate in predicting the measured outcome.

  19. Paleoparasitological report on Ascaris aDNA from an ancient East Asian sample

    Directory of Open Access Journals (Sweden)

    Chang Seok Oh

    2010-03-01

    Full Text Available In this study, Ascaris DNA was extracted and sequenced from a medieval archaeological sample in Korea. While Ascaris eggs were confirmed to be of human origin by archaeological evidence, it was not possible to pinpoint the exact species due to close genetic relationships among them. Despite this shortcoming, this is the first Ascaris ancient DNA (aDNA report from a medieval Asian country and thus will expand the scope of Ascaris aDNA research.

  20. MERCURY AND ARSENIC CONTAMINATION FROM SMALL SCALE GOLD MINING ACTIVITIES AT SELOGIRI AREA, CENTRAL JAVA, INDONESIA

    OpenAIRE

    Harijoko, Agung; Htun, Tin May; Saputra, Rodhie; Warmada, I Wayan; Setijadji, Lucas Donny; Imai, Akira; Watanabe, Koichiro

    2015-01-01

    Small scale gold mines discussed here are located at Selogiri area, Central Java, Indonesia which was mined by local community mainly during gold rush in 1990s. This Selogiri gold deposit genetically is characterized by porphyry mineralization overprinted by epithermal system. The ore minerals assemblage consists of pyrite, sphalerite, chalcopyrite, galena, chalcocite and rare arsenopyrite. Chemical analysis of soil and stream sediment sampled over 1.5 km across at the Selogiri gold extra...

  1. Leadership solves collective action problems in small-scale societies

    Science.gov (United States)

    Glowacki, Luke; von Rueden, Chris

    2015-01-01

    Observation of leadership in small-scale societies offers unique insights into the evolution of human collective action and the origins of sociopolitical complexity. Using behavioural data from the Tsimane forager-horticulturalists of Bolivia and Nyangatom nomadic pastoralists of Ethiopia, we evaluate the traits of leaders and the contexts in which leadership becomes more institutional. We find that leaders tend to have more capital, in the form of age-related knowledge, body size or social connections. These attributes can reduce the costs leaders incur and increase the efficacy of leadership. Leadership becomes more institutional in domains of collective action, such as resolution of intragroup conflict, where collective action failure threatens group integrity. Together these data support the hypothesis that leadership is an important means by which collective action problems are overcome in small-scale societies. PMID:26503683

  2. Biofuels in Africa: growing small-scale opportunities

    Energy Technology Data Exchange (ETDEWEB)

    Sulle, Emmanuel [Tanzania Natural Resources Forum (Tanzania, United Republic of); Fauveaud, Swan [Renewable Energy Group, Environment and Solidarity (France); Vermeulen, Sonja

    2009-11-15

    Global demand for climate-friendly transport fuels is driving vast commercial biofuels projects in developing countries. At the opposite end of the spectrum is small-scale bioenergy production. This offers a way for the poor to meet their energy needs and diversify their livelihoods without compromising food security or environmental integrity. Governments hope that it will be possible to combine the advantages of both large- and small-scale production of biofuels to generate energy security and GDP at the national level, while opening up local opportunities. In Africa, most governments are keen to attract foreign direct investment, and see big business as a strategic means of scaling up rural development. But there is a middle way. By encouraging business models that bridge large and small enterprise, African governments could show that commercial competition can go hand in hand with a range of real local benefits.

  3. Sustainability Metrics of a Small Scale Turbojet Engine

    Science.gov (United States)

    Ekici, Selcuk; Sohret, Yasin; Coban, Kahraman; Altuntas, Onder; Karakoc, T. Hikmet

    2018-05-01

    Over the last decade, sustainable energy consumption has attracted the attention of scientists and researchers. The current paper presents sustainability indicators of a small scale turbojet engine, operated on micro-aerial vehicles, for discussion of the sustainable development of the aviation industry from a different perspective. Experimental data was obtained from an engine at full power load and utilized to conduct an exergy-based sustainability analysis. Exergy efficiency, waste exergy ratio, recoverable exergy ratio, environmental effect factor, exergy destruction factor and exergetic sustainability index are evaluated as exergetic sustainability indicators of the turbojet engine under investigation in the current study. The exergy efficiency of the small scale turbojet engine is calculated as 27.25 % whereas the waste exergy ratio, the exergy destruction factor and the sustainability index of the engine are found to be 0.9756, 0.5466 and 0.2793, respectively.

  4. Leadership solves collective action problems in small-scale societies.

    Science.gov (United States)

    Glowacki, Luke; von Rueden, Chris

    2015-12-05

    Observation of leadership in small-scale societies offers unique insights into the evolution of human collective action and the origins of sociopolitical complexity. Using behavioural data from the Tsimane forager-horticulturalists of Bolivia and Nyangatom nomadic pastoralists of Ethiopia, we evaluate the traits of leaders and the contexts in which leadership becomes more institutional. We find that leaders tend to have more capital, in the form of age-related knowledge, body size or social connections. These attributes can reduce the costs leaders incur and increase the efficacy of leadership. Leadership becomes more institutional in domains of collective action, such as resolution of intragroup conflict, where collective action failure threatens group integrity. Together these data support the hypothesis that leadership is an important means by which collective action problems are overcome in small-scale societies. © 2015 The Author(s).

  5. Financing small-scale infrastructure investments in developing countries

    OpenAIRE

    Daniel L. Bond; Daniel Platz; Magnus Magnusson

    2012-01-01

    In most developing countries a shortage of long-term, local-currency financing for small-scale infrastructure projects impedes local economic development. Inadequate fiscal transfers, little own source revenue and low creditworthiness make it difficult for local governments to fully fund projects on their own. This paper proposes the use of project finance as a means to attract financing from domestic banks and institutional investors. Donors can play a catalytic role by providing technical a...

  6. Managing Small-Scale Fisheries : Alternative Directions and Methods

    International Development Research Centre (IDRC) Digital Library (Canada)

    Managing Small-scale Fisheries va plus loin que le champ d'application de la gestion classique des pêches pour aborder d'autres concepts, outils, méthodes et ... Les gestionnaires des pêches, tant du secteur public que du secteur privé, les chargés de cours et les étudiants en gestion des pêches, les organisations et les ...

  7. Acetone facilitated DNA sampling from electrical tapes improves DNA recovery and enables latent fingerprints development.

    Science.gov (United States)

    Feine, Ilan; Shpitzen, Moshe; Geller, Boris; Salmon, Eran; Peleg, Tsach; Roth, Jonathan; Gafny, Ron

    2017-07-01

    Electrical tapes (ETs) are a common component of improvised explosive devices (IEDs) used by terrorists or criminal organizations and represent a valuable forensic resource for DNA and latent fingerprints recovery. However, DNA recovery rates are typically low and usually below the minimal amount required for amplification. In addition, most DNA extraction methods are destructive and do not allow further latent fingerprints development. In the present study a cell culture based touch DNA model was used to demonstrate a two-step acetone-water DNA recovery protocol from ETs. This protocol involves only the adhesive side of the ET and increases DNA recovery rates by up to 70%. In addition, we demonstrated partially successful latent fingerprints development from the non-sticky side of the ETs. Taken together, this protocol maximizes the forensic examination of ETs and is recommended for routine casework processing. Copyright © 2017 Elsevier B.V. All rights reserved.

  8. Empirical spatial econometric modelling of small scale neighbourhood

    Science.gov (United States)

    Gerkman, Linda

    2012-07-01

    The aim of the paper is to model small scale neighbourhood in a house price model by implementing the newest methodology in spatial econometrics. A common problem when modelling house prices is that in practice it is seldom possible to obtain all the desired variables. Especially variables capturing the small scale neighbourhood conditions are hard to find. If there are important explanatory variables missing from the model, the omitted variables are spatially autocorrelated and they are correlated with the explanatory variables included in the model, it can be shown that a spatial Durbin model is motivated. In the empirical application on new house price data from Helsinki in Finland, we find the motivation for a spatial Durbin model, we estimate the model and interpret the estimates for the summary measures of impacts. By the analysis we show that the model structure makes it possible to model and find small scale neighbourhood effects, when we know that they exist, but we are lacking proper variables to measure them.

  9. The legalization of small scale mining in Colombia

    Directory of Open Access Journals (Sweden)

    Alexandra Urán

    2013-11-01

    Full Text Available The following article presents conceptual and analytical elements that allow us to broaden the debate about the legalization of the mining in Colombia. Looking for items to be able to propose alternatives in order to consolidate a new mining process socially and environmentally sustainable, claiming the value of the ancestral practices and forms of the redistributive production. To this end, it is necessary to start with the discussion of the concepts of formalization and legality, so that we can generate a theoretical framework that will allow us to explore such delicate matter, we will continue to make the framework socio-political, in which it is based that strategy. Then there is a brief context of thereformulation of legal mining, focusing our attention particularly standards which involves or has effects on artisanal mining and/or small-scale mining. There we will find ourselves with a debate on the typology of the mining and the current difficulties to define schemasof legalization or formalization of small-scale mining in Colombia. To conclude with a proposal to formalize as a mechanism of transition to an administrative system - legislativethat will connect more effectively with the realities and skills of the ethnic communities that practice small-scale mining.

  10. a Model Study of Small-Scale World Map Generalization

    Science.gov (United States)

    Cheng, Y.; Yin, Y.; Li, C. M.; Wu, W.; Guo, P. P.; Ma, X. L.; Hu, F. M.

    2018-04-01

    With the globalization and rapid development every filed is taking an increasing interest in physical geography and human economics. There is a surging demand for small scale world map in large formats all over the world. Further study of automated mapping technology, especially the realization of small scale production on a large scale global map, is the key of the cartographic field need to solve. In light of this, this paper adopts the improved model (with the map and data separated) in the field of the mapmaking generalization, which can separate geographic data from mapping data from maps, mainly including cross-platform symbols and automatic map-making knowledge engine. With respect to the cross-platform symbol library, the symbol and the physical symbol in the geographic information are configured at all scale levels. With respect to automatic map-making knowledge engine consists 97 types, 1086 subtypes, 21845 basic algorithm and over 2500 relevant functional modules.In order to evaluate the accuracy and visual effect of our model towards topographic maps and thematic maps, we take the world map generalization in small scale as an example. After mapping generalization process, combining and simplifying the scattered islands make the map more explicit at 1 : 2.1 billion scale, and the map features more complete and accurate. Not only it enhance the map generalization of various scales significantly, but achieve the integration among map-makings of various scales, suggesting that this model provide a reference in cartographic generalization for various scales.

  11. Sterile paper points as a bacterial DNA-contamination source in microbiome profiles of clinical samples

    NARCIS (Netherlands)

    van der Horst, J.; Buijs, M.J.; Laine, M.L.; Wismeijer, D.; Loos, B.G.; Crielaard, W.; Zaura, E.

    2013-01-01

    Objectives High throughput sequencing of bacterial DNA from clinical samples provides untargeted, open-ended information on the entire microbial community. The downside of this approach is the vulnerability to DNA contamination from other sources than the clinical sample. Here we describe

  12. Analysis of multiple single nucleotide polymorphisms (SNP) on DNA traces from plasma and dried blood samples

    NARCIS (Netherlands)

    Catsburg, Arnold; van der Zwet, Wil C.; Morre, Servaas A.; Ouburg, Sander; Vandenbroucke-Grauls, Christina M. J. E.; Savelkoul, Paul H. M.

    2007-01-01

    Reliable analysis of single nucleotide polymorphisms (SNPs) in DNA derived from samples containing low numbers of cells or from suboptimal sources can be difficult. A new procedure to characterize multiple SNPs in traces of DNA from plasma and old dried blood samples was developed. Six SNPs in the

  13. Passive Plasma Contact Mechanisms for Small-Scale Spacecraft

    Science.gov (United States)

    McTernan, Jesse K.

    Small-scale spacecraft represent a paradigm shift in how entities such as academia, industry, engineering firms, and the scientific community operate in space. However, although the paradigm shift produces unique opportunities to build satellites in unique ways for novel missions, there are also significant challenges that must be addressed. This research addresses two of the challenges associated with small-scale spacecraft: 1) the miniaturization of spacecraft and associated instrumentation and 2) the need to transport charge across the spacecraft-environment boundary. As spacecraft decrease in size, constraints on the size, weight, and power of on-board instrumentation increase--potentially limiting the instrument's functionality or ability to integrate with the spacecraft. These constraints drive research into mechanisms or techniques that use little or no power and efficiently utilize existing resources. One limited resource on small-scale spacecraft is outer surface area, which is often covered with solar panels to meet tight power budgets. This same surface area could also be needed for passive neutralization of spacecraft charging. This research explores the use of a transparent, conductive layer on the solar cell coverglass that is electrically connected to spacecraft ground potential. This dual-purpose material facilitates the use of outer surfaces for both energy harvesting of solar photons as well as passive ion collection. Mission capabilities such as in-situ plasma measurements that were previously infeasible on small-scale platforms become feasible with the use of indium tin oxide-coated solar panel coverglass. We developed test facilities that simulate the space environment in low Earth orbit to test the dual-purpose material and the various application of this approach. Particularly, this research is in support of two upcoming missions: OSIRIS-3U, by Penn State's Student Space Programs Lab, and MiTEE, by the University of Michigan. The purpose of

  14. Sources of pre-analytical variations in yield of DNA extracted from blood samples: analysis of 50,000 DNA samples in EPIC.

    Directory of Open Access Journals (Sweden)

    Elodie Caboux

    Full Text Available The European Prospective Investigation into Cancer and nutrition (EPIC is a long-term, multi-centric prospective study in Europe investigating the relationships between cancer and nutrition. This study has served as a basis for a number of Genome-Wide Association Studies (GWAS and other types of genetic analyses. Over a period of 5 years, 52,256 EPIC DNA samples have been extracted using an automated DNA extraction platform. Here we have evaluated the pre-analytical factors affecting DNA yield, including anthropometric, epidemiological and technical factors such as center of subject recruitment, age, gender, body-mass index, disease case or control status, tobacco consumption, number of aliquots of buffy coat used for DNA extraction, extraction machine or procedure, DNA quantification method, degree of haemolysis and variations in the timing of sample processing. We show that the largest significant variations in DNA yield were observed with degree of haemolysis and with center of subject recruitment. Age, gender, body-mass index, cancer case or control status and tobacco consumption also significantly impacted DNA yield. Feedback from laboratories which have analyzed DNA with different SNP genotyping technologies demonstrate that the vast majority of samples (approximately 88% performed adequately in different types of assays. To our knowledge this study is the largest to date to evaluate the sources of pre-analytical variations in DNA extracted from peripheral leucocytes. The results provide a strong evidence-based rationale for standardized recommendations on blood collection and processing protocols for large-scale genetic studies.

  15. Risk management strategies on small-scale commercial farms in three zobatat of Eritrea

    Directory of Open Access Journals (Sweden)

    MA Mohammed

    2014-05-01

    Full Text Available In this study the perceptions of small-scale commercial farmers in Eritrea of the importance of various risk responses are ascertained and analysed to gain insight into their risk-management strategies.  Data were elicited through a survey of 186 small-scale commercial farmers conducted in three zobatat (regions of Eritrea. Factor Analysis is used to investigate heterogeneity in sample farmers’ responses.  Results indicate that relatively more important risk responses include the use of internal and external sources of information, on-farm and off-farm diversification, choice of production system and product marketing arrangements. Farmers’ perceptions of risk responses vary according to farm type, geographical location, farm and farmer characteristics, as well as the existence of enterprise specific risk responses (e.g. livestock insurance and differences in the marketing regulations of various agricultural products.

  16. Computational analyses of ancient pathogen DNA from herbarium samples: challenges and prospects.

    Science.gov (United States)

    Yoshida, Kentaro; Sasaki, Eriko; Kamoun, Sophien

    2015-01-01

    The application of DNA sequencing technology to the study of ancient DNA has enabled the reconstruction of past epidemics from genomes of historically important plant-associated microbes. Recently, the genome sequences of the potato late blight pathogen Phytophthora infestans were analyzed from 19th century herbarium specimens. These herbarium samples originated from infected potatoes collected during and after the Irish potato famine. Herbaria have therefore great potential to help elucidate past epidemics of crops, date the emergence of pathogens, and inform about past pathogen population dynamics. DNA preservation in herbarium samples was unexpectedly good, raising the possibility of a whole new research area in plant and microbial genomics. However, the recovered DNA can be extremely fragmented resulting in specific challenges in reconstructing genome sequences. Here we review some of the challenges in computational analyses of ancient DNA from herbarium samples. We also applied the recently developed linkage method to haplotype reconstruction of diploid or polyploid genomes from fragmented ancient DNA.

  17. Impact of temperature and time storage on the microbial detection of oral samples by Checkerboard DNA-DNA hybridization method.

    Science.gov (United States)

    do Nascimento, Cássio; dos Santos, Janine Navarro; Pedrazzi, Vinícius; Pita, Murillo Sucena; Monesi, Nadia; Ribeiro, Ricardo Faria; de Albuquerque, Rubens Ferreira

    2014-01-01

    Molecular diagnosis methods have been largely used in epidemiological or clinical studies to detect and quantify microbial species that may colonize the oral cavity in healthy or disease. The preservation of genetic material from samples remains the major challenge to ensure the feasibility of these methodologies. Long-term storage may compromise the final result. The aim of this study was to evaluate the effect of temperature and time storage on the microbial detection of oral samples by Checkerboard DNA-DNA hybridization. Saliva and supragingival biofilm were taken from 10 healthy subjects, aliquoted (n=364) and processed according to proposed protocols: immediate processing and processed after 2 or 4 weeks, and 6 or 12 months of storage at 4°C, -20°C and -80°C. Either total or individual microbial counts were recorded in lower values for samples processed after 12 months of storage, irrespective of temperatures tested. Samples stored up to 6 months at cold temperatures showed similar counts to those immediately processed. The microbial incidence was also significantly reduced in samples stored during 12 months in all temperatures. Temperature and time of oral samples storage have relevant impact in the detection and quantification of bacterial and fungal species by Checkerboard DNA-DNA hybridization method. Samples should be processed immediately after collection or up to 6 months if conserved at cold temperatures to avoid false-negative results. Copyright © 2013 Elsevier Ltd. All rights reserved.

  18. Identification of Forensic Samples via Mitochondrial DNA in the Undergraduate Biochemistry Laboratory

    Science.gov (United States)

    Millard, Julie T.; Pilon, André M.

    2003-04-01

    A recent forensic approach for identification of unknown biological samples is mitochondrial DNA (mtDNA) sequencing. We describe a laboratory exercise suitable for an undergraduate biochemistry course in which the polymerase chain reaction is used to amplify a 440 base pair hypervariable region of human mtDNA from a variety of "crime scene" samples (e.g., teeth, hair, nails, cigarettes, envelope flaps, toothbrushes, and chewing gum). Amplification is verified via agarose gel electrophoresis and then samples are subjected to cycle sequencing. Sequence alignments are made via the program CLUSTAL W, allowing students to compare samples and solve the "crime."

  19. Influence of Sampling Practices on the Appearance of DNA Image Histograms of Prostate Cells in FNAB Samples

    Directory of Open Access Journals (Sweden)

    Abdelbaset Buhmeida

    1999-01-01

    Full Text Available Twenty‐one fine needle aspiration biopsies (FNAB of the prostate, diagnostically classified as definitely malignant, were studied. The Papanicolaou or H&E stained samples were destained and then stained for DNA with the Feulgen reaction. DNA cytometry was applied after different sampling rules. The histograms varied according to the sampling rule applied. Because free cells between cell groups were easier to measure than cells in the cell groups, two sampling rules were tested in all samples: (i cells in the cell groups were measured, and (ii free cells between cell groups were measured. Abnormal histograms were more common after the sampling rule based on free cells, suggesting that abnormal patterns are best revealed through the free cells in these samples. The conclusions were independent of the applied histogram interpretation method.

  20. Improved reproducibility in genome-wide DNA methylation analysis for PAXgene® fixed samples compared to restored FFPE DNA

    DEFF Research Database (Denmark)

    Andersen, Gitte Brinch; Hager, Henrik; Hansen, Lise Lotte

    2014-01-01

    Chip. Quantitative DNA methylation analysis demonstrated that the methylation profile in PAXgene-fixed tissues showed, in comparison with restored FFPE samples, a higher concordance with the profile detected in frozen samples. We demonstrate, for the first time, that DNA from PAXgene conserved tissue performs better......Formalin fixation has been the standard method for conservation of clinical specimens for decades. However, a major drawback is the high degradation of nucleic acids, which complicates its use in genome-wide analyses. Unbiased identification of biomarkers, however, requires genome-wide studies......, precluding the use of the valuable archives of specimens with long-term follow-up data. Therefore, restoration protocols for DNA from formalin-fixed and paraffin-embedded (FFPE) samples have been developed, although they are cost-intensive and time-consuming. An alternative to FFPE and snap...

  1. Small-Scale Combined Heat and Power Plants Using Biofuels

    Energy Technology Data Exchange (ETDEWEB)

    Salomon-Popa, Marianne [Royal Inst. of Tech., Stockholm (Sweden). Dept. of Energy Technology

    2002-11-01

    In this time period where energy supply and climate change are of special concern, biomass-based fuels have attracted much interest due to their plentiful supply and favorable environmental characteristics (if properly managed). The effective capture and continued sustainability of this renewable resource requires a new generation of biomass power plants with high fuel energy conversion. At the same time, deregulation of the electricity market offers new opportunities for small-scale power plants in a decentralized scheme. These two important factors have opened up possibilities for small-scale combined heat and power (CHP) plants based on biofuels. The objective of this pre-study is to assess the possibilities and technical limitations for increased efficiency and energy utilization of biofuels in small size plants (approximately 10 MWe or lower). Various energy conversion technologies are considered and proven concepts for large-scale fossil fuel plants are an especially important area. An analysis has been made to identify the problems, technical limitations and different possibilities as recognized in the literature. Beyond published results, a qualitative survey was conducted to gain first-hand, current knowledge from experts in the field. At best, the survey results together with the results of personal interviews and a workshop on the role of small-scale plants in distributed generation will serve a guideline for future project directions and ideas. Conventional and novel technologies are included in the survey such as Stirling engines, combustion engines, gas turbines, steam turbines, steam motors, fuel cells and other novel technologies/cycles for biofuels. State-of-the-art heat and power plants will be identified to clarify of the advantages and disadvantages as well as possible obstacles for their implementation.

  2. Small-scale power plant potential in Finland

    International Nuclear Information System (INIS)

    Helynen, S.

    1993-01-01

    The presentation discusses the small-scale power plant potential in Finland. The study of the potential is limited to W-scale power plants producing both electric power and heat using solid fuels. The basic power plant dimensioning and electric power load determination is based on traditional boiler and gas turbine technology. The possible sites for power plants are communities using district heating, and industrialized sites needing process steam or heat. In 1990 70 % (17 TWh) of district heat was produced by gas turbines. Ten communities have an own back-pressure power plant, and 40 communities buy heat from industrial plants, owing back-pressure power generation. Additionally about 40 communes buy district heat from companies, owned by power companies and industry. Estimates of small-scale power plant potential has been made plant wise on the basis of district heat loads and industrial heat needs. The scale of the plants has been limited to scale 3 MWe or more. The choosing of the fuel depends on the local conditions. The cheapest indigenous fuels in many communes are industrial wood wastes, and both milled and sod peat. The potential of steam technology based small-scale power plants has been estimated to be about 50 plants in 1992/1993, the total power of which is 220-260 MW. The largest estimate is base situation, in which there would be energy cooperation between the communes and industry. The fuel used by the power plants would be about 5.4-6.6 TWh/a corresponding to 270-330 million FIM/a. The total investment costs of the plants would be about 2.0 billion FIM. The plants would employ about 250 persons, and the fuel supply (wood or peat) about 100 persons

  3. Examples of backreaction of small-scale inhomogeneities in cosmology

    Science.gov (United States)

    Green, Stephen R.; Wald, Robert M.

    2013-06-01

    In previous work, we introduced a new framework to treat large-scale backreaction effects due to small-scale inhomogeneities in general relativity. We considered one-parameter families of spacetimes for which such backreaction effects can occur, and we proved that, provided the weak energy condition on matter is satisfied, the leading effect of small-scale inhomogeneities on large-scale dynamics is to produce a traceless effective stress-energy tensor that itself satisfies the weak energy condition. In this work, we illustrate the nature of our framework by providing two explicit examples of one-parameter families with backreaction. The first, based on previous work of Berger, is a family of polarized vacuum Gowdy spacetimes on a torus, which satisfies all of the assumptions of our framework. As the parameter approaches its limiting value, the metric uniformly approaches a smooth background metric, but spacetime derivatives of the deviation of the metric from the background metric do not converge uniformly to zero. The limiting metric has nontrivial backreaction from the small-scale inhomogeneities, with an effective stress energy that is traceless and satisfies the weak energy condition, in accord with our theorems. Our second one-parameter family consists of metrics which have a uniform Friedmann-Lemaître-Robertson-Walker limit. This family satisfies all of our assumptions with the exception of the weak energy condition for matter. In this case, the limiting metric has an effective stress-energy tensor which is not traceless. We emphasize the importance of imposing energy conditions on matter in studies of backreaction.

  4. Evaluating Ethanol-based Sample Preservation to Facilitate Use of DNA Barcoding in Routine Freshwater Biomonitoring Programs Using Benthic Macroinvertebrates

    Science.gov (United States)

    Molecular methods, such as DNA barcoding, have the potential in enhance biomonitoring programs worldwide. Altering routinely used sample preservation methods to protect DNA from degradation may pose a potential impediment to application of DNA barcoding and metagenomics for biom...

  5. Aerodynamics of small-scale vertical-axis wind turbines

    Science.gov (United States)

    Paraschivoiu, I.; Desy, P.

    1985-12-01

    The purpose of this work is to study the influence of various rotor parameters on the aerodynamic performance of a small-scale Darrieus wind turbine. To do this, a straight-bladed Darrieus rotor is calculated by using the double-multiple-streamtube model including the streamtube expansion effects through the rotor (CARDAAX computer code) and the dynamicstall effects. The straight-bladed Darrieus turbine is as expected more efficient with respect the curved-bladed rotor but for a given solidity is operates at higher wind speeds.

  6. Interactive economic analysis of small-scale heating plant

    Energy Technology Data Exchange (ETDEWEB)

    Landen, R.A.; Sanders, D.L.; Douglas, B.H.

    1998-11-01

    This report contains the work that has been undertaken by LRZ Limited in pursuance of this agreement. The potential for small-scale biomass heating systems is identified, and surrounding issues relating to acceptance are discussed. Such systems are described, and the origins of capital and running costs examined. A full review of the calculation methods for boiler plant size and fuel consumption is made, and subsequently expounded in four varying case studies. The results of this work are discussed, and the final development of the computer models is reviewed, incorporating further refinements to the method. Finally, data not contained in the text is incorporated in comprehensive appendices. (author)

  7. Small-scale generator opportunities in the competitive supply market

    International Nuclear Information System (INIS)

    Scrivener, G.

    1998-01-01

    The last franchises for electricity supply held by Public Electricity Suppliers are due to expire early in 1998. As a consequence from then on, after a phased start-up, all electricity consumers will be free to choose their supplier, completing the process of introducing competition into the electricity market which started in 1990 with the privatisation of the Industry. Then the framework by which the industry operates will become very different. This paper will review the changes to the operation of the market and assess the opportunities for small scale embedded generators post 1998. (Author)

  8. Analysis of small-scale rotor hover performance data

    Science.gov (United States)

    Kitaplioglu, Cahit

    1990-01-01

    Rotor hover-performance data from a 1/6-scale helicopter rotor are analyzed and the data sets compared for the effects of ambient wind, test stand configuration, differing test facilities, and scaling. The data are also compared to full scale hover data. The data exhibited high scatter, not entirely due to ambient wind conditions. Effects of download on the test stand proved to be the most significant influence on the measured data. Small-scale data correlated resonably well with full scale data; the correlation did not improve with Reynolds number corrections.

  9. Thermodynamic comparison of three small-scale gas liquefaction systems

    DEFF Research Database (Denmark)

    Nguyen, Tuong-Van; Rothuizen, Erasmus Damgaard; Markussen, Wiebke Brix

    2017-01-01

    . The present work investigates three configurations suitable for small-scale applications because of their simplicity and compactness: the single-mixed refrigerant, single and dual reverse Brayton cycles. The impact of different feed compositions and refrigerant properties is analysed. A detailed assessment...... to be more efficient (1000-2000 kJ/kgLNG) than expander-based ones (2500-5000 kJ/kgLNG) over larger ranges of operating conditions, at the expense of a greater system complexity and higher thermal conductance (250-500kW/K against 80-160 kW/K). The results show that the use of different thermodynamic models...

  10. Development of small scale soft x-ray lasers

    International Nuclear Information System (INIS)

    Kim, D.; Suckewer, S.; Princeton Univ., NJ; Skinner, C.H.; Voorhees, D.

    1991-05-01

    At present rapid progress is being made in the application of soft x-ray lasers to fields such as microscopy and microlithography. A critical factor in the range of suitable applications is the scale and hence cost of the soft x-ray lasers. At Princeton, gain at 183 angstrom has been obtained with relatively low pump laser energies (as low as 6J) in a ''portable'' small-scale soft x-ray laser system. We will also discuss aspects of data interpretation and pitfalls to be avoided in measurements of gain in such systems. 14 refs., 7 figs

  11. Small scale pelletizing equipment for agriculture; Smaaskalig pelleteringsanlaeggning foer lantbruket

    Energy Technology Data Exchange (ETDEWEB)

    Paulrud, Susanne (The Swedish Environmental Research Inst. Ltd., Stockholm (Sweden)); Wallin, Mikael (Sweden Powers Chippers AB, Boraas (Sweden))

    2009-06-15

    Refining agricultural raw materials is one way for farmers to increase the value of their products. For example, briquettes or pellets made from straw, reed canary grass or hemp can sell for a higher price than in loose or baled forms. The aim of this project was to develop and build a plant for small-scale production of pellets on the farm. Working together with the farmer, the plant would then be tested and adapted for small-scale production of pellets from straw, reed canary grass and hemp. The project also aimed to investigate and summarise suitable systems and solutions for breaking up bales in preparation for use in the pellets module. A pelleting system has been developed and built as a container module (measuring 6 x 2.80 x 2.50 m) by Sweden Power Chippers (SPC). The container system includes a fuel store with push floor, a grinder, an SPC pellet press (pp150, capacity 150 kg/hour for woodbased material), a conveyor belt and a cooling system. The practical operation of the plant was tested on two Swedish farms: Laattra gaard in Vingaaker and Ek gaard in Vara. The bales were broken up in preparation for pelleting using a straw mill of model Tomahawk 505M. The project has demonstrated that the SPC plant has the capacity to be used for agricultural pelleting of fuels from straw, canary reed grass and hemp. Some modification and continued adjustment of the feed system for the fuel remains to be done in order to optimise and ensure the reliability of the pelleting process. A certain amount of modifications to the plant is required to enable cost-effective transportation between different locations. Tests showed that each batch of fuel was unique, even from the same raw material, and that optimisation of the dies is necessary for each specific case. Training is required to run the plant. The farmers have been able to run the plant themselves, for example, starting up the plant, changing the sieve on the grinder, changing dies etc. In order for such small-scale

  12. Small-scale generator opportunities in the competitive supply market

    Energy Technology Data Exchange (ETDEWEB)

    Scrivener, G. [Energy Technology Support Unit (ETSU), Harwell (United Kingdom)

    1998-07-01

    The last franchises for electricity supply held by Public Electricity Suppliers are due to expire early in 1998. As a consequence from then on, after a phased start-up, all electricity consumers will be free to choose their supplier, completing the process of introducing competition into the electricity market which started in 1990 with the privatisation of the Industry. Then the framework by which the industry operates will become very different. This paper will review the changes to the operation of the market and assess the opportunities for small scale embedded generators post 1998. (Author)

  13. Model Predictive Control for a Small Scale Unmanned Helicopter

    Directory of Open Access Journals (Sweden)

    Jianfu Du

    2008-11-01

    Full Text Available Kinematical and dynamical equations of a small scale unmanned helicoper are presented in the paper. Based on these equations a model predictive control (MPC method is proposed for controlling the helicopter. This novel method allows the direct accounting for the existing time delays which are used to model the dynamics of actuators and aerodynamics of the main rotor. Also the limits of the actuators are taken into the considerations during the controller design. The proposed control algorithm was verified in real flight experiments where good perfomance was shown in postion control mode.

  14. Dimensional analysis of small-scale steam explosion experiments

    International Nuclear Information System (INIS)

    Huh, K.; Corradini, M.L.

    1986-01-01

    Dimensional analysis applied to Nelson's small-scale steam explosion experiments to determine the qualitative effect of each relevant parameter for triggering a steam explosion. According to experimental results, the liquid entrapment model seems to be a consistent explanation for the steam explosion triggering mechanism. The three-dimensional oscillatory wave motion of the vapor/liquid interface is analyzed to determine the necessary conditions for local condensation and production of a coolant microjet to be entrapped in fuel. It is proposed that different contact modes between fuel and coolant may involve different initiation mechanisms of steam explosions

  15. Small scale studies of production of fissium aerosols

    International Nuclear Information System (INIS)

    Lindqvist, O.; Rydberg, J.

    1983-02-01

    A small scale study concerning the production and analysis of fission product aerosols formed at various temperatures as a function of the chemical composition of the fissium/corium mixture at the source is presented. CsOH, CsJ and Te are the main aerosol components to be expected. The thermodynamic characterization of occuring Te-iodides and other phases is of great importance for reactor core meltdown chemistry and for the evaluation of the aerosol transport tests. Elemental iodine seems not to be released in significant amounts in reducing atmosphere. Analysis data concerning elements, phases, themral analysis and gases are presented. (G.B.)

  16. Decreased mitochondrial DNA content in blood samples of patients with stage I breast cancer

    International Nuclear Information System (INIS)

    Xia, Peng; An, Han-Xiang; Dang, Cheng-Xue; Radpour, Ramin; Kohler, Corina; Fokas, Emmanouil; Engenhart-Cabillic, Rita; Holzgreve, Wolfgang; Zhong, Xiao Yan

    2009-01-01

    Alterations of mitochondrial DNA (mtDNA) have been implicated in carcinogenesis. We developed an accurate multiplex quantitative real-time PCR for synchronized determination of mtDNA and nuclear DNA (nDNA). We sought to investigate whether mtDNA content in the peripheral blood of breast cancer patients is associated with clinical and pathological parameters. Peripheral blood samples were collected from 60 patients with breast cancer and 51 age-matched healthy individuals as control. DNA was extracted from peripheral blood for the quantification of mtDNA and nDNA, using a one-step multiplex real-time PCR. A FAM labeled MGB probe and primers were used to amplify the mtDNA sequence of the ATP 8 gene, and a VIC labeled MGB probe and primers were employed to amplify the glyceraldehyde-3-phosphate-dehydrogenase gene. mtDNA content was correlated with tumor stage, menstruation status, and age of patients as well as lymph node status and the expression of estrogen receptor (ER), progesterone receptor (PR) and Her-2/neu protein. The content of mtDNA in stage I breast cancer patients was significantly lower than in other stages (overall P = 0.023). Reduced mtDNA was found often in post menopausal cancer group (P = 0.024). No difference in mtDNA content, in regards to age (p = 0.564), lymph node involvement (p = 0.673), ER (p = 0.877), PR (p = 0.763), and Her-2/neu expression (p = 0.335), was observed. Early detection of breast cancer has proved difficult and current detection methods are inadequate. In the present study, decreased mtDNA content in the peripheral blood of patients with breast cancer was strongly associated with stage I. The use of mtDNA may have diagnostic value and further studies are required to validate it as a potential biomarker for early detection of breast cancer

  17. Evaluation of Skin Surface as an Alternative Source of Reference DNA Samples: A Pilot Study.

    Science.gov (United States)

    Albujja, Mohammed H; Bin Dukhyil, Abdul Aziz; Chaudhary, Abdul Rauf; Kassab, Ahmed Ch; Refaat, Ahmed M; Babu, Saranya Ramesh; Okla, Mohammad K; Kumar, Sachil

    2018-01-01

    An acceptable area for collecting DNA reference sample is a part of the forensic DNA analysis development. The aim of this study was to evaluate skin surface cells (SSC) as an alternate source of reference DNA sample. From each volunteer (n = 10), six samples from skin surface areas (forearm and fingertips) and two traditional samples (blood and buccal cells) were collected. Genomic DNA was extracted and quantified then genotyped using standard techniques. The highest DNA concentration of SSC samples was collected using the tape/forearm method of collection (2.1 ng/μL). Cotton swabs moistened with ethanol yielded higher quantities of DNA than swabs moistened with salicylic acid, and it gave the highest percentage of full STR profiles (97%). This study supports the use of SSC as a noninvasive sampling technique and as a extremely useful source of DNA reference samples among certain cultures where the use of buccal swabs can be considered socially unacceptable. © 2017 American Academy of Forensic Sciences.

  18. Protocol for collecting eDNA samples from streams [Version 2.3

    Science.gov (United States)

    K. J. Carim; T. Wilcox; M. K. Young; K. S. McKelvey; M. K. Schwartz

    2015-01-01

    Throughout the 2014 field season, we had over two dozen biologist throughout the western US collect over 300 samples for eDNA analysis with paired controls. Control samples were collected by filtering 0.5 L of distilled water. No samples had any evidence of field contamination. This method of sampling verifies the cleanliness of the field equipment, as well as the...

  19. Forensic genetic SNP typing of low-template DNA and highly degraded DNA from crime case samples.

    Science.gov (United States)

    Børsting, Claus; Mogensen, Helle Smidt; Morling, Niels

    2013-05-01

    Heterozygote imbalances leading to allele drop-outs and disproportionally large stutters leading to allele drop-ins are known stochastic phenomena related to STR typing of low-template DNA (LtDNA). The large stutters and the many drop-ins in typical STR stutter positions are artifacts from the PCR amplification of tandem repeats. These artifacts may be avoided by typing bi-allelic markers instead of STRs. In this work, the SNPforID multiplex assay was used to type LtDNA. A sensitized SNP typing protocol was introduced, that increased signal strengths without increasing noise and without affecting the heterozygote balance. Allele drop-ins were only observed in experiments with 25 pg of DNA and not in experiments with 50 and 100 pg of DNA. The allele drop-in rate in the 25 pg experiments was 0.06% or 100 times lower than what was previously reported for STR typing of LtDNA. A composite model and two different consensus models were used to interpret the SNP data. Correct profiles with 42-49 SNPs were generated from the 50 and 100 pg experiments, whereas a few incorrect genotypes were included in the generated profiles from the 25 pg experiments. With the strict consensus model, between 35 and 48 SNPs were correctly typed in the 25 pg experiments and only one allele drop-out (error rate: 0.07%) was observed in the consensus profiles. A total of 28 crime case samples were selected for typing with the sensitized SNPforID protocol. The samples were previously typed with old STR kits during the crime case investigation and only partial profiles (0-6 STRs) were obtained. Eleven of the samples could not be quantified with the Quantifiler™ Human DNA Quantification kit because of partial or complete inhibition of the PCR. For eight of these samples, SNP typing was only possible when the buffer and DNA polymerase used in the original protocol was replaced with the AmpFℓSTR(®) SEfiler Plus™ Master Mix, which was developed specifically for challenging forensic samples. All

  20. Small-scale impacts as potential trigger for landslides on small Solar system bodies

    Science.gov (United States)

    Hofmann, Marc; Sierks, Holger; Blum, Jürgen

    2017-07-01

    We conducted a set of experiments to investigate whether millimetre-sized impactors impinging on a granular material at several m s-1 are able to trigger avalanches on small, atmosphereless planetary bodies. These experiments were carried out at the Zentrum für angewandte Raumfahrttechnologie und Mikrogravitation (ZARM) drop tower facility in Bremen, Germany to facilitate a reduced gravity environment. Additional data were gathered at Earth gravity levels in the laboratory. As sample materials we used a ground Howardites, Eucrites and Diogenites (HED) meteorite and the Johnson Space Center (JSC) Mars-1 Martian soil simulant. We found that this type of small-scale impact can trigger avalanches with a moderate probability, if the target material is tilted to an angle close to the angle of repose. We additionally simulated a small-scale impact using the discrete element method code esys-particle. These simulations show that energy transfer from impactor to the target material is most efficient at low- and moderate-impactor inclinations and the transferred energy is retained in particles close to the surface due to a rapid dissipation of energy in lower material layers driven by inelastic collisions. Through Monte Carlo simulations we estimate the time-scale on which small-scale impacts with the observed characteristics will trigger avalanches covering all steep slopes on the surface of a small planetary body to be of the order 105 yr.

  1. Thermal characteristics of various biomass fuels in a small-scale biomass combustor

    International Nuclear Information System (INIS)

    Al-Shemmeri, T.T.; Yedla, R.; Wardle, D.

    2015-01-01

    Biomass combustion is a mature and reliable technology, which has been used for heating and cooking. In the UK, biomass currently qualifies for financial incentives such as the Renewable Heat Incentive (RHI). Therefore, it is vital to select the right type of fuel for a small-scale combustor to address different types of heat energy needs. In this paper, the authors attempt to investigate the performance of a small-scale biomass combustor for heating, and the impact of burning different biomass fuels on useful output energy from the combustor. The test results of moisture content, calorific value and combustion products of various biomass samples were presented. Results from this study are in general agreement with published data as far as the calorific values and moisture contents are concerned. Six commonly available biomass fuels were tested in a small-scale combustion system, and the factors that affect the performance of the system were analysed. In addition, the study has extended to examine the magnitude and proportion of useful heat, dissipated by convection and radiation while burning different biomass fuels in the small-scale combustor. It is concluded that some crucial factors have to be carefully considered before selecting biomass fuels for any particular heating application. - Highlights: • Six biomass materials combustion performance in a small combustor was examined. • Fuel combustion rate and amount of heat release has varied between materials. • Heat release by radiation, convection and flue gasses varied between materials. • Study helps engineers and users of biomass systems to select right materials

  2. Community-Weighted Mean Plant Traits Predict Small Scale Distribution of Insect Root Herbivore Abundance.

    Directory of Open Access Journals (Sweden)

    Ilja Sonnemann

    Full Text Available Small scale distribution of insect root herbivores may promote plant species diversity by creating patches of different herbivore pressure. However, determinants of small scale distribution of insect root herbivores, and impact of land use intensity on their small scale distribution are largely unknown. We sampled insect root herbivores and measured vegetation parameters and soil water content along transects in grasslands of different management intensity in three regions in Germany. We calculated community-weighted mean plant traits to test whether the functional plant community composition determines the small scale distribution of insect root herbivores. To analyze spatial patterns in plant species and trait composition and insect root herbivore abundance we computed Mantel correlograms. Insect root herbivores mainly comprised click beetle (Coleoptera, Elateridae larvae (43% in the investigated grasslands. Total insect root herbivore numbers were positively related to community-weighted mean traits indicating high plant growth rates and biomass (specific leaf area, reproductive- and vegetative plant height, and negatively related to plant traits indicating poor tissue quality (leaf C/N ratio. Generalist Elaterid larvae, when analyzed independently, were also positively related to high plant growth rates and furthermore to root dry mass, but were not related to tissue quality. Insect root herbivore numbers were not related to plant cover, plant species richness and soil water content. Plant species composition and to a lesser extent plant trait composition displayed spatial autocorrelation, which was not influenced by land use intensity. Insect root herbivore abundance was not spatially autocorrelated. We conclude that in semi-natural grasslands with a high share of generalist insect root herbivores, insect root herbivores affiliate with large, fast growing plants, presumably because of availability of high quantities of food. Affiliation of

  3. Small-Scale High Temperature Melter-1 (SSHTM-1) Data Package. Appendix B

    Energy Technology Data Exchange (ETDEWEB)

    NONE

    1996-03-01

    This appendix provides the data for Alternate HTM Flowsheet 2 (Glycolic Acid) melter feed preparation activities in both the laboratory- and small-scale testing. The first section provides an outline of this appendix. The melter feed preparation data are presented in the next two main sections, laboratory melter feed preparation data and small-scale melter feed preparation data. Section 3.0 provides the laboratory data which is discussed in the main body of the Small-Scale High Temperature-1 (SSHTM-1) Data Package, milestone C95-02.02Y. Section 3.1 gives the flowsheet in outline form as used in the laboratory-scale tests. This section also includes the ``Laboratory Melter Feed Preparation Activity Log`` which gives A chronological account of the test in terms of time, temperature, slurry pH, and specific observations about slurry appearance, acid addition rates, and samples taken. The ``Laboratory Melter Feed Preparation Activity Log`` provides a road map to the reader by which all the activity and data from the laboratory can be easily accessed. A summary of analytical data is presented next, section 3.2, which covers starting materials and progresses to the analysis of the melter feed. The next section, 3.3, characterizes the off-gas generation that occurs during the slurry processing. The following section, 3.4, provides the rheology data gathered including gram waste oxide loading information for the various slurries tested. The final section, 3.5, includes data from standard crucible redox testing. Section 4.0 provides the small-scale data in parallel form to section 3.0. Section 5.0 concludes with the references for this appendix.

  4. Permanganate-assisted removal of PCR inhibitors during the DNA Chelex extraction from stained denim samples.

    Science.gov (United States)

    Pîrlea, Sorina; Puiu, Mihaela; Răducan, Adina; Oancea, Dumitru

    2017-03-01

    In this study, it was demonstrated that the DNA Chelex extraction combined with the permanganate assisted-oxidation is highly efficient in removing the PCR inhibitors often found in clothing materials, such as phthalocyanine. The extraction assays were conducted in saliva, blood and epithelial cells samples mixed with three oxidation-resistant dye copper(II) α-phthalocyanine, copper(II) β-phthalocyanine and tetrasulfonated copper(II) β-phthalocyanine. After DNA amplification, all samples were able to provide full DNA profiles. The permanganate/Chelex system was tested further on denim-stained samples and displayed the same ability to remove the PCR inhibitors from the commercial textile materials.

  5. Detection of Toxoplasma gondii DNA in sera samples of mice experimentally infected

    Directory of Open Access Journals (Sweden)

    H. Langoni

    2006-04-01

    Full Text Available Detection of Toxoplasma gondii (T. gondii DNA in blood can help to diagnose the disease in its acute phase; however, it must be considered that hemoglobin, present in blood, can inhibit polymerase activity, making impracticable the detection of DNA in samples. Mice were experimentally infected via oral route with ME49 and BTU2 strains cysts and RH strain tachyzoites; polymerase chain reaction was used to detect T. gondii DNA in mice sera 18, 24, 48, 96, and 192 hours post infection (PI. Toxoplama gondii DNA was detected in only one animal infected with BTU2 strain, genotype III (isolated from a dog with neurological signs 18 hours PI. The agent's DNA was not detected in any sample of the other experimental groups. New studies must be carried out to verify the technique sensitivity in researches on this agent's genetic material using sera samples of acute-phase toxoplasmosis patients, especially in cases of immunosuppression.

  6. High frequency of parvovirus B19 DNA in bone marrow samples from rheumatic patients

    DEFF Research Database (Denmark)

    Lundqvist, Anders; Isa, Adiba; Tolfvenstam, Thomas

    2005-01-01

    BACKGROUND: Human parvovirus B19 (B19) polymerase chain reaction (PCR) is now a routine analysis and serves as a diagnostic marker as well as a complement or alternative to B19 serology. The clinical significance of a positive B19 DNA finding is however dependent on the type of tissue or body fluid...... analysed and of the immune status of the patient. OBJECTIVES: To analyse the clinical significance of B19 DNA positivity in bone marrow samples from rheumatic patients. STUDY DESIGN: Parvovirus B19 DNA was analysed in paired bone marrow and serum samples by nested PCR technique. Serum was also analysed...... negative group. A high frequency of parvovirus B19 DNA was thus detected in bone marrow samples in rheumatic patients. The clinical data does not support a direct association between B19 PCR positivity and rheumatic disease manifestation. Therefore, the clinical significance of B19 DNA positivity in bone...

  7. Small-Scale Renewable Energy Converters for Battery Charging

    Directory of Open Access Journals (Sweden)

    Mohd Nasir Ayob

    2018-03-01

    Full Text Available This paper presents two wave energy concepts for small-scale electricity generation. In the presented case, these concepts are installed on the buoy of a heaving, point-absorbing wave energy converter (WEC for large scale electricity production. In the studied WEC, developed by Uppsala University, small-scale electricity generation in the buoy is needed to power a tidal compensating system designed to increase the performance of the WEC in areas with high tides. The two considered and modeled concepts are an oscillating water column (OWC and a heaving point absorber. The results indicate that the OWC is too small for the task and does not produce enough energy. On the other hand, the results show that a hybrid system composed of a small heaving point absorber combined with a solar energy system would be able to provide a requested minimum power of around 37.7 W on average year around. The WEC and solar panel complement each other, as the WEC produces enough energy by itself during wintertime (but not in the summer, while the solar panel produces enough energy in the summer (but not in the winter.

  8. Development of small scale cluster computer for numerical analysis

    Science.gov (United States)

    Zulkifli, N. H. N.; Sapit, A.; Mohammed, A. N.

    2017-09-01

    In this study, two units of personal computer were successfully networked together to form a small scale cluster. Each of the processor involved are multicore processor which has four cores in it, thus made this cluster to have eight processors. Here, the cluster incorporate Ubuntu 14.04 LINUX environment with MPI implementation (MPICH2). Two main tests were conducted in order to test the cluster, which is communication test and performance test. The communication test was done to make sure that the computers are able to pass the required information without any problem and were done by using simple MPI Hello Program where the program written in C language. Additional, performance test was also done to prove that this cluster calculation performance is much better than single CPU computer. In this performance test, four tests were done by running the same code by using single node, 2 processors, 4 processors, and 8 processors. The result shows that with additional processors, the time required to solve the problem decrease. Time required for the calculation shorten to half when we double the processors. To conclude, we successfully develop a small scale cluster computer using common hardware which capable of higher computing power when compare to single CPU processor, and this can be beneficial for research that require high computing power especially numerical analysis such as finite element analysis, computational fluid dynamics, and computational physics analysis.

  9. Biomedical device prototype based on small scale hydrodynamic cavitation

    Directory of Open Access Journals (Sweden)

    Morteza Ghorbani

    2018-03-01

    Full Text Available This study presents a biomedical device prototype based on small scale hydrodynamic cavitation. The application of small scale hydrodynamic cavitation and its integration to a biomedical device prototype is offered as an important alternative to other techniques, such as ultrasound therapy, and thus constitutes a local, cheap, and energy-efficient solution, for urinary stone therapy and abnormal tissue ablation (e.g., benign prostate hyperplasia (BPH. The destructive nature of bubbly, cavitating, flows was exploited, and the potential of the prototype was assessed and characterized. Bubbles generated in a small flow restrictive element (micro-orifice based on hydrodynamic cavitation were utilized for this purpose. The small bubbly, cavitating, flow generator (micro-orifice was fitted to a small flexible probe, which was actuated with a micromanipulator using fine control. This probe also houses an imaging device for visualization so that the emerging cavitating flow could be locally targeted to the desired spot. In this study, the feasibility of this alternative treatment method and its integration to a device prototype were successfully accomplished.

  10. Biomedical device prototype based on small scale hydrodynamic cavitation

    Science.gov (United States)

    Ghorbani, Morteza; Sozer, Canberk; Alcan, Gokhan; Unel, Mustafa; Ekici, Sinan; Uvet, Huseyin; Koşar, Ali

    2018-03-01

    This study presents a biomedical device prototype based on small scale hydrodynamic cavitation. The application of small scale hydrodynamic cavitation and its integration to a biomedical device prototype is offered as an important alternative to other techniques, such as ultrasound therapy, and thus constitutes a local, cheap, and energy-efficient solution, for urinary stone therapy and abnormal tissue ablation (e.g., benign prostate hyperplasia (BPH)). The destructive nature of bubbly, cavitating, flows was exploited, and the potential of the prototype was assessed and characterized. Bubbles generated in a small flow restrictive element (micro-orifice) based on hydrodynamic cavitation were utilized for this purpose. The small bubbly, cavitating, flow generator (micro-orifice) was fitted to a small flexible probe, which was actuated with a micromanipulator using fine control. This probe also houses an imaging device for visualization so that the emerging cavitating flow could be locally targeted to the desired spot. In this study, the feasibility of this alternative treatment method and its integration to a device prototype were successfully accomplished.

  11. Effects of thermal inflation on small scale density perturbations

    Energy Technology Data Exchange (ETDEWEB)

    Hong, Sungwook E. [School of Physics, Korea Institute for Advanced Study, 85 Hoegiro, Seoul 130-722 (Korea, Republic of); Lee, Hyung-Joo; Lee, Young Jae; Stewart, Ewan D. [Department of Physics, KAIST, 291 Daehak-ro, Yuseong-gu, Daejeon 305-338 (Korea, Republic of); Zoe, Heeseung, E-mail: swhong@kias.re.kr, E-mail: ohsk111@kaist.ac.kr, E-mail: noasac@kaist.ac.kr, E-mail: jcap@profstewart.org, E-mail: heezoe@dgist.ac.kr [School of Basic Science, Daegu Gyeongbuk Institute of Science and Technology (DGIST), 333 Techno jungang-daero, Daegu 711-873 (Korea, Republic of)

    2015-06-01

    In cosmological scenarios with thermal inflation, extra eras of moduli matter domination, thermal inflation and flaton matter domination exist between primordial inflation and the radiation domination of Big Bang nucleosynthesis. During these eras, cosmological perturbations on small scales can enter and re-exit the horizon, modifying the power spectrum on those scales. The largest modified scale, k{sub b}, touches the horizon size when the expansion changes from deflation to inflation at the transition from moduli domination to thermal inflation. We analytically calculate the evolution of perturbations from moduli domination through thermal inflation and evaluate the curvature perturbation on the constant radiation density hypersurface at the end of thermal inflation to determine the late time curvature perturbation. Our resulting transfer function suppresses the power spectrum by a factor 0∼ 5 at k >> k{sub b}, with k{sub b} corresponding to anywhere from megaparsec to subparsec scales depending on the parameters of thermal inflation. Thus, thermal inflation might be constrained or detected by small scale observations such as CMB distortions or 21cm hydrogen line observations.

  12. Small-scale engagement model with arrivals: analytical solutions

    International Nuclear Information System (INIS)

    Engi, D.

    1977-04-01

    This report presents an analytical model of small-scale battles. The specific impetus for this effort was provided by a need to characterize hypothetical battles between guards at a nuclear facility and their potential adversaries. The solution procedure can be used to find measures of a number of critical parameters; for example, the win probabilities and the expected duration of the battle. Numerical solutions are obtainable if the total number of individual combatants on the opposing sides is less than 10. For smaller force size battles, with one or two combatants on each side, symbolic solutions can be found. The symbolic solutions express the output parameters abstractly in terms of symbolic representations of the input parameters while the numerical solutions are expressed as numerical values. The input parameters are derived from the probability distributions of the attrition and arrival processes. The solution procedure reduces to solving sets of linear equations that have been constructed from the input parameters. The approach presented in this report does not address the problems associated with measuring the inputs. Rather, this report attempts to establish a relatively simple structure within which small-scale battles can be studied

  13. Small-Scale Smart Grid Construction and Analysis

    Science.gov (United States)

    Surface, Nicholas James

    The smart grid (SG) is a commonly used catch-phrase in the energy industry yet there is no universally accepted definition. The objectives and most useful concepts have been investigated extensively in economic, environmental and engineering research by applying statistical knowledge and established theories to develop simulations without constructing physical models. In this study, a small-scale version (SSSG) is constructed to physically represent these ideas so they can be evaluated. Results of construction show data acquisition three times more expensive than the grid itself although mainly due to the incapability to downsize 70% of data acquisition costs to small-scale. Experimentation on the fully assembled grid exposes the limitations of low cost modified sine wave power, significant enough to recommend pure sine wave investment in future SSSG iterations. Findings can be projected to full-size SG at a ratio of 1:10, based on the appliance representing average US household peak daily load. However this exposes disproportionalities in the SSSG compared with previous SG investigations and recommended changes for future iterations are established to remedy this issue. Also discussed are other ideas investigated in the literature and their suitability for SSSG incorporation. It is highly recommended to develop a user-friendly bidirectional charger to more accurately represent vehicle-to-grid (V2G) infrastructure. Smart homes, BEV swap stations and pumped hydroelectric storage can also be researched on future iterations of the SSSG.

  14. The case for small-scale domestic cannabis cultivation.

    Science.gov (United States)

    Decorte, Tom

    2010-07-01

    The shift to (inter)regional production, trade and domestic cultivation has become an irreversible international trend. Until now, the focus of most empirical work has been on large-scale, commercially oriented and professionally organized segments of the cannabis industry, often based on police data and on the perspective of law enforcement agencies. This paper offers a review of recent Dutch-language research that focuses on cannabis cultivation. Empirical studies were identified through literature searches using relevant search terms and Web of Science, Elin, Social Science Research Network and Elsevier ScienceDirect. The paper presents the main findings of Dutch and Belgian empirical work on the factors that stimulated the import substitution process on the cannabis market, aspects related to quality and potency issues, typologies of cannabis growers, and (unintended) effects of pursued policies. In the light of this (selective) review the author offers some commentary and analysis concerning the claims made by different stakeholders, and concludes with some reflections on future research and on policy implications. The author outlines the importance of small-scale, independent or ideologically oriented cannabis cultivation as an under-researched market segment. The author also makes a case for greater toleration of small-scale cannabis cultivation, to secure the least worst of cannabis markets. Copyright (c) 2010 Elsevier B.V. All rights reserved.

  15. Atmospheric dispersion modelling over complex terrain at small scale

    Science.gov (United States)

    Nosek, S.; Janour, Z.; Kukacka, L.; Jurcakova, K.; Kellnerova, R.; Gulikova, E.

    2014-03-01

    Previous study concerned of qualitative modelling neutrally stratified flow over open-cut coal mine and important surrounding topography at meso-scale (1:9000) revealed an important area for quantitative modelling of atmospheric dispersion at small-scale (1:3300). The selected area includes a necessary part of the coal mine topography with respect to its future expansion and surrounding populated areas. At this small-scale simultaneous measurement of velocity components and concentrations in specified points of vertical and horizontal planes were performed by two-dimensional Laser Doppler Anemometry (LDA) and Fast-Response Flame Ionization Detector (FFID), respectively. The impact of the complex terrain on passive pollutant dispersion with respect to the prevailing wind direction was observed and the prediction of the air quality at populated areas is discussed. The measured data will be used for comparison with another model taking into account the future coal mine transformation. Thus, the impact of coal mine transformation on pollutant dispersion can be observed.

  16. DNA damage in preserved specimens and tissue samples: a molecular assessment

    Directory of Open Access Journals (Sweden)

    Cantin Elizabeth

    2008-10-01

    Full Text Available Abstract The extraction of genetic information from preserved tissue samples or museum specimens is a fundamental component of many fields of research, including the Barcode of Life initiative, forensic investigations, biological studies using scat sample analysis, and cancer research utilizing formaldehyde-fixed, paraffin-embedded tissue. Efforts to obtain genetic information from these sources are often hampered by an inability to amplify the desired DNA as a consequence of DNA damage. Previous studies have described techniques for improved DNA extraction from such samples or focused on the effect of damaging agents – such as light, oxygen or formaldehyde – on free nucleotides. We present ongoing work to characterize lesions in DNA samples extracted from preserved specimens. The extracted DNA is digested to single nucleosides with a combination of DNase I, Snake Venom Phosphodiesterase, and Antarctic Phosphatase and then analyzed by HPLC-ESI-TOF-MS. We present data for moth specimens that were preserved dried and pinned with no additional preservative and for frog tissue samples that were preserved in either ethanol, or formaldehyde, or fixed in formaldehyde and then preserved in ethanol. These preservation methods represent the most common methods of preserving animal specimens in museum collections. We observe changes in the nucleoside content of these samples over time, especially a loss of deoxyguanosine. We characterize the fragmentation state of the DNA and aim to identify abundant nucleoside lesions. Finally, simple models are introduced to describe the DNA fragmentation based on nicks and double-strand breaks.

  17. A combined method for DNA analysis and radiocarbon dating from a single sample.

    Science.gov (United States)

    Korlević, Petra; Talamo, Sahra; Meyer, Matthias

    2018-03-07

    Current protocols for ancient DNA and radiocarbon analysis of ancient bones and teeth call for multiple destructive samplings of a given specimen, thereby increasing the extent of undesirable damage to precious archaeological material. Here we present a method that makes it possible to obtain both ancient DNA sequences and radiocarbon dates from the same sample material. This is achieved by releasing DNA from the bone matrix through incubation with either EDTA or phosphate buffer prior to complete demineralization and collagen extraction utilizing the acid-base-acid-gelatinization and ultrafiltration procedure established in most radiocarbon dating laboratories. Using a set of 12 bones of different ages and preservation conditions we demonstrate that on average 89% of the DNA can be released from sample powder with minimal, or 38% without any, detectable collagen loss. We also detect no skews in radiocarbon dates compared to untreated samples. Given the different material demands for radiocarbon dating (500 mg of bone/dentine) and DNA analysis (10-100 mg), combined DNA and collagen extraction not only streamlines the sampling process but also drastically increases the amount of DNA that can be recovered from limited sample material.

  18. Assessment of mercury exposure among small-scale gold miners using mercury stable isotopes

    International Nuclear Information System (INIS)

    Sherman, Laura S.; Blum, Joel D.; Basu, Niladri; Rajaee, Mozhgon; Evers, David C.; Buck, David G.; Petrlik, Jindrich; DiGangi, Joseph

    2015-01-01

    Total mercury (Hg) concentrations in hair and urine are often used as biomarkers of exposure to fish-derived methylmercury (MeHg) and gaseous elemental Hg, respectively. We used Hg stable isotopes to assess the validity of these biomarkers among small-scale gold mining populations in Ghana and Indonesia. Urine from Ghanaian miners displayed similar Δ 199 Hg values to Hg derived from ore deposits (mean urine Δ 199 Hg=0.01‰, n=6). This suggests that urine total Hg concentrations accurately reflect exposure to inorganic Hg among this population. Hair samples from Ghanaian miners displayed low positive Δ 199 Hg values (0.23–0.55‰, n=6) and low percentages of total Hg as MeHg (7.6–29%, n=7). These data suggest that the majority of the Hg in these miners' hair samples is exogenously adsorbed inorganic Hg and not fish-derived MeHg. Hair samples from Indonesian gold miners who eat fish daily displayed a wider range of positive Δ 199 Hg values (0.21–1.32‰, n=5) and percentages of total Hg as MeHg (32–72%, n=4). This suggests that total Hg in the hair samples from Indonesian gold miners is likely a mixture of ingested fish MeHg and exogenously adsorbed inorganic Hg. Based on data from both populations, we suggest that total Hg concentrations in hair samples from small-scale gold miners likely overestimate exposure to MeHg from fish consumption. - Highlights: • Mercury isotopes were measured in hair and urine from small-scale gold miners. • Mercury isotopes indicate that Hg in urine comes from mining activity. • Mercury isotopes suggest Hg in hair is a mixture of fish MeHg and inorganic Hg. • A large percentage of Hg in miner’s hair is released during amalgam burning and adsorbed

  19. High-resolution DNA content analysis of microbiopsy samples in oral lichen planus.

    Science.gov (United States)

    Pentenero, M; Monticone, M; Marino, R; Aiello, C; Marchitto, G; Malacarne, D; Giaretti, W; Gandolfo, S; Castagnola, P

    2017-04-01

    DNA aneuploidy has been reported to be a predictor of poor prognosis in both premalignant and malignant lesions. In oral lichen planus (OLP), this hypothesis remains to be proved. This study aimed to determine the rate of occurrence of DNA aneuploidy in patients with OLP by high-resolution DNA flow cytometry. Patients with OLP were consecutively enrolled. Tissue samples were subdivided for formalin fixation and routine histological assessment and for immediate storage at -20°C for later DNA ploidy analysis, which was performed by DAPI staining of the extracted nuclei and excitation with a UV lamp. The DNA aneuploid sublines were characterized by the DNA Index. A DNA aneuploid status was observed in two of 77 patients with OLP (2.6%). When considering the clinical aspect of the OLP lesions, both DNA aneuploid cases had a reticular clinical aspect. DNA aneuploidy is an uncommon event in OLP and less frequent compared to other non-dysplastic and non-OLP oral potentially malignant disorders. The extremely low rate of DNA aneuploidy could represent an occasional finding or reflect the low rate of malignant transformation observed in patients with OLP even if the real prognostic value of DNA ploidy analysis in patients with OLP remains to be confirmed. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  20. Repurposing environmental DNA samples: Detecting the western pearlshell (Margaritifera falcata) as a proof of concept

    Science.gov (United States)

    Joseph C. Dysthe; Torrey Rodgers; Thomas W. Franklin; Kellie J. Carim; Michael K. Young; Kevin S. McKelvey; Karen E. Mock; Michael K. Schwartz

    2018-01-01

    Information on the distribution of multiple species in a common landscape is fundamental to effective conservation and management. However, distribution data are expensive to obtain and often limited to high-profile species in a system. A recently developed technique, environmental DNA (eDNA) sampling, has been shown to be more sensitive than traditional detection...

  1. Comparing different post-mortem human samples as DNA sources for downstream genotyping and identification.

    Science.gov (United States)

    Calacal, Gayvelline C; Apaga, Dame Loveliness T; Salvador, Jazelyn M; Jimenez, Joseph Andrew D; Lagat, Ludivino J; Villacorta, Renato Pio F; Lim, Maria Cecilia F; Fortun, Raquel D R; Datar, Francisco A; De Ungria, Maria Corazon A

    2015-11-01

    The capability of DNA laboratories to perform genotyping procedures from post-mortem remains, including those that had undergone putrefaction, continues to be a challenge in the Philippines, a country characterized by very humid and warm conditions all year round. These environmental conditions accelerate the decomposition of human remains that were recovered after a disaster and those that were left abandoned after a crime. When considerable tissue decomposition of human remains has taken place, there is no other option but to extract DNA from bone and/or teeth samples. Routinely, femur shafts are obtained from recovered bodies for human identification because the calcium matrix protects the DNA contained in the osteocytes. In the Philippines, there is difficulty in collecting femur samples after natural disasters or even human-made disasters, because these events are usually characterized by a large number of fatalities. Identification of casualties is further delayed by limitation in human and material resources. Hence, it is imperative to test other types of biological samples that are easier to collect, transport, process and store. We analyzed DNA that were obtained from body fluid, bone marrow, muscle tissue, clavicle, femur, metatarsal, patella, rib and vertebral samples from five recently deceased untreated male cadavers and seven male human remains that were embalmed, buried for ∼ 1 month and then exhumed. The bodies had undergone different environmental conditions and were in various stages of putrefaction. A DNA extraction method utilizing a detergent-washing step followed by an organic procedure was used. The utility of bone marrow and vitreous fluid including bone marrow and vitreous fluid that was transferred on FTA(®) cards and subjected to autosomal STR and Y-STR DNA typing were also evaluated. DNA yield was measured and the presence or absence of PCR inhibitors in DNA extracts was assessed using Plexor(®)HY. All samples were amplified using

  2. Tri-allelic SNP markers enable analysis of mixed and degraded DNA samples.

    Science.gov (United States)

    Westen, Antoinette A; Matai, Anuska S; Laros, Jeroen F J; Meiland, Hugo C; Jasper, Mandy; de Leeuw, Wiljo J F; de Knijff, Peter; Sijen, Titia

    2009-09-01

    For the analysis of degraded DNA in disaster victim identification (DVI) and criminal investigations, single nucleotide polymorphisms (SNPs) have been recognized as promising markers mainly because they can be analyzed in short sized amplicons. Most SNPs are bi-allelic and are thereby ineffective to detect mixtures, which may lead to incorrect genotyping. We developed an algorithm to find non-binary (i.e. tri-allelic or tetra-allelic) SNPs in the NCBI dbSNP database. We selected 31 potential tri-allelic SNPs with a minor allele frequency of at least 10%. The tri-allelic nature was confirmed for 15 SNPs residing on 14 different chromosomes. Multiplex SNaPshot assays were developed, and the allele frequencies of 16 SNPs were determined among 153 Dutch and 111 Netherlands Antilles reference samples. Using these multiplex SNP assays, the presence of a mixture of two DNA samples in a ratio up to 1:8 could be recognized reliably. Furthermore, we compared the genotyping efficiency of the tri-allelic SNP markers and short tandem repeat (STR) markers by analyzing artificially degraded DNA and DNA from 30 approximately 500-year-old bone and molar samples. In both types of degraded DNA samples, the larger sized STR amplicons failed to amplify whereas the tri-allelic SNP markers still provided valuable information. In conclusion, tri-allelic SNP markers are suited for the analysis of degraded DNA and enable the detection of a second DNA source in a sample.

  3. LAMP assay for rapid diagnosis of cow DNA in goat milk and meat samples.

    Science.gov (United States)

    Deb, R; Sengar, G S; Singh, U; Kumar, S; Raja, T V; Alex, R; Alyethodi, R R; Prakash, B

    2017-01-01

    Animal species detection is one of the crucial steps for consumer's food analysis. In the present study we developed an in-house built loop-mediated isothermal amplification (LAMP) assay for rapid detection of adulterated cow DNA in goat milk/meat samples. The cow milk/tissue DNA in goat milk/meat samples were identified in the developed LAMP assay by either naked eye visualizing with SYBR Green I dyes or by detecting the typical ladder pattern on gel electrophoresis. This test can detect up to minimum 5% level of cow components admixed in goat milk/meat samples and can be completed within 1 h 40 min starting from DNA extraction from milk/meat samples and can be performed in a water bath. Developed LAMP methodology is simple; rapid and sensitive techniques that can detect adulterant like cow components in goat milk/meat are more accurate than other existing DNA based technologies.

  4. Preservation and rapid purification of DNA from decomposing human tissue samples.

    Science.gov (United States)

    Sorensen, Amy; Rahman, Elizabeth; Canela, Cassandra; Gangitano, David; Hughes-Stamm, Sheree

    2016-11-01

    One of the key features to be considered in a mass disaster is victim identification. However, the recovery and identification of human remains are sometimes complicated by harsh environmental conditions, limited facilities, loss of electricity and lack of refrigeration. If human remains cannot be collected, stored, or identified immediately, bodies decompose and DNA degrades making genotyping more difficult and ultimately decreasing DNA profiling success. In order to prevent further DNA damage and degradation after collection, tissue preservatives may be used. The goal of this study was to evaluate three customized (modified TENT, DESS, LST) and two commercial DNA preservatives (RNAlater and DNAgard ® ) on fresh and decomposed human skin and muscle samples stored in hot (35°C) and humid (60-70% relative humidity) conditions for up to three months. Skin and muscle samples were harvested from the thigh of three human cadavers placed outdoors for up to two weeks. In addition, the possibility of purifying DNA directly from the preservative solutions ("free DNA") was investigated in order to eliminate lengthy tissue digestion processes and increase throughput. The efficiency of each preservative was evaluated based on the quantity of DNA recovered from both the "free DNA" in solution and the tissue sample itself in conjunction with the quality and completeness of downstream STR profiles. As expected, DNA quantity and STR success decreased with time of decomposition. However, a marked decrease in DNA quantity and STR quality was observed in all samples after the bodies entered the bloat stage (approximately six days of decomposition in this study). Similar amounts of DNA were retrieved from skin and muscle samples over time, but slightly more complete STR profiles were obtained from muscle tissue. Although higher amounts of DNA were recovered from tissue samples than from the surrounding preservative, the average number of reportable alleles from the "free DNA" was

  5. Effect of DNA extraction and sample preservation method on rumen bacterial population.

    Science.gov (United States)

    Fliegerova, Katerina; Tapio, Ilma; Bonin, Aurelie; Mrazek, Jakub; Callegari, Maria Luisa; Bani, Paolo; Bayat, Alireza; Vilkki, Johanna; Kopečný, Jan; Shingfield, Kevin J; Boyer, Frederic; Coissac, Eric; Taberlet, Pierre; Wallace, R John

    2014-10-01

    The comparison of the bacterial profile of intracellular (iDNA) and extracellular DNA (eDNA) isolated from cow rumen content stored under different conditions was conducted. The influence of rumen fluid treatment (cheesecloth squeezed, centrifuged, filtered), storage temperature (RT, -80 °C) and cryoprotectants (PBS-glycerol, ethanol) on quality and quantity parameters of extracted DNA was evaluated by bacterial DGGE analysis, real-time PCR quantification and metabarcoding approach using high-throughput sequencing. Samples clustered according to the type of extracted DNA due to considerable differences between iDNA and eDNA bacterial profiles, while storage temperature and cryoprotectants additives had little effect on sample clustering. The numbers of Firmicutes and Bacteroidetes were lower (P rumen fluid subjected to the eDNA isolation procedure considerably changed the ratio of molecular operational taxonomic units (MOTUs) of Bacteroidetes and Firmicutes. Intracellular DNA extraction using bead-beating method from cheesecloth sieved rumen content mixed with PBS-glycerol and stored at -80 °C was found as the optimal method to study ruminal bacterial profile. Copyright © 2013 Elsevier Ltd. All rights reserved.

  6. Small scale tests on the progressive retreat of soil slopes

    Science.gov (United States)

    Voulgari, Chrysoula; Utili, Stefano; Castellanza, Riccardo

    2015-04-01

    In this paper, the influence due to the presence of cracks on the morphologic evolution of natural cliffs subject to progressive retreat induced by weathering is investigated through small scale laboratory tests. Weathering turns hard rocks into soft rocks that maintain the structure of the intact rocks, but are characterised by higher void ratios and reduced bond strengths; soft rocks are transformed into granular soils generally called residual soils. A number of landslides develop in slopes due to weathering which results in the progressive retrogression of the slope face and the further degradation within the weathering zone. Cracks, that are widely present, can be a result of weathering and they can cause a significant decrease in their stability, as they provide preferential flow channels which increase the soil permeability and decrease the soil strength. The geological models employed until now are mainly empirical. Several researchers have tried to study the stability of slopes through experimental procedures. Centrifuge modelling is widely used to investigate the failure of slopes. Small scale tests are also an important approach, in order to study the behaviour of a slope under certain conditions, such as the existence of water, as they allow the observation of the infiltration processes, the movement of the weathering front, deformation and failure. However, the deformation response of a slope subject to weathering is not yet thoroughly clarified. In this work, a set of experiments were conducted to investigate weathering induced successive landslides. Weathering was applied to the slope model by wetting the slope crest through a rainfall simulator device. The moisture content of the soil during the tests was monitored by soil moisture sensors that were buried inside the slope model. High resolution cameras were recording the behaviour of the slope model. GeoPIV was used to analyse the frames and obtain the deformations of the slope model during the

  7. Assessing genetic polymorphisms using DNA extracted from cells present in saliva samples

    Directory of Open Access Journals (Sweden)

    Nemoda Zsofia

    2011-12-01

    Full Text Available Abstract Background Technical advances following the Human Genome Project revealed that high-quality and -quantity DNA may be obtained from whole saliva samples. However, usability of previously collected samples and the effects of environmental conditions on the samples during collection have not been assessed in detail. In five studies we document the effects of sample volume, handling and storage conditions, type of collection device, and oral sampling location, on quantity, quality, and genetic assessment of DNA extracted from cells present in saliva. Methods Saliva samples were collected from ten adults in each study. Saliva volumes from .10-1.0 ml, different saliva collection devices, sampling locations in the mouth, room temperature storage, and multiple freeze-thaw cycles were tested. One representative single nucleotide polymorphism (SNP in the catechol-0-methyltransferase gene (COMT rs4680 and one representative variable number of tandem repeats (VNTR in the serotonin transporter gene (5-HTTLPR: serotonin transporter linked polymorphic region were selected for genetic analyses. Results The smallest tested whole saliva volume of .10 ml yielded, on average, 1.43 ± .77 μg DNA and gave accurate genotype calls in both genetic analyses. The usage of collection devices reduced the amount of DNA extracted from the saliva filtrates compared to the whole saliva sample, as 54-92% of the DNA was retained on the device. An "adhered cell" extraction enabled recovery of this DNA and provided good quality and quantity DNA. The DNA from both the saliva filtrates and the adhered cell recovery provided accurate genotype calls. The effects of storage at room temperature (up to 5 days, repeated freeze-thaw cycles (up to 6 cycles, and oral sampling location on DNA extraction and on genetic analysis from saliva were negligible. Conclusions Whole saliva samples with volumes of at least .10 ml were sufficient to extract good quality and quantity DNA. Using

  8. Australian attitudes to DNA sample banks and genetic screening.

    Science.gov (United States)

    Williams, Carolyn

    2005-11-01

    An exploration via an anonymous questionnaire of Australian public attitudes towards medical genetics and sample banking revealed the overwhelming majority views these developments with thoughtful confidence. Continued public education and awareness of these issues will allow the public to make informed decisions and enhance vigilance towards the sometimes misleading coverage in the press and media.

  9. Evaluation and optimization of DNA extraction and purification procedures for soil and sediment samples.

    Science.gov (United States)

    Miller, D N; Bryant, J E; Madsen, E L; Ghiorse, W C

    1999-11-01

    We compared and statistically evaluated the effectiveness of nine DNA extraction procedures by using frozen and dried samples of two silt loam soils and a silt loam wetland sediment with different organic matter contents. The effects of different chemical extractants (sodium dodecyl sulfate [SDS], chloroform, phenol, Chelex 100, and guanadinium isothiocyanate), different physical disruption methods (bead mill homogenization and freeze-thaw lysis), and lysozyme digestion were evaluated based on the yield and molecular size of the recovered DNA. Pairwise comparisons of the nine extraction procedures revealed that bead mill homogenization with SDS combined with either chloroform or phenol optimized both the amount of DNA extracted and the molecular size of the DNA (maximum size, 16 to 20 kb). Neither lysozyme digestion before SDS treatment nor guanidine isothiocyanate treatment nor addition of Chelex 100 resin improved the DNA yields. Bead mill homogenization in a lysis mixture containing chloroform, SDS, NaCl, and phosphate-Tris buffer (pH 8) was found to be the best physical lysis technique when DNA yield and cell lysis efficiency were used as criteria. The bead mill homogenization conditions were also optimized for speed and duration with two different homogenizers. Recovery of high-molecular-weight DNA was greatest when we used lower speeds and shorter times (30 to 120 s). We evaluated four different DNA purification methods (silica-based DNA binding, agarose gel electrophoresis, ammonium acetate precipitation, and Sephadex G-200 gel filtration) for DNA recovery and removal of PCR inhibitors from crude extracts. Sephadex G-200 spin column purification was found to be the best method for removing PCR-inhibiting substances while minimizing DNA loss during purification. Our results indicate that for these types of samples, optimum DNA recovery requires brief, low-speed bead mill homogenization in the presence of a phosphate-buffered SDS-chloroform mixture, followed

  10. Economic feasibility of small scale button mushroom production in pakistan

    International Nuclear Information System (INIS)

    Tahir, A.; Hassan, S.

    2013-01-01

    Abstract:- Mushroom is widely cultivated as a proteineous vegetable in many countries of the world including Pakistan. Its cultivation requires less space, care, equipment and cost compared to many other crops and livestock. The present study was conducted in 2010 to estimate the profitability of small scale button mushroom production at National Agricultural Research Centre (NARC) Islamabad, Pakistan. The cost of production methodology was used for this study. The yield and gross return of mushroom was estimated at 155.6 kg ha and Rs.77,800 ha , respectively. The results indicated the fact that mushroom production is very much remunerative to its producers as it can give maximum net return by reducing their cost of production as its cultivation is dependent on the agricultural raw material which is cheaply available. (author)

  11. Small scale wind energy harvesting with maximum power tracking

    Directory of Open Access Journals (Sweden)

    Joaquim Azevedo

    2015-07-01

    Full Text Available It is well-known that energy harvesting from wind can be used to power remote monitoring systems. There are several studies that use wind energy in small-scale systems, mainly with wind turbine vertical axis. However, there are very few studies with actual implementations of small wind turbines. This paper compares the performance of horizontal and vertical axis wind turbines for energy harvesting on wireless sensor network applications. The problem with the use of wind energy is that most of the time the wind speed is very low, especially at urban areas. Therefore, this work includes a study on the wind speed distribution in an urban environment and proposes a controller to maximize the energy transfer to the storage systems. The generated power is evaluated by simulation and experimentally for different load and wind conditions. The results demonstrate the increase in efficiency of wind generators that use maximum power transfer tracking, even at low wind speeds.

  12. Numerical simulation of small scale soft impact tests

    International Nuclear Information System (INIS)

    Varpasuo, Pentti

    2008-01-01

    This paper describes the small scale soft missile impact tests. The purpose of the test program is to provide data for the calibration of the numerical simulation models for impact simulation. In the experiments, both dry and fluid filled missiles are used. The tests with fluid filled missiles investigate the release speed and the droplet size of the fluid release. This data is important in quantifying the fire hazard of flammable liquid after the release. The spray release velocity and droplet size are also input data for analytical and numerical simulation of the liquid spread in the impact. The behaviour of the impact target is the second investigative goal of the test program. The response of reinforced and pre-stressed concrete walls is studied with the aid of displacement and strain monitoring. (authors)

  13. Concepts for Small-Scale Testing of Used Nuclear Fuel

    Energy Technology Data Exchange (ETDEWEB)

    Marschman, Steven Craig [Idaho National Lab. (INL), Idaho Falls, ID (United States); Winston, Philip Lon [Idaho National Lab. (INL), Idaho Falls, ID (United States)

    2015-09-01

    This report documents a concept for a small-scale test involving between one and three Boiling Water Rector (BWR) high burnup (HBU) fuel assemblies. This test would be similar to the DOE funded High Burn-Up (HBU) Confirmatory Data Project to confirm the behavior of used high burn-up fuel under prototypic conditions, only on a smaller scale. The test concept proposed would collect data from fuel stored under prototypic dry storage conditions to mimic, as closely as possible, the conditions HBU UNF experiences during all stages of dry storage: loading, cask drying, inert gas backfilling, and transfer to an Independent Spent Fuel Storage Installation (ISFSI) for multi-year storage.

  14. A multi scale model for small scale plasticity

    International Nuclear Information System (INIS)

    Zbib, Hussein M.

    2002-01-01

    Full text.A framework for investigating size-dependent small-scale plasticity phenomena and related material instabilities at various length scales ranging from the nano-microscale to the mesoscale is presented. The model is based on fundamental physical laws that govern dislocation motion and their interaction with various defects and interfaces. Particularly, a multi-scale model is developed merging two scales, the nano-microscale where plasticity is determined by explicit three-dimensional dislocation dynamics analysis providing the material length-scale, and the continuum scale where energy transport is based on basic continuum mechanics laws. The result is a hybrid simulation model coupling discrete dislocation dynamics with finite element analyses. With this hybrid approach, one can address complex size-dependent problems, including dislocation boundaries, dislocations in heterogeneous structures, dislocation interaction with interfaces and associated shape changes and lattice rotations, as well as deformation in nano-structured materials, localized deformation and shear band

  15. Small-Scale Pellet Boiler with Thermoelectric Generator

    Energy Technology Data Exchange (ETDEWEB)

    Moser, Wilhelm; Friedl, Guenther; Haslinger, Walter [Austrian Bioenergy Centre GmbH, Wieselburg (Austria); Hofbauer, Hermann [Vienna Univ. of Technology (Austria). Inst. of Chemical Engineering

    2006-07-15

    Pellet burners need auxiliary electrical power to provide CO{sub 2}-balanced heat in a comfortable and environment-friendly way. The idea is to produce this and some extra electricity within the furnace in order to save resources and to gain operation reliability and independency. Thermoelectric generators (TEGs) allow the direct conversion of heat to electrical power to a certain extent. They have the advantages of a maintenance-free long life and soundless operation without moving parts or any working fluid. A novel kind of decentralised small-scale biomass-based combined heat and power generation will be developed. The basic system allows grid-independent operation of automatically running biomass furnaces including fuel delivery from storage and circulating the cooling respectively heating water or air. The advanced system also provides electricity for network supply or for other electrical devices and is an additional benefit.

  16. Exergoeconomic analysis of small-scale biomass steam cogeneration

    Energy Technology Data Exchange (ETDEWEB)

    Rodriguez Sotomonte, Cesar Adolfo; Lora, Electo Eduardo Silva [Universidade Federal de Itajuba, MG (Brazil)], e-mails: c.rodriguez32@unifei.edu.br, electo@unifei.edu.br; Venturini, Osvaldo Jose; Escobar, Jose Carlos [Universidad Federal de Itajuba, MG (Brazil)], e-mail: osvaldo@unifei.edu.br

    2010-07-01

    The principal objective of this work is to develop a calculation process, based on the second law of thermodynamics, for evaluating the thermoeconomic potential of a small steam cogeneration plant using waste from pulp processing and/or sawmills as fuel. Four different configurations are presented and assessed. The exergetic efficiency of the cycles that use condensing turbines is found to be around 11%, which has almost 3 percent higher efficiency than cycles with back pressure turbines. The thermoeconomic equations used in this paper estimated the production costs varying the fuel price. The main results show that present cost of technologies in a small-scale steam cycle cogeneration do not justify the implementation of more efficient systems for biomass prices less than 100 R$/t. (author)

  17. The Multifractal Structure of Small-Scale Artificial Ionospheric Turbulence

    Directory of Open Access Journals (Sweden)

    Vybornov F. I.

    2013-03-01

    Full Text Available We present the results of investigation of a multifractal structure of the artificial ionospheric turbulence when the midlatitude ionosphere is affected by high-power radio waves. The experimental studies were performed on the basis of the SURA heating facility with the help of radio sounding of the disturbed region of ionospheric plasma by signals from the Earth’s orbital satellities. In the case of vertical radio sounding of the disturbed ionosphere region, the measured multipower and generalized multifractal spectra of turbulence coincide well with similar multifractal characteristics of the ionosperic turbulence under the natural conditions. In the case of oblique sounding of the disturbance region at small angles between the line of sight to the satellite and the direction of the Earth’s magnetic field, a nonuniform structure of the small-scale turbulence with a relatively narrow multipower spectrum and small variations in the generalized multifractal spectrum of the electron density was detected.

  18. Small scale renewable solar energy and the best result project

    Energy Technology Data Exchange (ETDEWEB)

    Bilbao, J.; Miguel, A.H.; Perez-Burgos, A.M. [Valladolid Univ. (Spain)

    2008-07-01

    The European Community has established programmes with different Projects in relation with the develop of an energy system according to de Kyoto objectives, improving energy efficiency, maintaining security supply and doubling the share of renewable energy use. The Best Result Project (Building and Energy Systems and Technology in Renewable Energy Sources Update and Linked Training), is financed by the European Commission, Intelligent Energy Agency (EIE) and the project objectives are to develop training and diffusion activities in the field of Renewable Energy Technology. The project aims to raise the renewable energy knowledge among suppliers and general public. The project activities are: basis and specialized training events, workshops, meetings, visits and e-learning common platform. The final objective is to extend the market of small scale RES applications in the building and energy sector through common and local activities addressing RES suppliers and consumers. (orig.)

  19. Optimal Combustion Conditions for a Small-scale Biomass Boiler

    Directory of Open Access Journals (Sweden)

    Viktor Plaček

    2012-01-01

    Full Text Available This paper reports on an attempt to achieve maximum efficiency and lowest possible emissions for a small-scale biomass boiler. This aim can be attained only by changing the control algorithm of the boiler, and in this way not raising the acquisition costs for the boiler. This paper describes the experimental facility, the problems that arose while establishing the facility, and how we have dealt with them. The focus is on discontinuities arising after periodic grate sweeping, and on finding the parameters of the PID control loops. Alongside these methods, which need a lambda probe signal for proper functionality, we inroduce another method, which is able to intercept the optimal combustion working point without the need to use a lambda sensor.

  20. Pervasive Rise of Small-scale Deforestation in Amazonia.

    Science.gov (United States)

    Kalamandeen, Michelle; Gloor, Emanuel; Mitchard, Edward; Quincey, Duncan; Ziv, Guy; Spracklen, Dominick; Spracklen, Benedict; Adami, Marcos; Aragão, Luiz E O C; Galbraith, David

    2018-01-25

    Understanding forest loss patterns in Amazonia, the Earth's largest rainforest region, is critical for effective forest conservation and management. Following the most detailed analysis to date, spanning the entire Amazon and extending over a 14-year period (2001-2014), we reveal significant shifts in deforestation dynamics of Amazonian forests. Firstly, hotspots of Amazonian forest loss are moving away from the southern Brazilian Amazon to Peru and Bolivia. Secondly, while the number of new large forest clearings (>50 ha) has declined significantly over time (46%), the number of new small clearings (<1 ha) increased by 34% between 2001-2007 and 2008-2014. Thirdly, we find that small-scale low-density forest loss expanded markedly in geographical extent during 2008-2014. This shift presents an important and alarming new challenge for forest conservation, despite reductions in overall deforestation rates.

  1. Emissions from small scale biomass combustion - Research needs

    International Nuclear Information System (INIS)

    Gustavsson, L.; Karlsson, M.L.; Larfeldt, J.; Leckner, B.

    1994-01-01

    Earlier investigations have shown that small scale biomass combustion leads to unacceptable emissions in the air. The most important problem is high levels of unburnt hydrocarbons. This report analyzes which are the most important reasons to these emissions and which research efforts that are necessary to increase the knowledge about the combustion processes, thereby promoting the development of environmentally feasible equipment. The following factors are defined as most crucial to emission levels: size of combustion chamber, air excess ratio, means of combustion air supply, mixing between air and fuel, transient events, and fuel quality. It is concluded that both basic and research within the area is needed. More specific, research in the form of systematic analysis of best available technology, reactor experiments, compilation of knowledge about relevant basic combustion processes, mathematical modelling as well as development of measurement techniques are called for. 15 refs, 11 figs, 1 tab

  2. Performance analysis of small-scale experimental facility of TWDEC

    International Nuclear Information System (INIS)

    Kawana, Ryoh; Ishikawa, Motoo; Takeno, Hiromasa; Yamamoto, Takayoshi; Yasaka, Yasuyoshi

    2008-01-01

    The objective of the present paper is to analyze small-scale experimental facilities of TWDEC (Travelling Wave type Direct Energy Converter) and to propose a modification in regard to a measuring device of the facilities by means of numerical simulation with the axisymmetrical two-dimensional approximation (a PIC method). The numerical simulation has given the following results: (1) tendency of the numerical results agree with the experimental results on the measured deceleration efficiency, (2) the deceleration efficiency measured in the experiment will increase if the radius of Faraday cup installed in the experiment increases and (3) the wave of condensation and rarefaction of measured electric charge density, which is averaged in the r-direction below the radius of Faraday cup, is not formed enough with a small radius of Faraday cup because of the r component of electric field which is induced by the electrode geometry

  3. Rural electrification in Malaysia via small scale biomass gasifier

    International Nuclear Information System (INIS)

    Zainal Alimuddin Zainal Alauddin

    2000-01-01

    It is the government of Malaysia's vision to see that the rural community is not left behind in its endeavour to be an industrialised nation in the year 2020. The standard of living in the rural areas is very far different from that in the urban areas. To obtain equality the standard of living of the rural folks need to be ungraded. This is done largely by electrification. Electricity has been in the past the catalyst for development and raising the standard of living of the poor. Electricity supplied by the nation's electricity company might not reach all remote areas and therefore there must be a means to provide alternative electrical supply to these places. Present method employ the use of diesel generator sets to provide electricity. The availability of biomass source of supply in the rural areas could be effectively exploited to provide alternative source of energy via a gasification system to run a reciprocating engine coupled to a generator to generated electricity. A small-scale biomass gasification generator set in the range of 2-5 kW is suitable to provide electrical supply to a typical house in the rural area. The present use of biomass source of energy is in its utilisation to provide source of heat for cooking. Several tests have been conducted and the performance is very good. Alternatively another medium scale system generating about 50-20O kW would be suitable for a typical village having about 50 houses. A small-scale system has been developed in USM to provide 5 kW of electrical power. The system used a petrol engine and produces an overall efficiency of 7% with a specific consumption of about 3 kg/kWh. The biomass material used is wood. However for application in the rural areas the biomass material will depend on the type available. A further 50 kW system is being develop in USM. (Author)

  4. Dark matter self-interactions and small scale structure

    Science.gov (United States)

    Tulin, Sean; Yu, Hai-Bo

    2018-02-01

    We review theories of dark matter (DM) beyond the collisionless paradigm, known as self-interacting dark matter (SIDM), and their observable implications for astrophysical structure in the Universe. Self-interactions are motivated, in part, due to the potential to explain long-standing (and more recent) small scale structure observations that are in tension with collisionless cold DM (CDM) predictions. Simple particle physics models for SIDM can provide a universal explanation for these observations across a wide range of mass scales spanning dwarf galaxies, low and high surface brightness spiral galaxies, and clusters of galaxies. At the same time, SIDM leaves intact the success of ΛCDM cosmology on large scales. This report covers the following topics: (1) small scale structure issues, including the core-cusp problem, the diversity problem for rotation curves, the missing satellites problem, and the too-big-to-fail problem, as well as recent progress in hydrodynamical simulations of galaxy formation; (2) N-body simulations for SIDM, including implications for density profiles, halo shapes, substructure, and the interplay between baryons and self-interactions; (3) semi-analytic Jeans-based methods that provide a complementary approach for connecting particle models with observations; (4) merging systems, such as cluster mergers (e.g., the Bullet Cluster) and minor infalls, along with recent simulation results for mergers; (5) particle physics models, including light mediator models and composite DM models; and (6) complementary probes for SIDM, including indirect and direct detection experiments, particle collider searches, and cosmological observations. We provide a summary and critical look for all current constraints on DM self-interactions and an outline for future directions.

  5. Emissions from small scale combustion of pelletized wood fuels

    International Nuclear Information System (INIS)

    Bachs, A.

    1998-01-01

    Combustion of wood pellets in small scale heating systems with an effect below 20 kW has increased. During the winter season 1995/96 1500 small plants for heating houses are estimated to be in operation. Stack emissions from three pellet burners and two pellet stoves have been studied at laboratory. Different pellet qualities were tested. When the fraction of fines increased also the NO x emissions increased with about 10 %. As reference fuel 8 mm pellets was used. Tests with 6 mm pellets gave, in most cases, significant lower emissions of CO and THC. Eleven stoves, burners and boilers were studied in a field test. The results show that all the plants generally have higher emissions in the field than during conditions when the plants are adjusted with a stack gas monitoring instrument. A conclusion is that it is difficult for the operator to adjust the plant without a monitoring instrument. The emissions from the tested plants give an estimation of stack gas emissions from small scale pellet plants. The difference between the 'best' and 'worst' technologies is big. The span of emissions with the best technology to the worst is given below. The interval is concerning normal combustion . During abnormal conditions the emissions are on a significant higher level: * CO 80-1 000 mg/MJ; * Tar 0,3-19 mg/MJ; * THC (as methane equivalents) 2-100 mg/MJ; * NO x 50-70 mg/W;, and * Dust emissions 20-40 mg/MJ. Emissions from pellets heating are lower than from wood combustion and the best technology is close to the emission from oil burners. Wood and pellets have the same origin but the conditions to burn them in an environmental friendly way differ. Combustion of pellets could be improved through improved control of the air and fuel ratio that will create more stable conditions for the combustion

  6. Small-scale distribution and diel vertical migration of zooplankton in a shallow lake (Lake Naardermeer, the Netherlands)

    NARCIS (Netherlands)

    Cerbin, S.; Balayla, D.; Van de Bund, W.J.

    2003-01-01

    Small scale distribution and diurnal migration of zooplankton were investigated in lake Naardermeer, a shallow lake largely covered by uniform Chara beds. For sampling, pattern samplers with a number of inverted funnels facing towards the lake bottom and held in a frame were used. Samplers were

  7. Fuel from farms: a guide to small-scale ethanol production

    Energy Technology Data Exchange (ETDEWEB)

    None

    1980-02-01

    A guide on fermentation processes with emphasis on small-scale production of ethanol using farm crops as a source of raw material is published. The current status of on-farm ethanol production as well as an overview of some of the technical and economic factors is presented. Decision and planning worksheets and a sample business plan for use in decision making are included. Specifics in production including information on the raw materials, system components, and operational requirements are also provided. Diagrams of fermentors and distilling apparatus are included. (DC)

  8. Inspecting close maternal relatedness: Towards better mtDNA population samples in forensic databases.

    Science.gov (United States)

    Bodner, Martin; Irwin, Jodi A; Coble, Michael D; Parson, Walther

    2011-03-01

    Reliable data are crucial for all research fields applying mitochondrial DNA (mtDNA) as a genetic marker. Quality control measures have been introduced to ensure the highest standards in sequence data generation, validation and a posteriori inspection. A phylogenetic alignment strategy has been widely accepted as a prerequisite for data comparability and database searches, for forensic applications, for reconstructions of human migrations and for correct interpretation of mtDNA mutations in medical genetics. There is continuing effort to enhance the number of worldwide population samples in order to contribute to a better understanding of human mtDNA variation. This has often lead to the analysis of convenience samples collected for other purposes, which might not meet the quality requirement of random sampling for mtDNA data sets. Here, we introduce an additional quality control means that deals with one aspect of this limitation: by combining autosomal short tandem repeat (STR) marker with mtDNA information, it helps to avoid the bias introduced by related individuals included in the same (small) sample. By STR analysis of individuals sharing their mitochondrial haplotype, pedigree construction and subsequent software-assisted calculation of likelihood ratios based on the allele frequencies found in the population, closely maternally related individuals can be identified and excluded. We also discuss scenarios that allow related individuals in the same set. An ideal population sample would be representative for its population: this new approach represents another contribution towards this goal. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

  9. Intelligent Network Flow Optimization (INFLO) prototype : Seattle small-scale demonstration report.

    Science.gov (United States)

    2015-05-01

    This report describes the performance and results of the INFLO Prototype Small-Scale Demonstration. The purpose of : the Small-Scale Demonstration was to deploy the INFLO Prototype System to demonstrate its functionality and : performance in an opera...

  10. design of a small scale wind generator for low wind speed areas

    African Journals Online (AJOL)

    USER

    Most small scale level wind turbine generators are directly driven system, variable speed, and partially ... the best solutions for small-scale wind power plants. Low-speed multi-pole PM generators ..... Designs of the Same Magnet Structure for.

  11. Direct PCR amplification of forensic touch and other challenging DNA samples: A review.

    Science.gov (United States)

    Cavanaugh, Sarah E; Bathrick, Abigail S

    2018-01-01

    DNA evidence sample processing typically involves DNA extraction, quantification, and STR amplification; however, DNA loss can occur at both the DNA extraction and quantification steps, which is not ideal for forensic evidence containing low levels of DNA. Direct PCR amplification of forensic unknown samples has been suggested as a means to circumvent extraction and quantification, thereby retaining the DNA typically lost during those procedures. Direct PCR amplification is a method in which a sample is added directly to an amplification reaction without being subjected to prior DNA extraction, purification, or quantification. It allows for maximum quantities of DNA to be targeted, minimizes opportunities for error and contamination, and reduces the time and monetary resources required to process samples, although data analysis may take longer as the increased DNA detection sensitivity of direct PCR may lead to more instances of complex mixtures. ISO 17025 accredited laboratories have successfully implemented direct PCR for limited purposes (e.g., high-throughput databanking analysis), and recent studies indicate that direct PCR can be an effective method for processing low-yield evidence samples. Despite its benefits, direct PCR has yet to be widely implemented across laboratories for the processing of evidentiary items. While forensic DNA laboratories are always interested in new methods that will maximize the quantity and quality of genetic information obtained from evidentiary items, there is often a lag between the advent of useful methodologies and their integration into laboratories. Delayed implementation of direct PCR of evidentiary items can be attributed to a variety of factors, including regulatory guidelines that prevent laboratories from omitting the quantification step when processing forensic unknown samples, as is the case in the United States, and, more broadly, a reluctance to validate a technique that is not widely used for evidence samples. The

  12. Simple DNA extraction of urine samples: Effects of storage temperature and storage time.

    Science.gov (United States)

    Ng, Huey Hian; Ang, Hwee Chen; Hoe, See Ying; Lim, Mae-Lynn; Tai, Hua Eng; Soh, Richard Choon Hock; Syn, Christopher Kiu-Choong

    2018-06-01

    Urine samples are commonly analysed in cases with suspected illicit drug consumption. In events of alleged sample mishandling, urine sample source identification may be necessary. A simple DNA extraction procedure suitable for STR typing of urine samples was established on the Promega Maxwell ® 16 paramagnetic silica bead platform. A small sample volume of 1.7mL was used. Samples were stored at room temperature, 4°C and -20°C for 100days to investigate the influence of storage temperature and time on extracted DNA quantity and success rate of STR typing. Samples stored at room temperature exhibited a faster decline in DNA yield with time and lower typing success rates as compared to those at 4°C and -20°C. This trend can likely be attributed to DNA degradation. In conclusion, this study presents a quick and effective DNA extraction protocol from a small urine volume stored for up to 100days at 4°C and -20°C. Copyright © 2018 Elsevier B.V. All rights reserved.

  13. Digital Droplet Multiple Displacement Amplification (ddMDA for Whole Genome Sequencing of Limited DNA Samples.

    Directory of Open Access Journals (Sweden)

    Minsoung Rhee

    Full Text Available Multiple displacement amplification (MDA is a widely used technique for amplification of DNA from samples containing limited amounts of DNA (e.g., uncultivable microbes or clinical samples before whole genome sequencing. Despite its advantages of high yield and fidelity, it suffers from high amplification bias and non-specific amplification when amplifying sub-nanogram of template DNA. Here, we present a microfluidic digital droplet MDA (ddMDA technique where partitioning of the template DNA into thousands of sub-nanoliter droplets, each containing a small number of DNA fragments, greatly reduces the competition among DNA fragments for primers and polymerase thereby greatly reducing amplification bias. Consequently, the ddMDA approach enabled a more uniform coverage of amplification over the entire length of the genome, with significantly lower bias and non-specific amplification than conventional MDA. For a sample containing 0.1 pg/μL of E. coli DNA (equivalent of ~3/1000 of an E. coli genome per droplet, ddMDA achieves a 65-fold increase in coverage in de novo assembly, and more than 20-fold increase in specificity (percentage of reads mapping to E. coli compared to the conventional tube MDA. ddMDA offers a powerful method useful for many applications including medical diagnostics, forensics, and environmental microbiology.

  14. Preservation of RNA and DNA from mammal samples under field conditions.

    Science.gov (United States)

    Camacho-Sanchez, Miguel; Burraco, Pablo; Gomez-Mestre, Ivan; Leonard, Jennifer A

    2013-07-01

    Ecological and conservation genetics require sampling of organisms in the wild. Appropriate preservation of the collected samples, usually by cryostorage, is key to the quality of the genetic data obtained. Nevertheless, cryopreservation in the field to ensure RNA and DNA stability is not always possible. We compared several nucleic acid preservation solutions appropriate for field sampling and tested them on rat (Rattus rattus) blood, ear and tail tip, liver, brain and muscle. We compared the efficacy of a nucleic acid preservation (NAP) buffer for DNA preservation against 95% ethanol and Longmire buffer, and for RNA preservation against RNAlater (Qiagen) and Longmire buffer, under simulated field conditions. For DNA, the NAP buffer was slightly better than cryopreservation or 95% ethanol, but high molecular weight DNA was preserved in all conditions. The NAP buffer preserved RNA as well as RNAlater. Liver yielded the best RNA and DNA quantity and quality; thus, liver should be the tissue preferentially collected from euthanized animals. We also show that DNA persists in nonpreserved muscle tissue for at least 1 week at ambient temperature, although degradation is noticeable in a matter of hours. When cryopreservation is not possible, the NAP buffer is an economical alternative for RNA preservation at ambient temperature for at least 2 months and DNA preservation for at least 10 months. © 2013 John Wiley & Sons Ltd.

  15. A rapid and efficient DNA extraction protocol from fresh and frozen human blood samples.

    Science.gov (United States)

    Guha, Pokhraj; Das, Avishek; Dutta, Somit; Chaudhuri, Tapas Kumar

    2018-01-01

    Different methods available for extraction of human genomic DNA suffer from one or more drawbacks including low yield, compromised quality, cost, time consumption, use of toxic organic solvents, and many more. Herein, we aimed to develop a method to extract DNA from 500 μL of fresh or frozen human blood. Five hundred microliters of fresh and frozen human blood samples were used for standardization of the extraction procedure. Absorbance at 260 and 280 nm, respectively, (A 260 /A 280 ) were estimated to check the quality and quantity of the extracted DNA sample. Qualitative assessment of the extracted DNA was checked by Polymerase Chain reaction and double digestion of the DNA sample. Our protocol resulted in average yield of 22±2.97 μg and 20.5±3.97 μg from 500 μL of fresh and frozen blood, respectively, which were comparable to many reference protocols and kits. Besides yielding bulk amount of DNA, our protocol is rapid, economical, and avoids toxic organic solvents such as Phenol. Due to unaffected quality, the DNA is suitable for downstream applications. The protocol may also be useful for pursuing basic molecular researches in laboratories having limited funds. © 2017 Wiley Periodicals, Inc.

  16. Experimental, theoretical, and numerical studies of small scale combustion

    Science.gov (United States)

    Xu, Bo

    Recently, the demand increased for the development of microdevices such as microsatellites, microaerial vehicles, micro reactors, and micro power generators. To meet those demands the biggest challenge is obtaining stable and complete combustion at relatively small scale. To gain a fundamental understanding of small scale combustion in this thesis, thermal and kinetic coupling between the gas phase and the structure at meso and micro scales were theoretically, experimentally, and numerically studied; new stabilization and instability phenomena were identified; and new theories for the dynamic mechanisms of small scale combustion were developed. The reduction of thermal inertia at small scale significantly reduces the response time of the wall and leads to a strong flame-wall coupling and extension of burning limits. Mesoscale flame propagation and extinction in small quartz tubes were theoretically, experimentally and numerically studied. It was found that wall-flame interaction in mesoscale combustion led to two different flame regimes, a heat-loss dominant fast flame regime and a wall-flame coupling slow flame regime. The nonlinear transition between the two flame regimes was strongly dependent on the channel width and flow velocity. It is concluded that the existence of multiple flame regimes is an inherent phenomenon in mesoscale combustion. In addition, all practical combustors have variable channel width in the direction of flame propagation. Quasi-steady and unsteady propagations of methane and propane-air premixed flames in a mesoscale divergent channel were investigated experimentally and theoretically. The emphasis was the impact of variable cross-section area and the flame-wall coupling on the flame transition between different regimes and the onset of flame instability. For the first time, spinning flames were experimentally observed for both lean and rich methane and propane-air mixtures in a broad range of equivalence ratios. An effective Lewis number

  17. [Acidity and microbial flora contaminating Senegalese reconstituted curdled milk produced on small scale].

    Science.gov (United States)

    Seydi, M; Ndiaye, M

    1993-01-01

    The present study is carried out to appreciate the acidity, and survey the microbiological quality of reconstituted curdled milk (R.C.M.) obtained on small scale. For his, a total of 100 samples collected from Dakar's sellers were examined. The results show that: pH of R.C.M. is low and very variable: 4.17 +/- 0.30, titrable acidity is high: 152.6 +/- 26.5 degrees D, 5% of samples are contaminated by fecal coliforms and yielded counts of 20 germs/g, 19% of samples are polluted by Staphylococcus aureus to level equal to 10(2) germs/g or higher, yeasts and moulds are present in all samples, salmonella were absent. Saphylococcus aureus survival in curdled milk despite a dysgenesic acidity may be the result of very unhygienic conditions of preparation. Sellers and consumers must be encouraged to respect hygienic rules of preparation. It is the only way to prevent food poisoning.

  18. Investigation of the feasibility of a small scale transmutation device

    Science.gov (United States)

    Sit, Roger Carson

    This dissertation presents the design and feasibility of a small-scale, fusion-based transmutation device incorporating a commercially available neutron generator. It also presents the design features necessary to optimize the device and render it practical for the transmutation of selected long-lived fission products and actinides. Four conceptual designs of a transmutation device were used to study the transformation of seven radionuclides: long-lived fission products (Tc-99 and I-129), short-lived fission products (Cs-137 and Sr-90), and selective actinides (Am-241, Pu-238, and Pu-239). These radionuclides were chosen because they are major components of spent nuclear fuel and also because they exist as legacy sources that are being stored pending a decision regarding their ultimate disposition. The four designs include the use of two different devices; a Deuterium-Deuterium (D-D) neutron generator (for one design) and a Deuterium-Tritium (D-T) neutron generator (for three designs) in configurations which provide different neutron energy spectra for targeting the radionuclide for transmutation. Key parameters analyzed include total fluence and flux requirements; transmutation effectiveness measured as irradiation effective half-life; and activation products generated along with their characteristics: activity, dose rate, decay, and ingestion and inhalation radiotoxicity. From this investigation, conclusions were drawn about the feasibility of the device, the design and technology enhancements that would be required to make transmutation practical, the most beneficial design for each radionuclide, the consequence of the transmutation, and radiation protection issues that are important for the conceptual design of the transmutation device. Key conclusions from this investigation include: (1) the transmutation of long-lived fission products and select actinides can be practical using a small-scale, fusion driven transmutation device; (2) the transmutation of long

  19. Species-specific identification from incomplete sampling: applying DNA barcodes to monitoring invasive solanum plants.

    Science.gov (United States)

    Zhang, Wei; Fan, Xiaohong; Zhu, Shuifang; Zhao, Hong; Fu, Lianzhong

    2013-01-01

    Comprehensive sampling is crucial to DNA barcoding, but it is rarely performed because materials are usually unavailable. In practice, only a few rather than all species of a genus are required to be identified. Thus identification of a given species using a limited sample is of great importance in current application of DNA barcodes. Here, we selected 70 individuals representing 48 species from each major lineage of Solanum, one of the most species-rich genera of seed plants, to explore whether DNA barcodes can provide reliable specific-species discrimination in the context of incomplete sampling. Chloroplast genes ndhF and trnS-trnG and the nuclear gene waxy, the commonly used markers in Solanum phylogeny, were selected as the supplementary barcodes. The tree-building and modified barcode gap methods were employed to assess species resolution. The results showed that four Solanum species of quarantine concern could be successfully identified through the two-step barcoding sampling strategy. In addition, discrepancies between nuclear and cpDNA barcodes in some samples demonstrated the ability to discriminate hybrid species, and highlights the necessity of using barcode regions with different modes of inheritance. We conclude that efficient phylogenetic markers are good candidates as the supplementary barcodes in a given taxonomic group. Critically, we hypothesized that a specific-species could be identified from a phylogenetic framework using incomplete sampling-through this, DNA barcoding will greatly benefit the current fields of its application.

  20. Small-Scale Spray Releases: Additional Aerosol Test Results

    Energy Technology Data Exchange (ETDEWEB)

    Schonewill, Philip P.; Gauglitz, Phillip A.; Kimura, Marcia L.; Brown, G. N.; Mahoney, Lenna A.; Tran, Diana N.; Burns, Carolyn A.; Kurath, Dean E.

    2013-08-01

    One of the events postulated in the hazard analysis at the Waste Treatment and Immobilization Plant (WTP) and other U.S. Department of Energy (DOE) nuclear facilities is a breach in process piping that produces aerosols with droplet sizes in the respirable range. The current approach for predicting the size and concentration of aerosols produced in a spray leak involves extrapolating from correlations reported in the literature. These correlations are based on results obtained from small engineered spray nozzles using pure liquids with Newtonian fluid behavior. The narrow ranges of physical properties on which the correlations are based do not cover the wide range of slurries and viscous materials that will be processed in the WTP and across processing facilities in the DOE complex. To expand the data set upon which the WTP accident and safety analyses were based, an aerosol spray leak testing program was conducted by Pacific Northwest National Laboratory (PNNL). PNNL’s test program addressed two key technical areas to improve the WTP methodology (Larson and Allen 2010). The first technical area was to quantify the role of slurry particles in small breaches where slurry particles may plug the hole and prevent high-pressure sprays. The results from an effort to address this first technical area can be found in Mahoney et al. (2012a). The second technical area was to determine aerosol droplet size distribution and total droplet volume from prototypic breaches and fluids, including sprays from larger breaches and sprays of slurries for which literature data are largely absent. To address the second technical area, the testing program collected aerosol generation data at two scales, commonly referred to as small-scale and large-scale. The small-scale testing and resultant data are described in Mahoney et al. (2012b) and the large-scale testing and resultant data are presented in Schonewill et al. (2012). In tests at both scales, simulants were used to mimic the

  1. Quantifying seismic anisotropy induced by small-scale chemical heterogeneities

    Science.gov (United States)

    Alder, C.; Bodin, T.; Ricard, Y.; Capdeville, Y.; Debayle, E.; Montagner, J. P.

    2017-12-01

    Observations of seismic anisotropy are usually used as a proxy for lattice-preferred orientation (LPO) of anisotropic minerals in the Earth's mantle. In this way, seismic anisotropy observed in tomographic models provides important constraints on the geometry of mantle deformation associated with thermal convection and plate tectonics. However, in addition to LPO, small-scale heterogeneities that cannot be resolved by long-period seismic waves may also produce anisotropy. The observed (i.e. apparent) anisotropy is then a combination of an intrinsic and an extrinsic component. Assuming the Earth's mantle exhibits petrological inhomogeneities at all scales, tomographic models built from long-period seismic waves may thus display extrinsic anisotropy. In this paper, we investigate the relation between the amplitude of seismic heterogeneities and the level of induced S-wave radial anisotropy as seen by long-period seismic waves. We generate some simple 1-D and 2-D isotropic models that exhibit a power spectrum of heterogeneities as what is expected for the Earth's mantle, that is, varying as 1/k, with k the wavenumber of these heterogeneities. The 1-D toy models correspond to simple layered media. In the 2-D case, our models depict marble-cake patterns in which an anomaly in shear wave velocity has been advected within convective cells. The long-wavelength equivalents of these models are computed using upscaling relations that link properties of a rapidly varying elastic medium to properties of the effective, that is, apparent, medium as seen by long-period waves. The resulting homogenized media exhibit extrinsic anisotropy and represent what would be observed in tomography. In the 1-D case, we analytically show that the level of anisotropy increases with the square of the amplitude of heterogeneities. This relation is numerically verified for both 1-D and 2-D media. In addition, we predict that 10 per cent of chemical heterogeneities in 2-D marble-cake models can

  2. Controls on sublithospheric small-scale convection on Curie depths

    Science.gov (United States)

    Likerman, Jeremias; Zlotnik, Sergio; Chun-Feng, Li

    2017-04-01

    As the ocean lithosphere cools and thickens, its bottom layer goes unstable leading to sub-lithospheric small-scale convection (SSC). Since SSC was originally proposed, there have been considerable efforts regarding the understanding of the physics that rules the thermal instabilities of the SSC (e.g. Dumoulin et al, 1999; Solomatov and Moresi, 2000). Over the last several years, it is understood that the interaction between the plate movement and the SSC tends to form longitudinal (LRs or also called 'Richter rolls') and transverse rolls (TRs), of which the axis is parallel and perpendicular to the plate motion, respectively. The geometry of these rolls have been been recently inferred by Li et al (2013) using Curie depths from the North Atlantic as proxies for plates temperatures. They showed that Curie depths have a large oscillating and heterogeneous patterns that could be related to SSC. In the North Atlantic transverse rolls seem predominant. In this work we analyze, by means of 3D dynamical numerical simulations, the influence of SSC on the Curie depths patterns observed in the North Atlantic and Pacific plates. We investigate the behaviour of the Curie isotherms trying to determine if SSC is able to reproduce the observed data, and the influence of several poorly constrained rheological parameters. Our numerical simulations show that: a) using realistic laboratory-constrained rheologies and temperature it is possible to modify temperatures as low as those at Curie depths; b) transverse rolls are generated as well as longitudinal rolls on those isotherms; c) the spreading rate is a first order control on the developing of transverse rolls. References Dumoulin, C., Doin, M. P., & Fleitout, L. (1999). Heat transport in stagnant lid convection with temperature-and pressure-dependent Newtonian or non-Newtonian rheology. Journal of Geophysical Research: Solid Earth, 104(B6), 12759-12777. Li, C. F., Wang, J., Lin, J., & Wang, T. (2013). Thermal evolution of the

  3. Ehrlichia canis morulae and DNA detection in whole blood and spleen aspiration samples.

    Science.gov (United States)

    Faria, Joice Lara Maia; Dagnone, Ana Sílvia; Munhoz, Thiago Demarchi; João, Carolina Franchi; Pereira, Wanderson Adriano Biscola; Machado, Rosângela Zacarias; Tinucci-Costa, Mirela

    2010-01-01

    The aim of this study was to compare the detection of Ehrlichia canis morulae and DNA by nPCR in whole blood and spleen aspiration. The sample included 40 dogs showing thrombocytopenia associated to clinical signs suggestive of canine ehrlichiosis. Morulae detection showed that in 35 of the dogs studied, 17 had morulae in spleen tissue, and two in buffy coat smears. E. canis DNA was detected in 29/40 blood samples. We verified that morulae detection is more efficient in cytological preparations from spleen aspiration. On the other hand, nPCR on spleen and blood samples were equally efficient for disease diagnosis.

  4. Diagnosis of becker muscular dystrophy: Results of Re-analysis of DNA samples.

    Science.gov (United States)

    Straathof, Chiara S M; Van Heusden, Dave; Ippel, Pieternella F; Post, Jan G; Voermans, Nicol C; De Visser, Marianne; Brusse, Esther; Van Den Bergen, Janneke C; Van Der Kooi, Anneke J; Verschuuren, Jan J G M; Ginjaar, Hendrika B

    2016-01-01

    The phenotype of Becker muscular dystrophy (BMD) is highly variable, and the disease may be underdiagnosed. We searched for new mutations in the DMD gene in a cohort of previously undiagnosed patients who had been referred in the period 1985-1995. All requests for DNA analysis of the DMD gene in probands with suspected BMD were re-evaluated. If the phenotype was compatible with BMD, and no deletions or duplications were detected, DNA samples were screened for small mutations. In 79 of 185 referrals, no mutation was found. Analysis could be performed on 31 DNA samples. Seven different mutations, including 3 novel ones, were found. Long-term clinical follow-up is described. Refining DNA analysis in previously undiagnosed cases can identify mutations in the DMD gene and provide genetic diagnosis of BMD. A delayed diagnosis can still be valuable for the proband or the relatives of BMD patients. © 2015 Wiley Periodicals, Inc.

  5. DNA-methylation profiling of fetal tissues reveals marked epigenetic differences between chorionic and amniotic samples.

    Directory of Open Access Journals (Sweden)

    Christel Eckmann-Scholz

    Full Text Available Epigenetic mechanisms including DNA methylation are supposed to play a key role in fetal development. Here we have investigated fetal DNA-methylation levels of 27,578 CpG loci in 47 chorionic villi (CVS and 16 amniotic cell (AC samples. Methylation levels differed significantly between karyotypically normal AC and CVS for 2,014 genes. AC showed more extreme DNA-methylation levels of these genes than CVS and the differentially methylated genes are significantly enriched for processes characteristic for the different cell types sampled. Furthermore, we identified 404 genes differentially methylated in CVS with trisomy 21. These genes were significantly enriched for high CG dinucleotid (CpG content and developmental processes associated with Down syndrome. Our study points to major tissue-specific differences of fetal DNA-methylation and gives rise to the hypothesis that part of the Down syndrome phenotype is epigenetically programmed in the first trimester of pregnancy.

  6. Environmental DNA from seawater samples correlate with trawl catches of Subarctic, deepwater fishes

    DEFF Research Database (Denmark)

    Thomsen, Philip Francis; Møller, Peter Rask; Sigsgaard, Eva Egelyng

    2016-01-01

    depths in Southwest Greenland. We collected seawater samples at depths of 188-918 m and compared seawater eDNA to catch data from trawling. We used Illumina sequencing of PCR products to demonstrate that eDNA reads show equivalence to fishing catch data obtained from trawling. Twenty-six families were......Remote polar and deepwater fish faunas are under pressure from ongoing climate change and increasing fishing effort. However, these fish communities are difficult to monitor for logistic and financial reasons. Currently, monitoring of marine fishes largely relies on invasive techniques...... such as bottom trawling, and on official reporting of global catches, which can be unreliable. Thus, there is need for alternative and non-invasive techniques for qualitative and quantitative oceanic fish surveys. Here we report environmental DNA (eDNA) metabarcoding of seawater samples from continental slope...

  7. Environmental DNA from Seawater Samples Correlate with Trawl Catches of Subarctic, Deepwater Fishes.

    Directory of Open Access Journals (Sweden)

    Philip Francis Thomsen

    Full Text Available Remote polar and deepwater fish faunas are under pressure from ongoing climate change and increasing fishing effort. However, these fish communities are difficult to monitor for logistic and financial reasons. Currently, monitoring of marine fishes largely relies on invasive techniques such as bottom trawling, and on official reporting of global catches, which can be unreliable. Thus, there is need for alternative and non-invasive techniques for qualitative and quantitative oceanic fish surveys. Here we report environmental DNA (eDNA metabarcoding of seawater samples from continental slope depths in Southwest Greenland. We collected seawater samples at depths of 188-918 m and compared seawater eDNA to catch data from trawling. We used Illumina sequencing of PCR products to demonstrate that eDNA reads show equivalence to fishing catch data obtained from trawling. Twenty-six families were found with both trawling and eDNA, while three families were found only with eDNA and two families were found only with trawling. Key commercial fish species for Greenland were the most abundant species in both eDNA reads and biomass catch, and interpolation of eDNA abundances between sampling sites showed good correspondence with catch sizes. Environmental DNA sequence reads from the fish assemblages correlated with biomass and abundance data obtained from trawling. Interestingly, the Greenland shark (Somniosus microcephalus showed high abundance of eDNA reads despite only a single specimen being caught, demonstrating the relevance of the eDNA approach for large species that can probably avoid bottom trawls in most cases. Quantitative detection of marine fish using eDNA remains to be tested further to ascertain whether this technique is able to yield credible results for routine application in fisheries. Nevertheless, our study demonstrates that eDNA reads can be used as a qualitative and quantitative proxy for marine fish assemblages in deepwater oceanic

  8. An Improved Method for High Quality Metagenomics DNA Extraction from Human and Environmental Samples

    DEFF Research Database (Denmark)

    Bag, Satyabrata; Saha, Bipasa; Mehta, Ojasvi

    2016-01-01

    and human origin samples. We introduced a combination of physical, chemical and mechanical lysis methods for proper lysis of microbial inhabitants. The community microbial DNA was precipitated by using salt and organic solvent. Both the quality and quantity of isolated DNA was compared with the existing...... methodologies and the supremacy of our method was confirmed. Maximum recovery of genomic DNA in the absence of substantial amount of impurities made the method convenient for nucleic acid extraction. The nucleic acids obtained using this method are suitable for different downstream applications. This improved...

  9. Study of DNA damage with a new system for irradiation of samples in a nuclear reactor

    Energy Technology Data Exchange (ETDEWEB)

    Gual, Maritza R., E-mail: mrgual@instec.c [Instituto Superior de Tecnologias y Ciencias Aplicadas, InSTEC, Avenida Salvador Allende y Luaces, Quinta de Los Molinos, Plaza de la Revolucion, Havana, AP 6163 (Cuba); Milian, Felix M. [Universidade Estadual de Santa Cruz, UESC (Brazil); Deppman, Airton [Instituto de Fisica, Universidad de Sao Paulo, IF-USP, Rua do Matao, Travessa R, no. 187, Ciudade Universitaria, Butanta, CEP 05508-900, Sao Paulo (Brazil); Coelho, Paulo R.P. [Instituto de Pesquisas Energeticas e Nucleares, IPEN-CNEN/SP (Brazil)

    2011-02-15

    In this paper, we report results of a quantitative analysis of the effects of neutrons on DNA, and, specifically, the production of simple and double breaks of plasmid DNA in aqueous solutions with different concentrations of free-radical scavengers. The radiation damage to DNA was evaluated by electrophoresis through agarose gels. The neutron and gamma doses were measured separately with thermoluminescent detectors. In this work, we have also demonstrated usefulness of a new system for positioning and removing samples in channel BH3 of the IEA-R1 reactor at the Instituto de Pesquisas Energeticas e Nucleares (Brazil) without necessity of interrupting the reactor operation.

  10. Quantitative Field Testing Rotylenchulus reniformis DNA from Metagenomic Samples Isolated Directly from Soil

    Science.gov (United States)

    Showmaker, Kurt; Lawrence, Gary W.; Lu, Shien; Balbalian, Clarissa; Klink, Vincent P.

    2011-01-01

    A quantitative PCR procedure targeting the β-tubulin gene determined the number of Rotylenchulus reniformis Linford & Oliveira 1940 in metagenomic DNA samples isolated from soil. Of note, this outcome was in the presence of other soil-dwelling plant parasitic nematodes including its sister genus Helicotylenchus Steiner, 1945. The methodology provides a framework for molecular diagnostics of nematodes from metagenomic DNA isolated directly from soil. PMID:22194958

  11. Latent hardening size effect in small-scale plasticity

    Science.gov (United States)

    Bardella, Lorenzo; Segurado, Javier; Panteghini, Andrea; Llorca, Javier

    2013-07-01

    We aim at understanding the multislip behaviour of metals subject to irreversible deformations at small-scales. By focusing on the simple shear of a constrained single-crystal strip, we show that discrete Dislocation Dynamics (DD) simulations predict a strong latent hardening size effect, with smaller being stronger in the range [1.5 µm, 6 µm] for the strip height. We attempt to represent the DD pseudo-experimental results by developing a flow theory of Strain Gradient Crystal Plasticity (SGCP), involving both energetic and dissipative higher-order terms and, as a main novelty, a strain gradient extension of the conventional latent hardening. In order to discuss the capability of the SGCP theory proposed, we implement it into a Finite Element (FE) code and set its material parameters on the basis of the DD results. The SGCP FE code is specifically developed for the boundary value problem under study so that we can implement a fully implicit (Backward Euler) consistent algorithm. Special emphasis is placed on the discussion of the role of the material length scales involved in the SGCP model, from both the mechanical and numerical points of view.

  12. Latent hardening size effect in small-scale plasticity

    International Nuclear Information System (INIS)

    Bardella, Lorenzo; Panteghini, Andrea; Segurado, Javier; Llorca, Javier

    2013-01-01

    We aim at understanding the multislip behaviour of metals subject to irreversible deformations at small-scales. By focusing on the simple shear of a constrained single-crystal strip, we show that discrete Dislocation Dynamics (DD) simulations predict a strong latent hardening size effect, with smaller being stronger in the range [1.5 µm, 6 µm] for the strip height. We attempt to represent the DD pseudo-experimental results by developing a flow theory of Strain Gradient Crystal Plasticity (SGCP), involving both energetic and dissipative higher-order terms and, as a main novelty, a strain gradient extension of the conventional latent hardening. In order to discuss the capability of the SGCP theory proposed, we implement it into a Finite Element (FE) code and set its material parameters on the basis of the DD results. The SGCP FE code is specifically developed for the boundary value problem under study so that we can implement a fully implicit (Backward Euler) consistent algorithm. Special emphasis is placed on the discussion of the role of the material length scales involved in the SGCP model, from both the mechanical and numerical points of view. (paper)

  13. Small-scale variability in tropical tropopause layer humidity

    Science.gov (United States)

    Jensen, E. J.; Ueyama, R.; Pfister, L.; Karcher, B.; Podglajen, A.; Diskin, G. S.; DiGangi, J. P.; Thornberry, T. D.; Rollins, A. W.; Bui, T. V.; Woods, S.; Lawson, P.

    2016-12-01

    Recent advances in statistical parameterizations of cirrus cloud processes for use in global models are highlighting the need for information about small-scale fluctuations in upper tropospheric humidity and the physical processes that control the humidity variability. To address these issues, we have analyzed high-resolution airborne water vapor measurements obtained in the Airborne Tropical TRopopause EXperiment over the tropical Pacific between 14 and 20 km. Using accurate and precise 1-Hz water vapor measurements along approximately-level aircraft flight legs, we calculate structure functions spanning horizontal scales ranging from about 0.2 to 50 km, and we compare the water vapor variability in the lower (about 14 km) and upper (16-19 km) Tropical Tropopause Layer (TTL). We also compare the magnitudes and scales of variability inside TTL cirrus versus in clear-sky regions. The measurements show that in the upper TTL, water vapor concentration variance is stronger inside cirrus than in clear-sky regions. Using simulations of TTL cirrus formation, we show that small variability in clear-sky humidity is amplified by the strong sensitivity of ice nucleation rate to supersaturation, which results in highly-structured clouds that subsequently drive variability in the water vapor field. In the lower TTL, humidity variability is correlated with recent detrainment from deep convection. The structure functions indicate approximately power-law scaling with spectral slopes ranging from about -5/3 to -2.

  14. Small-scale electric generators for arctic applications

    International Nuclear Information System (INIS)

    Lamp, T.R.

    1995-01-01

    Forest fires that have endangered remote US Air Force sites equipped with radioisotope thermoelectric generators (RTGs) has prompted the assessment of power generating systems as substitutes for RTGs in small scale (10--120 watt) applications. A team of scientists and engineers of the US Air Forces' Wright Laboratory conductd an assessment of electrical power technologies for use by the Air Force in remote, harsh environments. The surprisingly high logistics costs of operating fossil fuel generators resulted in the extension of the assessment to non-RTG sites. The candidate power sources must operate unattended for long periods at a high level of operational reliability. Selection of the optimum power generation technology is complicated and heavily driven by the severe operating environment and compounded by the remoteness of the location. It is these site-related characteristics, more than any other, that drive the selection of a safe and economical power source for Arctic applications. A number of proven power generation technologies were evaluated. The assessment concluded that RGTs are clearly the safest, most reliable, and most economical approach to supplying electrical power for remote, difficult to assess locations. The assessment also indicated that the logistics costs associated with combustion driven generator systems could be substantially reduced through the use of conversion technologies which have been previously developed for space power applications. copyright 1995 American Institute of Physics

  15. Development of a small-scale computer cluster

    Science.gov (United States)

    Wilhelm, Jay; Smith, Justin T.; Smith, James E.

    2008-04-01

    An increase in demand for computing power in academia has necessitated the need for high performance machines. Computing power of a single processor has been steadily increasing, but lags behind the demand for fast simulations. Since a single processor has hard limits to its performance, a cluster of computers can have the ability to multiply the performance of a single computer with the proper software. Cluster computing has therefore become a much sought after technology. Typical desktop computers could be used for cluster computing, but are not intended for constant full speed operation and take up more space than rack mount servers. Specialty computers that are designed to be used in clusters meet high availability and space requirements, but can be costly. A market segment exists where custom built desktop computers can be arranged in a rack mount situation, gaining the space saving of traditional rack mount computers while remaining cost effective. To explore these possibilities, an experiment was performed to develop a computing cluster using desktop components for the purpose of decreasing computation time of advanced simulations. This study indicates that small-scale cluster can be built from off-the-shelf components which multiplies the performance of a single desktop machine, while minimizing occupied space and still remaining cost effective.

  16. Small scale lithium-lead/water-interaction studies

    International Nuclear Information System (INIS)

    Kranert, O.; Kottowski, H.

    1991-01-01

    One current concept in fusion blanket design is to utilize water as the coolant and liquid lithium-lead as the breeding/neutron multiplier material. Considering the complex design of the blanket module, it is likely that a water leakage into the liquid alloy may occur due to a tube rupture provoking an intolerable pressure increase in the blanket module. The pressure increase is caused by the combined chemical and thermohydraulic reaction of lithium-lead with water. Experiments which simulate such a transient event are necessary to obtain information which is important for the blanket module design. The interaction has been investigated by conducting small-scale experiments at various injection pressures, alloy- and coolant temperatures. Besides using eutectic Li 17 Pb 83 , Li 7 Pb 2 , lithium and lead have been used. Among other results, the experiments indicate increasing chemical reaction with increasing lithium concentration. At the same time, the chemical reaction inhibits violent thermohydaulic reactions due to the attenuating effect of the hydrogen produced. The preliminary epxerimental results from Li 17 Pb 83 and Li 7 Pb 2 reveal that the pressure- and temperature transients caused by the chemical and thermohydraulic reactions lie within technically manageable limits. (orig.)

  17. Small-Scale Fabrication of Biomimetic Structures for Periodontal Regeneration

    Science.gov (United States)

    Green, David W.; Lee, Jung-Seok; Jung, Han-Sung

    2016-01-01

    The periodontium is the supporting tissues for the tooth organ and is vulnerable to destruction, arising from overpopulating pathogenic bacteria and spirochaetes. The presence of microbes together with host responses can destroy large parts of the periodontium sometimes leading tooth loss. Permanent tissue replacements are made possible with tissue engineering techniques. However, existing periodontal biomaterials cannot promote proper tissue architectures, necessary tissue volumes within the periodontal pocket and a “water-tight” barrier, to become clinically acceptable. New kinds of small-scale engineered biomaterials, with increasing biological complexity are needed to guide proper biomimetic regeneration of periodontal tissues. So the ability to make compound structures with small modules, filled with tissue components, is a promising design strategy for simulating the anatomical complexity of the periodotium attachment complexes along the tooth root and the abutment with the tooth collar. Anatomical structures such as, intima, adventitia, and special compartments such as the epithelial cell rests of Malassez or a stellate reticulum niche need to be engineered from the start of regeneration to produce proper periodontium replacement. It is our contention that the positioning of tissue components at the origin is also necessary to promote self-organizing cell–cell connections, cell–matrix connections. This leads to accelerated, synchronized and well-formed tissue architectures and anatomies. This strategy is a highly effective preparation for tackling periodontitis, periodontium tissue resorption, and to ultimately prevent tooth loss. Furthermore, such biomimetic tissue replacements will tackle problems associated with dental implant support and perimimplantitis. PMID:26903872

  18. Small Scale Turbopump Manufacturing Technology and Material Processes

    Science.gov (United States)

    Alvarez, Erika; Morgan, Kristin; Wells, Doug; Zimmerman, Frank

    2011-01-01

    As part of an internal research and development project, NASA Marshall Space Flight Center (MSFC) has been developing a high specific impulse 9,000-lbf LOX/LH2 pump-fed engine testbed with the capability to throttle 10:1. A Fuel Turbopump (FTP) with the ability to operate across a speed range of 30,000-rpm to 100,000-rpm was developed and analyzed. This small size and flight-like Fuel Turbopump has completed the design and analysis phase and is currently in the manufacturing phase. This paper highlights the manufacturing and processes efforts to fabricate an approximately 20-lb turbopump with small flow passages, intricately bladed components and approximately 3-in diameter impellers. As a result of the small scale and tight tolerances of the hardware on this turbopump, several unique manufacturing and material challenges were encountered. Some of the technologies highlighted in this paper include the use of powder metallurgy technology to manufacture small impellers, electron beam welding of a turbine blisk shroud, and casting challenges. The use of risk reduction efforts such as non-destructive testing (NDT) and evaluation (NDE), fractography, material testing, and component spin testing are also discussed in this paper.

  19. Small-Scale Testing of Laterally Loaded Monopiles in Sand

    DEFF Research Database (Denmark)

    Thomassen, Kristina; Roesen, Hanne Ravn; Ibsen, Lars Bo

    2011-01-01

    of small-scale laboratory tests. Six quasi-static tests are conducted on piles with diameters of 40mm and 100mm and a slenderness ratio, L/D, of 5. To minimise scale effects, the tests are carried out in a pressure tank at various stress levels. From the obtained load-deflection relationships......In current designs of offshore wind turbines, monopiles are often used as foundation. The behaviour of the monopoles when subjected to lateral loading has not been fully investigated. In this paper, the behaviour of two non-slender piles in sand subjected to lateral loading are analysed by means...... it is revealed that the uncertainties of the results for the pile with a diameter of 40mm are large. The load-deflection relationships normalised as H/(L2Dγ’) and y/D indicate that the lateral load, H, is proportional to L2D. Comparison of the normalised load-deflection relationships for different stress levels...

  20. Small-scale dislocation plasticity in strontium titanate

    Energy Technology Data Exchange (ETDEWEB)

    Stukowski, Alexander; Javaid, Farhan; Durst, Karsten; Albe, Karsten [Technische Universitaet Darmstadt (Germany)

    2016-07-01

    Strontium titanate (STO) is an optically transparent perovskite oxide ceramic material. In contrast to other ceramics, single crystal STO plastically deforms under ambient condition, without showing a phase transition or early fracture. This remarkable ductility makes it a prime candidate for different technological applications. However, while the mechanical behavior of bulk STO has been studied extensively using uniaxial compression testing techniques, little is known about the local, small-scale behavior and the details of dislocation-based nanoplasticity in this perovskite material. In this contribution we compare results obtained from new nanoindentation experiments and corresponding large-scale molecular dynamics simulations. The evolution of the plastic zone and dislocation structures that form underneath the indenter is investigated using etch-pit methods in experiments and a novel three-dimensional defect identification technique in atomistic computer models. The latter allows tracing the evolution of the complete dislocation line network as function of indentation depth, quantifying the activity of different slip systems, and correlating this information with the recorded load-displacement curves and hardness data.

  1. Small-Scale Fabrication of Biomimetic Structures for Periodontal Regeneration

    Directory of Open Access Journals (Sweden)

    David William Green

    2016-02-01

    Full Text Available The periodontium is the supporting tissues for the tooth organ and is vulnerable to destruction, arising from overpopulating pathogenic bacteria and spirochaetes. The presence of microbes together with host responses can destroy large parts of the periodontium sometimes leading tooth loss. Permanent tissue replacements are made possible with tissue engineering techniques. However, existing periodontal biomaterials cannot promote proper tissue architectures, necessary tissue volumes within the periodontal pocket and a water-tight barrier, to become clinically acceptable. New kinds of small-scale engineered biomaterials, with increasing biological complexity are needed to guide proper biomimetic regeneration of periodontal tissues. So the ability to make compound structures with small modules, filled with tissue components, is a promising design strategy for simulating the anatomical complexity of the periodotium attachement complexes along the tooth root and the abutment with the tooth collar. Anatomical structures such as, intima, adventitia and special compartments such as the epithelial cell rests of Malassez or a stellate reticulum niche need to be engineered from the start of regeneration to produce proper periodontium replacement.. It is our contention that the positioning of tissue components at the origin is also necessary to promote self-organising cell-cell connections, cell-matrix connections. This leads to accelerated, synchronized and well-formed tissue architectures and anatomies. This strategy is a highly effective preparation for tackling periodontitis, periodontium tissue resorption and to ultimately prevent tooth loss. Furthermore, such biomimetic tissue replacements will tackle problems associated with dental implant support and perimimplantitis.

  2. Impact of small-scale geometric roughness on wetting behavior.

    Science.gov (United States)

    Kumar, Vaibhaw; Errington, Jeffrey R

    2013-09-24

    We examine the extent to which small-scale geometric substrate roughness influences the wetting behavior of fluids at solid surfaces. Molecular simulation is used to construct roughness wetting diagrams wherein the progression of the contact angle is traced from the Cassie to Wenzel to impregnation regime with increasing substrate strength for a collection of systems with rectangularly shaped grooves. We focus on the evolution of these diagrams as the length scale of the substrate features approaches the size of a fluid molecule. When considering a series of wetting diagrams for substrates with fixed shape and variable feature periodicity, we find that the diagrams progressively shift away from a common curve as the substrate features become smaller than approximately 10 fluid diameters. It is at this length scale that the macroscopic models of Cassie and Wenzel become unreliable. Deviations from the macroscopic models are attributed to the manner in which the effective substrate-fluid interaction strength evolves with periodicity and the important role that confinement effects play for substrates with small periodicities.

  3. Structures and Intermittency in Small Scales Solar Wind Turbulence

    International Nuclear Information System (INIS)

    Sahraoui, Fouad; Goldstein, Melvyn

    2010-01-01

    Several observations in space plasmas have reported the presence of coherent structures at different plasma scales. Structure formation is believed to result from nonlinear interactions between the plasma modes, which depend strongly on their phase synchronization. Despite this important role of the phases in turbulence, very limited work has been devoted to study the phases as potential tracers of nonlinearities in comparison with the wealth of literature on power spectra of turbulence where phases are totally missed. The reason why the phases are seldom used is probably because they usually appear to be completely mixed (due to their dependence on an arbitrary time origin and to 2π periodicity). To handle the phases properly, a new method based on using surrogate data has been developed recently to detect coherent structures in magnetized plasmas [Sahraoui, PRE, 2008]. Here, we show new applications of the technique to study the nature (weak vs strong, self-similar vs intermittent) of the small scale turbulence in the solar wind using the Cluster observations.

  4. Small-scale structure in the diffuse interstellar medium

    International Nuclear Information System (INIS)

    Meyer, D.M.

    1990-01-01

    The initial results of a study to probe the small-scale structure in the diffuse interstellar medium (ISM) through IUE and optical observations of interstellar absorption lines toward both components of resolvable binary stars is reported. The binaries (Kappa CrA, 57 Aql, 59 And, HR 1609/10, 19 Lyn, and Theta Ser) observed with IUE have projected linear separations ranging from 5700 to 700 Au. Except for Kappa CrA, the strengths of the interstellar absorption lines toward both components of these binaries agree to within 10 percent. In the case of Kappa CrA, the optically thin interstellar Mg I and Mn II lines are about 50 percent stronger toward Kappa-2 CrA than Kappa-1 CrA. Higher resolution observations of interstellar Ca II show that this difference is concentrated in the main interstellar component at V(LSR) = 9 + or - 2 km/s. Interestingly, this velocity corresponds to an intervening cloud that may be associated with the prominent Loop I shell in the local ISM. Given the separation (23 arcsec) and distance (120 pc) of Kappa CrA, the line strength variations indicate that this cloud has structure on scales of 2800 AU or less. 21 refs

  5. Small-scale fixed wing airplane software verification flight test

    Science.gov (United States)

    Miller, Natasha R.

    The increased demand for micro Unmanned Air Vehicles (UAV) driven by military requirements, commercial use, and academia is creating a need for the ability to quickly and accurately conduct low Reynolds Number aircraft design. There exist several open source software programs that are free or inexpensive that can be used for large scale aircraft design, but few software programs target the realm of low Reynolds Number flight. XFLR5 is an open source, free to download, software program that attempts to take into consideration viscous effects that occur at low Reynolds Number in airfoil design, 3D wing design, and 3D airplane design. An off the shelf, remote control airplane was used as a test bed to model in XFLR5 and then compared to flight test collected data. Flight test focused on the stability modes of the 3D plane, specifically the phugoid mode. Design and execution of the flight tests were accomplished for the RC airplane using methodology from full scale military airplane test procedures. Results from flight test were not conclusive in determining the accuracy of the XFLR5 software program. There were several sources of uncertainty that did not allow for a full analysis of the flight test results. An off the shelf drone autopilot was used as a data collection device for flight testing. The precision and accuracy of the autopilot is unknown. Potential future work should investigate flight test methods for small scale UAV flight.

  6. Hydropower harvesting from a small scale reciprocating system

    Energy Technology Data Exchange (ETDEWEB)

    Malla, Ramesh B.; Shrestha, Binu; Bagtzoglou, Amvrossios; Drasdis, Jonathon [Department of Civil and Environmental Engineering, University of Connecticut, 261 Glenbrook Road, Storrs, CT 06269-2037 (United States); Johnson, Paul [eGen LLC, 1084 Shennecossett Road, Groton, CT 06340 (United States)

    2011-05-15

    Conventional hydropower systems that can take advantage of low head movement of water require substantial flow rates. However, these systems cannot harvest hydro energy from small sources of water with low head and low discharge, such as streams and creeks. The reciprocating hydropower system discussed in this paper can harvest power from such low flow discharge and low head sources. This paper presents a detailed proof-of-concept study of the hydropower model, including the underlining theoretical principles. Laboratory test results demonstrating the dependence of the lift force in the reciprocating small scale hydropower model as a function of flow velocity, size and rotational speed of the cylinder and comparison of the results with a previous study are also included. Two methods of power harvesting from the output displacement obtained from the hydropower system are discussed. The first employs electromagnetic induction principles and the other is based on a linear inertial generator using a conventional second order spring mass damper system. Finally, results from a finite element analysis of the hydropower system are presented and facilitate future design of the structural aspects of the housing for the reciprocating cylinder. (author)

  7. Numerical simulation of a small-scale biomass boiler

    International Nuclear Information System (INIS)

    Collazo, J.; Porteiro, J.; Míguez, J.L.; Granada, E.; Gómez, M.A.

    2012-01-01

    Highlights: ► Simplified model for biomass combustion was developed. ► Porous zone conditions are used in the bed. ► Model is fully integrated in a commercial CFD code to simulate a small scale pellet boiler. ► Pollutant emissions are well predicted. ► Simulation provides extensive information about the behaviour of the boiler. - Abstract: This paper presents a computational fluid dynamic simulation of a domestic pellet boiler. Combustion of the solid fuel in the burner is an important issue when discussing the simulation of this type of system. A simplified method based on a thermal balance was developed in this work to introduce the effects provoked by pellet combustion in the boiler simulation. The model predictions were compared with the experimental measurements, and a good agreement was found. The results of the boiler analysis show that the position of the water tubes, the distribution of the air inlets and the air infiltrations are the key factors leading to the high emission levels present in this type of system.

  8. Impact of small-scale structures on estuarine circulation

    Science.gov (United States)

    Liu, Zhuo; Zhang, Yinglong J.; Wang, Harry V.; Huang, Hai; Wang, Zhengui; Ye, Fei; Sisson, Mac

    2018-05-01

    We present a novel and challenging application of a 3D estuary-shelf model to the study of the collective impact of many small-scale structures (bridge pilings of 1 m × 2 m in size) on larger-scale circulation in a tributary (James River) of Chesapeake Bay. We first demonstrate that the model is capable of effectively transitioning grid resolution from 400 m down to 1 m near the pilings without introducing undue numerical artifact. We then show that despite their small sizes and collectively small area as compared to the total channel cross-sectional area, the pilings exert a noticeable impact on the large-scale circulation, and also create a rich structure of vortices and wakes around the pilings. As a result, the water quality and local sedimentation patterns near the bridge piling area are likely to be affected as well. However, when evaluating over the entire waterbody of the project area, the near field effects are weighed with the areal percentage which is small compared to that for the larger unaffected area, and therefore the impact on the lower James River as a whole becomes relatively insignificant. The study highlights the importance of the use of high resolution in assessing the near-field impact of structures.

  9. Social Norms of Cooperation in Small-Scale Societies.

    Directory of Open Access Journals (Sweden)

    Fernando P Santos

    2016-01-01

    Full Text Available Indirect reciprocity, besides providing a convenient framework to address the evolution of moral systems, offers a simple and plausible explanation for the prevalence of cooperation among unrelated individuals. By helping someone, an individual may increase her/his reputation, which may change the pre-disposition of others to help her/him in the future. This, however, depends on what is reckoned as a good or a bad action, i.e., on the adopted social norm responsible for raising or damaging a reputation. In particular, it remains an open question which social norms are able to foster cooperation in small-scale societies, while enduring the wide plethora of stochastic affects inherent to finite populations. Here we address this problem by studying the stochastic dynamics of cooperation under distinct social norms, showing that the leading norms capable of promoting cooperation depend on the community size. However, only a single norm systematically leads to the highest cooperative standards in small communities. That simple norm dictates that only whoever cooperates with good individuals, and defects against bad ones, deserves a good reputation, a pattern that proves robust to errors, mutations and variations in the intensity of selection.

  10. Social Norms of Cooperation in Small-Scale Societies.

    Science.gov (United States)

    Santos, Fernando P; Santos, Francisco C; Pacheco, Jorge M

    2016-01-01

    Indirect reciprocity, besides providing a convenient framework to address the evolution of moral systems, offers a simple and plausible explanation for the prevalence of cooperation among unrelated individuals. By helping someone, an individual may increase her/his reputation, which may change the pre-disposition of others to help her/him in the future. This, however, depends on what is reckoned as a good or a bad action, i.e., on the adopted social norm responsible for raising or damaging a reputation. In particular, it remains an open question which social norms are able to foster cooperation in small-scale societies, while enduring the wide plethora of stochastic affects inherent to finite populations. Here we address this problem by studying the stochastic dynamics of cooperation under distinct social norms, showing that the leading norms capable of promoting cooperation depend on the community size. However, only a single norm systematically leads to the highest cooperative standards in small communities. That simple norm dictates that only whoever cooperates with good individuals, and defects against bad ones, deserves a good reputation, a pattern that proves robust to errors, mutations and variations in the intensity of selection.

  11. A diagnostic model to estimate winds and small-scale drag from Mars Observer PMIRR data

    Science.gov (United States)

    Barnes, J. R.

    1993-01-01

    Theoretical and modeling studies indicate that small-scale drag due to breaking gravity waves is likely to be of considerable importance for the circulation in the middle atmospheric region (approximately 40-100 km altitude) on Mars. Recent earth-based spectroscopic observations have provided evidence for the existence of circulation features, in particular, a warm winter polar region, associated with gravity wave drag. Since the Mars Observer PMIRR experiment will obtain temperature profiles extending from the surface up to about 80 km altitude, it will be extensively sampling middle atmospheric regions in which gravity wave drag may play a dominant role. Estimating the drag then becomes crucial to the estimation of the atmospheric winds from the PMIRR-observed temperatures. An interative diagnostic model based upon one previously developed and tested with earth satellite temperature data will be applied to the PMIRR measurements to produce estimates of the small-scale zonal drag and three-dimensional wind fields in the Mars middle atmosphere. This model is based on the primitive equations, and can allow for time dependence (the time tendencies used may be based upon those computed in a Fast Fourier Mapping procedure). The small-scale zonal drag is estimated as the residual in the zonal momentum equation; the horizontal winds having first been estimated from the meridional momentum equation and the continuity equation. The scheme estimates the vertical motions from the thermodynamic equation, and thus needs estimates of the diabatic heating based upon the observed temperatures. The latter will be generated using a radiative model. It is hoped that the diagnostic scheme will be able to produce good estimates of the zonal gravity wave drag in the Mars middle atmosphere, estimates that can then be used in other diagnostic or assimilation efforts, as well as more theoretical studies.

  12. On Spatial Resolution in Habitat Models: Can Small-scale Forest Structure Explain Capercaillie Numbers?

    Directory of Open Access Journals (Sweden)

    Ilse Storch

    2002-06-01

    Full Text Available This paper explores the effects of spatial resolution on the performance and applicability of habitat models in wildlife management and conservation. A Habitat Suitability Index (HSI model for the Capercaillie (Tetrao urogallus in the Bavarian Alps, Germany, is presented. The model was exclusively built on non-spatial, small-scale variables of forest structure and without any consideration of landscape patterns. The main goal was to assess whether a HSI model developed from small-scale habitat preferences can explain differences in population abundance at larger scales. To validate the model, habitat variables and indirect sign of Capercaillie use (such as feathers or feces were mapped in six study areas based on a total of 2901 20 m radius (for habitat variables and 5 m radius sample plots (for Capercaillie sign. First, the model's representation of Capercaillie habitat preferences was assessed. Habitat selection, as expressed by Ivlev's electivity index, was closely related to HSI scores, increased from poor to excellent habitat suitability, and was consistent across all study areas. Then, habitat use was related to HSI scores at different spatial scales. Capercaillie use was best predicted from HSI scores at the small scale. Lowering the spatial resolution of the model stepwise to 36-ha, 100-ha, 400-ha, and 2000-ha areas and relating Capercaillie use to aggregated HSI scores resulted in a deterioration of fit at larger scales. Most importantly, there were pronounced differences in Capercaillie abundance at the scale of study areas, which could not be explained by the HSI model. The results illustrate that even if a habitat model correctly reflects a species' smaller scale habitat preferences, its potential to predict population abundance at larger scales may remain limited.

  13. Detection of Merkel Cell Polyomavirus DNA in Serum Samples of Healthy Blood Donors

    Science.gov (United States)

    Mazzoni, Elisa; Rotondo, John C.; Marracino, Luisa; Selvatici, Rita; Bononi, Ilaria; Torreggiani, Elena; Touzé, Antoine; Martini, Fernanda; Tognon, Mauro G.

    2017-01-01

    Merkel cell polyomavirus (MCPyV) has been detected in 80% of Merkel cell carcinomas (MCC). In the host, the MCPyV reservoir remains elusive. MCPyV DNA sequences were revealed in blood donor buffy coats. In this study, MCPyV DNA sequences were investigated in the sera (n = 190) of healthy blood donors. Two MCPyV DNA sequences, coding for the viral oncoprotein large T antigen (LT), were investigated using polymerase chain reaction (PCR) methods and DNA sequencing. Circulating MCPyV sequences were detected in sera with a prevalence of 2.6% (5/190), at low-DNA viral load, which is in the range of 1–4 and 1–5 copies/μl by real-time PCR and droplet digital PCR, respectively. DNA sequencing carried out in the five MCPyV-positive samples indicated that the two MCPyV LT sequences which were analyzed belong to the MKL-1 strain. Circulating MCPyV LT sequences are present in blood donor sera. MCPyV-positive samples from blood donors could represent a potential vehicle for MCPyV infection in receivers, whereas an increase in viral load may occur with multiple blood transfusions. In certain patient conditions, such as immune-depression/suppression, additional disease or old age, transfusion of MCPyV-positive samples could be an additional risk factor for MCC onset. PMID:29238698

  14. Small scale thermal violence experiments for combined insensitive high explosive and booster materials

    Energy Technology Data Exchange (ETDEWEB)

    Rae, Philip J [Los Alamos National Laboratory; Bauer, Clare L [AWE, UK; Stennett, C [DCMT SHRIVENHAM, UK; Flower, H M [AWE, UK

    2010-01-01

    A small scale cook-off experiment has been designed to provide a violence metric for both booster and IHE materials, singly and in combination. The experiment has a simple, axisymmetric geometry provided by a 10 mm internal diameter cylindrical steel confinement up to 80 mm in length. Heating is applied from one end of the sample length creating pseudo 1-D heating profile and a thermal gradient across the sample(s). At the opposite end of the confinement to the heating block, a machined groove provides a point of rupture that generates a cylindrical fragment. The displacement of the external face of the fragment is detected by Heterodyne Velocimetry. Proof of concept experiments are reported focusing on HMX and TATB formulations, and are described in relation to confinement, ullage and heating profile. The development of a violence metric, based upon fragment velocity records is discussed.

  15. Usefulness of FTA® cards as a Pneumocystis-DNA extraction method in bronchoalveolar lavage samples.

    Science.gov (United States)

    Rodiño, Jenniffer M; Aguilar, Yudy A; Rueda, Zulma Vanessa; Vélez, Lázaro A

    2016-01-01

    FTA® cards (Fast Technology for Analysis of Nucleic Acids) are an alternative DNA extraction method in bronchoalveolar lavage (BAL) samples for Pneumocystis jirovecii molecular analyses. The goal was to evaluate the usefulness of FTA® cards to detect P. jirovecii-DNA by PCR in BAL samples compared to silica adsorption chromatography (SAC). This study used 134 BAL samples from immunocompromised patients previously studied to establish microbiological aetiology of pneumonia, among them 15 cases of Pneumocystis pneumonia (PCP) documented by staining and 119 with other alternative diagnoses. The FTA® system and SAC were used for DNA extraction and then amplified by nested PCR to detect P. jirovecii. Performance and concordance of the two DNA extraction methods compared to P. jirovecii microscopy were calculated. The influence of the macroscopic characteristics, transportation of samples and the duration of the FTA® card storage (1, 7, 10 or 12 months) were also evaluated. Among 134 BAL samples, 56% were positive for P. jirovecii-DNA by SAC and 27% by FTA®. All 15 diagnosed by microscopy were detected by FTA® and SAC. Specificity of the FTA® system and SAC were 82.4% and 49.6%, respectively. Compared to SAC, positivity by FTA® decreased with the presence of blood in BAL (62% vs 13.5%). The agreement between samples at 7, 10 and 12 months was 92.5% for FTA®. Positive cases by FTA® remained the same after shipment by mail. Results suggest that FTA® is a practical, safe and economical method to preserve P. jirovecii-DNA in BAL samples for molecular studies.

  16. Study of microtip-based extraction and purification of DNA from human samples for portable devices

    Science.gov (United States)

    Fotouhi, Gareth

    DNA sample preparation is essential for genetic analysis. However, rapid and easy-to-use methods are a major challenge to obtaining genetic information. Furthermore, DNA sample preparation technology must follow the growing need for point-of-care (POC) diagnostics. The current use of centrifuges, large robots, and laboratory-intensive protocols has to be minimized to meet the global challenge of limited access healthcare by bringing the lab to patients through POC devices. To address these challenges, a novel extraction method of genomic DNA from human samples is presented by using heat-cured polyethyleneimine-coated microtips generating a high electric field. The microtip extraction method is based on recent work using an electric field and capillary action integrated into an automated device. The main challenges to the method are: (1) to obtain a stable microtip surface for the controlled capture and release of DNA and (2) to improve the recovery of DNA from samples with a high concentration of inhibitors, such as human samples. The present study addresses these challenges by investigating the heat curing of polyethyleneimine (PEI) coated on the surface of the microtip. Heat-cured PEI-coated microtips are shown to control the capture and release of DNA. Protocols are developed for the extraction and purification of DNA from human samples. Heat-cured PEI-coated microtip methods of DNA sample preparation are used to extract genomic DNA from human samples. It is discovered through experiment that heat curing of a PEI layer on a gold-coated surface below 150°C could inhibit the signal of polymerase chain reaction (PCR). Below 150°C, the PEI layer is not completely cured and dissolved off the gold-coated surface. Dissolved PEI binds with DNA to inhibit PCR. Heat curing of a PEI layer above 150°C on a gold-coated surface prevents inhibition to PCR and gel electrophoresis. In comparison to gold-coated microtips, the 225°C-cured PEI-coated microtips improve the

  17. DNA extraction in Echinococcus granulosus and Taenia spp. eggs in dogs stool samples applying thermal shock.

    Science.gov (United States)

    Hidalgo, Alejandro; Melo, Angélica; Romero, Fernando; Hidalgo, Víctor; Villanueva, José; Fonseca-Salamanca, Flery

    2018-03-01

    The extraction of DNA in taeniid eggs shows complications attached to the composition of stool samples and the high resistance of eggs to degradation. The objective of this study was to test a method of DNA extraction in taeniid eggs by applying a thermal shock to facilitate the chemical-enzymatic degradation of these elements. A group of six tubes containing 1 ml of dog stool sample was spiked with eggs of Echinococcus granulosus and another group of six with Taenia pisiformis. Samples were floated with supersaturated sugar solution and centrifuged. The upper portion of each tube (500 μl) was aspirated and deposited in 1.5 ml tubes. Three tubes from each group were incubated at -20 °C and then at 90 °C, the remaining three from each group, incubated at room temperature. Proteinase K and lysis buffer were added to each tube and incubated for 12 h at 58 °C. The lysis effect was evaluated by microscopy at 3, 6 and 12 h and integrity by electrophoresis in 1% agarose gels. With the same experimental scheme, the thermal shock effect was evaluated in extractions of 1, 2, 3 and 4 eggs of each species and the DNA was quantified. Additionally, the protocol was applied in samples of 4 dogs diagnosed with natural infection by Taeniidae worms. Finally, all the extractions were tested by PCR amplification. Both E. granulosus and T. pisiformis eggs showed a similar response in the tests. In samples without treatment, the lysis effect was poor and showed no differences over time, but in those subjected to thermal shock, eggs degradation increased with time. In both treatments, there was no DNA loss integrity. The protocol applied to limited amounts of eggs yielded PCR products in 100% of the samples exposed to thermal shock, allowing PCR amplifications up to 1 egg. In non-exposed samples, the results were not replicable. However, DNA quantification showed low values in both treatments. In turn, DNA extractions with thermal shock in infected dog samples

  18. Gas explosion characterization, wave propagation (small-scale experiments)

    International Nuclear Information System (INIS)

    Larsen, G.C.

    1985-01-01

    A number of experiments have been performed with blast waves arising from the ignition of homogeneous and well defined mixtures of methane, oxygen and nitrogen, contained within spherical balloons with controlled initial dimensions. In the initial small scale experiments pressure characteristics, ground reflection phenomena and pressure distribution on box like obstacles were studied. Both configurations with one box and two closely spaced boxes have been considered, and a wave-wave interaction phenomenom was observed in the case of closely spaced obstacles. Main emphasis has been placed on the half scale field experiments. In these, the maximum flame speed has been of the order of 100 m/s, resulting in positive peak pressures of 50-100.10 2 Pa in 5 - 10 m distance from the source. The explosion process was found to be reasonable symmetric. The attenuation of the blast wave due to vegetation and the influence of obstacles as banks, walls and houses on the pressure field have been investigated. The presence of the bank and the house was felt in a zone with a length corresponding to a typical dimension of the obstacles, whereas the overall pressure field is shown to be unaffected by the type of obstacles and vegetation investigated. For the wall and house, reflection factors have been established, and some variation over the surface has been measured. The scatter of the pressure measurements is estimated for stable, neutral and unstable atmospheric conditions, and an attempt to determine the ground reflection factor has been performed. Finally the accelerations of a house exposed to the blast wave have been examined

  19. ARCADE small-scale docking mechanism for micro-satellites

    Science.gov (United States)

    Boesso, A.; Francesconi, A.

    2013-05-01

    The development of on-orbit autonomous rendezvous and docking (ARD) capabilities represents a key point for a number of appealing mission scenarios that include activities of on-orbit servicing, automated assembly of modular structures and active debris removal. As of today, especially in the field of micro-satellites ARD, many fundamental technologies are still missing or require further developments and micro-gravity testing. In this framework, the University of Padova, Centre of Studies and Activities for Space (CISAS), developed the Autonomous Rendezvous Control and Docking Experiment (ARCADE), a technology demonstrator intended to fly aboard a BEXUS stratospheric balloon. The goal was to design, build and test, in critical environment conditions, a proximity relative navigation system, a custom-made reaction wheel and a small-size docking mechanism. The ARCADE docking mechanism was designed against a comprehensive set of requirements and it can be classified as small-scale, central, gender mating and unpressurized. The large use of commercial components makes it low-cost and simple to be manufactured. Last, it features a good tolerance to off-nominal docking conditions and a by-design soft docking capability. The final design was extensively verified to be compliant with its requirements by means of numerical simulations and physical testing. In detail, the dynamic behaviour of the mechanism in both nominal and off-nominal conditions was assessed with the multibody dynamics analysis software MD ADAMS 2010 and functional tests were carried out within the fully integrated ARCADE experiment to ensure the docking system efficacy and to highlight possible issues. The most relevant results of the study will be presented and discussed in conclusion to this paper.

  20. Small Scales Structure of MHD Turbulence, Tubes or Ribbons?

    Science.gov (United States)

    Verdini, A.; Grappin, R.; Alexandrova, O.; Lion, S.

    2017-12-01

    Observations in the solar wind indicate that turbulent eddies change their anisotropy with scales [1]. At large scales eddies are elongated in direction perpendicular to the mean-field axis. This is the result of solar wind expansion that affects both the anisotropy and single-spacecraft measurments [2,3]. At small scales one recovers the anisotropy expected in strong MHD turbulence and constrained by the so-called critical balance: eddies are elongated along the mean-field axis. However, the actual eddy shape is intermediate between tubes and ribbons, preventing us to discriminate between two concurrent theories that predict 2D axysimmetric anisotropy [4] or full 3D anisotropy [5]. We analyse 10 years of WIND data and apply a numerically-derived criterion to select intervals in which solar wind expansion is expected to be negligible. By computing the anisotropy of structure functions with respect to the local mean field we obtain for the first time scaling relations that are in agreement with full 3D anisotropy, i.e. ribbons-like structures. However, we cannot obtain the expected scaling relations for the alignment angle which, according to the theory, is physically responsible for the departure from axisymmetry. In addition, a further change of anisotropy occurs well above the proton scales. We discuss the implication of our findings and how numerical simulations can help interpreting the observed spectral anisotropy. [1] Chen et al., ApJ, 768:120, 2012 [2] Verdini & Grappin, ApJL, 808:L34, 2015 [3] Vech & Chen, ApJL, 832:L16, 2016 [4] Goldreich & Shridar, ApJ, 438:763, 1995 [5] Boldyrev, ApJL, 626:L37, 2005

  1. Comparison of three methods for recovery of Brucella canis DNA from canine blood samples.

    Science.gov (United States)

    Batinga, Maria Cryskely A; Dos Santos, Jaíne C; Lima, Julia T R; Bigotto, Maria Fernanda D; Muner, Kerstin; Faita, Thalita; Soares, Rodrigo M; da Silva, David A V; Oliveira, Trícia M F S; Ferreira, Helena L; Diniz, Jaqueline A; Keid, Lara B

    2017-12-01

    Brucella canis, a gram-negative, facultative intracellular and zoonotic bacterium causes canine brucellosis. Direct methods are the most appropriate for the detection of canine brucellosis and bacterial isolation from blood samples has been employed as gold-standard method. However, due to the delay in obtaining results and the biological risk of the bacterial culturing, the polymerase chain reaction (PCR) has been successfully used as an alternative method for the diagnosis of the infection. Sample preparation is a key step for successful PCR and protocols that provide high DNA yield and purity are recommended to ensure high diagnostic sensitivity. The objective of this study was to evaluate the performance of PCR for the diagnosis of B. canis infection in 36 dogs by testing DNA of whole blood obtained through different extraction and purification protocols. Methods 1 and 2 were based on a commercial kit, using protocols recommended for DNA purification of whole blood and tissue samples, respectively. Method 3 was an in-house method based on enzymatic lysis and purification using organic solvents. The results of the PCR on samples obtained through three different DNA extraction protocols were compared to the blood culture. Of the 36 dogs, 13 (36.1%) were positive by blood culturing, while nine (25.0%), 14 (38.8%), and 15 (41.6%) were positive by PCR after DNA extraction using methods 1, 2 and 3, respectively. PCR performed on DNA purified by Method 2 was as efficient as blood culturing and PCR performed on DNA purified with in-house method, but had the advantage of being less laborious and, therefore, a suitable alternative for the direct B. canis detection in dogs. Copyright © 2017. Published by Elsevier B.V.

  2. Assessment of mercury exposure among small-scale gold miners using mercury stable isotopes

    Energy Technology Data Exchange (ETDEWEB)

    Sherman, Laura S., E-mail: lsaylors@umich.edu [University of Michigan, Department of Earth and Environmental Sciences, 1100 North University Avenue, Ann Arbor, MI 48109 (United States); Blum, Joel D. [University of Michigan, Department of Earth and Environmental Sciences, 1100 North University Avenue, Ann Arbor, MI 48109 (United States); Basu, Niladri [McGill University, Faculty of Agricultural and Environmental Sciences, 21,111 Lakeshore Road, Ste. Anne de Bellevue, Quebec, Canada H9X3V9 (Canada); Rajaee, Mozhgon [University of Michigan, Department of Environmental Health Sciences, 1415 Washington Heights, Ann Arbor, MI 48109 (United States); Evers, David C.; Buck, David G. [Biodiversity Research Institute, 19 Flaggy Meadow Road, Gorham, ME 04038 (United States); Petrlik, Jindrich [Arnika Association, Chlumova 17, Prague 3 (Czech Republic); DiGangi, Joseph [IPEN, Box 7256, SE-402 35 Gothenburg (Sweden)

    2015-02-15

    Total mercury (Hg) concentrations in hair and urine are often used as biomarkers of exposure to fish-derived methylmercury (MeHg) and gaseous elemental Hg, respectively. We used Hg stable isotopes to assess the validity of these biomarkers among small-scale gold mining populations in Ghana and Indonesia. Urine from Ghanaian miners displayed similar Δ{sup 199}Hg values to Hg derived from ore deposits (mean urine Δ{sup 199}Hg=0.01‰, n=6). This suggests that urine total Hg concentrations accurately reflect exposure to inorganic Hg among this population. Hair samples from Ghanaian miners displayed low positive Δ{sup 199}Hg values (0.23–0.55‰, n=6) and low percentages of total Hg as MeHg (7.6–29%, n=7). These data suggest that the majority of the Hg in these miners' hair samples is exogenously adsorbed inorganic Hg and not fish-derived MeHg. Hair samples from Indonesian gold miners who eat fish daily displayed a wider range of positive Δ{sup 199}Hg values (0.21–1.32‰, n=5) and percentages of total Hg as MeHg (32–72%, n=4). This suggests that total Hg in the hair samples from Indonesian gold miners is likely a mixture of ingested fish MeHg and exogenously adsorbed inorganic Hg. Based on data from both populations, we suggest that total Hg concentrations in hair samples from small-scale gold miners likely overestimate exposure to MeHg from fish consumption. - Highlights: • Mercury isotopes were measured in hair and urine from small-scale gold miners. • Mercury isotopes indicate that Hg in urine comes from mining activity. • Mercury isotopes suggest Hg in hair is a mixture of fish MeHg and inorganic Hg. • A large percentage of Hg in miner’s hair is released during amalgam burning and adsorbed.

  3. Small Scale Yielding Correction of Constraint Loss in Small Sized Fracture Toughness Test Specimens

    International Nuclear Information System (INIS)

    Kim, Maan Won; Kim, Min Chul; Lee, Bong Sang; Hong, Jun Hwa

    2005-01-01

    Fracture toughness data in the ductile-brittle transition region of ferritic steels show scatter produced by local sampling effects and specimen geometry dependence which results from relaxation in crack tip constraint. The ASTM E1921 provides a standard test method to define the median toughness temperature curve, so called Master Curve, for the material corresponding to a 1T crack front length and also defines a reference temperature, T 0 , at which median toughness value is 100 MPam for a 1T size specimen. The ASTM E1921 procedures assume that high constraint, small scaling yielding (SSY) conditions prevail at fracture along the crack front. Violation of the SSY assumption occurs most often during tests of smaller specimens. Constraint loss in such cases leads to higher toughness values and thus lower T 0 values. When applied to a structure with low constraint geometry, the standard fracture toughness estimates may lead to strongly over-conservative estimates. A lot of efforts have been made to adjust the constraint effect. In this work, we applied a small-scale yielding correction (SSYC) to adjust the constraint loss of 1/3PCVN and PCVN specimens which are relatively smaller than 1T size specimen at the fracture toughness Master Curve test

  4. Small-scale instrumentation for nuclear magnetic resonance of porous media

    International Nuclear Information System (INIS)

    Bluemich, Bernhard; Casanova, Federico; Dabrowski, Martin; Danieli, Ernesto; Haber, Agnes; Van Landeghem, Maxime; Haber-Pohlmeier, Sabina; Olaru, Alexandra; Perlo, Juan; Sucre, Oscar; Evertz, Loribeth

    2011-01-01

    The investigation of fluids confined to porous media is the oldest topic of investigation with small-scale nuclear magnetic resonance (NMR) instruments, as such instruments are mobile and can be moved to the site of the object, such as the borehole of an oil well. While the analysis was originally restricted by the inferior homogeneity of the employed magnets to relaxation measurements, today, portable magnets are available for all types of NMR measurements concerning relaxometry, imaging and spectroscopy in two types of geometries. These geometries refer to closed magnets that surround the sample and open magnets, which are brought close to the object for measurement. The current state of the art of portable, small-scale NMR instruments is reviewed and recent applications of such instruments are featured. These include the porosity analysis and description of diesel particulate filters, the determination of the moisture content in walls from gray concrete, new approaches to analyze the pore space and moisture migration in soil, and the constitutional analysis of the mortar base of ancient wall paintings.

  5. Effect of water purification process in radioactive content: analysis on small scale purification plants

    International Nuclear Information System (INIS)

    Lopez del Rio, H.; Quiroga S, J. C.; Davila R, J. I.; Mireles G, F.

    2009-10-01

    Water from small scale purification plants is a low cost alternative for consumers in comparison to the bottled commercial presentations. Because of its low cost per liter, the consumption of this product has increased in recent years, stimulating in turn the installation of purification systems for these small businesses. The purpose of this study was to estimate the efficiency of small scale purification systems located in the cities of Zacatecas and Guadalupe, Zacatecas, to reduce the radioactive content of water. It was measured the total alpha and beta activity in water samples of entry and exit to process, through the liquid scintillation technique. In general it was observed that the process is more efficient in removing alpha that beta activity. The fraction of total alpha activity removed varied between 27 and 100%, while between 0 and 77% of the total beta activity was removed by the analyzed plants. In all cases, the total radioactivity level was lower than the maximum permissible value settled by the official mexican standard for drinking water. (Author)

  6. Sequence analysis of the canine mitochondrial DNA control region from shed hair samples in criminal investigations.

    Science.gov (United States)

    Berger, C; Berger, B; Parson, W

    2012-01-01

    In recent years, evidence from domestic dogs has increasingly been analyzed by forensic DNA testing. Especially, canine hairs have proved most suitable and practical due to the high rate of hair transfer occurring between dogs and humans. Starting with the description of a contamination-free sample handling procedure, we give a detailed workflow for sequencing hypervariable segments (HVS) of the mtDNA control region from canine evidence. After the hair material is lysed and the DNA extracted by Phenol/Chloroform, the amplification and sequencing strategy comprises the HVS I and II of the canine control region and is optimized for DNA of medium-to-low quality and quantity. The sequencing procedure is based on the Sanger Big-dye deoxy-terminator method and the separation of the sequencing reaction products is performed on a conventional multicolor fluorescence detection capillary electrophoresis platform. Finally, software-aided base calling and sequence interpretation are addressed exemplarily.

  7. Occurrence of Eimeria species parasites on small-scale commercial chicken farms in Africa and indication of economic profitability.

    Directory of Open Access Journals (Sweden)

    Kimberly M Fornace

    Full Text Available Small-scale commercial poultry production is emerging as an important form of livestock production in Africa, providing sources of income and animal protein to many poor households, yet the occurrence and impact of coccidiosis on this relatively new production system remains unknown. The primary objective of this study was to examine Eimeria parasite occurrence on small-scale commercial poultry farms in Ghana, Tanzania and Zambia. Additionally, farm economic viability was measured by calculating the farm gross margin and enterprise budget. Using these economic measures as global assessments of farm productivity, encompassing the diversity present in regional husbandry systems with a measure of fundamental local relevance, we investigated the detection of specific Eimeria species as indicators of farm profitability. Faecal samples and data on production parameters were collected from small-scale (less than 2,000 birds per batch intensive broiler and layer farms in peri-urban Ghana, Tanzania and Zambia. All seven Eimeria species recognised to infect the chicken were detected in each country. Furthermore, two of the three genetic variants (operational taxonomic units identified previously in Australia have been described outside of Australia for the first time. Detection of the most pathogenic Eimeria species associated with decreased farm profitability and may be considered as an indicator of likely farm performance. While a causal link remains to be demonstrated, the presence of highly pathogenic enteric parasites may pose a threat to profitable, sustainable small-scale poultry enterprises in Africa.

  8. Occurrence of Eimeria Species Parasites on Small-Scale Commercial Chicken Farms in Africa and Indication of Economic Profitability

    Science.gov (United States)

    Fornace, Kimberly M.; Clark, Emily L.; Macdonald, Sarah E.; Namangala, Boniface; Karimuribo, Esron; Awuni, Joseph A.; Thieme, Olaf; Blake, Damer P.; Rushton, Jonathan

    2013-01-01

    Small-scale commercial poultry production is emerging as an important form of livestock production in Africa, providing sources of income and animal protein to many poor households, yet the occurrence and impact of coccidiosis on this relatively new production system remains unknown. The primary objective of this study was to examine Eimeria parasite occurrence on small-scale commercial poultry farms in Ghana, Tanzania and Zambia. Additionally, farm economic viability was measured by calculating the farm gross margin and enterprise budget. Using these economic measures as global assessments of farm productivity, encompassing the diversity present in regional husbandry systems with a measure of fundamental local relevance, we investigated the detection of specific Eimeria species as indicators of farm profitability. Faecal samples and data on production parameters were collected from small-scale (less than 2,000 birds per batch) intensive broiler and layer farms in peri-urban Ghana, Tanzania and Zambia. All seven Eimeria species recognised to infect the chicken were detected in each country. Furthermore, two of the three genetic variants (operational taxonomic units) identified previously in Australia have been described outside of Australia for the first time. Detection of the most pathogenic Eimeria species associated with decreased farm profitability and may be considered as an indicator of likely farm performance. While a causal link remains to be demonstrated, the presence of highly pathogenic enteric parasites may pose a threat to profitable, sustainable small-scale poultry enterprises in Africa. PMID:24391923

  9. Occurrence of Eimeria species parasites on small-scale commercial chicken farms in Africa and indication of economic profitability.

    Science.gov (United States)

    Fornace, Kimberly M; Clark, Emily L; Macdonald, Sarah E; Namangala, Boniface; Karimuribo, Esron; Awuni, Joseph A; Thieme, Olaf; Blake, Damer P; Rushton, Jonathan

    2013-01-01

    Small-scale commercial poultry production is emerging as an important form of livestock production in Africa, providing sources of income and animal protein to many poor households, yet the occurrence and impact of coccidiosis on this relatively new production system remains unknown. The primary objective of this study was to examine Eimeria parasite occurrence on small-scale commercial poultry farms in Ghana, Tanzania and Zambia. Additionally, farm economic viability was measured by calculating the farm gross margin and enterprise budget. Using these economic measures as global assessments of farm productivity, encompassing the diversity present in regional husbandry systems with a measure of fundamental local relevance, we investigated the detection of specific Eimeria species as indicators of farm profitability. Faecal samples and data on production parameters were collected from small-scale (less than 2,000 birds per batch) intensive broiler and layer farms in peri-urban Ghana, Tanzania and Zambia. All seven Eimeria species recognised to infect the chicken were detected in each country. Furthermore, two of the three genetic variants (operational taxonomic units) identified previously in Australia have been described outside of Australia for the first time. Detection of the most pathogenic Eimeria species associated with decreased farm profitability and may be considered as an indicator of likely farm performance. While a causal link remains to be demonstrated, the presence of highly pathogenic enteric parasites may pose a threat to profitable, sustainable small-scale poultry enterprises in Africa.

  10. Environmental Health and Safety Hazards of Indigenous Small-Scale Gold Mining Using Cyanidation in the Philippines.

    Science.gov (United States)

    Leung, Ana Marie R; Lu, Jinky Leilanie Dp

    2016-01-01

    This cross-sectional study aimed at the environmental health hazards at work and cyanide exposure of small-scale gold miners engaged in gold extraction from ores in a mining area in the Philippines. Methods consisted of structured questionnaire-guided interviews, work process observation tools, physical health assessment by medical doctors, and laboratory examination and blood cyanide determination in the blood samples of 34 indigenous small-scale gold miners from Benguet, Philippines. The small-scale gold miners worked for a mean of 10.3 years, had a mean age of 36 years, with mean lifetime mining work hours of 18,564. All were involved in tunneling work (100%) while a considerable number were involved in mixing cyanide with the ore (44%). A considerable number were injured (35%) during the mining activity, and an alarming number (35%) had elevated blood cyanide level. The most prevalent hazard was exposure to chemicals, particularly to cyanide and nitric acid, which were usually handled with bare hands. The small-scale gold miners were exposed to occupational and environmental hazards at work.

  11. Environmental Health and Safety Hazards of Indigenous Small-Scale Gold Mining Using Cyanidation in the Philippines

    Science.gov (United States)

    Leung, Ana Marie R.; Lu, Jinky Leilanie DP.

    2016-01-01

    OBJECTIVES This cross-sectional study aimed at the environmental health hazards at work and cyanide exposure of small-scale gold miners engaged in gold extraction from ores in a mining area in the Philippines. METHODS Methods consisted of structured questionnaire-guided interviews, work process observation tools, physical health assessment by medical doctors, and laboratory examination and blood cyanide determination in the blood samples of 34 indigenous small-scale gold miners from Benguet, Philippines. RESULTS The small-scale gold miners worked for a mean of 10.3 years, had a mean age of 36 years, with mean lifetime mining work hours of 18,564. All were involved in tunneling work (100%) while a considerable number were involved in mixing cyanide with the ore (44%). A considerable number were injured (35%) during the mining activity, and an alarming number (35%) had elevated blood cyanide level. The most prevalent hazard was exposure to chemicals, particularly to cyanide and nitric acid, which were usually handled with bare hands. CONCLUSION The small-scale gold miners were exposed to occupational and environmental hazards at work. PMID:27547035

  12. Mercury exposure of workers and health problems related with small-scale gold panning and extraction

    International Nuclear Information System (INIS)

    Khan, S.; Shah, M.T.; Din, I.U.; Rehman, S.

    2012-01-01

    This study was conducted to investigate mercury (Hg) exposure and health problems related to small-scale gold panning and extraction (GPE) in the northern Pakistan. Urine and blood samples of occupational and non-occupational persons were analyzed for total Hg, while blood's fractions including red blood cells and plasma were analyzed for total Hg and its inorganic and organic species. The concentrations of Hg in urine and blood samples were significantly (P<0.01) higher in occupational persons as compared to non-occupational and exceeded the permissible limits set by World Health Organization (WHO) and United State Environmental Protection Agency (US-EPA). Furthermore, the data indicated that numerous health problems were present in occupational persons involved in GPE. (author)

  13. Materials identification using a small-scale pixellated x-ray diffraction system

    International Nuclear Information System (INIS)

    O’Flynn, D; Crews, C; Drakos, I; Christodoulou, C; Speller, R D; Wilson, M D; Veale, M C; Seller, P

    2016-01-01

    A transmission x-ray diffraction system has been developed using a pixellated, energy-resolving detector (HEXITEC) and a small-scale, mains operated x-ray source (Amptek Mini-X). HEXITEC enables diffraction to be measured without the requirement of incident spectrum filtration, or collimation of the scatter from the sample, preserving a large proportion of the useful signal compared with other diffraction techniques. Due to this efficiency, sufficient molecular information for material identification can be obtained within 5 s despite the relatively low x-ray source power. Diffraction data are presented from caffeine, hexamine, paracetamol, plastic explosives and narcotics. The capability to determine molecular information from aspirin tablets inside their packaging is demonstrated. Material selectivity and the potential for a sample classification model is shown with principal component analysis, through which each different material can be clearly resolved. (paper)

  14. A Study of the Radio Continuum Far Infrared Correlation at Small Scales in the Galaxy

    Science.gov (United States)

    Rodriguez-Martinez, Monica I.; Allen, R. J.; Wiklind, T.; Loinard, L.

    2006-12-01

    We present a study of the behavior of the Radio Continuum (RC) Far Infrared (FIR) correlation on scales corresponding to the size of small molecular clouds. This was done by comparing the spatial distribution of RC emission and FIR emission from a sample of several regions, distributed within the range 79∘ ≤ l ≤ 174∘ in the Galaxy. We have examined the 408 and 1420 MHz mosaic images of the sample, from the Canadian Galactic Plane Survey (CGPS), which later were compared with images at 60 and 100 μm. Preliminary results suggest that the RC -FIR correlation still holds at small scales, since a good qualitative correlation between RC and FIR emission is found. The physical process involved that may cause such correlation will be discussed as well as the nature of the RC emission. This research makes use of data from the Canadian Galactic Plane Survey.

  15. Prevalence and persistence of male DNA identified in mixed saliva samples after intense kissing.

    Science.gov (United States)

    Kamodyová, Natália; Durdiaková, Jaroslava; Celec, Peter; Sedláčková, Tatiana; Repiská, Gabriela; Sviežená, Barbara; Minárik, Gabriel

    2013-01-01

    Identification of foreign biological material by genetic profiling is widely used in forensic DNA testing in different cases of sexual violence, sexual abuse or sexual harassment. In all these kinds of sexual assaults, the perpetrator could constrain the victim to kissing. The value of the victim's saliva taken after such an assault has not been investigated in the past with currently widely used molecular methods of extremely high sensitivity (e.g. qPCR) and specificity (e.g. multiplex Y-STR PCR). In our study, 12 voluntary pairs were tested at various intervals after intense kissing and saliva samples were taken from the women to assess the presence of male DNA. Sensitivity-focused assays based on the SRY (single-copy gene) and DYS (multi-copy gene) sequence motifs confirmed the presence of male DNA in female saliva after 10 and even 60min after kissing, respectively. For specificity, standard multiplex Y-STR PCR profiling was performed and male DNA was found in female saliva samples, as the entire Y-STR profile, even after 30min in one sample. Our study confirms that foreign DNA tends to persist for a restricted period of time in the victim's mouth, can be isolated from saliva after prompt collection and can be used as a valuable source of evidence. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  16. Applications of pooled DNA samples to the assessment of population affinities: short tandem repeats.

    Science.gov (United States)

    Crawford, M H; Banerjee, P; Demarchi, D A; Zlojutro, M; McComb, J; Livshits, G; Henneberg, M; Mosher, M J; Schanfield, M S; Knowles, J A

    2005-12-01

    Pooled DNA samples have been used in association studies of Mendelian disease genes. This method involves combining equal quantities of DNA from patients and control subjects into separate pools and comparing the pools for distributions of genetic markers. In this study identical quantities of DNA from 300 individuals representing 6 populations were pooled and amplified for 296 loci using the touchdown polymerase chain reaction (PCR) method. The purpose of this study is to test the efficacy of pooled DNA markers in the reconstruction of the genetic structure of human populations. The populations sampled included Chuvash, Buryats, Kizhi, Native Americans, South Africans, and New York City whites. To test the accuracy of the allele-frequency distributions, we genotyped the Buryats and New York samples individually for six microsatellite markers and compared their frequencies to the allele frequencies derived from the electropherogram peak heights for the pooled DNA, producing a correlation of 0.9811 with a variance of less than 0.04. Two-dimensional scaling of genetic distances among the six populations produced clusters that reflected known historical relationships. A distance matrix was created using all 296 loci, and matrices based on individual chromosomes were correlated against the total matrix. As expected, the largest chromosomes had the highest correlations with the total matrix, whereas one of the smallest chromosomes, chromosome 22, had the lowest correlation and differed most from the combined STR distance matrix.

  17. Sample preparation methods for quantitative detection of DNA by molecular assays and marine biosensors.

    Science.gov (United States)

    Cox, Annie M; Goodwin, Kelly D

    2013-08-15

    The need for quantitative molecular methods is growing in environmental, food, and medical fields but is hindered by low and variable DNA extraction and by co-extraction of PCR inhibitors. DNA extracts from Enterococcus faecium, seawater, and seawater spiked with E. faecium and Vibrio parahaemolyticus were tested by qPCR for target recovery and inhibition. Conventional and novel methods were tested, including Synchronous Coefficient of Drag Alteration (SCODA) and lysis and purification systems used on an automated genetic sensor (the Environmental Sample Processor, ESP). Variable qPCR target recovery and inhibition were measured, significantly affecting target quantification. An aggressive lysis method that utilized chemical, enzymatic, and mechanical disruption enhanced target recovery compared to commercial kit protocols. SCODA purification did not show marked improvement over commercial spin columns. Overall, data suggested a general need to improve sample preparation and to accurately assess and account for DNA recovery and inhibition in qPCR applications. Published by Elsevier Ltd.

  18. Experimental investigation of small-scale gasification of woody biomass

    Energy Technology Data Exchange (ETDEWEB)

    Barrio, Maria

    2002-05-01

    A small-scale stratified down draft gasifier has been built and operated under stable conditions using wood pellets as fuel and air as gasification agent. The problems observed during the preliminary experiments have been described and explained; they are mainly related to the stability of the process. The stable operation of the gasifier has been characterised by the gas composition and the product gas tar and particle content. The biomass feeding rate has varied between 4,5 and 6,5 kg/h. The CO content of the product gas (23-26 % vol.) is higher than in similar gasifiers and the H{sub 2} content has been found to vary between 14 and 16 % vol. The tar content in the product gas (Ca. 3 g/Nm{sup 3}) is rather high compared with similar gasifiers. The temperature profile, together with other relevant parameters like the air-excess ratio, the air to fuel ratio and gas to fuel ratio have been calculated. The experiments show that the air excess ratio is rather constant, varying between 0,25 and 0,3. Experiments have been conducted with a gas engine using mixtures of CH{sub 4}, CO, H{sub 2}, CO{sub 2} and N{sub 2} as a fuel. NO{sub x} and CO emissions are analysed. The char gasification process has been studied in detail by means of Thermogravimetric Analysis. The study comprises the chemical kinetics of the gasification reactions of wood char in CO{sub 2} and H{sub 2}O, including the inhibition effect of CO and H{sub 2}. A kinetic model based on Langmuir-Hinshelwood kinetics has been found which relates the mass loss rate to the temperature, gas composition and degree of conversion for each reaction. The ratio CO/CO{sub 2} has been found to be a relevant parameter for reactivity. The gasification experiments in mixtures of CO{sub 2} and H{sub 2}O give reasons to believe that the rate of desorption for the complex C(O) varies depending on the gas mixture surrounding the char. It has been found that if the experimental data are obtained from separate H{sub 2}O/N{sub 2

  19. Integrated bioenergy conversion concepts for small scale gasification power systems

    Science.gov (United States)

    Aldas, Rizaldo Elauria

    Thermal and biological gasification are promising technologies for addressing the emerging concerns in biomass-based renewable energy, environmental protection and waste management. However, technical barriers such as feedstock quality limitations, tars, and high NOx emissions from biogas fueled engines impact their full utilization and make them suffer at the small scale from the need to purify the raw gas for most downstream processes, including power generation other than direct boiler use. The two separate gasification technologies may be integrated to better address the issues of power generation and waste management and to complement some of each technologies' limitations. This research project investigated the technical feasibility of an integrated thermal and biological gasification concept for parameters critical to appropriately matching an anaerobic digester with a biomass gasifier. Specific studies investigated the thermal gasification characteristics of selected feedstocks in four fixed-bed gasification experiments: (1) updraft gasification of rice hull, (2) indirect-heated gasification of rice hull, (3) updraft gasification of Athel wood, and (4) downdraft gasification of Athel and Eucalyptus woods. The effects of tars and other components of producer gas on anaerobic digestion at mesophilic temperature of 36°C and the biodegradation potentials and soil carbon mineralization of gasification tars during short-term aerobic incubation at 27.5°C were also examined. Experiments brought out the ranges in performance and quality and quantity of gasification products under different operating conditions and showed that within the conditions considered in the study, these gasification products did not adversely impact the overall digester performance. Short-term aerobic incubation demonstrated variable impacts on carbon mineralization depending on tar and soil conditions. Although tars exhibited low biodegradation indices, degradation may be improved if the

  20. Small-scale geodiversity and dirt road management, Ede (NL)

    Science.gov (United States)

    van den Ancker, Hanneke; Jungerius, Pieter Dirk

    2016-04-01

    A large part of the countryside roads on the Pleistocene sands of The Netherlands are dirt roads. Most are footpaths, but a small percentage are relatively heavily used by motorized vehicles. These latter roads are a cause subject of debate. Puddles and potholes develop during periods of wet weather, while dust whirls from the roads form during spells of dry weather as do washboard ripples. They cause problems for people living along these roads and tourists (walkers and bikers. The community of Ede (NL), like many other communities on the sand, wants to keep its 80 km of dirt roads because of the natural values they harbour as well as for their characteristic landscape quality and cultural heritage value. A part of the dirt roads in Ede is heavily used. In 2009, the community of Ede developed a decision model to support management of the dirt roads. Ede acknowledges that each dirt road is unique and asks for a tailor-made solution. Road maintenance measures include grading, making a camber, digging pits, applying loam or sandy loam. If problems become too large, one-way traffic can be an option. In more and more cases the dirt roads are barred for motorized through traffic (Gemeente Ede, 2009). As a reconnaissance we have studied the dirt roads of the Horabos/Horalaan over the last year. Incidentally we looked at other parts of the main Horalaan and the footpaths in the adjacent forest of Hoekelum. All dirt roads lie near the top of a Saalian push-moraine in which the upper course of dry valleys are present. Some results of the reconnaissance: - Most dirt roads sections in the Horabos lie lower than the surrounding terrain; - The problems develop in a short period of time during special weather conditions; - Certain dirt road sections e.g. those sections crossing a slight depression are quickly developing potholes; - Even a small slope of the road (differences that have consequences for its maintenance. Knowledge of geodiversity of the terrain and study of small-scale

  1. DNA barcoding of selected UAE medicinal plant species: a comparative assessment of herbarium and fresh samples.

    Science.gov (United States)

    Enan, Mohamed Rizk; Palakkott, Abdul Rasheed; Ksiksi, Taoufik Saleh

    2017-01-01

    It is commonly difficult to extract and amplify DNA from herbarium samples as they are old and preserved using different compounds. In addition, such samples are subjected to the accumulation of intrinsically produced plant substances over long periods (up to hundreds of years). DNA extraction from desert flora may pause added difficulties as many contain high levels of secondary metabolites. Herbarium samples from the Biology Department (UAE University) plant collection and fresh plant samples, collected from around Al-Ain (UAE), were used in this study. The three barcode loci for the coding genes matK, rbcL and rpoC1-were amplified. Our results showed that T. terresteris , H. robustum , T. pentandrus and Z. qatarense were amplified using all three primers for both fresh and herbaium samples. Both fresh and herbarium samples of C. comosum , however, were not amplified at all, using the three primers. Herbarium samples from A. javanica , C. imbricatum , T. aucherana and Z. simplex were not amplified with any of the three primers. For fresh samples 90, 90 and 80% of the samples were amplified using matK, rbcL and rpoC1, respectively. In short, fresh samples were significantly better amplified than those from herbarium sources, using the three primers. Both fresh and herbarium samples from one species ( C. comosum ), however, were not successfully amplified. It is also concluded that the rbcL regions showed real potentials to distinguish the UAE species under investigation into the appropriate family and genus.

  2. Just in Time Strategy and Financial Performance of Small Scale Industry in Ogun State: A Study of ADO-ODO/OTA Local Government

    Directory of Open Access Journals (Sweden)

    Patrick Amaechi Egbunike

    2017-10-01

    Full Text Available Many manufacturing firms have decided to implement just in time technique as a strategic cost management to survive and remain competitive in their business environment. The study examines how just in time technique has assisted in reducing inventory cost management and improve the firm profit level. The specific objective is to ascertain the influence of purchases and sales on return on equity of small scale manufacturing industry. Survey design was used for the study. Sample frame was purposively selected for convenience sake. Data was collected though secondary source. Regression analysis was employed to analyze the data. The study found positive relationship between just in time implementation and profit level of small scale business industry. We recommend other small scale businesses that have not started implementing just in time strategy to start the strategy. We encourage future researcher to examine the efficiency of just in time strategy among petty small scale trader in our urban centers.

  3. Use of SCGE method for detection of DNA comet in irradiated samples of poultry and shrimp

    International Nuclear Information System (INIS)

    Rajaei, R.; Hosseini, S.L.

    2005-01-01

    DNA in food may sustain damage by gamma irradiation.This damage can be detected by a sensitive technique, called single cell gel electrophoresis. This is a simple and low-cost technique for rapid screening of the cells of irradiated foodstuffs. For this purpose, poultry and shrimp samples were irradiated by the 60 Co gamma radiation. The radiation doses for poultry were 2,5 and 7 kGy and for shrimp were 3 and 7kGy, respectively. The irradiation samples were compared with those of unirradiated types (control). In addition, the effects of shelf-life and temperature were considered on the poultry samples only. We have found that this technique is easily applicable for identification of irradiated from unirradiated samples and it is found to be irrespective of the applied dose. It is worth mentioning that any DNA change arising from any source, for example temperature fluctuation, may be detected by the single cell gel electrophoresis technique

  4. Optimized mtDNA Control Region Primer Extension Capture Analysis for Forensically Relevant Samples and Highly Compromised mtDNA of Different Age and Origin

    Directory of Open Access Journals (Sweden)

    Mayra Eduardoff

    2017-09-01

    Full Text Available The analysis of mitochondrial DNA (mtDNA has proven useful in forensic genetics and ancient DNA (aDNA studies, where specimens are often highly compromised and DNA quality and quantity are low. In forensic genetics, the mtDNA control region (CR is commonly sequenced using established Sanger-type Sequencing (STS protocols involving fragment sizes down to approximately 150 base pairs (bp. Recent developments include Massively Parallel Sequencing (MPS of (multiplex PCR-generated libraries using the same amplicon sizes. Molecular genetic studies on archaeological remains that harbor more degraded aDNA have pioneered alternative approaches to target mtDNA, such as capture hybridization and primer extension capture (PEC methods followed by MPS. These assays target smaller mtDNA fragment sizes (down to 50 bp or less, and have proven to be substantially more successful in obtaining useful mtDNA sequences from these samples compared to electrophoretic methods. Here, we present the modification and optimization of a PEC method, earlier developed for sequencing the Neanderthal mitochondrial genome, with forensic applications in mind. Our approach was designed for a more sensitive enrichment of the mtDNA CR in a single tube assay and short laboratory turnaround times, thus complying with forensic practices. We characterized the method using sheared, high quantity mtDNA (six samples, and tested challenging forensic samples (n = 2 as well as compromised solid tissue samples (n = 15 up to 8 kyrs of age. The PEC MPS method produced reliable and plausible mtDNA haplotypes that were useful in the forensic context. It yielded plausible data in samples that did not provide results with STS and other MPS techniques. We addressed the issue of contamination by including four generations of negative controls, and discuss the results in the forensic context. We finally offer perspectives for future research to enable the validation and accreditation of the PEC MPS

  5. Accurate Digital Polymerase Chain Reaction Quantification of Challenging Samples Applying Inhibitor-Tolerant DNA Polymerases.

    Science.gov (United States)

    Sidstedt, Maja; Romsos, Erica L; Hedell, Ronny; Ansell, Ricky; Steffen, Carolyn R; Vallone, Peter M; Rådström, Peter; Hedman, Johannes

    2017-02-07

    Digital PCR (dPCR) enables absolute quantification of nucleic acids by partitioning of the sample into hundreds or thousands of minute reactions. By assuming a Poisson distribution for the number of DNA fragments present in each chamber, the DNA concentration is determined without the need for a standard curve. However, when analyzing nucleic acids from complex matrixes such as soil and blood, the dPCR quantification can be biased due to the presence of inhibitory compounds. In this study, we evaluated the impact of varying the DNA polymerase in chamber-based dPCR for both pure and impure samples using the common PCR inhibitor humic acid (HA) as a model. We compared the TaqMan Universal PCR Master Mix with two alternative DNA polymerases: ExTaq HS and Immolase. By using Bayesian modeling, we show that there is no difference among the tested DNA polymerases in terms of accuracy of absolute quantification for pure template samples, i.e., without HA present. For samples containing HA, there were great differences in performance: the TaqMan Universal PCR Master Mix failed to correctly quantify DNA with more than 13 pg/nL HA, whereas Immolase (1 U) could handle up to 375 pg/nL HA. Furthermore, we found that BSA had a moderate positive effect for the TaqMan Universal PCR Master Mix, enabling accurate quantification for 25 pg/nL HA. Increasing the amount of DNA polymerase from 1 to 5 U had a strong effect for ExTaq HS, elevating HA-tolerance four times. We also show that the average Cq values of positive reactions may be used as a measure of inhibition effects, e.g., to determine whether or not a dPCR quantification result is reliable. The statistical models developed to objectively analyze the data may also be applied in quality control. We conclude that the choice of DNA polymerase in dPCR is crucial for the accuracy of quantification when analyzing challenging samples.

  6. Payments for Environmental Services as source of development funding for small-scale farmers in northern Namibia: preliminary results

    Science.gov (United States)

    Angombe, Simon; Bloemertz, Lena; Käch, Simon; Asino, Josefina; Kuhn, Nikolaus J.

    2013-04-01

    Studies in Africa suggest that improving Soil Organic Carbon (SOC) on cropland soils increases yields, but also offers the opportunity of earning carbon credits. Further potential for earning carbon credits and generating Payments for Environmental Services (PES) lies in an integrated approach to landscape carbon management, including shrubland and pasture used for grazing and timber supply. These studies indicate that funds raised from PES could be used to foster the development of small-scale farming in northern Namibia. However, the limited information on soil quality and the rationale for particular soil management and land use practices applied by small-scale farmers in Namibia prohibits a conclusive assessment of the potential of Payment for PES as a source of income or funding opportunity for development initiatives in Northern Central Regions of Namibia. Therefore, the aim of this study is the identification of potential intervention mechanisms to improve the livelihood of small scale-farmers and reducing land degradation with the support of PES in the communal regions of northern Namibia. The work in Namibia aimed at identifying existing soil management and land use practices as well as soil quality, including carbon stocks, on land used by small-scale farmers in the densely populated northern central region. The main objective of the first part of the field work was to develop an overview of farming practices and soil quality as well as sampling and interviewing approaches. Four settlements were selected for the field work based on their distance to the urbanized road corridor between Oshakati and the Angolan border. Initial results confirm the potential to increase productivity on land used by small-scale farmers as well as the opportunity to develop landscape carbon stocks. However, limits to earning PES might be the lack of a market, and thus incentive for the farmers, to shift from subsistence to commercial farming.

  7. Comparison of Waste Feed Delivery Small Scale Mixing Demonstration Simulant to Hanford Waste

    Energy Technology Data Exchange (ETDEWEB)

    Wells, Beric E.; Gauglitz, Phillip A.; Rector, David R.

    2012-07-10

    The Hanford double-shell tank (DST) system provides the staging location for waste that will be transferred to the Hanford Tank Waste Treatment and Immobilization Plant (WTP). Specific WTP acceptance criteria for waste feed delivery describe the physical and chemical characteristics of the waste that must be met before the waste is transferred from the DSTs to the WTP. One of the more challenging requirements relates to the sampling and characterization of the undissolved solids (UDS) in a waste feed DST because the waste contains solid particles that settle and their concentration and relative proportion can change during the transfer of the waste in individual batches. A key uncertainty in the waste feed delivery system is the potential variation in UDS transferred in individual batches in comparison to an initial sample used for evaluating the acceptance criteria. To address this uncertainty, a number of small-scale mixing tests have been conducted as part of Washington River Protection Solutions' Small Scale Mixing Demonstration (SSMD) project to determine the performance of the DST mixing and sampling systems. A series of these tests have used a five-part simulant composed of particles of different size and density and designed to be equal or more challenging than AY-102 waste. This five-part simulant, however, has not been compared with the broad range of Hanford waste, and thus there is an additional uncertainty that this simulant may not be as challenging as the most difficult Hanford waste. The purpose of this study is to quantify how the current five-part simulant compares to all of the Hanford sludge waste, and to suggest alternate simulants that could be tested to reduce the uncertainty in applying the current testing results to potentially more challenging wastes.

  8. A modular method for the extraction of DNA and RNA, and the separation of DNA pools from diverse environmental sample types

    DEFF Research Database (Denmark)

    Lever, Mark; Torti, Andrea; Eickenbusch, Philip

    2015-01-01

    tests, in which permutations of all nucleic acid extraction steps were compared. The final modular protocol is suitable for extractions from igneous rock, air, water, and sediments. Sediments range from high-biomass, organic rich coastal samples to samples from the most oligotrophic region of the world...... DNA pools without cell lysis from intracellular and particle-complexed DNA pools may enable new insights into the cycling and preservation of DNA in environmental samples in the future. A general protocol is outlined, along with recommendations for optimizing this general protocol for specific sample...

  9. Mercury Pollution Due to Small-Scale Gold Mining in the Philippines: An Economic Analysis

    OpenAIRE

    Orbeta, Aniceto C.; Israel, Danilo C.; Asirot, Jasminda

    2000-01-01

    The study reviews small-scale gold mining in the Philippines and economically assesses mercury pollution and other development problems in the industry. The end purpose is to suggest measures to address the problems and promote better environmental and overall management of small-scale mining. The study has used secondary data from mining institutions and primary data from key informants and small-scale gold miners and processors in the two case study sites.

  10. Mercury Pollution Due to Small-Scale Gold Mining in the Philippines: An Economic Analysis

    OpenAIRE

    Israel, Danilo C.; Asirot, Jasminda

    2002-01-01

    The study reviews small-scale gold mining in the Philippines and economically assesses mercury pollution and other development problems in the industry. The end purpose is to suggest measures to address the problems and promote better environmental and overall management of small-scale mining. The study has used secondary data from mining institutions and primary data from key informants and small-scale gold miners and processors in the two case study sites. brazzer

  11. Small-Scale Spray Releases: Initial Aerosol Test Results

    Energy Technology Data Exchange (ETDEWEB)

    Mahoney, Lenna A.; Gauglitz, Phillip A.; Kimura, Marcia L.; Brown, Garrett N.; Kurath, Dean E.; Buchmiller, William C.; Smith, Dennese M.; Blanchard, Jeremy; Song, Chen; Daniel, Richard C.; Wells, Beric E.; Tran, Diana N.; Burns, Carolyn A.

    2013-05-29

    rectangular slots. For the combination of both test stands, the round holes ranged in size from 0.2 to 4.46 mm. The slots ranged from (width × length) 0.3 × 5 to 2.74 × 76.2 mm. Most slots were oriented longitudinally along the pipe, but some were oriented circumferentially. In addition, a limited number of multi-hole test pieces were tested in an attempt to assess the impact of a more complex breach. Much of the testing was conducted at pressures of 200 and 380 psi, but some tests were conducted at 100 psi. Testing the largest postulated breaches was deemed impractical because of the much larger flow rates and equipment that would be required. This report presents the experimental results and analyses for the aerosol measurements obtained in the small-scale test stand. It includes a description of the simulants used and their properties, equipment and operations, data analysis methodologies, and test results. The results of tests investigating the role of slurry particles in plugging small breaches are reported in Mahoney et al. (2012). The results of the aerosol measurements in the large-scale test stand are reported in Schonewill et al. (2012) along with an analysis of the combined results from both test scales.

  12. Small-Scale Spray Releases: Initial Aerosol Test Results

    Energy Technology Data Exchange (ETDEWEB)

    Mahoney, Lenna A.; Gauglitz, Phillip A.; Kimura, Marcia L.; Brown, Garrett N.; Kurath, Dean E.; Buchmiller, William C.; Smith, Dennese M.; Blanchard, Jeremy; Song, Chen; Daniel, Richard C.; Wells, Beric E.; Tran, Diana N.; Burns, Carolyn A.

    2012-11-01

    rectangular slots. The round holes ranged in size from 0.2 to 4.46 mm. The slots ranged from (width × length) 0.3 × 5 to 2.74 × 76.2 mm. Most slots were oriented longitudinally along the pipe, but some were oriented circumferentially. In addition, a limited number of multi-hole test pieces were tested in an attempt to assess the impact of a more complex breach. Much of the testing was conducted at pressures of 200 and 380 psi, but some tests were conducted at 100 psi. Testing the largest postulated breaches was deemed impractical because of the large size of some of the WTP equipment. This report presents the experimental results and analyses for the aerosol measurements obtained in the small-scale test stand. It includes a description of the simulants used and their properties, equipment and operations, data analysis methodologies, and test results. The results of tests investigating the role of slurry particles in plugging small breaches are reported in Mahoney et al. (2012). The results of the aerosol measurements in the large-scale test stand are reported in Schonewill et al. (2012) along with an analysis of the combined results from both test scales.

  13. Preanalytical blood sample workup for cell-free DNA analysis using Droplet Digital PCR for future molecular cancer diagnostics

    NARCIS (Netherlands)

    van Ginkel, Joost H.; van den Broek, Daan A.; van Kuik, Joyce; Linders, Dorothé; de Weger, Roel; Willems, Stefan M.; Huibers, Manon M.H.

    2017-01-01

    In current molecular cancer diagnostics, using blood samples of cancer patients for the detection of genetic alterations in plasma (cell-free) circulating tumor DNA (ctDNA) is an emerging practice. Since ctDNA levels in blood are low, highly sensitive Droplet Digital PCR (ddPCR) can be used for

  14. The potential use of indigenous nickel hyperaccumulators for small-scale mining in The Philippines

    Directory of Open Access Journals (Sweden)

    E S Fernando

    2013-10-01

    Full Text Available Uptake of nickel and three other heavy metals (copper, cobalt, and chromium was examined in 33 species of the common and rare native vascular plants growing in an ultramafic area currently subjected to mining in Zambales Province, Luzon, Philippines. Leaf tissue samples were initially screened in the field using filter paper impregnated with dimethylglyoxime (1% solution in 70% ethyl alcohol and later analyzed by atomic absorption spectroscopy. One species was found to be a hypernickelophore (>10,000 µg/g, eight species were nickel hyperaccumulators (>1,000 µg/g, nineteen species were hemi-accumulators (>100-1,000 µg/g, and five species were non-accumulators (<100 µg/g. This paper significantly adds to the list of hyperaccumulator species first reported for the Philippines in 1992. The findings will be discussed in context of using indigenous species for post mining ecological restoration and nickel phytoextraction in small-scale mining in the Philippines

  15. Trace DNA Sampling Success from Evidence Items Commonly Encountered in Forensic Casework.

    Science.gov (United States)

    Dziak, Renata; Peneder, Amy; Buetter, Alicia; Hageman, Cecilia

    2018-05-01

    Trace DNA analysis is a significant part of a forensic laboratory's workload. Knowing optimal sampling strategies and item success rates for particular item types can assist in evidence selection and examination processes and shorten turnaround times. In this study, forensic short tandem repeat (STR) casework results were reviewed to determine how often STR profiles suitable for comparison were obtained from "handler" and "wearer" areas of 764 items commonly submitted for examination. One hundred and fifty-five (155) items obtained from volunteers were also sampled. Items were analyzed for best sampling location and strategy. For casework items, headwear and gloves provided the highest success rates. Experimentally, eyeglasses and earphones, T-shirts, fabric gloves and watches provided the highest success rates. Eyeglasses and latex gloves provided optimal results if the entire surfaces were swabbed. In general, at least 10%, and up to 88% of all trace DNA analyses resulted in suitable STR profiles for comparison. © 2017 American Academy of Forensic Sciences.

  16. Insights into the processes behind the contamination of degraded human teeth and bone samples with exogenous sources of DNA

    DEFF Research Database (Denmark)

    Gilbert, M. T. P.; Hansen, Anders J.; Willerslev, E.

    2006-01-01

    A principal problem facing human DNA studies that use old and degraded remains is contamination from other sources of human DNA. In this study we have attempted to contaminate deliberately bones and teeth sampled from a medieval collection excavated in Trondheim, Norway, in order to investigate......, prior to assaying for the residual presence of the handler's DNA. Surprisingly, although our results suggest that a large proportion of the teeth were contaminated with multiple sources of human DNA prior to our investigation, we were unable to contaminate the samples with further human DNA. One...

  17. Microdosimetry calculations for monoenergetic electrons using Geant4-DNA combined with a weighted track sampling algorithm.

    Science.gov (United States)

    Famulari, Gabriel; Pater, Piotr; Enger, Shirin A

    2017-07-07

    The aim of this study was to calculate microdosimetric distributions for low energy electrons simulated using the Monte Carlo track structure code Geant4-DNA. Tracks for monoenergetic electrons with kinetic energies ranging from 100 eV to 1 MeV were simulated in an infinite spherical water phantom using the Geant4-DNA extension included in Geant4 toolkit version 10.2 (patch 02). The microdosimetric distributions were obtained through random sampling of transfer points and overlaying scoring volumes within the associated volume of the tracks. Relative frequency distributions of energy deposition f(>E)/f(>0) and dose mean lineal energy ([Formula: see text]) values were calculated in nanometer-sized spherical and cylindrical targets. The effects of scoring volume and scoring techniques were examined. The results were compared with published data generated using MOCA8B and KURBUC. Geant4-DNA produces a lower frequency of higher energy deposits than MOCA8B. The [Formula: see text] values calculated with Geant4-DNA are smaller than those calculated using MOCA8B and KURBUC. The differences are mainly due to the lower ionization and excitation cross sections of Geant4-DNA for low energy electrons. To a lesser extent, discrepancies can also be attributed to the implementation in this study of a new and fast scoring technique that differs from that used in previous studies. For the same mean chord length ([Formula: see text]), the [Formula: see text] calculated in cylindrical volumes are larger than those calculated in spherical volumes. The discrepancies due to cross sections and scoring geometries increase with decreasing scoring site dimensions. A new set of [Formula: see text] values has been presented for monoenergetic electrons using a fast track sampling algorithm and the most recent physics models implemented in Geant4-DNA. This dataset can be combined with primary electron spectra to predict the radiation quality of photon and electron beams.

  18. Development of a real-time PCR to detect Demodex canis DNA in different tissue samples.

    Science.gov (United States)

    Ravera, Ivan; Altet, Laura; Francino, Olga; Bardagí, Mar; Sánchez, Armand; Ferrer, Lluís

    2011-02-01

    The present study reports the development of a real-time polymerase chain reaction (PCR) to detect Demodex canis DNA on different tissue samples. The technique amplifies a 166 bp of D. canis chitin synthase gene (AB 080667) and it has been successfully tested on hairs extracted with their roots and on formalin-fixed paraffin embedded skin biopsies. The real-time PCR amplified on the hairs of all 14 dogs with a firm diagnosis of demodicosis and consistently failed to amplify on negative controls. Eleven of 12 skin biopsies with a morphologic diagnosis of canine demodicosis were also positive. Sampling hairs on two skin points (lateral face and interdigital skin), D. canis DNA was detected on nine of 51 healthy dogs (17.6%) a much higher percentage than previously reported with microscopic studies. Furthermore, it is foreseen that if the number of samples were increased, the percentage of positive dogs would probably also grow. Moreover, in four of the six dogs with demodicosis, the samples taken from non-lesioned skin were positive. This finding, if confirmed in further studies, suggests that demodicosis is a generalized phenomenon in canine skin, due to proliferation of local mite populations, even though macroscopic lesions only appear in certain areas. The real-time PCR technique to detect D. canis DNA described in this work is a useful tool to advance our understanding of canine demodicosis.

  19. SYBR green-based detection of Leishmania infantum DNA using peripheral blood samples.

    Science.gov (United States)

    Ghasemian, Mehrdad; Gharavi, Mohammad Javad; Akhlaghi, Lame; Mohebali, Mehdi; Meamar, Ahmad Reza; Aryan, Ehsan; Oormazdi, Hormozd; Ghayour, Zahra

    2016-03-01

    Parasitological methods for the diagnosis of visceral leishmaniasis (VL) require invasive sampling procedures. The aim of this study was to detect Leishmania infantum (L. infantum) DNA by real time-PCR method in peripheral blood of symptomatic VL patient and compared its performance with nested PCR, an established molecular method with very high diagnostic indices. 47 parasitologically confirmed VL patients diagnosed by direct agglutination test (DAT > 3200), bone marrow aspiration and presented characteristic clinical features (fever, hepatosplenomegaly, and anemia) and 40 controls (non-endemic healthy control-30, Malaria-2, Toxoplasma gondii-2, Mycobacterium tuberculosis-2, HBV-1, HCV-1, HSV-1 and CMV-1) were enrolled in this study. SYBR-green based real time-PCR and nested PCR was performed to amplify the Kinetoplast DNA minicircle gene using the DNA extracted from Buffy coat. From among 47 patients, 45 (95.7 %) were positive by both nested-PCR and real time-PCR. These results indicate that real time-PCR was not only as sensitive as a nested-PCR assay for detection of Leishmania kDNA in clinical sample, but also more rapid. The advantage of real time-PCR based methods over nested-PCR is simple to perform, more faster in which nested-PCR requires post-PCR processing and reducing contamination risk.

  20. Sample preparation methods for quantitative detection of DNA by molecular assays and marine biosensors

    International Nuclear Information System (INIS)

    Cox, Annie M.; Goodwin, Kelly D.

    2013-01-01

    Highlights: • DNA extraction methods affected measured qPCR target recovery. • Recovery and variability differed, sometimes by more than an order of magnitude. • SCODA did not offer significant improvement with PCR-inhibited seawater. • Aggressive lysis did appear to improve target recovery. • Reliable and affordable correction methods are needed for quantitative PCR. -- Abstract: The need for quantitative molecular methods is growing in environmental, food, and medical fields but is hindered by low and variable DNA extraction and by co-extraction of PCR inhibitors. DNA extracts from Enterococcus faecium, seawater, and seawater spiked with E. faecium and Vibrio parahaemolyticus were tested by qPCR for target recovery and inhibition. Conventional and novel methods were tested, including Synchronous Coefficient of Drag Alteration (SCODA) and lysis and purification systems used on an automated genetic sensor (the Environmental Sample Processor, ESP). Variable qPCR target recovery and inhibition were measured, significantly affecting target quantification. An aggressive lysis method that utilized chemical, enzymatic, and mechanical disruption enhanced target recovery compared to commercial kit protocols. SCODA purification did not show marked improvement over commercial spin columns. Overall, data suggested a general need to improve sample preparation and to accurately assess and account for DNA recovery and inhibition in qPCR applications

  1. Effect of Various Packaging Methods on Small-Scale Hanwoo (Korean Native Cattle) during Refrigerated Storage

    Science.gov (United States)

    Yu, Hwan Hee; Song, Myung Wook; Kim, Tae-Kyung; Choi, Yun-Sang; Cho, Gyu Yong; Lee, Na-Kyoung; Paik, Hyun-Dong

    2018-01-01

    Abstract The objective of this study was to investigate comparison of physicochemical, microbiological, and sensory characteristics of Hanwoo eye of round by various packaging methods [wrapped packaging (WP), modified atmosphere packaging (MAP), vacuum packaging (VP) with three different vacuum films, and vacuum skin packaging (VSP)] at a small scale. Packaged Hanwoo beef samples were stored in refrigerated conditions (4±1°C) for 28 days. Packaged beef was sampled on days 0, 7, 14, 21, and 28. Physicochemical [pH, surface color, thiobarbituric acid reactive substances (TBARS), and volatile basic nitrogen (VBN) values], microbiological, and sensory analysis of packaged beef samples were performed. VP and VSP samples showed low TBARS and VBN values, and pH and surface color did not change substantially during the 28-day period. For VSP, total viable bacteria, psychrotrophic bacteria, lactic acid bacteria, and coliform counts were lower than those for other packaging systems. Salmonella spp. and Escherichia coli O157:H7 were not detected in any packaged beef samples. A sensory analysis showed that the scores for appearance, flavor, color, and overall acceptability did not change significantly until day 7. In total, VSP was effective with respect to significantly higher a* values, physicochemical stability, and microbial safety in Hanwoo packaging (p<0.05). PMID:29805283

  2. Small scale processors' engagement in cassava postharvest and ...

    African Journals Online (AJOL)

    harvest activities for ensuring households'food provision in Imo State, Nigeria. A multi-stage random sampling technique was used in selecting one hundred and eighty (180) respondents across the three agricultural zones of the State.

  3. Preanalytical blood sample workup for cell-free DNA analysis using Droplet Digital PCR for future molecular cancer diagnostics.

    Science.gov (United States)

    van Ginkel, Joost H; van den Broek, Daan A; van Kuik, Joyce; Linders, Dorothé; de Weger, Roel; Willems, Stefan M; Huibers, Manon M H

    2017-10-01

    In current molecular cancer diagnostics, using blood samples of cancer patients for the detection of genetic alterations in plasma (cell-free) circulating tumor DNA (ctDNA) is an emerging practice. Since ctDNA levels in blood are low, highly sensitive Droplet Digital PCR (ddPCR) can be used for detecting rare mutational targets. In order to perform ddPCR on blood samples, a standardized procedure for processing and analyzing blood samples is necessary to facilitate implementation into clinical practice. Therefore, we assessed the technical sample workup procedure for ddPCR on blood plasma samples. Blood samples from healthy individuals, as well as lung cancer patients were analyzed. We compared different methods and protocols for sample collection, storage, centrifugation, isolation, and quantification. Cell-free DNA (cfDNA) concentrations of several wild-type targets and BRAF and EGFR-mutant ctDNA concentrations quantified by ddPCR were primary outcome measurements. Highest cfDNA concentrations were measured in blood collected in serum tubes. No significant differences in cfDNA concentrations were detected between various time points of up to 24 h until centrifugation. Highest cfDNA concentrations were detected after DNA isolation with the Quick cfDNA Serum & Plasma Kit, while plasma isolation using the QIAamp Circulating Nucleic Acid Kit yielded the most consistent results. DdPCR results on cfDNA are highly dependent on multiple factors during preanalytical sample workup, which need to be addressed during the development of this diagnostic tool for cancer diagnostics in the future. © 2017 The Authors. Cancer Medicine published by John Wiley & Sons Ltd.

  4. The Impact of Small Scale Mining on Irrigation Water Quality in ...

    African Journals Online (AJOL)

    Small scale mining is a major threat to water resources and agricultural activities in most mining communities across Ghana. This study investigated the effect of small scale mining on the quality of water for irrigation from some selected sites along a river and a reservoir which was used as a control. The physical and ...

  5. Methodological foundations of evaluation of effectiveness indicators of small-scale business activities

    Directory of Open Access Journals (Sweden)

    Ivanova T.

    2013-01-01

    Full Text Available The methodological approach to the measurement of financial indicators of small-scale enterprises has been developed. It enables to secure the comparability of financial condition indicators and the results of small-scale enterprise activities, and also to develop the methods of vertical integral estimate calculation at separate aspects of financial condition and the results of smallscale enterprise activities.

  6. Enhancing stewardship in Latin America and Caribbean small-scale fisheries : challenges and opportunities

    NARCIS (Netherlands)

    Gasalla, M.A.; de Castro, F.

    2016-01-01

    This thematic series, entitled “Enhancing Stewardship in Latin America and Caribbean Small-Scale Fisheries”, emerged as part of a joint effort to bridge Latin-American scholars interested in networking on small-scale fisheries in the region. Built on results presented at two meetings (‘Too Big to

  7. Socio-technical study of small-scale gold mining in Suriname

    NARCIS (Netherlands)

    Seccatore, J; de Theije, M.E.M.

    2017-01-01

    Small-scale gold mining is Suriname’s main economic sector, producing about two thirds of the nation’s gold. Despite this, the sector is only very loosely regulated and most small-scale mining activities are informal. Surinamese miners are only a minority: the majority are Brazilian migrants, who

  8. Category, narrative and value in the governance of small-scale fisheries

    NARCIS (Netherlands)

    Johnson, D.S.

    2006-01-01

    Since the 1970s, small-scale fisheries have had an important place in fisheries social science and in fisheries management. While there has been substantial discussion of what constitutes the category of small-scale fisheries, its considerable ambiguity is nevertheless often passed over. This paper

  9. A review of advanced small-scale parallel bioreactor technology for accelerated process development: current state and future need.

    Science.gov (United States)

    Bareither, Rachel; Pollard, David

    2011-01-01

    The pharmaceutical and biotech industries face continued pressure to reduce development costs and accelerate process development. This challenge occurs alongside the need for increased upstream experimentation to support quality by design initiatives and the pursuit of predictive models from systems biology. A small scale system enabling multiple reactions in parallel (n ≥ 20), with automated sampling and integrated to purification, would provide significant improvement (four to fivefold) to development timelines. State of the art attempts to pursue high throughput process development include shake flasks, microfluidic reactors, microtiter plates and small-scale stirred reactors. The limitations of these systems are compared to desired criteria to mimic large scale commercial processes. The comparison shows that significant technological improvement is still required to provide automated solutions that can speed upstream process development. Copyright © 2010 American Institute of Chemical Engineers (AIChE).

  10. Bisulfite-Based DNA Methylation Analysis from Recent and Archived Formalin-Fixed, Paraffin Embedded Colorectal Tissue Samples.

    Science.gov (United States)

    Kalmár, Alexandra; Péterfia, Bálint; Hollósi, Péter; Wichmann, Barnabás; Bodor, András; Patai, Árpád V; Schöller, Andrea; Krenács, Tibor; Tulassay, Zsolt; Molnár, Béla

    2015-09-01

    We aimed to test the applicability of formalin-fixed and paraffin-embedded (FFPE) tissue samples for gene specific DNA methylation analysis after using two commercially available DNA isolation kits. Genomic DNA was isolated from 5 colorectal adenocarcinomas and 5 normal adjacent tissues from "recent", collected within 6 months, and "archived", collected more than 5 years ago, FFPE tissues using either High Pure FFPET DNA Isolation kit or QIAamp DNA FFPE Tissue kit. DNA methylation analysis of MAL, SFRP1 and SFRP2 genes, known to be hypermethylated in CRC, was performed using methylation-sensitive high resolution melting (MS-HRM) analysis and sequencing. QIAamp (Q) method resulted in slightly higher recovery in archived (HP: 1.22 ± 3.18 μg DNA; Q: 3.00 ± 4.04 μg DNA) and significantly (p < 0.05) higher recovery in recent samples compared to High Pure method (HP) (HP: 4.10 ± 2.91 μg DNA; Q: 11.51 ± 7.50 μg DNA). Both OD260/280 and OD260/230 ratios were lower, but still high in the High Pure isolated archived and recent samples compared to those isolated with QIAamp. Identical DNA methylation patterns were detected for all 3 genes tested by MS-HRM with both isolation kits in the recent group. However, despite of higher DNA recovery in QIAamp slightly more reproducible methylation results were obtained from High Pure isolated archived samples. Sequencing confirmed DNA hypermethylation in CRCs. In conclusion, reproducible DNA methylation patterns were obtained from recent samples using both isolation kits. However, long term storage may affect the reliability of the results leading to moderate differences between the efficiency of isolation kits.

  11. Comparison of three mycobacterial DNA extraction methods from extrapulmonary samples for PCR assay

    Directory of Open Access Journals (Sweden)

    Khandaker Shadia

    2012-01-01

    Full Text Available Sensitivity of the molecular diagnostic tests of extrapulmonary tuberculosis largely depends upon the efficiency of DNA extraction methods. The objective of our study was to compare three methods of extracting DNA of Mycobacterium tuberculosis for testing by polymerase chain reaction. All three methods; heating, heating with sonication and addition of lysis buffer with heating and sonication were implicated on 20 extrapulmonary samples. PCR positivity was 2 (10%, 4 (20% and 7 (35% in the samples extracted by heating, heat+sonication and heat+sonication+lysis buffer method respectively. Of the extraction methods evaluated, maximum PCR positive results were achieved by combined heat, sonication and lysis buffer method which can be applied in routine clinical practice. Ibrahim Med. Coll. J. 2012; 6(1: 9-11

  12. Vertebrate DNA in fecal samples from bonobos and gorillas: evidence for meat consumption or artefact?

    Directory of Open Access Journals (Sweden)

    Michael Hofreiter

    Full Text Available BACKGROUND: Deciphering the behavioral repertoire of great apes is a challenge for several reasons. First, due to their elusive behavior in dense forest environments, great ape populations are often difficult to observe. Second, members of the genus Pan are known to display a great variety in their behavioral repertoire; thus, observations from one population are not necessarily representative for other populations. For example, bonobos (Pan paniscus are generally believed to consume almost no vertebrate prey. However, recent observations show that at least some bonobo populations may consume vertebrate prey more commonly than previously believed. We investigated the extent of their meat consumption using PCR amplification of vertebrate mitochondrial DNA (mtDNA segments from DNA extracted from bonobo feces. As a control we also attempted PCR amplifications from gorilla feces, a species assumed to be strictly herbivorous. PRINCIPAL FINDINGS: We found evidence for consumption of a variety of mammalian species in about 16% of the samples investigated. Moreover, 40% of the positive DNA amplifications originated from arboreal monkeys. However, we also found duiker and monkey mtDNA in the gorilla feces, albeit in somewhat lower percentages. Notably, the DNA sequences isolated from the two ape species fit best to the species living in the respective regions. This result suggests that the sequences are of regional origin and do not represent laboratory contaminants. CONCLUSIONS: Our results allow at least three possible and mutually not exclusive conclusions. First, all results may represent contamination of the feces by vertebrate DNA from the local environment. Thus, studies investigating a species' diet from feces DNA may be unreliable due to the low copy number of DNA originating from diet items. Second, there is some inherent difference between the bonobo and gorilla feces, with only the later ones being contaminated. Third, similar to bonobos, for

  13. Vertebrate DNA in fecal samples from bonobos and gorillas: evidence for meat consumption or artefact?

    Science.gov (United States)

    Hofreiter, Michael; Kreuz, Eva; Eriksson, Jonas; Schubert, Grit; Hohmann, Gottfried

    2010-02-25

    Deciphering the behavioral repertoire of great apes is a challenge for several reasons. First, due to their elusive behavior in dense forest environments, great ape populations are often difficult to observe. Second, members of the genus Pan are known to display a great variety in their behavioral repertoire; thus, observations from one population are not necessarily representative for other populations. For example, bonobos (Pan paniscus) are generally believed to consume almost no vertebrate prey. However, recent observations show that at least some bonobo populations may consume vertebrate prey more commonly than previously believed. We investigated the extent of their meat consumption using PCR amplification of vertebrate mitochondrial DNA (mtDNA) segments from DNA extracted from bonobo feces. As a control we also attempted PCR amplifications from gorilla feces, a species assumed to be strictly herbivorous. We found evidence for consumption of a variety of mammalian species in about 16% of the samples investigated. Moreover, 40% of the positive DNA amplifications originated from arboreal monkeys. However, we also found duiker and monkey mtDNA in the gorilla feces, albeit in somewhat lower percentages. Notably, the DNA sequences isolated from the two ape species fit best to the species living in the respective regions. This result suggests that the sequences are of regional origin and do not represent laboratory contaminants. Our results allow at least three possible and mutually not exclusive conclusions. First, all results may represent contamination of the feces by vertebrate DNA from the local environment. Thus, studies investigating a species' diet from feces DNA may be unreliable due to the low copy number of DNA originating from diet items. Second, there is some inherent difference between the bonobo and gorilla feces, with only the later ones being contaminated. Third, similar to bonobos, for which the consumption of monkeys has only recently been

  14. Small-scale density variations in the lunar crust revealed by GRAIL

    Science.gov (United States)

    Jansen, J. C.; Andrews-Hanna, J. C.; Li, Y.; Lucey, P. G.; Taylor, G. J.; Goossens, S.; Lemoine, F. G.; Mazarico, E.; Head, J. W.; Milbury, C.; Kiefer, W. S.; Soderblom, J. M.; Zuber, M. T.

    2017-07-01

    Data from the Gravity Recovery and Interior Laboratory (GRAIL) mission have revealed that ∼98% of the power of the gravity signal of the Moon at high spherical harmonic degrees correlates with the topography. The remaining 2% of the signal, which cannot be explained by topography, contains information about density variations within the crust. These high-degree Bouguer gravity anomalies are likely caused by small-scale (10‧s of km) shallow density variations. Here we use gravity inversions to model the small-scale three-dimensional variations in the density of the lunar crust. Inversion results from three non-descript areas yield shallow density variations in the range of 100-200 kg/m3. Three end-member scenarios of variations in porosity, intrusions into the crust, and variations in bulk crustal composition were tested as possible sources of the density variations. We find that the density anomalies can be caused entirely by changes in porosity. Characteristics of density anomalies in the South Pole-Aitken basin also support porosity as a primary source of these variations. Mafic intrusions into the crust could explain many, but not all of the anomalies. Additionally, variations in crustal composition revealed by spectral data could only explain a small fraction of the density anomalies. Nevertheless, all three sources of density variations likely contribute. Collectively, results from this study of GRAIL gravity data, combined with other studies of remote sensing data and lunar samples, show that the lunar crust exhibits variations in density by ± 10% over scales ranging from centimeters to 100‧s of kilometers.

  15. Small-Scale Density Variations in the Lunar Crust Revealed by GRAIL

    Science.gov (United States)

    Jansen, J. C.; Andrews-Hanna, J. C.; Li, Y.; Lucey, P. G.; Taylor, G. J.; Goossens, S.; Lemoine, F. G.; Mazarico, E.; Head, J. W., III; Milbury, C.; hide

    2017-01-01

    Data from the Gravity Recovery and Interior Laboratory (GRAIL) mission have revealed that approximately 98 percent of the power of the gravity signal of the Moon at high spherical harmonic degrees correlates with the topography. The remaining 2 percent of the signal, which cannot be explained by topography, contains information about density variations within the crust. These high-degree Bouguer gravity anomalies are likely caused by small-scale (10's of km) shallow density variations. Here we use gravity inversions to model the small-scale three-dimensional variations in the density of the lunar crust. Inversion results from three non-descript areas yield shallow density variations in the range of 100-200 kg/m3. Three end-member scenarios of variations in porosity, intrusions into the crust, and variations in bulk crustal composition were tested as possible sources of the density variations. We find that the density anomalies can be caused entirely by changes in porosity. Characteristics of density anomalies in the South Pole-Aitken basin also support porosity as a primary source of these variations. Mafic intrusions into the crust could explain many, but not all of the anomalies. Additionally, variations in crustal composition revealed by spectral data could only explain a small fraction of the density anomalies. Nevertheless, all three sources of density variations likely contribute. Collectively, results from this study of GRAIL gravity data, combined with other studies of remote sensing data and lunar samples, show that the lunar crust exhibits variations in density by plus or minus 10 percent over scales ranging from centimeters to 100’s of kilometers.

  16. The underlying processes of a soil mite metacommunity on a small scale.

    Directory of Open Access Journals (Sweden)

    Chengxu Dong

    Full Text Available Metacommunity theory provides an understanding of how ecological processes regulate local community assemblies. However, few field studies have evaluated the underlying mechanisms of a metacommunity on a small scale through revealing the relative roles of spatial and environmental filtering in structuring local community composition. Based on a spatially explicit sampling design in 2012 and 2013, this study aims to evaluate the underlying processes of a soil mite metacommunity on a small spatial scale (50 m in a temperate deciduous forest located at the Maoershan Ecosystem Research Station, Northeast China. Moran's eigenvector maps (MEMs were used to model independent spatial variables. The relative importance of spatial (including trend variables, i.e., geographical coordinates, and broad- and fine-scale spatial variables and environmental factors in driving the soil mite metacommunity was determined by variation partitioning. Mantel and partial Mantel tests and a redundancy analysis (RDA were also used to identify the relative contributions of spatial and environmental variables. The results of variation partitioning suggested that the relatively large and significant variance was a result of spatial variables (including broad- and fine-scale spatial variables and trend, indicating the importance of dispersal limitation and autocorrelation processes. The significant contribution of environmental variables was detected in 2012 based on a partial Mantel test, and soil moisture and soil organic matter were especially important for the soil mite metacommunity composition in both years. The study suggested that the soil mite metacommunity was primarily regulated by dispersal limitation due to broad-scale and neutral biotic processes at a fine-scale and that environmental filtering might be of subordinate importance. In conclusion, a combination of metacommunity perspectives between neutral and species sorting theories was suggested to be important

  17. Intensive land use drives small-scale homogenization of plant- and leafhopper communities and promotes generalists.

    Science.gov (United States)

    Chisté, Melanie N; Mody, Karsten; Kunz, Gernot; Gunczy, Johanna; Blüthgen, Nico

    2018-02-01

    The current biodiversity decline through anthropogenic land-use not only involves local species losses, but also homogenization of communities, with a few generalist species benefitting most from human activities. Most studies assessed community heterogeneity (β-diversity) on larger scales by comparing different sites, but little is known about impacts on β-diversity within each site, which is relevant for understanding variation in the level of α-diversity, the small-scale distribution of species and associated habitat heterogeneity. To obtain our dataset with 36,899 individuals out of 117 different plant- and leafhopper (Auchenorrhyncha) species, we sampled communities of 140 managed grassland sites across Germany by quantitative vacuum suction of five 1 m 2 plots on each site. Sites differed in land-use intensity as characterized by intensity of fertilization, mowing and grazing. Our results demonstrate a significant within-site homogenization of plant- and leafhopper communities with increasing land-use intensity. Correspondingly, density (- 78%) and γ-diversity (- 35%) declined, particularly with fertilization and mowing intensity. More than 34% of plant- and leafhopper species were significant losers and only 6% were winners of high land-use intensity, with abundant and widespread species being less affected. Increasing land-use intensity adversely affected dietary specialists and promoted generalist species. Our study emphasizes considerable, multifaceted effects of land-use intensification on species loss, with a few dominant generalists winning, and an emerging trend towards more homogenized assemblages. By demonstrating homogenization for the first time within sites, our study highlights that anthropogenic influences on biodiversity even occur on small scales.

  18. The underlying processes of a soil mite metacommunity on a small scale

    Science.gov (United States)

    Guo, Chuanwei; Lin, Lin; Wu, Donghui; Zhang, Limin

    2017-01-01

    Metacommunity theory provides an understanding of how ecological processes regulate local community assemblies. However, few field studies have evaluated the underlying mechanisms of a metacommunity on a small scale through revealing the relative roles of spatial and environmental filtering in structuring local community composition. Based on a spatially explicit sampling design in 2012 and 2013, this study aims to evaluate the underlying processes of a soil mite metacommunity on a small spatial scale (50 m) in a temperate deciduous forest located at the Maoershan Ecosystem Research Station, Northeast China. Moran’s eigenvector maps (MEMs) were used to model independent spatial variables. The relative importance of spatial (including trend variables, i.e., geographical coordinates, and broad- and fine-scale spatial variables) and environmental factors in driving the soil mite metacommunity was determined by variation partitioning. Mantel and partial Mantel tests and a redundancy analysis (RDA) were also used to identify the relative contributions of spatial and environmental variables. The results of variation partitioning suggested that the relatively large and significant variance was a result of spatial variables (including broad- and fine-scale spatial variables and trend), indicating the importance of dispersal limitation and autocorrelation processes. The significant contribution of environmental variables was detected in 2012 based on a partial Mantel test, and soil moisture and soil organic matter were especially important for the soil mite metacommunity composition in both years. The study suggested that the soil mite metacommunity was primarily regulated by dispersal limitation due to broad-scale and neutral biotic processes at a fine-scale and that environmental filtering might be of subordinate importance. In conclusion, a combination of metacommunity perspectives between neutral and species sorting theories was suggested to be important in the

  19. Evaluation of Sample Stability and Automated DNA Extraction for Fetal Sex Determination Using Cell-Free Fetal DNA in Maternal Plasma

    Directory of Open Access Journals (Sweden)

    Elena Ordoñez

    2013-01-01

    Full Text Available Objective. The detection of paternally inherited sequences in maternal plasma, such as the SRY gene for fetal sexing or RHD for fetal blood group genotyping, is becoming part of daily routine in diagnostic laboratories. Due to the low percentage of fetal DNA, it is crucial to ensure sample stability and the efficiency of DNA extraction. We evaluated blood stability at 4°C for at least 24 hours and automated DNA extraction, for fetal sex determination in maternal plasma. Methods. A total of 158 blood samples were collected, using EDTA-K tubes, from women in their 1st trimester of pregnancy. Samples were kept at 4°C for at least 24 hours before processing. An automated DNA extraction was evaluated, and its efficiency was compared with a standard manual procedure. The SRY marker was used to quantify cfDNA by real-time PCR. Results. Although lower cfDNA amounts were obtained by automated DNA extraction (mean 107,35 GE/mL versus 259,43 GE/mL, the SRY sequence was successfully detected in all 108 samples from pregnancies with male fetuses. Conclusion. We successfully evaluated the suitability of standard blood tubes for the collection of maternal blood and assessed samples to be suitable for analysis at least 24 hours later. This would allow shipping to a central reference laboratory almost from anywhere in Europe.

  20. Detection of Babesia DNA in blood and spleen samples from Eurasian badgers (Meles meles) in Scotland.

    Science.gov (United States)

    Bartley, Paul M; Wilson, Cari; Innes, Elisabeth A; Katzer, Frank

    2017-08-01

    Babesia are intraerythrocytic parasites of importance worldwide within the fields of human and veterinary medicine, as some Babesia sp., including Babesia microti are potentially zoonotic and can cause fatal disease in both humans and animals. The aims of this study were to use a nested PCR (amplifying the 18S rRNA gene) to determine the presence and species of Babesia parasite DNA found in blood (n = 47) and spleen (n = 47) samples collected from Eurasian badgers (Meles meles) in Scotland. The results showed 28/47 (59·6%) blood and 14/47 (29·8%) spleen samples tested positive for the presence of Babesia DNA. Initial sequence analysis of the Babesia DNA identified three distinct sequence types (submitted to GenBank KX528553, KX528554 and KX528555), which demonstrated ⩾99% identity to Babesia sp. parasites previously identified in badgers in Spain (KT223484 and KT223485). Phylogenetic analysis showed that the three isolates are closely related to Babesia annae, B. microti and other Piroplasmida species found in wildlife. Further sequence analysis of the samples demonstrated that the badgers were routinely infected with more than one parasite isolate and there was also evidence of genetic recombination between the Babesia parasite isolates (submitted to GenBank KY250472 - KY250477).

  1. Silica Exposures in Artisanal Small-Scale Gold Mining in Tanzania and Implications for Tuberculosis Prevention.

    Science.gov (United States)

    Gottesfeld, Perry; Andrew, Damian; Dalhoff, Jeffrey

    2015-01-01

    Gold miners exposed to crystalline silica are at risk of silicosis, lung cancer, and experience higher incidence rates of pulmonary tuberculosis (TB). Although the hazards associated with mercury exposure in artisanal small-scale gold mining (ASGM) have been well documented, no published data was available on crystalline silica exposures in this population. Air sampling was conducted in the breathing zone of workers in five villages in Tanzania with battery-operated sampling pumps and bulk samples were collected to measure the type and concentration of crystalline silica in the ore. Samples were analyzed at an accredited laboratory with X-ray diffraction. Airborne crystalline silica exposures exceeded recommended limits for all tasks monitored with an average exposure of 16.85 mg/m(3) for underground drilling that was 337 fold greater than the recommended exposure limit (REL) published by the U.S. National Institute for Occupational Safety and Health (NIOSH) and 0.19 mg/m(3) for aboveground operations or 4-fold greater than the REL. The exposures measured raise concern for possible acute and chronic silicosis and are known to significantly contribute to TB incidence rates in mining communities. The use of wet methods could greatly reduce exposures and the risk of TB and silicosis in ASGM. Ongoing efforts to address mercury and other hazards in ASGM should incorporate crystalline silica dust controls.

  2. Nanoparticle sensor for label free detection of swine DNA in mixed biological samples

    Energy Technology Data Exchange (ETDEWEB)

    Ali, M E; Hashim, U [Institute of Nano Electronic Engineering (INNE), Universiti Malaysia Perlis, Lot 104-108, Tingkat 1, Block A, Taman Pertiwi Indah, Jalan Kangar-Alor Star, Seriab, 01000 Kangar, Perlis (Malaysia); Mustafa, S; Che Man, Y B; Yusop, M H M [Halal Products Research Institute, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor (Malaysia); Bari, M F [School of Materials Engineering, University Malaysia Perlis, Seriab 01000, Kangar, Perlis (Malaysia); Islam, Kh N [Department of Preclinical Sciences, Faculty of Veterinary Medicine, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor (Malaysia); Hasan, M F, E-mail: uda@unimap.edu.my [Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400 UPM Serdang, Selangor (Malaysia)

    2011-05-13

    We used 40 {+-} 5 nm gold nanoparticles (GNPs) as colorimetric sensor to visually detect swine-specific conserved sequence and nucleotide mismatch in PCR-amplified and non-amplified mitochondrial DNA mixtures to authenticate species. Colloidal GNPs changed color from pinkish-red to gray-purple in 2 mM PBS. Visually observed results were clearly reflected by the dramatic reduction of surface plasmon resonance peak at 530 nm and the appearance of new features in the 620-800 nm regions in their absorption spectra. The particles were stabilized against salt-induced aggregation upon the adsorption of single-stranded DNA. The PCR products, without any additional processing, were hybridized with a 17-base probe prior to exposure to GNPs. At a critical annealing temperature (55 {sup 0}C) that differentiated matched and mismatched base pairing, the probe was hybridized to pig PCR product and dehybridized from the deer product. The dehybridized probe stuck to GNPs to prevent them from salt-induced aggregation and retained their characteristic red color. Hybridization of a 27-nucleotide probe to swine mitochondrial DNA identified them in pork-venison, pork-shad and venison-shad binary admixtures, eliminating the need of PCR amplification. Thus the assay was applied to authenticate species both in PCR-amplified and non-amplified heterogeneous biological samples. The results were determined visually and validated by absorption spectroscopy. The entire assay (hybridization plus visual detection) was performed in less than 10 min. The LOD (for genomic DNA) of the assay was 6 {mu}g ml{sup -1} swine DNA in mixed meat samples. We believe the assay can be applied for species assignment in food analysis, mismatch detection in genetic screening and homology studies between closely related species.

  3. Nanoparticle sensor for label free detection of swine DNA in mixed biological samples

    International Nuclear Information System (INIS)

    Ali, M E; Hashim, U; Mustafa, S; Che Man, Y B; Yusop, M H M; Bari, M F; Islam, Kh N; Hasan, M F

    2011-01-01

    We used 40 ± 5 nm gold nanoparticles (GNPs) as colorimetric sensor to visually detect swine-specific conserved sequence and nucleotide mismatch in PCR-amplified and non-amplified mitochondrial DNA mixtures to authenticate species. Colloidal GNPs changed color from pinkish-red to gray-purple in 2 mM PBS. Visually observed results were clearly reflected by the dramatic reduction of surface plasmon resonance peak at 530 nm and the appearance of new features in the 620-800 nm regions in their absorption spectra. The particles were stabilized against salt-induced aggregation upon the adsorption of single-stranded DNA. The PCR products, without any additional processing, were hybridized with a 17-base probe prior to exposure to GNPs. At a critical annealing temperature (55 0 C) that differentiated matched and mismatched base pairing, the probe was hybridized to pig PCR product and dehybridized from the deer product. The dehybridized probe stuck to GNPs to prevent them from salt-induced aggregation and retained their characteristic red color. Hybridization of a 27-nucleotide probe to swine mitochondrial DNA identified them in pork-venison, pork-shad and venison-shad binary admixtures, eliminating the need of PCR amplification. Thus the assay was applied to authenticate species both in PCR-amplified and non-amplified heterogeneous biological samples. The results were determined visually and validated by absorption spectroscopy. The entire assay (hybridization plus visual detection) was performed in less than 10 min. The LOD (for genomic DNA) of the assay was 6 μg ml -1 swine DNA in mixed meat samples. We believe the assay can be applied for species assignment in food analysis, mismatch detection in genetic screening and homology studies between closely related species.

  4. Wetland use and resource degradation among small-scale farmers ...

    African Journals Online (AJOL)

    economic life of smallholders in Cross River State, and the relationship between socio-economic factors and wetland degradation. A multi-stage sampling procedure was used in selecting respondents for the study. Data for this study was analyzed ...

  5. Comparative analysis of five DNA isolation protocols and three drying methods for leaves samples of Nectandra megapotamica (Spreng. Mez

    Directory of Open Access Journals (Sweden)

    Leonardo Severo da Costa

    2016-06-01

    Full Text Available The aim of the study was to establish a DNA isolation protocol Nectandra megapotamica (Spreng. Mez., able to obtain samples of high yield and quality for use in genomic analysis. A commercial kit and four classical methods of DNA extraction were tested, including three cetyltrimethylammonium bromide (CTAB-based and one sodium dodecyl sulfate (SDS-based methods. Three drying methods for leaves samples were also evaluated including drying at room temperature (RT, in an oven at 40ºC (S40, and in a microwave oven (FMO. The DNA solutions obtained from different types of leaves samples using the five protocols were assessed in terms of cost, execution time, and quality and yield of extracted DNA. The commercial kit did not extract DNA with sufficient quantity or quality for successful PCR reactions. Among the classic methods, only the protocols of Dellaporta and of Khanuja yielded DNA extractions for all three types of foliar samples that resulted in successful PCR reactions and subsequent enzyme restriction assays. Based on the evaluated variables, the most appropriate DNA extraction method for Nectandra megapotamica (Spreng. Mez. was that of Dellaporta, regardless of the method used to dry the samples. The selected method has a relatively low cost and total execution time. Moreover, the quality and quantity of DNA extracted using this method was sufficient for DNA sequence amplification using PCR reactions and to get restriction fragments.

  6. Developmental validation of the Quantifiler(®) HP and Trio Kits for human DNA quantification in forensic samples.

    Science.gov (United States)

    Holt, Allison; Wootton, Sharon Chao; Mulero, Julio J; Brzoska, Pius M; Langit, Emanuel; Green, Robert L

    2016-03-01

    The quantification of human genomic DNA is a necessary first step in the DNA casework sample analysis workflow. DNA quantification determines optimal sample input amounts for subsequent STR (short tandem repeat) genotyping procedures, as well as being a useful screening tool to identify samples most likely to provide probative genotypic evidence. To better mesh with the capabilities of newest-generation STR analysis assays, the Quantifiler(®) HP and Quantifiler(®) Trio DNA Quantification Kits were designed for greater detection sensitivity and more robust performance with samples that contain PCR inhibitors or degraded DNA. The new DNA quantification kits use multiplex TaqMan(®) assay-based fluorescent probe technology to simultaneously quantify up to three human genomic targets, allowing samples to be assessed for total human DNA, male contributor (i.e., Y-chromosome) DNA, as well as a determination of DNA degradation state. The Quantifiler HP and Trio Kits use multiple-copy loci to allow for significantly improved sensitivity compared to earlier-generation kits that employ single-copy target loci. The kits' improved performance provides better predictive ability for results with downstream, newest-generation STR assays, and their shortened time-to-result allows more efficient integration into the forensic casework analysis workflow. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

  7. [Real-time quantification to analyze historical Colombian samples detecting a short fragment of hypervariable region II of mitochondrial DNA].

    Science.gov (United States)

    Pérez, Luz Adriana; Rodríguez, Freddy; Langebaek, Carl Henrik; Groot, Helena

    2016-09-01

    Unlike other molecular biology studies, the analysis of ancient DNA (aDNA) requires special infrastructure and methodological conditions to guarantee the quality of the results. One of the main authenticity criteria is DNA quantification, where quantitative real-time PCR is often used given its sensitivity and specificity. Nevertheless, the implementation of these conditions and methodologies to fulfill authenticity criteria imply higher costs. Objective: To develop a simple and less costly method for mitochondrial DNA quantification suitable for highly degraded samples. Materials and methods: The proposed method is based on the use of mini-primers for the specific amplification of short fragments of mitochondrial DNA. The subsequent purification of these amplified fragments allows a standard curve to be constructed with concentrations in accordance to the state of degradation of the samples. Results: The proposed method successfully detected DNA from ancient samples including bone remains and mummified tissue. DNA inhibitory substances were also detected. Conclusion: The proposed method represents a simpler and cost-effective way to detect low amounts of aDNA, and a tool to differentiate DNA-free samples from samples with inhibitory substances.

  8. Amplification volume reduction on DNA database samples using FTA™ Classic Cards.

    Science.gov (United States)

    Wong, Hang Yee; Lim, Eng Seng Simon; Tan-Siew, Wai Fun

    2012-03-01

    The DNA forensic community always strives towards improvements in aspects such as sensitivity, robustness, and efficacy balanced with cost efficiency. Therefore our laboratory decided to study the feasibility of PCR amplification volume reduction using DNA entrapped in FTA™ Classic Card and to bring cost savings to the laboratory. There were a few concerns the laboratory needed to address. First, the kinetics of the amplification reaction could be significantly altered. Second, an increase in sensitivity might affect interpretation due to increased stochastic effects even though they were pristine samples. Third, statics might cause FTA punches to jump out of its allocated well into another thus causing sample-to-sample contamination. Fourth, the size of the punches might be too small for visual inspection. Last, there would be a limit to the extent of volume reduction due to evaporation and the possible need of re-injection of samples for capillary electrophoresis. The laboratory had successfully optimized a reduced amplification volume of 10 μL for FTA samples. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

  9. DNA damage focus analysis in blood samples of minipigs reveals acute partial body irradiation.

    Directory of Open Access Journals (Sweden)

    Andreas Lamkowski

    Full Text Available Radiation accidents frequently involve acute high dose partial body irradiation leading to victims with radiation sickness and cutaneous radiation syndrome that implements radiation-induced cell death. Cells that are not lethally hit seek to repair ionizing radiation (IR induced damage, albeit at the expense of an increased risk of mutation and tumor formation due to misrepair of IR-induced DNA double strand breaks (DSBs. The response to DNA damage includes phosphorylation of histone H2AX in the vicinity of DSBs, creating foci in the nucleus whose enumeration can serve as a radiation biodosimeter. Here, we investigated γH2AX and DNA repair foci in peripheral blood lymphocytes of Göttingen minipigs that experienced acute partial body irradiation (PBI with 49 Gy (± 6% Co-60 γ-rays of the upper lumbar region. Blood samples taken 4, 24 and 168 hours post PBI were subjected to γ-H2AX, 53BP1 and MRE11 focus enumeration. Peripheral blood lymphocytes (PBL of 49 Gy partial body irradiated minipigs were found to display 1-8 DNA damage foci/cell. These PBL values significantly deceed the high foci numbers observed in keratinocyte nuclei of the directly γ-irradiated minipig skin regions, indicating a limited resident time of PBL in the exposed tissue volume. Nonetheless, PBL samples obtained 4 h post IR in average contained 2.2% of cells displaying a pan-γH2AX signal, suggesting that these received a higher IR dose. Moreover, dispersion analysis indicated partial body irradiation for all 13 minipigs at 4 h post IR. While dose reconstruction using γH2AX DNA repair foci in lymphocytes after in vivo PBI represents a challenge, the DNA damage focus assay may serve as a rapid, first line indicator of radiation exposure. The occurrence of PBLs with pan-γH2AX staining and of cells with relatively high foci numbers that skew a Poisson distribution may be taken as indicator of acute high dose partial body irradiation, particularly when samples are available

  10. Effect of DNA extraction methods and sampling techniques on the apparent structure of cow and sheep rumen microbial communities.

    Directory of Open Access Journals (Sweden)

    Gemma Henderson

    Full Text Available Molecular microbial ecology techniques are widely used to study the composition of the rumen microbiota and to increase understanding of the roles they play. Therefore, sampling and DNA extraction methods that result in adequate yields of microbial DNA that also accurately represents the microbial community are crucial. Fifteen different methods were used to extract DNA from cow and sheep rumen samples. The DNA yield and quality, and its suitability for downstream PCR amplifications varied considerably, depending on the DNA extraction method used. DNA extracts from nine extraction methods that passed these first quality criteria were evaluated further by quantitative PCR enumeration of microbial marker loci. Absolute microbial numbers, determined on the same rumen samples, differed by more than 100-fold, depending on the DNA extraction method used. The apparent compositions of the archaeal, bacterial, ciliate protozoal, and fungal communities in identical rumen samples were assessed using 454 Titanium pyrosequencing. Significant differences in microbial community composition were observed between extraction methods, for example in the relative abundances of members of the phyla Bacteroidetes and Firmicutes. Microbial communities in parallel samples collected from cows by oral stomach-tubing or through a rumen fistula, and in liquid and solid rumen digesta fractions, were compared using one of the DNA extraction methods. Community representations were generally similar, regardless of the rumen sampling technique used, but significant differences in the abundances of some microbial taxa such as the Clostridiales and the Methanobrevibacter ruminantium clade were observed. The apparent microbial community composition differed between rumen sample fractions, and Prevotellaceae were most abundant in the liquid fraction. DNA extraction methods that involved phenol-chloroform extraction and mechanical lysis steps tended to be more comparable. However

  11. A probe-based quantitative PCR assay for detecting Tetracapsuloides bryosalmonae in fish tissue and environmental DNA water samples

    Science.gov (United States)

    Hutchins, Patrick; Sepulveda, Adam; Martin, Renee; Hopper, Lacey

    2017-01-01

    A probe-based quantitative real-time PCR assay was developed to detect Tetracapsuloides bryosalmonae, which causes proliferative kidney disease in salmonid fish, in kidney tissue and environmental DNA (eDNA) water samples. The limits of detection and quantification were 7 and 100 DNA copies for calibration standards and T. bryosalmonae was reliably detected down to 100 copies in tissue and eDNA samples. The assay presented here is a highly sensitive and quantitative tool for detecting T. bryosalmonae with potential applications for tissue diagnostics and environmental detection.

  12. Small scale temporal variability in the phytoplankton of Independencia Bay, Pisco, Perú

    Directory of Open Access Journals (Sweden)

    Noemí Ochoa

    2013-06-01

    Full Text Available Temporal variations at small scale of the coastal marine phytoplankton assemblages were studied. Water samples were collected at a fixed station in Bahia Independencia (Pisco-Peru. The sampling took place in the morning (08:00 h. and afternoon (15:00 h over a period of 29 days (March 28 to April 25, 1988. Surface temperatures also were taken, fluctuating from 15,4 °C to 17,2 °C. Diatoms were the principal component of the phytoplankton community and were more related with the total of phytoplankton. Other groups as Dinoflagellates, Coccolitophorids, Silicoflagellates and small flagellates were present but were less important. Skeletonema costatum was the dominant specie during the first nine days of sampling, after that it was substituted by Thalassionema nitzschioides, which remained as dominant until the end of the study. Small variation in species composition but large fluctuations in density of phytoplankton were recorded over a period of few hours. Small increments in temperature influenced in the phytoplankton assemblages.

  13. Usefulness of in-house real time PCR for HBV DNA quantification in serum and oral fluid samples.

    Science.gov (United States)

    Portilho, Moyra Machado; Mendonça, Ana Carolina da Fonseca; Bezerra, Cristianne Sousa; do Espirito-Santo, Márcia Paschoal; de Paula, Vanessa Salete; Nabuco, Leticia Cancella; Villela-Nogueira, Cristiane Alves; Lewis-Ximenez, Lia Laura; Lampe, Elisabeth; Villar, Livia Melo

    2018-06-01

    For quantification of hepatitis B virus DNA (HBV DNA), commercial assays are used with serum or plasma samples, but oral fluid samples could be an alternative for HBV diagnosis due to ease of collection. This study aims to develop in-house real time PCR using synthetic curve for HBV DNA quantification for serum and oral fluid samples. Samples were collected from 103 individuals (55 HBsAg reactive and HBV DNA reactive by commercial assay and 48 without HBV markers) and submitted to two in-house real time PCR assays for HBV pre-S/S region with different standard curves: qPCR plasmidial and qPCR synthetic. A total of 27 serum samples were HBV DNA positive by qPCR plasmidial and 40 with qPCR synthetic (72% and 85% of concordance, respectively). Quantitative PCR synthetic presented efficiency of 99% and sensitivity of 2log10 copies/mL. Among oral fluid samples, five and ten were detected using qPCR plasmidial and synthetic, respectively. This study demonstrated that qPCR synthetic using serum samples could be used as alternative for HBV DNA quantification due to its sensitivity. In addition, it was possible to quantify HBV DNA in oral fluid samples suggesting the potential of this specimen for molecular diagnosis of HBV. Copyright © 2018 Elsevier B.V. All rights reserved.

  14. Automation and integration of multiplexed on-line sample preparation with capillary electrophoresis for DNA sequencing

    Energy Technology Data Exchange (ETDEWEB)

    Tan, H.

    1999-03-31

    The purpose of this research is to develop a multiplexed sample processing system in conjunction with multiplexed capillary electrophoresis for high-throughput DNA sequencing. The concept from DNA template to called bases was first demonstrated with a manually operated single capillary system. Later, an automated microfluidic system with 8 channels based on the same principle was successfully constructed. The instrument automatically processes 8 templates through reaction, purification, denaturation, pre-concentration, injection, separation and detection in a parallel fashion. A multiplexed freeze/thaw switching principle and a distribution network were implemented to manage flow direction and sample transportation. Dye-labeled terminator cycle-sequencing reactions are performed in an 8-capillary array in a hot air thermal cycler. Subsequently, the sequencing ladders are directly loaded into a corresponding size-exclusion chromatographic column operated at {approximately} 60 C for purification. On-line denaturation and stacking injection for capillary electrophoresis is simultaneously accomplished at a cross assembly set at {approximately} 70 C. Not only the separation capillary array but also the reaction capillary array and purification columns can be regenerated after every run. DNA sequencing data from this system allow base calling up to 460 bases with accuracy of 98%.

  15. THE DEVELOPMENT OF SMALL-SCALE BUSINESS IN RUSSIA, TYPES OF FUNDING

    Directory of Open Access Journals (Sweden)

    Kirill O. Voronin

    2015-01-01

    Full Text Available In Russia small-scale business originated in the end of 1980s duringRestructuring. It has been developing as fast as Russian economics.Unlike large industrial companies, which just continued to run businessas they used to, small-scale businessmen had to start from scratch ordisaffiliate with large organizations. Basically, in 1990-s small-scale business as a financial institute was self-regulated due to its highcriminalization and nonpayment of tax.For a period of only 25 years small-scale business has improved muchand now provides well-being to the country. The improvement happeneddue to the following factors:- propitious economic and political climate of the country against thebackground of global economy and the years of restricting- important and useful measures for economic development were taken - important and useful measures for development of small-scale enterprises were takenThe development of this new financial institute is quite fast, but historyhas other examples of such phenomenon. In the 21st century RussianFederation adopted experience of advanced countries and imposed it onits historic experience. However, we can’t say that small-scale business is on its top of development in our country. Nowadays development of small-scale business is one of the priorities of the Russian government.

  16. C-14 bomb peak dating of human DNA samples at the microgram level

    International Nuclear Information System (INIS)

    Liebl, J. C.

    2011-01-01

    Radiocarbon (14C, t 1/2 = 5700 ± 30 years) is probably the radionuclide with the most versatile applications, spanning from archaeology to geoscience and medicine. Many of these applications are finally limited by the minimum amount of carbon in which the isotopic ratio 14C/12C can be measured. The required carbon sample size has dramatically decreased with the development of Accelerator Mass Spectrometry (AMS), typically from gram amounts for the classical beta counting method to about 1 milligram for AMS. The current work presents a further reduction into the few-μg carbon range. This means a decrease by a factor of one million compared to classical beta counting and is essential for the field of retrospective birth dating of human cells by means of radiocarbon from above-ground nuclear weapons testing between 1955 and 1963. The determination of 14C levels in genomic DNA can be used to retrospectively establish the birth date of cells in the human body. The main motive of the current work was to reduce the amount of carbon required for reliable 14C measurements to such an extent that investigations of neurons of particularly interesting small sections of the human brain (e.g. the olfactory bulb, bulbus olfactorius) were possible. In-depth investigations and development of 14C AMS sample preparation and measurement methods for μg-size DNA samples were carried out in close collaboration with the Department of Cell and Molecular Biology of the Karolinska Institute in Stockholm. As the most significant result, 14C measurements of 4.6 μg carbon DNA samples were performed with an overall precision of 2.3%. This allowed to study neurogenesis in the human olfactory bulb, which turned out to take place primarily at birth. Assuming throughout life a constant annual renewal rate of neurons in the human olfactory bulb, an upper limit of 0.34% for the renewal rate (95% confidence) was determined. At the Vienna Environmental Research Accelerator (VERA) the μg carbon

  17. Expression of DNA repair genes in ovarian cancer samples: biological and clinical considerations.

    Science.gov (United States)

    Ganzinelli, M; Mariani, P; Cattaneo, D; Fossati, R; Fruscio, R; Corso, S; Ricci, F; Broggini, M; Damia, G

    2011-05-01

    The purpose of this study was to investigate retrospectively the mRNA expression of genes involved in different DNA repair pathways implicated in processing platinum-induced damage in 171 chemotherapy-naïve ovarian tumours and correlate the expression of the different genes with clinical parameters. The expression of genes involved in DNA repair pathways (PARP1, ERCC1, XPA, XPF, XPG, BRCA1, FANCA, FANCC, FANCD2, FANCF and PolEta), and in DNA damage transduction (Chk1 and Claspin) was measured by RT-PCR in 13 stage I borderline and 77 stage I and 88 III ovarian carcinomas. ERCC1, XPA, XPF and XPG genes were significantly less expressed in stage III than in stage I carcinoma; BRCA1, FANCA, FANCC, FANCD2 gene expressions were low in borderline tumours, higher in stage I carcinomas and lower in stage III samples. High levels of ERCC1, XPA, FANCC, XPG and PolEta correlated with an increase in Overall Survival (OS) and Progression Free Survival (PFS), whilst high BRCA1 levels were associated with PFS on univariate analysis. With multivariate analyses no genes retained an association when adjusted by stage, grade and residual tumour. A tendency towards a better PFS was observed in patients with the highest level of ERCC1 and BRCA1 after platinum-based therapy than those given both platinum and taxol. The expression of DNA repair genes differed in borderline stage I, stage I and stage III ovarian carcinomas. The role of DNA repair genes in predicting the response in ovarian cancer patients seems far from being established. Copyright © 2010 Elsevier Ltd. All rights reserved.

  18. Small-scale hot facility for reprocessing and alpha research

    International Nuclear Information System (INIS)

    Abdel-Rassoul, A.A.

    1976-01-01

    The experimental hot facility at Inchas is planned for research activities related to the decontamination of radioactive wastes, analytical chemistry of alpha emitters and chemical treatment of spent UO 2 -Mg fuel samples. The design concept permits safe handling of source materials with radioactivity levels up to 10000Ci. The laboratory includes a reception area, process hall, a number of research laboratories and other facilities for chemical and physical analysis, nuclear measurements and health physics control. The radioactive waste management plant allows for control and decontamination of intermediate- and low-level laboratory effluents. Fixation of radioactive residues will be carried out in the sludge immobilization plant. High-level fission-product waste liquors are subject to preconcentration and transformation to a glassy matrix before ultimate storage. (author)

  19. Establishing a novel automated magnetic bead-based method for the extraction of DNA from a variety of forensic samples.

    Science.gov (United States)

    Witt, Sebastian; Neumann, Jan; Zierdt, Holger; Gébel, Gabriella; Röscheisen, Christiane

    2012-09-01

    Automated systems have been increasingly utilized for DNA extraction by many forensic laboratories to handle growing numbers of forensic casework samples while minimizing the risk of human errors and assuring high reproducibility. The step towards automation however is not easy: The automated extraction method has to be very versatile to reliably prepare high yields of pure genomic DNA from a broad variety of sample types on different carrier materials. To prevent possible cross-contamination of samples or the loss of DNA, the components of the kit have to be designed in a way that allows for the automated handling of the samples with no manual intervention necessary. DNA extraction using paramagnetic particles coated with a DNA-binding surface is predestined for an automated approach. For this study, we tested different DNA extraction kits using DNA-binding paramagnetic particles with regard to DNA yield and handling by a Freedom EVO(®)150 extraction robot (Tecan) equipped with a Te-MagS magnetic separator. Among others, the extraction kits tested were the ChargeSwitch(®)Forensic DNA Purification Kit (Invitrogen), the PrepFiler™Automated Forensic DNA Extraction Kit (Applied Biosystems) and NucleoMag™96 Trace (Macherey-Nagel). After an extensive test phase, we established a novel magnetic bead extraction method based upon the NucleoMag™ extraction kit (Macherey-Nagel). The new method is readily automatable and produces high yields of DNA from different sample types (blood, saliva, sperm, contact stains) on various substrates (filter paper, swabs, cigarette butts) with no evidence of a loss of magnetic beads or sample cross-contamination. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

  20. Molecular species identification with rich floristic sampling: DNA barcoding the pteridophyte flora of Japan.

    Directory of Open Access Journals (Sweden)

    Atsushi Ebihara

    Full Text Available BACKGROUND: DNA barcoding is expected to be an effective identification tool for organisms with heteromorphic generations such as pteridophytes, which possess a morphologically simple gametophyte generation. Although a reference data set including complete coverage of the target local flora/fauna is necessary for accurate identification, DNA barcode studies including such rich taxonomic sampling on a countrywide scale are lacking. METHODOLOGY/PRINCIPAL FINDINGS: The Japanese pteridophyte flora (733 taxa including subspecies and varieties was used to test the utility of two plastid DNA barcode regions (rbcL and trnH-psbA with the intention of developing an identification system for native gametophytes. DNA sequences were obtained from each of 689 (94.0% taxa for rbcL and 617 (84.2% taxa for trnH-psbA. Mean interspecific divergence values across all taxon pairs (K2P genetic distances did not reveal a significant difference in rate between trnH-psbA and rbcL, but mean K2P distances of each genus showed significant heterogeneity according to systematic position. The minimum fail rate of taxon discrimination in an identification test using BLAST (12.52% was obtained when rbcL and trnH-psbA were combined, and became lower in datasets excluding infraspecific taxa or apogamous taxa, or including sexual diploids only. CONCLUSIONS/SIGNIFICANCE: This study demonstrates the overall effectiveness of DNA barcodes for species identification in the Japanese pteridophyte flora. Although this flora is characterized by a high occurrence of apogamous taxa that pose a serious challenge to identification using DNA barcodes, such taxa are limited to a small number of genera, and only minimally detract from the overall success rate. In the case that a query sequence is matched to a known apogamous genus, routine species identification may not be possible. Otherwise, DNA barcoding is a practical tool for identification of most Japanese pteridophytes, and is especially

  1. Small-scale upgrading and refinement of biogas; Smaaskalig uppgradering och foeraedling av biogas

    Energy Technology Data Exchange (ETDEWEB)

    Blom, Helena; Mccann, Michael; Westman, Johan (Poeyry SwedPower AB, Stockholm (Sweden))

    2012-02-15

    Small-scale upgrading and refinement of biogas is a report which aims to compile the state of knowledge in small-scale biogas upgrading. The project have been a collaboration with Agrovaest and Energy Farm and was funded by the Foundation for Agricultural Research, Western Goetaland and the Agriculture Department. The technology available for small scale upgrade has been examined from the technical and economic standpoint. An economic comparison has been made and the production of upgraded biogas has been estimated for different raw gas flows. The work also contains information related to biogas production, upgrading and a comparison of liquid biogas, DME and Ecopar-diesel

  2. Comparison between full- and small-scale sensory assessments of air quality

    DEFF Research Database (Denmark)

    Wargocki, Pawel; Sabikova, J.; Lagercrantz, Love Per

    2002-01-01

    Thirty-nine untrained subjects made small- and full-scale evaluations of the acceptability of the quality of air at 22 deg.C and 40% RH, polluted by either carpet, felt floor covering, painted gypsum board, linoleum or chipboard. Small-scale evaluations were made on the air extracted from 200-L......-scale sensory ratings of acceptability of air polluted by carpet and by linoleum were systematically better than small-scale assessments, but not for the other three materials. Calculated sensory emission rates from carpet and linoleum were significantly lower in full scale than in small scale. When modelling...

  3. Discordant genotyping results using DNA isolated from anti-doping control urine samples.

    Science.gov (United States)

    Choong, Eva; Schulze, Jenny J; Ericsson, Magnus; Rane, Anders; Ekström, Lena

    2017-07-01

    The UGT2B17 gene deletion polymorphism is known to correlate to urinary concentration of testosterone-glucuronide and hence this genotype exerts a large impact on the testosterone/epitestosterone (T/E) ratio, a biomarker for testosterone doping. The objective of this study was to assess if DNA isolated from athletes' urine samples (n = 713) obtained in routine doping controls could be targeted for genotyping analysis for future integration in the athlete's passport. A control population (n = 21) including both urine and blood DNA was used for genotyping concordance test. Another aim was to study a large group (n = 596) of authentic elite athletes in respect of urinary steroid profile in relation to genetic variation. First we found that the genotype results when using urine-derived DNA did not correlate sufficiently with the genotype obtained from whole blood DNA. Secondly we found males with one or two UGT2B17 alleles had higher T/E (mean 1.63 ± 0.93) than females (mean 1.28 ± 1.08), p˂0.001. Unexpectedly, we found that several male del/del athletes in power sports had a T/E ˃1. If men in power sport exert a different urinary steroid profile needs to be further investigated. The other polymorphisms investigated in the CYP17A1, UGT2B7 and UGT2B15 genes did not show any associations with testosterone and epitestosterone concentrations. Our results show that genotyping using urine samples according to our method is not useful in an anti-doping setting. Instead, it is of importance for the anti-doping test programs to include baseline values in the ABP to minimize any putative impact of genotype. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

  4. Polymorphism discovery and allele frequency estimation using high-throughput DNA sequencing of target-enriched pooled DNA samples

    Directory of Open Access Journals (Sweden)

    Mullen Michael P

    2012-01-01

    Full Text Available Abstract Background The central role of the somatotrophic axis in animal post-natal growth, development and fertility is well established. Therefore, the identification of genetic variants affecting quantitative traits within this axis is an attractive goal. However, large sample numbers are a pre-requisite for the identification of genetic variants underlying complex traits and although technologies are improving rapidly, high-throughput sequencing of large numbers of complete individual genomes remains prohibitively expensive. Therefore using a pooled DNA approach coupled with target enrichment and high-throughput sequencing, the aim of this study was to identify polymorphisms and estimate allele frequency differences across 83 candidate genes of the somatotrophic axis, in 150 Holstein-Friesian dairy bulls divided into two groups divergent for genetic merit for fertility. Results In total, 4,135 SNPs and 893 indels were identified during the resequencing of the 83 candidate genes. Nineteen percent (n = 952 of variants were located within 5' and 3' UTRs. Seventy-two percent (n = 3,612 were intronic and 9% (n = 464 were exonic, including 65 indels and 236 SNPs resulting in non-synonymous substitutions (NSS. Significant (P ® MassARRAY. No significant differences (P > 0.1 were observed between the two methods for any of the 43 SNPs across both pools (i.e., 86 tests in total. Conclusions The results of the current study support previous findings of the use of DNA sample pooling and high-throughput sequencing as a viable strategy for polymorphism discovery and allele frequency estimation. Using this approach we have characterised the genetic variation within genes of the somatotrophic axis and related pathways, central to mammalian post-natal growth and development and subsequent lactogenesis and fertility. We have identified a large number of variants segregating at significantly different frequencies between cattle groups divergent for calving

  5. New Detection Modality for Label-Free Quantification of DNA in Biological Samples via Superparamagnetic Bead Aggregation

    Science.gov (United States)

    Leslie, Daniel C.; Li, Jingyi; Strachan, Briony C.; Begley, Matthew R.; Finkler, David; Bazydlo, Lindsay L.; Barker, N. Scott; Haverstick, Doris; Utz, Marcel; Landers, James P.

    2012-01-01

    Combining DNA and superparamagnetic beads in a rotating magnetic field produces multiparticle aggregates that are visually striking, and enables label-free optical detection and quantification of DNA at levels in the picogram per microliter range. DNA in biological samples can be quantified directly by simple analysis of optical images of microfluidic wells placed on a magnetic stirrer without DNA purification. Aggregation results from DNA/bead interactions driven either by the presence of a chaotrope (a nonspecific trigger for aggregation) or by hybridization with oligonucleotides on functionalized beads (sequence-specific). This paper demonstrates quantification of DNA with sensitivity comparable to that of the best currently available fluorometric assays. The robustness and sensitivity of the method enable a wide range of applications, illustrated here by counting eukaryotic cells. Using widely available and inexpensive benchtop hardware, the approach provides a highly accessible low-tech microscale alternative to more expensive DNA detection and cell counting techniques. PMID:22423674

  6. MANU. Isostatic compression of buffer blocks. Small scale

    International Nuclear Information System (INIS)

    Laaksonen, R.

    2010-01-01

    The purpose of this study was to become familiar with the isostatic compression technique and to manufacture specimens to study various aspects of the manufacturing process. These included for example the effect of moisture, maximum compressive pressure, vibration, vacuum, specimen size, coating, multiple compressions and duration of load cycle on the density and other properties of bentonite specimens. Also the amount of volumetric contraction was of interest in this study together with the used mould technology. This work summarizes the tests done with isostatic compression technique during 2008. Tests were mainly carried out with MX-80 bentonite, which is a commercial product and currently the reference bentonite in the repository reference plan. Tests were made from June to November 2008 both in Finland and in Sweden. VTT made four test series in Finland. MABU Consulting Ab made two test series in Sweden. Also Posiva Oy carried out one preliminary series before this study in Finland. The test results show that there is a clear relationship between density and moisture content at all pressure levels. The calculated degree of saturation of more moist samples remained at the level of 95 -to 98 % of full saturation. It should be possible to manufacture buffer blocks with high accuracy (density, water content, degree of saturation), if similar preliminary tests are done. Tests did not support the assumption that vacuum (partial or full) in the specimen during compression increases the final density. Tests showed that pre-vibrated specimens had a slightly higher density but the difference was insignificant. Coarse raw bentonite produced the highest dry density of all sodium bentonites used. The highest dry density values were received with Minelco's Ca-bentonite, but the average water content was not extremely accurate. The following recommendations were derived from the results of this project: additional tests should be carried out to determine the relationship

  7. Analysis of fingerprint samples, testing various conditions, for forensic DNA identification.

    Science.gov (United States)

    Ostojic, Lana; Wurmbach, Elisa

    2017-01-01

    Fingerprints can be of tremendous value for forensic biology, since they can be collected from a wide variety of evident types, such as handles of weapons, tools collected in criminal cases, and objects with no apparent staining. DNA obtained from fingerprints varies greatly in quality and quantity, which ultimately affects the quality of the resulting STR profiles. Additional difficulties can arise when fingerprint samples show mixed STR profiles due to the handling of multiple persons. After applying a tested protocol for sample collection (swabbing with 5% Triton X-100), DNA extraction (using an enzyme that works at elevated temperatures), and PCR amplification (AmpFlSTR® Identifiler® using 31cycles) extensive analysis was performed to better understand the challenges inherent to fingerprint samples, with the ultimate goal of developing valuable profiles (≥50% complete). The impact of time on deposited fingerprints was investigated, revealing that while the quality of profiles deteriorated, full STR profiles could still be obtained from samples after 40days of storage at room temperature. By comparing the STR profiles from fingerprints of the dominant versus the non-dominant hand, we found a slightly better quality from the non-dominant hand, which was not always significant. Substrates seem to have greater effects on fingerprints. Tests on glass, plastic, paper and metal (US Quarter dollar, made of Cu and Ni), common substrates in offices and homes, showed best results for glass, followed by plastic and paper, while almost no profiles were obtained from a Quarter dollar. Important for forensic casework, we also assessed three-person mixtures of touched fingerprint samples. Unlike routinely used approaches for sampling evidence, the surface of an object (bottle) was sectioned into six equal parts and separate samples were taken from each section. The samples were processed separately for DNA extraction and STR amplification. The results included a few single

  8. Developing Ultra-small Scale Mechanical Testing Methods and Microstructural Investigation Procedures for Irradiated Materials

    Energy Technology Data Exchange (ETDEWEB)

    Hosemann, Peter; Kaoumi, Djamel

    2018-04-02

    -beam irradiations have been utilized for decades to foster the understanding of materials’ behavior under radiation, and significant efforts at comparing ion-beam irradiations to neutron irradiations are ongoing [1]. While extensive microstructural and chemical characterizations of neutron-irradiated and ion-irradiated materials are essential to the understanding of the underlying physics of materials’ degradation in nuclear environments, the ultimate test is the mechanical performance of a material under the anticipated condition, since it is the final criterion for a material to be accepted for use in a specific nuclear component. Again, standard, large-scale, bulk evaluations are key for the licensing of materials in a specific component, but additional, more basic scientific testing can accelerate the process by targeting specific areas of interest. Small-scale mechanical testing has been applied on nuclear materials for decades [2]. Traditionally the driving forces to use non-standard-size samples are the limited space in reactors, the availability of new alloys, and a reduction in radioactive-materials volume. Shear punch testing [3,5], sub-sized micro tensile testing [4], sub-sized compact tension and charpy testing [6,7], micro bulge testing [8], and micro hardness testing [3] have been used. Small-scale mechanical testing also allows the targeting of specific regions of interest, be they single grains to evaluate a specific deformation mechanism [9], grain boundaries, heat-affected zones in welds, or any other specific critical area of interest. With further reducing of the sample size, it also holds the promise to obtain quantitative data from ion-beam irradiations and to compare such data to the microstructural changes observed. Over the last few decades, a number of small-scale mechanical characterization techniques have been developed and utilized for irradiated materials. In addition to the above-mentioned sample test techniques at the mm and sub mm length scale

  9. Long-term frozen storage of urine samples: a trouble to get PCR results in Schistosoma spp. DNA detection?

    Science.gov (United States)

    Fernández-Soto, Pedro; Velasco Tirado, Virginia; Carranza Rodríguez, Cristina; Pérez-Arellano, José Luis; Muro, Antonio

    2013-01-01

    Human schistosomiasis remains a serious worldwide public health problem. At present, a sensitive and specific assay for routine diagnosis of schistosome infection is not yet available. The potential for detecting schistosome-derived DNA by PCR-based methods in human clinical samples is currently being investigated as a diagnostic tool with potential application in routine schistosomiasis diagnosis. Collection of diagnostic samples such as stool or blood is usually difficult in some populations. However, urine is a biological sample that can be collected in a non-invasive method, easy to get from people of all ages and easy in management, but as a sample for PCR diagnosis is still not widely used. This could be due to the high variability in the reported efficiency of detection as a result of the high variation in urine samples' storage or conditions for handling and DNA preservation and extraction methods. We evaluate different commercial DNA extraction methods from a series of long-term frozen storage human urine samples from patients with parasitological confirmed schistosomiasis in order to assess the PCR effectiveness for Schistosoma spp. detection. Patients urine samples were frozen for 18 months up to 7 years until use. Results were compared with those obtained in PCR assays using fresh healthy human urine artificially contaminated with Schistosoma mansoni DNA and urine samples from mice experimentally infected with S. mansoni cercariae stored frozen for at least 12 months before use. PCR results in fresh human artificial urine samples using different DNA based extraction methods were much more effective than those obtained when long-term frozen human urine samples were used as the source of DNA template. Long-term frozen human urine samples are probably not a good source for DNA extraction for use as a template in PCR detection of Schistosoma spp., regardless of the DNA method of extraction used.

  10. Long-term frozen storage of urine samples: a trouble to get PCR results in Schistosoma spp. DNA detection?

    Directory of Open Access Journals (Sweden)

    Pedro Fernández-Soto

    Full Text Available BACKGROUND: Human schistosomiasis remains a serious worldwide public health problem. At present, a sensitive and specific assay for routine diagnosis of schistosome infection is not yet available. The potential for detecting schistosome-derived DNA by PCR-based methods in human clinical samples is currently being investigated as a diagnostic tool with potential application in routine schistosomiasis diagnosis. Collection of diagnostic samples such as stool or blood is usually difficult in some populations. However, urine is a biological sample that can be collected in a non-invasive method, easy to get from people of all ages and easy in management, but as a sample for PCR diagnosis is still not widely used. This could be due to the high variability in the reported efficiency of detection as a result of the high variation in urine samples' storage or conditions for handling and DNA preservation and extraction methods. METHODOLOGY/PRINCIPAL FINDINGS: We evaluate different commercial DNA extraction methods from a series of long-term frozen storage human urine samples from patients with parasitological confirmed schistosomiasis in order to assess the PCR effectiveness for Schistosoma spp. detection. Patients urine samples were frozen for 18 months up to 7 years until use. Results were compared with those obtained in PCR assays using fresh healthy human urine artificially contaminated with Schistosoma mansoni DNA and urine samples from mice experimentally infected with S. mansoni cercariae stored frozen for at least 12 months before use. PCR results in fresh human artificial urine samples using different DNA based extraction methods were much more effective than those obtained when long-term frozen human urine samples were used as the source of DNA template. CONCLUSIONS/SIGNIFICANCE: Long-term frozen human urine samples are probably not a good source for DNA extraction for use as a template in PCR detection of Schistosoma spp., regardless of the DNA

  11. Monitoring of cotton dust and health risk assessment in small-scale weaving industry.

    Science.gov (United States)

    Tahir, Muhammad Wajid; Mumtaz, Muhammad Waseem; Tauseef, Shanza; Sajjad, Muqadas; Nazeer, Awais; Farheen, Nazish; Iqbal, Muddsar

    2012-08-01

    The present study describes the estimation of particulate matter (cotton dust) with different sizes, i.e., PM(1.0), PM(2.5), PM(4.0), and PM(10.0 μm) in small-scale weaving industry (power looms) situated in district Hafizabad, Punjab, Pakistan, and the assessment of health problems of workers associated with these pollutants. A significant difference was found in PM(1.0), PM(2.5), PM(4.0), and PM(10.0) with reference to nine different sampling stations with p values 4.0), and PM(10.0), depict that PM(1.0) differs significantly from PM(2.5), PM(4.0), and PM(10.0), with p values 4.0), with a p value >0.05 in defined sampling stations on an average basis. Majority of the workers were facing several diseases due to interaction with particulate matter (cotton dust) during working hours. Flue, cough, eye, and skin infections were the most common diseases among workers caused by particulate matter (cotton dust).

  12. Prevalence and Distribution of Campylobacter jejuni in Small-Scale Broiler Operations.

    Science.gov (United States)

    Tangkham, Wannee; Janes, Marlene; LeMieux, Frederick

    2016-01-01

    Campylobacter jejuni has been recognized as one of the most prevalent causes of foodborne bacterial illnesses in humans. Previous studies have focused on the transmission routes of C. jejuni from commercial flock farms to the final retail product. The objective of this study was to determine the prevalence of C. jejuni and Campylobacter spp. in eggshells, live birds, feed, drinking water, and the rearing environment in a small-scale broiler operation. Broilers were raised under two different production systems: (i) environmentally controlled housing and (ii) open-air housing with two replications. Each week, samples were collected from eggshells, bird feces, feed, drinking water, enclosures (vertical walls of bird housing), and feed troughs for enumeration and isolation testing. All samples were plated on modified charcoal-cefoperazone-deoxycholate agar to determine the log CFU per gram and percent prevalence of Campylobacter spp. Isolation of C. jejuni was verified with latex agglutination and hippurate hydrolysis tests. The results from this study suggest that vertical transmission of these bacteria from egg surfaces to newly hatched chicks is not a significant risk factor. The results also suggest that the prevalence of C. jejuni at time of harvest (week 6) was significantly higher (P < 0.05) in the open-air housing broilers than in those in the environmentally controlled housing. Elevated levels of cross-contaminants, especially water and feed, may have played a role in this outcome.

  13. Probing the Small-scale Structure in Strongly Lensed Systems via Transdimensional Inference

    Science.gov (United States)

    Daylan, Tansu; Cyr-Racine, Francis-Yan; Diaz Rivero, Ana; Dvorkin, Cora; Finkbeiner, Douglas P.

    2018-02-01

    Strong lensing is a sensitive probe of the small-scale density fluctuations in the Universe. We implement a pipeline to model strongly lensed systems using probabilistic cataloging, which is a transdimensional, hierarchical, and Bayesian framework to sample from a metamodel (union of models with different dimensionality) consistent with observed photon count maps. Probabilistic cataloging allows one to robustly characterize modeling covariances within and across lens models with different numbers of subhalos. Unlike traditional cataloging of subhalos, it does not require model subhalos to improve the goodness of fit above the detection threshold. Instead, it allows the exploitation of all information contained in the photon count maps—for instance, when constraining the subhalo mass function. We further show that, by not including these small subhalos in the lens model, fixed-dimensional inference methods can significantly mismodel the data. Using a simulated Hubble Space Telescope data set, we show that the subhalo mass function can be probed even when many subhalos in the sample catalogs are individually below the detection threshold and would be absent in a traditional catalog. The implemented software, Probabilistic Cataloger (PCAT) is made publicly available at https://github.com/tdaylan/pcat.

  14. Mendelian breeding units versus standard sampling strategies: mitochondrial DNA variation in southwest Sardinia

    Directory of Open Access Journals (Sweden)

    Daria Sanna

    2011-01-01

    Full Text Available We report a sampling strategy based on Mendelian Breeding Units (MBUs, representing an interbreeding group of individuals sharing a common gene pool. The identification of MBUs is crucial for case-control experimental design in association studies. The aim of this work was to evaluate the possible existence of bias in terms of genetic variability and haplogroup frequencies in the MBU sample, due to severe sample selection. In order to reach this goal, the MBU sampling strategy was compared to a standard selection of individuals according to their surname and place of birth. We analysed mitochondrial DNA variation (first hypervariable segment and coding region in unrelated healthy subjects from two different areas of Sardinia: the area around the town of Cabras and the western Campidano area. No statistically significant differences were observed when the two sampling methods were compared, indicating that the stringent sample selection needed to establish a MBU does not alter original genetic variability and haplogroup distribution. Therefore, the MBU sampling strategy can be considered a useful tool in association studies of complex traits.

  15. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample.

    Directory of Open Access Journals (Sweden)

    Chengwei Luo

    Full Text Available Next-generation sequencing (NGS is commonly used in metagenomic studies of complex microbial communities but whether or not different NGS platforms recover the same diversity from a sample and their assembled sequences are of comparable quality remain unclear. We compared the two most frequently used platforms, the Roche 454 FLX Titanium and the Illumina Genome Analyzer (GA II, on the same DNA sample obtained from a complex freshwater planktonic community. Despite the substantial differences in read length and sequencing protocols, the platforms provided a comparable view of the community sampled. For instance, derived assemblies overlapped in ~90% of their total sequences and in situ abundances of genes and genotypes (estimated based on sequence coverage correlated highly between the two platforms (R(2>0.9. Evaluation of base-call error, frameshift frequency, and contig length suggested that Illumina offered equivalent, if not better, assemblies than Roche 454. The results from metagenomic samples were further validated against DNA samples of eighteen isolate genomes, which showed a range of genome sizes and G+C% content. We also provide quantitative estimates of the errors in gene and contig sequences assembled from datasets characterized by different levels of complexity and G+C% content. For instance, we noted that homopolymer-associated, single-base errors affected ~1% of the protein sequences recovered in Illumina contigs of 10× coverage and 50% G+C; this frequency increased to ~3% when non-homopolymer errors were also considered. Collectively, our results should serve as a useful practical guide for choosing proper sampling strategies and data possessing protocols for future metagenomic studies.

  16. Direct comparisons of Illumina vs. Roche 454 sequencing technologies on the same microbial community DNA sample.

    Science.gov (United States)

    Luo, Chengwei; Tsementzi, Despina; Kyrpides, Nikos; Read, Timothy; Konstantinidis, Konstantinos T

    2012-01-01

    Next-generation sequencing (NGS) is commonly used in metagenomic studies of complex microbial communities but whether or not different NGS platforms recover the same diversity from a sample and their assembled sequences are of comparable quality remain unclear. We compared the two most frequently used platforms, the Roche 454 FLX Titanium and the Illumina Genome Analyzer (GA) II, on the same DNA sample obtained from a complex freshwater planktonic community. Despite the substantial differences in read length and sequencing protocols, the platforms provided a comparable view of the community sampled. For instance, derived assemblies overlapped in ~90% of their total sequences and in situ abundances of genes and genotypes (estimated based on sequence coverage) correlated highly between the two platforms (R(2)>0.9). Evaluation of base-call error, frameshift frequency, and contig length suggested that Illumina offered equivalent, if not better, assemblies than Roche 454. The results from metagenomic samples were further validated against DNA samples of eighteen isolate genomes, which showed a range of genome sizes and G+C% content. We also provide quantitative estimates of the errors in gene and contig sequences assembled from datasets characterized by different levels of complexity and G+C% content. For instance, we noted that homopolymer-associated, single-base errors affected ~1% of the protein sequences recovered in Illumina contigs of 10× coverage and 50% G+C; this frequency increased to ~3% when non-homopolymer errors were also considered. Collectively, our results should serve as a useful practical guide for choosing proper sampling strategies and data possessing protocols for future metagenomic studies.

  17. Chromatin Immunoprecipitation (ChIP): Revisiting the Efficacy of Sample Preparation, Sonication, Quantification of Sheared DNA, and Analysis via PCR

    Science.gov (United States)

    Schoppee Bortz, Pamela D.; Wamhoff, Brian R.

    2011-01-01

    The “quantitative” ChIP, a tool commonly used to study protein-DNA interactions in cells and tissue, is a difficult assay often plagued with technical error. We present, herein, the process required to merge multiple protocols into a quick, reliable and easy method and an approach to accurately quantify ChIP DNA prior to performing PCR. We demonstrate that high intensity sonication for at least 30 min is required for full cellular disruption and maximum DNA recovery because ChIP lysis buffers fail to lyse formaldehyde-fixed cells. In addition, extracting ChIP DNA with chelex-100 yields samples that are too dilute for evaluation of shearing efficiency or quantification via nanospectrophotometry. However, DNA extracted from the Mock-ChIP supernatant via the phenol-chloroform-isoamyl alcohol (PCIA) method can be used to evaluate DNA shearing efficiency and used as the standard in a fluorescence-based microplate assay. This enabled accurate quantification of DNA in chelex-extracted ChIP samples and normalization to total DNA concentration prior to performing real-time PCR (rtPCR). Thus, a quick ChIP assay that can be completed in nine bench hours over two days has been validated along with a rapid, accurate and repeatable way to quantify ChIP DNA. The resulting rtPCR data more accurately depicts treatment effects on protein-DNA interactions of interest. PMID:22046253

  18. Environmental DNA method for estimating salamander distribution in headwater streams, and a comparison of water sampling methods.

    Science.gov (United States)

    Katano, Izumi; Harada, Ken; Doi, Hideyuki; Souma, Rio; Minamoto, Toshifumi

    2017-01-01

    Environmental DNA (eDNA) has recently been used for detecting the distribution of macroorganisms in various aquatic habitats. In this study, we applied an eDNA method to estimate the distribution of the Japanese clawed salamander, Onychodactylus japonicus, in headwater streams. Additionally, we compared the detection of eDNA and hand-capturing methods used for determining the distribution of O. japonicus. For eDNA detection, we designed a qPCR primer/probe set for O. japonicus using the 12S rRNA region. We detected the eDNA of O. japonicus at all sites (with the exception of one), where we also observed them by hand-capturing. Additionally, we detected eDNA at two sites where we were unable to observe individuals using the hand-capturing method. Moreover, we found that eDNA concentrations and detection rates of the two water sampling areas (stream surface and under stones) were not significantly different, although the eDNA concentration in the water under stones was more varied than that on the surface. We, therefore, conclude that eDNA methods could be used to determine the distribution of macroorganisms inhabiting headwater systems by using samples collected from the surface of the water.

  19. Assessment of small-scale integrated water vapour variability during HOPE

    Science.gov (United States)

    Steinke, S.; Eikenberg, S.; Löhnert, U.; Dick, G.; Klocke, D.; Di Girolamo, P.; Crewell, S.

    2015-03-01

    The spatio-temporal variability of integrated water vapour (IWV) on small scales of less than 10 km and hours is assessed with data from the 2 months of the High Definition Clouds and Precipitation for advancing Climate Prediction (HD(CP)2) Observational Prototype Experiment (HOPE). The statistical intercomparison of the unique set of observations during HOPE (microwave radiometer (MWR), Global Positioning System (GPS), sun photometer, radiosondes, Raman lidar, infrared and near-infrared Moderate Resolution Imaging Spectroradiometer (MODIS) on the satellites Aqua and Terra) measuring close together reveals a good agreement in terms of random differences (standard deviation ≤1 kg m-2) and correlation coefficient (≥ 0.98). The exception is MODIS, which appears to suffer from insufficient cloud filtering. For a case study during HOPE featuring a typical boundary layer development, the IWV variability in time and space on scales of less than 10 km and less than 1 h is investigated in detail. For this purpose, the measurements are complemented by simulations with the novel ICOsahedral Nonhydrostatic modelling framework (ICON), which for this study has a horizontal resolution of 156 m. These runs show that differences in space of 3-4 km or time of 10-15 min induce IWV variabilities on the order of 0.4 kg m-2. This model finding is confirmed by observed time series from two MWRs approximately 3 km apart with a comparable temporal resolution of a few seconds. Standard deviations of IWV derived from MWR measurements reveal a high variability (> 1 kg m-2) even at very short time scales of a few minutes. These cannot be captured by the temporally lower-resolved instruments and by operational numerical weather prediction models such as COSMO-DE (an application of the Consortium for Small-scale Modelling covering Germany) of Deutscher Wetterdienst, which is included in the comparison. However, for time scales larger than 1 h, a sampling resolution of 15 min is

  20. Pseudogenes and DNA-based diet analyses: A cautionary tale from a relatively well sampled predator-prey system

    DEFF Research Database (Denmark)

    Dunshea, G.; Barros, N. B.; Wells, R. S.

    2008-01-01

    Mitochondrial ribosomal DNA is commonly used in DNA-based dietary analyses. In such studies, these sequences are generally assumed to be the only version present in DNA of the organism of interest. However, nuclear pseudogenes that display variable similarity to the mitochondrial versions...... are common in many taxa. The presence of nuclear pseudogenes that co-amplify with their mitochondrial paralogues can lead to several possible confounding interpretations when applied to estimating animal diet. Here, we investigate the occurrence of nuclear pseudogenes in fecal samples taken from bottlenose...... dolphins (Tursiops truncatus) that were assayed for prey DNA with a universal primer technique. We found pseudogenes in 13 of 15 samples and 1-5 pseudogene haplotypes per sample representing 5-100% of all amplicons produced. The proportion of amplicons that were pseudogenes and the diversity of prey DNA...

  1. Self-reference and random sampling approach for label-free identification of DNA composition using plasmonic nanomaterials.

    Science.gov (United States)

    Freeman, Lindsay M; Pang, Lin; Fainman, Yeshaiahu

    2018-05-09

    The analysis of DNA has led to revolutionary advancements in the fields of medical diagnostics, genomics, prenatal screening, and forensic science, with the global DNA testing market expected to reach revenues of USD 10.04 billion per year by 2020. However, the current methods for DNA analysis remain dependent on the necessity for fluorophores or conjugated proteins, leading to high costs associated with consumable materials and manual labor. Here, we demonstrate a potential label-free DNA composition detection method using surface-enhanced Raman spectroscopy (SERS) in which we identify the composition of cytosine and adenine within single strands of DNA. This approach depends on the fact that there is one phosphate backbone per nucleotide, which we use as a reference to compensate for systematic measurement variations. We utilize plasmonic nanomaterials with random Raman sampling to perform label-free detection of the nucleotide composition within DNA strands, generating a calibration curve from standard samples of DNA and demonstrating the capability of resolving the nucleotide composition. The work represents an innovative way for detection of the DNA composition within DNA strands without the necessity of attached labels, offering a highly sensitive and reproducible method that factors in random sampling to minimize error.

  2. Tracing Males From Different Continents by Genotyping JC Polyomavirus in DNA From Semen Samples.

    Science.gov (United States)

    Rotondo, John Charles; Candian, Tommaso; Selvatici, Rita; Mazzoni, Elisa; Bonaccorsi, Gloria; Greco, Pantaleo; Tognon, Mauro; Martini, Fernanda

    2017-05-01

    The human JC polyomavirus (JCPyV) is an ubiquitous viral agent infecting approximately 60% of humans. Recently, JCPyV sequences have been detected in semen samples. The aim of this investigation was to test whether semen JCPyV genotyping can be employed to trace the origin continent of males. Semen DNA samples (n = 170) from males of different Continents were investigated by PCR for the polymorphic JCPyV viral capsid protein 1 (VP1) sequences, followed by DNA sequencing. JCPyV sequences were detected with an overall prevalence of 27.6% (47/170). DNA sequencing revealed that European males carried JCPyV types 1A (71.4%), 4 (11.4%), 2B (2.9%), 2D1 (2.9%), and 3A (2.9%). Asians JCPyV type 2D1 (66.7%) and Africans JCPyV types 3A (33.3%) and 1A (33.3%). In 10.6% of males, two different JCPyV genotypes were detected, suggesting that the second JCPyV genotype was acquired in the destination country. This study indicates that the majority of semen samples found to be JCPyV-positive, were infected with the JCPyV genotype found in the geographic area of male origin. Therefore, semen JCPyV genotyping could be employed to trace the origin continent of males. Our findings could be applied to forensic investigations, in case of for instance sexual crimes. Indeed, JCPyV genotyping should enable investigators to make additional detailed profiling of the offender. J. Cell. Physiol. 232: 982-985, 2017. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  3. The Impact of Micro-Finance on the Performance of Small-Scale ...

    African Journals Online (AJOL)

    The Impact of Micro-Finance on the Performance of Small-Scale Enterprises: A Comparison of ... PROMOTING ACCESS TO AFRICAN RESEARCH ... the impact that the study-MFIs are making on their SMEs-client in the Wa Municipality.

  4. The Impact of Micro-Finance on the Performance of Small-Scale ...

    African Journals Online (AJOL)

    2014-10-02

    Oct 2, 2014 ... Department of Planning and Management ... Keywords: Small-scale Enterprises, Micro-Financing, Micro-Credit, Sales Revenue, .... The Wa Municipality is often acclaimed as a private-sector business enclave in the Upper.

  5. thermal analysis of a small scale solid waste-fired steam boiler

    African Journals Online (AJOL)

    user

    Thermal analysis of a small scale solid waste-fired steam generator is presented in this paper. The analysis was based on the chosen design specifications which are operating steam ... include: wind, bio-energy, geothermal, solar thermal,.

  6. Growth and Efficiency of Small Scale Industry and its Impact on Economic Development of Sindh

    Directory of Open Access Journals (Sweden)

    Mumtaz Ali Junejo

    2008-09-01

    Full Text Available The purpose of this study is to analyze the growth, efficiency, causes of sickness of small scale industry, emergence of entrepreneur and competencies of entrepreneurs at Larkana estate area of Sindh Province. The study examines the educational background of the entrepreneurs of small scale industry who are the helm of affairs and its impact on the growth of sales of the every year. Strong evidence emerges that owners of small industrial units are family concern and having a low educational background, lack of managerial knowledge and conservation-oriented attitude results in under utilization of capacity and low growth of units established every year. This research paper provides a survey of the theoretical and empirical literature relating to promote the small scale industry in the Larkana region. This study indicates effective policy measures to promote the small scale industry particularly in Larkana region and generally in Pakistan.

  7. Small-scale hydroelectric power in the Pacific Northwest: new impetus for an old energy source

    Energy Technology Data Exchange (ETDEWEB)

    1980-07-01

    Energy supply is one of the most important issues facing Northwestern legislators today. To meet the challenge, state legislatures must address the development of alternative energy sources. The Small-Scale Hydroelectric Power Policy Project of the National Conference of State Legislators (NCSL) was designed to assist state legislators in looking at the benefits of one alternative, small-scale hydro. Because of the need for state legislative support in the development of small-scale hydroelectric, NCSL, as part of its contract with the Department of Energy, conducted the following conference on small-scale hydro in the Pacific Northwest. The conference was designed to identify state obstacles to development and to explore options for change available to policymakers. A summary of the conference proceedings is presented.

  8. Small scale hydroelectric power potential in Nevada: a preliminary reconnaissance survey

    Energy Technology Data Exchange (ETDEWEB)

    Cochran, G.F.; Fordham, J.W.; Richard, K.; Loux, R.

    1981-04-01

    This preliminary reconnaissance survey is intended to: develop a first estimate as to the potential number, location and characteristics of small-scale (50 kW to 15 MW) hydroelectric sites in Nevada; provide a compilation of various Federal and state laws and regulations, including tax and financing regulations, that affect small-scale hydroelectric development and provide information on sources of small-scale hydroelectric generation hardware and consultants/ contractors who do small scale hydroelectric work. The entire survey has been conducted in the office working with various available data bases. The site survey and site evaluation methods used are described, and data are tabulated on the flow, power potential, predicted capital expenditures required, etc. for 61 potential sites with measured flows and for 77 sites with derived flows. A map showing potential site locations is included. (LCL)

  9. Intelligent Network Flow Optimization (INFLO) prototype : Seattle small-scale demonstration plan.

    Science.gov (United States)

    2015-01-01

    This report describes the INFLO Prototype Small-Scale Demonstration to be performed in Seattle Washington. This demonstration is intended to demonstrate that the INFLO Prototype, previously demonstrated in a controlled environment, functions well in ...

  10. Analysis of the Determinants of Small-Scale Farmers' Grain Market ...

    African Journals Online (AJOL)

    In some cases, farmers may sell at low price when they face financial constraints, especially ... Analysis of the Determinants of Small-Scale Farmers' Grain Market Participations. [76] ...... An MSc Thesis Presented to the School of Graduate.

  11. Food Security in Africa and Asia: Strategies for Small-scale ...

    African Journals Online (AJOL)

    GGBT_2

    chapters. The focus is on small-scale agricultural development. It identifies ... Asia through a system of producer and consumer subsidies (pp. 195-196). ... Doha Round of the WTO and the position of African countries. In what ways will.

  12. Improved Methods of Carnivore Faecal Sample Preservation, DNA Extraction and Quantification for Accurate Genotyping of Wild Tigers

    Science.gov (United States)

    Harika, Katakam; Mahla, Ranjeet Singh; Shivaji, Sisinthy

    2012-01-01

    Background Non-invasively collected samples allow a variety of genetic studies on endangered and elusive species. However due to low amplification success and high genotyping error rates fewer samples can be identified up to the individual level. Number of PCRs needed to obtain reliable genotypes also noticeably increase. Methods We developed a quantitative PCR assay to measure and grade amplifiable nuclear DNA in feline faecal extracts. We determined DNA degradation in experimentally aged faecal samples and tested a suite of pre-PCR protocols to considerably improve DNA retrieval. Results Average DNA concentrations of Grade I, II and III extracts were 982pg/µl, 9.5pg/µl and 0.4pg/µl respectively. Nearly 10% of extracts had no amplifiable DNA. Microsatellite PCR success and allelic dropout rates were 92% and 1.5% in Grade I, 79% and 5% in Grade II, and 54% and 16% in Grade III respectively. Our results on experimentally aged faecal samples showed that ageing has a significant effect on quantity and quality of amplifiable DNA (pDNA degradation occurs within 3 days of exposure to direct sunlight. DNA concentrations of Day 1 samples stored by ethanol and silica methods for a month varied significantly from fresh Day 1 extracts (p0.05). DNA concentrations of fresh tiger and leopard faecal extracts without addition of carrier RNA were 816.5pg/µl (±115.5) and 690.1pg/µl (±207.1), while concentrations with addition of carrier RNA were 49414.5pg/µl (±9370.6) and 20982.7pg/µl (±6835.8) respectively. Conclusions Our results indicate that carnivore faecal samples should be collected as freshly as possible, are better preserved by two-step method and should be extracted with addition of carrier RNA. We recommend quantification of template DNA as this facilitates several downstream protocols. PMID:23071624

  13. Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis

    DEFF Research Database (Denmark)

    Bahl, Martin Iain; Bergström, Anders; Licht, Tine Rask

    2012-01-01

    Freezing stool samples prior to DNA extraction and downstream analysis is widely used in metagenomic studies of the human microbiota but may affect the inferred community composition. In this study, DNA was extracted either directly or following freeze storage of three homogenized human fecal...

  14. Freezing fecal samples prior to DNA extraction affects the Firmicutes to Bacteroidetes ratio determined by downstream quantitative PCR analysis

    DEFF Research Database (Denmark)

    Bahl, Martin Iain; Bergström, Anders; Licht, Tine Rask

    Freezing stool samples prior to DNA extraction and downstream analysis is widely used in metagenomic studies of the human microbiota but may affect the inferred community composition. In this study DNA was extracted either directly or following freeze storage of three homogenized human fecal...

  15. Resolution of a serum sample mix-up through the use of short tandem repeat DNA typing.

    Science.gov (United States)

    Allen, Robert W; Pritchard, Jane K

    2004-12-01

    A sample mix-up occurred in a tissue procurement laboratory in which aliquots of serum from two tissue donors were accidentally mislabeled. The clues to the apparent mixup involved discrepant Hepatitis C test results. In an attempt to resolve the apparent mix up, DNA typing was performed using serum samples as a possible source of genomic DNA. Two hundred microliter aliquots of two reference sera and aliquots prepared from them were subjected to DNA extraction. PCR amplification of 9 STR loci was performed on the extracts and amplicons were analyzed by capillary electrophoresis. About 1 microg/ml of DNA was recovered from all serum samples and was of sufficient quality to direct the amplification of most, if not all STR loci allowing the mislabeled specimens to be traced to the proper tissue donor. Serum is a useful source of genomic DNA for STR analysis in situations in which such samples are the only source of DNA for testing. Interestingly, one of the tissue donors on life support and repeatedly receiving blood products, exhibited a mixed DNA profile indicative of the presence of DNA from multiple individuals in the bloodstream.

  16. A sampling strategy and methodology for assessment and monitoring of Mediterranean small-scale fisheries

    OpenAIRE

    Farrugio, Henri; Le Corre, Gildas

    1993-01-01

    Para realizar una evaluacion cuantitativa de las pesquerias mediterraneas de artes menores, uno de los mayores problemas es la estimacion espacio-temporal de los esfuerzos de pesca y rendimientos de cada componente elemental de las pesquerias y de las variacions correspondientes. Estos elementos son esenciales para la evaluacion de las producciones y de los esfuerzos globales que presentan un interes primordial para el estudio de la dinamica de las pesquerias y de los recursos explotados. Est...

  17. NMR studies of bent DNA using {sup 13}C-enriched samples

    Energy Technology Data Exchange (ETDEWEB)

    Zimmer, D.P.; Crothers, D.M. [Yale Univ., New Haven, CT (United States)

    1994-12-01

    Bending of the DNA double helix can be brought about by introducing runs of adenines (A-tracts) in phase with the helical repeat of the DNA. The requirements for bending of DNA by A-tracts are that the length of the A-tract be greater than 3 base pairs and that the A-tracts must be in phase with the helical repeat (every 10 or 11 bp). Other factors, such as the number of adenines in the run, flanking sequences, and whether the A-tracts are phased with respect to the 5{prime}A or the 3{prime}A, have effects upon the degree of bending as assayed by electrophoretic mobility on native polyacrylamide gels. There are a number of models for bending A-tract DNA. The junction-bending model postulates that the structure of A-tracts is similar to the fiber diffraction structure of poly A, in which there is a significant degree of base pair tilt with respect to the helix axis. In this model, bending occurs at the junction between the A-tract and the B-form helix to allow favorable stacking interactions to occur. The bend of the helix could arise as a result of some other perturbation of B-form DNA by A-tracts, such as propeller twist; bending also could be due to a combination of factors. Our goal is to find the structural features of A-tracts responsible for bending of the helix by performing NMR on oligonucleotides containing A-tracts to obtain higher resolution structural data. One of the problems encountered in NMR structure determination of nucleic acids and other macromolecules is the assignment of resonances to nuclei. This procedure can be greatly facilitated through the use of {sup 13}C-enriched nucleic acid samples. We are developing a technique for the enzymatic synthesis of labeled DNA for NMR. The technique we are developing is similar to RNA labeling techniques already in use. The technique involves growth of methylotrophic bacteria on {sup 13}CH{sub 3}OH.

  18. Particle integrity, sampling, and application of a DNA-tagged tracer for aerosol transport studies

    Energy Technology Data Exchange (ETDEWEB)

    Kaeser, Cynthia Jeanne [Michigan State Univ., East Lansing, MI (United States)

    2017-07-21

    formulations of two different food-grade sugars (maltodextrin and erythritol) to humidity as high as 66% had no significant effect on the DNA label’s degradation or the particle’s aerodynamic diameter, confirming particle stability under such conditions. In summary, confirmation of the DNATrax particles’ size and label integrity under variable conditions combined with experiment multiplexing and high resolution sampling provides a powerful experimental design for modeling aerosol transport through occupied indoor and outdoor locations.

  19. Genetically modified crops and small-scale farmers: main opportunities and challenges

    OpenAIRE

    Azadi, Hossein; Samiee, Atry; Mahmoudi, Hossein; Jouzi, Zeynab; Rafiaani Khachak, Parisa; De Maeyer, Philippe; Witlox, Frank

    2015-01-01

    Although some important features of genetically modified (GM) crops such as insect resistance, herbicide tolerance, and drought tolerance might seem to be beneficial for small-scale farmers, the adoption of GM technology by smallholders is still slight. Identifying pros and cons of using this technology is important to understand the impacts of GM crops on these farmers. This article reviews the main opportunities and challenges of GM crops for small-scale farmers in developing countrie...

  20. Effect of Integrated Pest Management Training on Ugandan Small-Scale Farmers

    DEFF Research Database (Denmark)

    Clausen, Anna Sabine; Jørs, Erik; Atuhaire, Aggrey

    2017-01-01

    Small-scale farmers in developing countries use hazardous pesticides taking few or no safety measures. Farmer field schools (FFSs) teaching integrated pest management (IPM) have been shown to reduce pesticide use among trained farmers. This cross-sectional study compares pesticide-related knowledge......-reported symptoms. The study supports IPM as a method to reduce pesticide use and potential exposure and to improve pesticide-related KAP among small-scale farmers in developing countries....

  1. Bioeffects on an In Vitro Model by Small-Scale Explosives and Shock Wave Overpressure Impacts

    Science.gov (United States)

    2017-11-01

    Many TBIs are associated with blast from improvised explosive devices.2–4 Explosions are physical, chemical , or nuclear reactions involving a rapid...ARL-TR-8210 ● NOV 2017 US Army Research Laboratory Bioeffects on an In Vitro Model by Small-Scale Explosives and Shock Wave...Research Laboratory Bioeffects on an In Vitro Model by Small-Scale Explosives and Shock Wave Overpressure Impacts by Nicole E Zander, Thuvan

  2. Basic principles of taxation of small-scale enterprises in the Russian Federation

    OpenAIRE

    Khodyreva Viktoriia Andreevna

    2015-01-01

    This research is devoted to general principles of taxation of small-scale enterprises. Development of small-scale enterprises is one of the most important lines of tax policy in Russian Federation. The development of principles of taxation is important while forming a strong state system of taxation. In this work basic principles and some specific are provided. This work is of great scientific interest to law students, graduates, teachers and other persons interested in law and particularly i...

  3. An accurate and computationally efficient small-scale nonlinear FEA of flexible risers

    OpenAIRE

    Rahmati, MT; Bahai, H; Alfano, G

    2016-01-01

    This paper presents a highly efficient small-scale, detailed finite-element modelling method for flexible risers which can be effectively implemented in a fully-nested (FE2) multiscale analysis based on computational homogenisation. By exploiting cyclic symmetry and applying periodic boundary conditions, only a small fraction of a flexible pipe is used for a detailed nonlinear finite-element analysis at the small scale. In this model, using three-dimensional elements, all layer components are...

  4. Notes on a Dramaturgical Analysis of Unequal Small-Scale Corruption Experiences

    OpenAIRE

    Edgar Daniel Manchinelly Mota

    2017-01-01

    In the last two decades, corruption has emerged as a relevant subject on a worldwide scale, because of its negative effects on the economy and State institutions, among other things. Research has focused on the macro aspects of corruption, emphasizing its causes and consequences. However, small-scale corruption has not been studied in such detail. This document proposes a theoretical-methodological framework for a dramaturgical analysis of small-scale corruption, with the aim of demonstrating...

  5. Marketing strategy for retailing small-scale wind energy turbines in Indian markets

    OpenAIRE

    Harjula, Nina

    2009-01-01

    The study analyzes the small-scale wind energy markets in Mumbai, focusing on questions: How feasible is the wind energy for SME businesses in Mumbai, and what are the main challenges and opportunities of small-scale wind energy in Mumbai? The study is a qualitative case study, in which, the data has been collected through observing the markets by visiting wind energy sites and companies, interviewing and meeting potential customers and other stakeholders in the market. Theoretical frame...

  6. Performance of small-scale photovoltaic systems and their potential for rural electrification in Ethiopia

    Energy Technology Data Exchange (ETDEWEB)

    Stutenbaeumer, Ulrich; Negash, Tesfaye; Abdi, Amensisa [Addis Ababa Univ., Dept. of Physics, Addis Ababa (Ethiopia)

    1999-09-01

    The performance of small-scale stand-alone photovoltaic systems is tested under the climatic conditions of Addis Ababa, Ethiopia. With climatic data obtained at a station in the Rift Valley, the photovoltaic systems performance is estimated for those climatic conditions. The economics of small-scale stand-alone photovoltaic system applications under Ethiopian conditions are analysed. The potential of photovoltaics for the rural electrification of Ethiopia is discussed. (Author)

  7. A spatial method to calculate small-scale fisheries effort in data poor scenarios.

    Science.gov (United States)

    Johnson, Andrew Frederick; Moreno-Báez, Marcia; Giron-Nava, Alfredo; Corominas, Julia; Erisman, Brad; Ezcurra, Exequiel; Aburto-Oropeza, Octavio

    2017-01-01

    To gauge the collateral impacts of fishing we must know where fishing boats operate and how much they fish. Although small-scale fisheries land approximately the same amount of fish for human consumption as industrial fleets globally, methods of estimating their fishing effort are comparatively poor. We present an accessible, spatial method of calculating the effort of small-scale fisheries based on two simple measures that are available, or at least easily estimated, in even the most data-poor fisheries: the number of boats and the local coastal human population. We illustrate the method using a small-scale fisheries case study from the Gulf of California, Mexico, and show that our measure of Predicted Fishing Effort (PFE), measured as the number of boats operating in a given area per day adjusted by the number of people in local coastal populations, can accurately predict fisheries landings in the Gulf. Comparing our values of PFE to commercial fishery landings throughout the Gulf also indicates that the current number of small-scale fishing boats in the Gulf is approximately double what is required to land theoretical maximum fish biomass. Our method is fishery-type independent and can be used to quantitatively evaluate the efficacy of growth in small-scale fisheries. This new method provides an important first step towards estimating the fishing effort of small-scale fleets globally.

  8. Macroscopic High-Temperature Structural Analysis Model of Small-Scale PCHE Prototype (II)

    International Nuclear Information System (INIS)

    Song, Kee Nam; Lee, Heong Yeon; Hong, Sung Deok; Park, Hong Yoon

    2011-01-01

    The IHX (intermediate heat exchanger) of a VHTR (very high-temperature reactor) is a core component that transfers the high heat generated by the VHTR at 950 .deg. C to a hydrogen production plant. Korea Atomic Energy Research Institute manufactured a small-scale prototype of a PCHE (printed circuit heat exchanger) that was being considered as a candidate for the IHX. In this study, as a part of high-temperature structural integrity evaluation of the small-scale PCHE prototype, we carried out high-temperature structural analysis modeling and macroscopic thermal and elastic structural analysis for the small-scale PCHE prototype under small-scale gas-loop test conditions. The modeling and analysis were performed as a precedent study prior to the performance test in the small-scale gas loop. The results obtained in this study will be compared with the test results for the small-scale PCHE. Moreover, these results will be used in the design of a medium-scale PCHE prototype

  9. Health and Safety Management for Small-scale Methane Fermentation Facilities

    Science.gov (United States)

    Yamaoka, Masaru; Yuyama, Yoshito; Nakamura, Masato; Oritate, Fumiko

    In this study, we considered health and safety management for small-scale methane fermentation facilities that treat 2-5 ton of biomass daily based on several years operation experience with an approximate capacity of 5 t·d-1. We also took account of existing knowledge, related laws and regulations. There are no qualifications or licenses required for management and operation of small-scale methane fermentation facilities, even though rural sewerage facilities with a relative similar function are required to obtain a legitimate license. Therefore, there are wide variations in health and safety consciousness of the operators of small-scale methane fermentation facilities. The industrial safety and health laws are not applied to the operation of small-scale methane fermentation facilities. However, in order to safely operate a small-scale methane fermentation facility, the occupational safety and health management system that the law recommends should be applied. The aims of this paper are to clarify the risk factors in small-scale methane fermentation facilities and encourage planning, design and operation of facilities based on health and safety management.

  10. Prevalence and concentration of Salmonella and Campylobacter in the processing environment of small-scale pastured broiler farms.

    Science.gov (United States)

    Trimble, Lisa M; Alali, Walid Q; Gibson, Kristen E; Ricke, Steven C; Crandall, Philip; Jaroni, Divya; Berrang, Mark; Habteselassie, Mussie Y

    2013-11-01

    A growing niche in the locally grown food movement is the small-scale production of broiler chickens using the pasture-raised poultry production model. Limited research exists that focuses on Salmonella and Campylobacter contamination in the environment associated with on-farm processing of pasture-raised broilers. The objective of this study was to establish data relative to Salmonella and Campylobacter prevalence and concentration in soil and mortality compost resulting from prior processing waste disposal in the small-scale, on-farm broiler processing environment. Salmonella and Campylobacter concentrations were determined in soil (n = 42), compost (n = 39), and processing wastewater (PWW; n = 46) samples from 4 small broiler farms using a 3-tube most probable number (MPN) method for Salmonella and direct plating method for Campylobacter. Salmonella prevalence and concentration (mean log10 MPN per sample weight or volume) in soil [60%, 0.97 (95% CI: 0.66 to 1.27)], compost [64%, 0.95 (95% CI: 0.66 to 1.24)], and wastewater [48%, 1.29 (95% CI: 0.87 to 1.71)] were not significantly different (P > 0.05). Although Campylobacter prevalence was not significantly different by sample type (64.3, 64.3, and 45.7% in soil, compost, and PWW, respectively), the concentration (mean log10 cfu) of this pathogen was significantly lower (P poultry production waste disposal practices and provides a record of data that may serve as a guide for future improvement of these practices. Further research is needed regarding the small-scale broiler production environment in relation to improving disposal of processing waste for optimum control of human pathogens.

  11. Occurrence of Staphylococcus aureus on Farms with Small Scale Production of Raw Milk Cheeses in Poland

    Directory of Open Access Journals (Sweden)

    Jolanta G. Rola

    2016-03-01

    Full Text Available This paper describes the results of a 3-year study on the prevalence, enterotoxinogenicity and resistance to antimicrobials of S. aureus isolated on dairy farms with small scale production of raw cow milk cheeses. The samples of raw milk, semi-finished products and the final products as well as swabs were collected between 2011 and 2013 from nine dairy farms in Poland. A total of 244 samples were examined, of which 122 (50.0% were contaminated with S. aureus including 18 of 26 (69.2% mature cheese samples with log10 CFU g−1 between <1- and 7.41. In swabs collected from the staff and production environment the highest contamination rate with coagulase positive staphylococci (CPS was detected on hands of cheese makers (4.34 log10 CFU/swab. None of the cheese samples contaminated with CPS contained staphylococcal enterotoxins (SEs. However, 55 of 122 (45.1% S. aureus isolates possessed SEs genes, mainly (26 of 55; 47.3% a combination of the sed, sej and ser genes. Furthermore, the sep (15 of 55; 27.3% as well as seg and sei (9 of 55; 16.4% genes were also identified. The remaining S. aureus isolates possessed the sea gene (one isolate, the combination of sec, seg and sei (three isolates as well as the sed, sej, sep and ser markers together (one CPS. Resistance to penicillin (62 of 122 isolates; 50.8% was the most common among the tested isolates. Some CPS were also resistant to chloramphenicol (7; 5.7% and tetracycline (5; 4.1%. The obtained results indicated that the analyzed cheeses were safe for consumers. To improve the microbiological quality of traditional cheese products more attention should be paid to animal welfare and hygiene practices during the process of cheese manufacturing in some dairy farms.

  12. Mercury Exposure Assessment and Spatial Distribution in A Ghanaian Small-Scale Gold Mining Community.

    Science.gov (United States)

    Rajaee, Mozhgon; Long, Rachel N; Renne, Elisha P; Basu, Niladri

    2015-09-01

    Mercury is utilized worldwide in artisanal and small-scale gold mining (ASGM) and may pose a risk for miners and mining communities. While a number of studies have characterized mercury in ASGM communities, most have focused on a single media and few have taken a holistic approach. Here, a multiple media exposure assessment and cross-sectional study of mercury was conducted in 2010 through 2012 in northeast Ghana with a small-scale gold mining community, Kejetia, a subsistence farming community, Gorogo, and an urban ASGM gold refinery in Bolgatanga. The objective was to assess mercury in a range of human (urine and hair) and ecological (household soil, sediment, fish, and ore) samples to increase understanding of mercury exposure pathways. All participants were interviewed on demographics, occupational and medical histories, and household characteristics. Participants included 90 women of childbearing age and 97 adults from Kejetia and 75 adults from Gorogo. Median total specific gravity-adjusted urinary, hair, and household soil mercury were significantly higher in Kejetia miners (5.18 µg/L, 0.967 µg/g, and 3.77 µg/g, respectively) than Kejetia non-miners (1.18 µg/L, 0.419 µg/g, and 2.00 µg/g, respectively) and Gorogo participants (0.154 µg/L, 0.181 µg/g, and 0.039 µg/g) in 2011. Sediment, fish, and ore Hg concentrations were below guideline values. Median soil mercury from the Bolgatanga refinery was very high (54.6 µg/g). Estimated mean mercury ingestion for Kejetia adults from soil and dust exceeded the U.S. Environmental Protection Agency reference dose (0.3 µg Hg/kg·day) for pica (0.409 µg Hg/kg·day) and geophagy (20.5 µg Hg/kg·day) scenarios. Most participants with elevated urinary and household soil mercury were miners, but some non-miners approached and exceeded guideline values, suggesting a health risk for non-mining residents living within these communities.

  13. Mercury Exposure Assessment and Spatial Distribution in A Ghanaian Small-Scale Gold Mining Community

    Directory of Open Access Journals (Sweden)

    Mozhgon Rajaee

    2015-09-01

    Full Text Available Mercury is utilized worldwide in artisanal and small-scale gold mining (ASGM and may pose a risk for miners and mining communities. While a number of studies have characterized mercury in ASGM communities, most have focused on a single media and few have taken a holistic approach. Here, a multiple media exposure assessment and cross-sectional study of mercury was conducted in 2010 through 2012 in northeast Ghana with a small-scale gold mining community, Kejetia, a subsistence farming community, Gorogo, and an urban ASGM gold refinery in Bolgatanga. The objective was to assess mercury in a range of human (urine and hair and ecological (household soil, sediment, fish, and ore samples to increase understanding of mercury exposure pathways. All participants were interviewed on demographics, occupational and medical histories, and household characteristics. Participants included 90 women of childbearing age and 97 adults from Kejetia and 75 adults from Gorogo. Median total specific gravity-adjusted urinary, hair, and household soil mercury were significantly higher in Kejetia miners (5.18 µg/L, 0.967 µg/g, and 3.77 µg/g, respectively than Kejetia non-miners (1.18 µg/L, 0.419 µg/g, and 2.00 µg/g, respectively and Gorogo participants (0.154 µg/L, 0.181 µg/g, and 0.039 µg/g in 2011. Sediment, fish, and ore Hg concentrations were below guideline values. Median soil mercury from the Bolgatanga refinery was very high (54.6 µg/g. Estimated mean mercury ingestion for Kejetia adults from soil and dust exceeded the U.S. Environmental Protection Agency reference dose (0.3 µg Hg/kg·day for pica (0.409 µg Hg/kg·day and geophagy (20.5 µg Hg/kg·day scenarios. Most participants with elevated urinary and household soil mercury were miners, but some non-miners approached and exceeded guideline values, suggesting a health risk for non-mining residents living within these communities.

  14. Mercury Exposure Assessment and Spatial Distribution in A Ghanaian Small-Scale Gold Mining Community

    Science.gov (United States)

    Rajaee, Mozhgon; Long, Rachel N.; Renne, Elisha P.; Basu, Niladri

    2015-01-01

    Mercury is utilized worldwide in artisanal and small-scale gold mining (ASGM) and may pose a risk for miners and mining communities. While a number of studies have characterized mercury in ASGM communities, most have focused on a single media and few have taken a holistic approach. Here, a multiple media exposure assessment and cross-sectional study of mercury was conducted in 2010 through 2012 in northeast Ghana with a small-scale gold mining community, Kejetia, a subsistence farming community, Gorogo, and an urban ASGM gold refinery in Bolgatanga. The objective was to assess mercury in a range of human (urine and hair) and ecological (household soil, sediment, fish, and ore) samples to increase understanding of mercury exposure pathways. All participants were interviewed on demographics, occupational and medical histories, and household characteristics. Participants included 90 women of childbearing age and 97 adults from Kejetia and 75 adults from Gorogo. Median total specific gravity-adjusted urinary, hair, and household soil mercury were significantly higher in Kejetia miners (5.18 µg/L, 0.967 µg/g, and 3.77 µg/g, respectively) than Kejetia non-miners (1.18 µg/L, 0.419 µg/g, and 2.00 µg/g, respectively) and Gorogo participants (0.154 µg/L, 0.181 µg/g, and 0.039 µg/g) in 2011. Sediment, fish, and ore Hg concentrations were below guideline values. Median soil mercury from the Bolgatanga refinery was very high (54.6 µg/g). Estimated mean mercury ingestion for Kejetia adults from soil and dust exceeded the U.S. Environmental Protection Agency reference dose (0.3 µg Hg/kg·day) for pica (0.409 µg Hg/kg·day) and geophagy (20.5 µg Hg/kg·day) scenarios. Most participants with elevated urinary and household soil mercury were miners, but some non-miners approached and exceeded guideline values, suggesting a health risk for non-mining residents living within these communities. PMID:26340636

  15. Effects of sampling conditions on DNA-based estimates of American black bear abundance

    Science.gov (United States)

    Laufenberg, Jared S.; Van Manen, Frank T.; Clark, Joseph D.

    2013-01-01

    DNA-based capture-mark-recapture techniques are commonly used to estimate American black bear (Ursus americanus) population abundance (N). Although the technique is well established, many questions remain regarding study design. In particular, relationships among N, capture probability of heterogeneity mixtures A and B (pA and pB, respectively, or p, collectively), the proportion of each mixture (π), number of capture occasions (k), and probability of obtaining reliable estimates of N are not fully understood. We investigated these relationships using 1) an empirical dataset of DNA samples for which true N was unknown and 2) simulated datasets with known properties that represented a broader array of sampling conditions. For the empirical data analysis, we used the full closed population with heterogeneity data type in Program MARK to estimate N for a black bear population in Great Smoky Mountains National Park, Tennessee. We systematically reduced the number of those samples used in the analysis to evaluate the effect that changes in capture probabilities may have on parameter estimates. Model-averaged N for females and males were 161 (95% CI = 114–272) and 100 (95% CI = 74–167), respectively (pooled N = 261, 95% CI = 192–419), and the average weekly p was 0.09 for females and 0.12 for males. When we reduced the number of samples of the empirical data, support for heterogeneity models decreased. For the simulation analysis, we generated capture data with individual heterogeneity covering a range of sampling conditions commonly encountered in DNA-based capture-mark-recapture studies and examined the relationships between those conditions and accuracy (i.e., probability of obtaining an estimated N that is within 20% of true N), coverage (i.e., probability that 95% confidence interval includes true N), and precision (i.e., probability of obtaining a coefficient of variation ≤20%) of estimates using logistic regression. The capture probability

  16. Rapid, sensitive and cost effective method for isolation of viral DNA from feacal samples of dogs

    Directory of Open Access Journals (Sweden)

    Savi.

    2010-06-01

    Full Text Available A simple method for viral DNA extraction using chelex resin was developed. The method used was eco-friendly and cost effective compared to other methods such as phenol chloroform method which use health hazardous organic reagents. Further, a polymerase chain reaction (PCR based detection of canine parvovirus (CPV using primers from conserved region of VP2 gene was developed. To increase the sensitivity and specificity of reaction, nested PCR was designed. PCR reaction was optimized to amplify 747bp product of VP2 gene. The assay can be completed in few hours and doesn’t need hazardous chemicals. Thus, the sample preparation using chelating resin along with nested PCR seems to be a sensitive, specific and practical method for the detection of CPV in diarrhoeal feacal samples. [Vet. World 2010; 3(3.000: 105-106

  17. Detection of multidrug-resistant tuberculosis from stored DNA Samples: A multicenter study

    Directory of Open Access Journals (Sweden)

    Marie Sylvianne Rabodoarivelo

    2018-01-01

    Full Text Available Background: In low-income countries, rapid detection of tuberculosis (TB drug resistance is often restricted by the difficulties of transporting and storing sputum samples from remote health centers to the reference laboratories where molecular tests are available. The aim of this study was to evaluate the performance of four transport and storage systems for molecular detection of rifampicin (RIF and isoniazid (INH resistance. Methods: This was a multicenter study. Molecular detection of RIF and INH resistance was performed directly from smear-positive TB sputa spotted on a slide, FTA card, GenoCard, and ethanol using the Genotype MTBDRplus assay. The performance of the DNA extraction method from each storage support to detect drug resistance was assessed by calculating their sensitivity and specificity compared to the phenotypic method. Results: From all sites, the overall sensitivity and specificity for RIF-resistance detection was 88% and 85%, respectively, for slides, 86% and 92%, respectively, for GenoCard, 87% and 89%, respectively, for FTA card, and 88% and 92%, respectively, for ethanol. For INH-resistance detection, the overall sensitivity and specificity was 82% and 90%, respectively, for slides, 85% and 96%, respectively, for GenoCard, 86% and 92%, respectively, for FTA card, and 86% and 94%, respectively, for ethanol. Conclusion: Smear slides and filter cards showed to be very useful tools to facilitate DNA extraction from sputum samples with the potential to accelerate the detection of drug resistance in remote areas.

  18. Detection of multidrug-resistant tuberculosis from stored DNA Samples: A multicenter study.

    Science.gov (United States)

    Rabodoarivelo, Marie Sylvianne; Brandao, A; Cergole Novella, M C; C Bombonatte, A G; Imperiale, B; Rakotosamimanana, N; Morcillo, N; Rasolofo, V; Palomino, J C; Martin, A

    2018-01-01

    In low-income countries, rapid detection of tuberculosis (TB) drug resistance is often restricted by the difficulties of transporting and storing sputum samples from remote health centers to the reference laboratories where molecular tests are available. The aim of this study was to evaluate the performance of four transport and storage systems for molecular detection of rifampicin (RIF) and isoniazid (INH) resistance. This was a multicenter study. Molecular detection of RIF and INH resistance was performed directly from smear-positive TB sputa spotted on a slide, FTA card, GenoCard, and ethanol using the Genotype MTBDRplus assay. The performance of the DNA extraction method from each storage support to detect drug resistance was assessed by calculating their sensitivity and specificity compared to the phenotypic method. From all sites, the overall sensitivity and specificity for RIF-resistance detection was 88% and 85%, respectively, for slides, 86% and 92%, respectively, for GenoCard, 87% and 89%, respectively, for FTA card, and 88% and 92%, respectively, for ethanol. For INH-resistance detection, the overall sensitivity and specificity was 82% and 90%, respectively, for slides, 85% and 96%, respectively, for GenoCard, 86% and 92%, respectively, for FTA card, and 86% and 94%, respectively, for ethanol. Smear slides and filter cards showed to be very useful tools to facilitate DNA extraction from sputum samples with the potential to accelerate the detection of drug resistance in remote areas.

  19. Removal of micro-organisms in a small-scale hydroponics wastewater treatment system.

    Science.gov (United States)

    Ottoson, J; Norström, A; Dalhammar, G

    2005-01-01

    To measure the microbial removal capacity of a small-scale hydroponics wastewater treatment plant. Paired samples were taken from untreated, partly-treated and treated wastewater and analysed for faecal microbial indicators, i.e. coliforms, Escherichia coli, enterococci, Clostridium perfringens spores and somatic coliphages, by culture based methods. Escherichia coli was never detected in effluent water after >5.8-log removal. Enterococci, coliforms, spores and coliphages were removed by 4.5, 4.1, 2.3 and 2.5 log respectively. Most of the removal (60-87%) took place in the latter part of the system because of settling, normal inactivation (retention time 12.7 d) and sand filtration. Time-dependent log-linear removal was shown for spores (k = -0.17 log d(-1), r(2) = 0.99). Hydroponics wastewater treatment removed micro-organisms satisfactorily. Investigations on the microbial removal capacity of hydroponics have only been performed for bacterial indicators. In this study it has been shown that virus and (oo)cyst process indicators were removed and that hydroponics can be an alternative to conventional wastewater treatment.

  20. Small-Scale Ion Exchange Removal of Cesium and Technetium from Hanford Tank 241-AN-102

    International Nuclear Information System (INIS)

    Hassan, N.M.

    2000-01-01

    The pretreatment process for BNFL, Inc.'s Hanford River Protection Project is to provide decontaminated low activity waste and concentrated eluate streams for vitrification into low and high activity waste glass, respectively. The pretreatment includes sludge washing, filtration, precipitation, and ion exchange processes to remove entrained solids, cesium, transuranics, technetium, and strontium. The cesium (Cs-137) and technetium (Tc-99) ion exchange removal is accomplished by using SuperLig 644, and 639 resins from IBC Advanced Technologies, American Fork, Utah. The resins were shown to selectively remove cesium and technetium (as anionic pertechnetate ) from alkaline salt solutions. The efficiency of ion exchange column loading and elution is a complex function involving feed compositions, equilibrium and kinetic behavior of ion exchange resins, diffusion, and the ionic strength and pH of the aqueous solution. A previous experimental program completed at the Savannah River Tech nology Center2 demonstrated the conceptualized flow sheet parameters with an Envelope C sample from Hanford Tank 241-AN-107. Those experiments also included determination of Cs and Tc batch distribution coefficients by SuperLig 644 and 639 resins and demonstration of small-scale column breakthrough and elution. The experimental findings were used in support of preliminary design bases and pretreatment flow sheet development by BNFL, Inc

  1. N2O emission hotspots at different spatial scales and governing factors for small scale hotspots

    International Nuclear Information System (INIS)

    Heuvel, R.N. van den; Hefting, M.M.; Tan, N.C.G.; Jetten, M.S.M.; Verhoeven, J.T.A.

    2009-01-01

    Chronically nitrate-loaded riparian buffer zones show high N 2 O emissions. Often, a large part of the N 2 O is emitted from small surface areas, resulting in high spatial variability in these buffer zones. These small surface areas with high N 2 O emissions (hotspots) need to be investigated to generate knowledge on the factors governing N 2 O emissions. In this study the N 2 O emission variability was investigated at different spatial scales. Therefore N 2 O emissions from three 32 m 2 grids were determined in summer and winter. Spatial variation and total emission were determined on three different scales (0.3 m 2 , 0.018 m 2 and 0.0013 m 2 ) at plots with different levels of N 2 O emissions. Spatial variation was high at all scales determined and highest at the smallest scale. To test possible factors inducing small scale hotspots, soil samples were collected for slurry incubation to determine responses to increased electron donor/acceptor availability. Acetate addition did increase N 2 O production, but nitrate addition failed to increase total denitrification or net N 2 O production. N 2 O production was similar in all soil slurries, independent of their origin from high or low emission soils, indicating that environmental conditions (including physical factors like gas diffusion) rather than microbial community composition governed N 2 O emission rates

  2. Impact of improved technologies on small-scale soybean production: empirical evidence from benue state, nigeria

    International Nuclear Information System (INIS)

    Adisa, R.S.; Balogun, K.S.

    2013-01-01

    The study examined the impact of improved technologies on the lives of small-scale soybean farmers in Benue State, Nigeria. A total of 160 respondents were selected using simple random sampling technique. Data were analyzed using descriptive statistics, Tobit model and the Kruskal-Wallis test. Findings revealed that 35.6% of the respondents were between 31 and 40 years old, 40.6% had household size of between 6 and 10 members. Majority of the respondents were male, married, and had secondary school education. Tobit analysis revealed that farmers socioeconomic characteristics which include gender, educational status and farming experience; and farmers knowledge on soybean innovations were significant factors determining the adoption of improved soybean production technologies. These factors were statistically significant at p=0.05. The adoption of improved soybean technologies has had a clear positive impact on farmers belief on soybean innovations. The major problems facing farmers in the adoption of improved soybean production technologies according to Kruskal-Wallis ranking were high cost of inputs, problem of labour availability and lack of credit/loan. The results of this study provide a strong case for the promotion of soybean as a solution for malnutrition and a means of poverty alleviation for poor people. (author)

  3. Applicability of two mobile analysers for mercury in urine in small-scale gold mining areas.

    Science.gov (United States)

    Baeuml, Jennifer; Bose-O'Reilly, Stephan; Lettmeier, Beate; Maydl, Alexandra; Messerer, Katalin; Roider, Gabriele; Drasch, Gustav; Siebert, Uwe

    2011-12-01

    Mercury is still used in developing countries to extract gold from the ore in small-scale gold mining areas. This is a major health hazard for people living in mining areas. The concentration of mercury in urine was analysed in different mining areas in Zimbabwe, Indonesia and Tanzania. First the urine samples were analysed by CV-AAS (cold vapour atomic absorption spectrometry) during the field projects with a mobile mercury analyser (Lumex(®) or Seefelder(®)) and secondly, in a laboratory with a stationary CV-AAS mercury analyser (PerkinElmer(®)). Caused by the different systems (reduction agent either SnCl(2) (Lumex(®) or Seefelder(®))) or NaBH(4) (PerkinElmer(®)), with the mobile analysers only the inorganic mercury was obtained and with the stationary system the total mercury concentration was measured. The aims of the study were whether the results obtained in field with the mobile equipments can be compared with the stationary reference method in the laboratory and allow the application of these mobile analysers in screening studies on concerned populations to select those, who are exposed to critical mercury levels. Overall, the concentrations obtained with the two mobile systems were approximately 25% lower than determined with the stationary system. Nevertheless, both mobile systems seem to be very useful for screening of volunteers in field. Moreover, regional staff may be trained on such analysers to perform screening tests by themselves. Copyright © 2011 Elsevier GmbH. All rights reserved.

  4. Small-scale, self-propagating combustion realized with on-chip porous silicon.

    Science.gov (United States)

    Piekiel, Nicholas W; Morris, Christopher J

    2015-05-13

    For small-scale energy applications, energetic materials represent a high energy density source that, in certain cases, can be accessed with a very small amount of energy input. Recent advances in microprocessing techniques allow for the implementation of a porous silicon energetic material onto a crystalline silicon wafer at the microscale; however, combustion at a small length scale remains to be fully investigated, particularly with regards to the limitations of increased relative heat loss during combustion. The present study explores the critical dimensions of an on-chip porous silicon energetic material (porous silicon + sodium perchlorate (NaClO4)) required to propagate combustion. We etched ∼97 μm wide and ∼45 μm deep porous silicon channels that burned at a steady rate of 4.6 m/s, remaining steady across 90° changes in direction. In an effort to minimize the potential on-chip footprint for energetic porous silicon, we also explored the minimum spacing between porous silicon channels. We demonstrated independent burning of porous silicon channels at a spacing of 0.5 m on a chip surface area of 1.65 cm(2). Smaller porous silicon channels of ∼28 μm wide and ∼14 μm deep were also utilized. These samples propagated combustion, but at times, did so unsteadily. This result may suggest that we are approaching a critical length scale for self-propagating combustion in a porous silicon energetic material.

  5. Comparative Study of Seven Commercial Kits for Human DNA Extraction from Urine Samples Suitable for DNA Biomarker-Based Public Health Studies

    Science.gov (United States)

    El Bali, Latifa; Diman, Aurélie; Bernard, Alfred; Roosens, Nancy H. C.; De Keersmaecker, Sigrid C. J.

    2014-01-01

    Human genomic DNA extracted from urine could be an interesting tool for large-scale public health studies involving characterization of genetic variations or DNA biomarkers as a result of the simple and noninvasive collection method. These studies, involving many samples, require a rapid, easy, and standardized extraction protocol. Moreover, for practicability, there is a necessity to collect urine at a moment different from the first void and to store it appropriately until analysis. The present study compared seven commercial kits to select the most appropriate urinary human DNA extraction procedure for epidemiological studies. DNA yield has been determined using different quantification methods: two classical, i.e., NanoDrop and PicoGreen, and two species-specific real-time quantitative (q)PCR assays, as DNA extracted from urine contains, besides human, microbial DNA also, which largely contributes to the total DNA yield. In addition, the kits giving a good yield were also tested for the presence of PCR inhibitors. Further comparisons were performed regarding the sampling time and the storage conditions. Finally, as a proof-of-concept, an important gene related to smoking has been genotyped using the developed tools. We could select one well-performing kit for the human DNA extraction from urine suitable for molecular diagnostic real-time qPCR-based assays targeting genetic variations, applicable to large-scale studies. In addition, successful genotyping was possible using DNA extracted from urine stored at −20°C for several months, and an acceptable yield could also be obtained from urine collected at different moments during the day, which is particularly important for public health studies. PMID:25365790

  6. Comparative study of seven commercial kits for human DNA extraction from urine samples suitable for DNA biomarker-based public health studies.

    Science.gov (United States)

    El Bali, Latifa; Diman, Aurélie; Bernard, Alfred; Roosens, Nancy H C; De Keersmaecker, Sigrid C J

    2014-12-01

    Human genomic DNA extracted from urine could be an interesting tool for large-scale public health studies involving characterization of genetic variations or DNA biomarkers as a result of the simple and noninvasive collection method. These studies, involving many samples, require a rapid, easy, and standardized extraction protocol. Moreover, for practicability, there is a necessity to collect urine at a moment different from the first void and to store it appropriately until analysis. The present study compared seven commercial kits to select the most appropriate urinary human DNA extraction procedure for epidemiological studies. DNA yield has been determined using different quantification methods: two classical, i.e., NanoDrop and PicoGreen, and two species-specific real-time quantitative (q)PCR assays, as DNA extracted from urine contains, besides human, microbial DNA also, which largely contributes to the total DNA yield. In addition, the kits giving a good yield were also tested for the presence of PCR inhibitors. Further comparisons were performed regarding the sampling time and the storage conditions. Finally, as a proof-of-concept, an important gene related to smoking has been genotyped using the developed tools. We could select one well-performing kit for the human DNA extraction from urine suitable for molecular diagnostic real-time qPCR-based assays targeting genetic variations, applicable to large-scale studies. In addition, successful genotyping was possible using DNA extracted from urine stored at -20°C for several months, and an acceptable yield could also be obtained from urine collected at different moments during the day, which is particularly important for public health studies.

  7. Application of the CometChip platform to assess DNA damage in field-collected blood samples from turtles.

    Science.gov (United States)

    Sykora, Peter; Chiari, Ylenia; Heaton, Andrew; Moreno, Nickolas; Glaberman, Scott; Sobol, Robert W

    2018-05-01

    DNA damage has been linked to genomic instability and the progressive breakdown of cellular and organismal homeostasis, leading to the onset of disease and reduced longevity. Insults to DNA from endogenous sources include base deamination, base hydrolysis, base alkylation, and metabolism-induced oxidative damage that can lead to single-strand and double-strand DNA breaks. Alternatively, exposure to environmental pollutants, radiation or ultra-violet light, can also contribute to exogenously derived DNA damage. We previously validated a novel, high through-put approach to measure levels of DNA damage in cultured mammalian cells. This new CometChip Platform builds on the classical single cell gel electrophoresis or comet methodology used extensively in environmental toxicology and molecular biology. We asked whether the CometChip Platform could be used to measure DNA damage in samples derived from environmental field studies. To this end, we determined that nucleated erythrocytes from multiple species of turtle could be successfully evaluated in the CometChip Platform to quantify levels of DNA damage. In total, we compared levels of DNA damage in 40 animals from two species: the box turtle (Terrapene carolina) and the red-eared slider (Trachemys scripta elegans). Endogenous levels of DNA damage were identical between the two species, yet we did discover some sex-linked differences and changes in DNA damage accumulation. Based on these results, we confirm that the CometChip Platform allows for the measurement of DNA damage in a large number of samples quickly and accurately, and is particularly adaptable to environmental studies using field-collected samples. Environ. Mol. Mutagen. 59:322-333, 2018. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

  8. Reverse sample genome probing, a new technique for identification of bacteria in environmental samples by DNA hybridization, and its application to the identification of sulfate-reducing bacteria in oil field samples

    International Nuclear Information System (INIS)

    Voordouw, G.; Voordouw, J.K.; Karkhoff-Schweizer, R.R.; Fedorak, P.M.; Westlake, D.W.S.

    1991-01-01

    A novel method for identification of bacteria in environmental samples by DNA hybridization is presented. It is based on the fact that, even within a genus, the genomes of different bacteria may have little overall sequence homology. This allows the use of the labeled genomic DNA of a given bacterium (referred to as a standard) to probe for its presence and that of bacteria with highly homologous genomes in total DNA obtained from an environmental sample. Alternatively, total DNA extracted from the sample can be labeled and used to probe filters on which denatured chromosomal DNA from relevant bacterial standards has been spotted. The latter technique is referred to as reverse sample genome probing, since it is the reverse of the usual practice of deriving probes from reference bacteria for analyzing a DNA sample. Reverse sample genome probing allows identification of bacteria in a sample in a single step once a master filter with suitable standards has been developed. Application of reverse sample genome probing to the identification of sulfate-reducing bacteria in 31 samples obtained primarily from oil fields in the province of Alberta has indicated that there are at least 20 genotypically different sulfate-reducing bacteria in these samples

  9. Critical points of DNA quantification by real-time PCR – effects of DNA extraction method and sample matrix on quantification of genetically modified organisms

    Directory of Open Access Journals (Sweden)

    Žel Jana

    2006-08-01

    Full Text Available Abstract Background Real-time PCR is the technique of choice for nucleic acid quantification. In the field of detection of genetically modified organisms (GMOs quantification of biotech products may be required to fulfil legislative requirements. However, successful quantification depends crucially on the quality of the sample DNA analyzed. Methods for GMO detection are generally validated on certified reference materials that are in the form of powdered grain material, while detection in routine laboratories must be performed on a wide variety of sample matrixes. Due to food processing, the DNA in sample matrixes can be present in low amounts and also degraded. In addition, molecules of plant origin or from other sources that affect PCR amplification of samples will influence the reliability of the quantification. Further, the wide variety of sample matrixes presents a challenge for detection laboratories. The extraction method must ensure high yield and quality of the DNA obtained and must be carefully selected, since even components of DNA extraction solutions can influence PCR reactions. GMO quantification is based on a standard curve, therefore similarity of PCR efficiency for the sample and standard reference material is a prerequisite for exact quantification. Little information on the performance of real-time PCR on samples of different matrixes is available. Results Five commonly used DNA extraction techniques were compared and their suitability for quantitative analysis was assessed. The effect of sample matrix on nucleic acid quantification was assessed by comparing 4 maize and 4 soybean matrixes. In addition 205 maize and soybean samples from routine analysis were analyzed for PCR efficiency to assess variability of PCR performance within each sample matrix. Together with the amount of DNA needed for reliable quantification, PCR efficiency is the crucial parameter determining the reliability of quantitative results, therefore it was

  10. Critical points of DNA quantification by real-time PCR--effects of DNA extraction method and sample matrix on quantification of genetically modified organisms.

    Science.gov (United States)

    Cankar, Katarina; Stebih, Dejan; Dreo, Tanja; Zel, Jana; Gruden, Kristina

    2006-08-14

    Real-time PCR is the technique of choice for nucleic acid quantification. In the field of detection of genetically modified organisms (GMOs) quantification of biotech products may be required to fulfil legislative requirements. However, successful quantification depends crucially on the quality of the sample DNA analyzed. Methods for GMO detection are generally validated on certified reference materials that are in the form of powdered grain material, while detection in routine laboratories must be performed on a wide variety of sample matrixes. Due to food processing, the DNA in sample matrixes can be present in low amounts and also degraded. In addition, molecules of plant origin or from other sources that affect PCR amplification of samples will influence the reliability of the quantification. Further, the wide variety of sample matrixes presents a challenge for detection laboratories. The extraction method must ensure high yield and quality of the DNA obtained and must be carefully selected, since even components of DNA extraction solutions can influence PCR reactions. GMO quantification is based on a standard curve, therefore similarity of PCR efficiency for the sample and standard reference material is a prerequisite for exact quantification. Little information on the performance of real-time PCR on samples of different matrixes is available. Five commonly used DNA extraction techniques were compared and their suitability for quantitative analysis was assessed. The effect of sample matrix on nucleic acid quantification was assessed by comparing 4 maize and 4 soybean matrixes. In addition 205 maize and soybean samples from routine analysis were analyzed for PCR efficiency to assess variability of PCR performance within each sample matrix. Together with the amount of DNA needed for reliable quantification, PCR efficiency is the crucial parameter determining the reliability of quantitative results, therefore it was chosen as the primary criterion by which to

  11. Critical points of DNA quantification by real-time PCR – effects of DNA extraction method and sample matrix on quantification of genetically modified organisms

    Science.gov (United States)

    Cankar, Katarina; Štebih, Dejan; Dreo, Tanja; Žel, Jana; Gruden, Kristina

    2006-01-01

    Background Real-time PCR is the technique of choice for nucleic acid quantification. In the field of detection of genetically modified organisms (GMOs) quantification of biotech products may be required to fulfil legislative requirements. However, successful quantification depends crucially on the quality of the sample DNA analyzed. Methods for GMO detection are generally validated on certified reference materials that are in the form of powdered grain material, while detection in routine laboratories must be performed on a wide variety of sample matrixes. Due to food processing, the DNA in sample matrixes can be present in low amounts and also degraded. In addition, molecules of plant origin or from other sources that affect PCR amplification of samples will influence the reliability of the quantification. Further, the wide variety of sample matrixes presents a challenge for detection laboratories. The extraction method must ensure high yield and quality of the DNA obtained and must be carefully selected, since even components of DNA extraction solutions can influence PCR reactions. GMO quantification is based on a standard curve, therefore similarity of PCR efficiency for the sample and standard reference material is a prerequisite for exact quantification. Little information on the performance of real-time PCR on samples of different matrixes is available. Results Five commonly used DNA extraction techniques were compared and their suitability for quantitative analysis was assessed. The effect of sample matrix on nucleic acid quantification was assessed by comparing 4 maize and 4 soybean matrixes. In addition 205 maize and soybean samples from routine analysis were analyzed for PCR efficiency to assess variability of PCR performance within each sample matrix. Together with the amount of DNA needed for reliable quantification, PCR efficiency is the crucial parameter determining the reliability of quantitative results, therefore it was chosen as the primary

  12. An economical mtDNA SNP assay detecting different mitochondrial haplogroups in identical HVR 1 samples of Caucasian ancestry.

    Science.gov (United States)

    Köhnemann, Stephan; Hohoff, Carsten; Pfeiffer, Heidi

    2009-09-01

    We had sequenced 329 Caucasian samples in Hypervariable Region 1 (HVR 1) and found that they belong to eleven different mitochondrial DNA (mtDNA) haplotypes. The sample set was further analysed by an mtDNA assay examining 32 single nucleotide polymorphisms (SNPs) for haplogroup discrimination. In a validation study on 160 samples of different origin it was shown that these SNPs were able to discriminate between the evolved superhaplogroups worldwide (L, M and N) and between the nine most common Caucasian haplogroups (H, I, J, K, T, U, V, W and X). The 32 mtDNA SNPs comprised 42 different SNP haplotypes instead of only eleven haplotypes after HVR 1 sequencing. The assay provided stable results in a range of 5ng genomic DNA down to virtually no genomic DNA per reaction. It was possible to detect samples of African, Asian and Eurasian ancestry, respectively. The 32 mtDNA SNP assay is a helpful adjunct to further distinguish between identical HVR 1 sequences of Caucasian origin. Our results suggest that haplogroup prediction using HVR 1 sequencing provides instable results. The use of coding region SNPs for haplogroup assignment is more suited than using HVR 1 haplotypes.

  13. The effect of DNA degradation bias in passive sampling devices on metabarcoding studies of arthropod communities and their associated microbiota.

    Science.gov (United States)

    Krehenwinkel, Henrik; Fong, Marisa; Kennedy, Susan; Huang, Edward Greg; Noriyuki, Suzuki; Cayetano, Luis; Gillespie, Rosemary

    2018-01-01

    PCR amplification bias is a well-known problem in metagenomic analysis of arthropod communities. In contrast, variation of DNA degradation rates is a largely neglected source of bias. Differential degradation of DNA molecules could cause underrepresentation of taxa in a community sequencing sample. Arthropods are often collected by passive sampling devices, like malaise traps. Specimens in such a trap are exposed to varying periods of suboptimal storage and possibly different rates of DNA degradation. Degradation bias could thus be a significant issue, skewing diversity estimates. Here, we estimate the effect of differential DNA degradation on the recovery of community diversity of Hawaiian arthropods and their associated microbiota. We use a simple DNA size selection protocol to test for degradation bias in mock communities, as well as passively collected samples from actual Malaise traps. We compare the effect of DNA degradation to that of varying PCR conditions, including primer choice, annealing temperature and cycle number. Our results show that DNA degradation does indeed bias community analyses. However, the effect of this bias is of minor importance compared to that induced by changes in PCR conditions. Analyses of the macro and microbiome from passively collected arthropod samples are thus well worth pursuing.

  14. International study to evaluate PCR methods for detection of Trypanosoma cruzi DNA in blood samples from Chagas disease patients.

    Directory of Open Access Journals (Sweden)

    Alejandro G Schijman

    Full Text Available BACKGROUND: A century after its discovery, Chagas disease still represents a major neglected tropical threat. Accurate diagnostics tools as well as surrogate markers of parasitological response to treatment are research priorities in the field. The purpose of this study was to evaluate the performance of PCR methods in detection of Trypanosoma cruzi DNA by an external quality evaluation. METHODOLOGY/FINDINGS: An international collaborative study was launched by expert PCR laboratories from 16 countries. Currently used strategies were challenged against serial dilutions of purified DNA from stocks representing T. cruzi discrete typing units (DTU I, IV and VI (set A, human blood spiked with parasite cells (set B and Guanidine Hidrochloride-EDTA blood samples from 32 seropositive and 10 seronegative patients from Southern Cone countries (set C. Forty eight PCR tests were reported for set A and 44 for sets B and C; 28 targeted minicircle DNA (kDNA, 13 satellite DNA (Sat-DNA and the remainder low copy number sequences. In set A, commercial master mixes and Sat-DNA Real Time PCR showed better specificity, but kDNA-PCR was more sensitive to detect DTU I DNA. In set B, commercial DNA extraction kits presented better specificity than solvent extraction protocols. Sat-DNA PCR tests had higher specificity, with sensitivities of 0.05-0.5 parasites/mL whereas specific kDNA tests detected 5.10(-3 par/mL. Sixteen specific and coherent methods had a Good Performance in both sets A and B (10 fg/µl of DNA from all stocks, 5 par/mL spiked blood. The median values of sensitivities, specificities and accuracies obtained in testing the Set C samples with the 16 tests determined to be good performing by analyzing Sets A and B samples varied considerably. Out of them, four methods depicted the best performing parameters in all three sets of samples, detecting at least 10 fg/µl for each DNA stock, 0.5 par/mL and a sensitivity between 83.3-94.4%, specificity of 85

  15. Small-scale variability in peatland pore-water biogeochemistry, Hudson Bay Lowland, Canada.

    Science.gov (United States)

    Ulanowski, T A; Branfireun, B A

    2013-06-01

    The Hudson Bay Lowland (HBL) of northern Ontario, Manitoba and Quebec, Canada is the second largest contiguous peatland complex in the world, currently containing more than half of Canada's soil carbon. Recent concerns about the ecohydrological impacts to these large northern peatlands resulting from climate change and resource extraction have catalyzed a resurgence in scientific research into this ecologically important region. However, the sheer size, heterogeneity and elaborate landscape arrangements of this ecosystem raise important questions concerning representative sampling of environmental media for chemical or physical characterization. To begin to quantify such variability, this study assessed the small-scale spatial (1m) and short temporal (21 day) variability of surface pore-water biogeochemistry (pH, dissolved organic carbon, and major ions) in a Sphagnum spp.-dominated, ombrotrophic raised bog, and a Carex spp.-dominated intermediate fen in the HBL. In general, pore-water pH and concentrations of dissolved solutes were similar to previously reported literature values from this region. However, systematic sampling revealed consistent statistically significant differences in pore-water chemistries between the bog and fen peatland types, and large within-site spatiotemporal variability. We found that microtopography in the bog was associated with consistent differences in most biogeochemical variables. Temporal changes in dissolved solute chemistry, particularly base cations (Na(+), Ca(2+) and Mg(2+)), were statistically significant in the intermediate fen, likely a result of a dynamic connection between surficial waters and mineral-rich deep groundwater. In both the bog and fen, concentrations of SO4(2-) showed considerable spatial variability, and a significant decrease in concentrations over the study period. The observed variability in peatland pore-water biogeochemistry over such small spatial and temporal scales suggests that under-sampling in

  16. Forensic genetic SNP typing of low-template DNA and highly degraded DNA from crime case samples

    DEFF Research Database (Denmark)

    Børsting, Claus; Mogensen, Helle Smidt; Morling, Niels

    2013-01-01

    the heterozygote balance. Allele drop-ins were only observed in experiments with 25 pg of DNA and not in experiments with 50 and 100 pg of DNA. The allele drop-in rate in the 25 pg experiments was 0.06% or 100 times lower than what was previously reported for STR typing of LtDNA. A composite model and two......Heterozygote imbalances leading to allele drop-outs and disproportionally large stutters leading to allele drop-ins are known stochastic phenomena related to STR typing of low-template DNA (LtDNA). The large stutters and the many drop-ins in typical STR stutter positions are artifacts from the PCR...... amplification of tandem repeats. These artifacts may be avoided by typing bi-allelic markers instead of STRs. In this work, the SNPforID multiplex assay was used to type LtDNA. A sensitized SNP typing protocol was introduced, that increased signal strengths without increasing noise and without affecting...

  17. High Throughput Sample Preparation and Analysis for DNA Sequencing, PCR and Combinatorial Screening of Catalysis Based on Capillary Array Technique

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yonghua [Iowa State Univ., Ames, IA (United States)

    2000-01-01

    Sample preparation has been one of the major bottlenecks for many high throughput analyses. The purpose of this research was to develop new sample preparation and integration approach for DNA sequencing, PCR based DNA analysis and combinatorial screening of homogeneous catalysis based on multiplexed capillary electrophoresis with laser induced fluorescence or imaging UV absorption detection. The author first introduced a method to integrate the front-end tasks to DNA capillary-array sequencers. protocols for directly sequencing the plasmids from a single bacterial colony in fused-silica capillaries were developed. After the colony was picked, lysis was accomplished in situ in the plastic sample tube using either a thermocycler or heating block. Upon heating, the plasmids were released while chromsomal DNA and membrane proteins were denatured and precipitated to the bottom of the tube. After adding enzyme and Sanger reagents, the resulting solution was aspirated into the reaction capillaries by a syringe pump, and cycle sequencing was initiated. No deleterious effect upon the reaction efficiency, the on-line purification system, or the capillary electrophoresis separation was observed, even though the crude lysate was used as the template. Multiplexed on-line DNA sequencing data from 8 parallel channels allowed base calling up to 620 bp with an accuracy of 98%. The entire system can be automatically regenerated for repeated operation. For PCR based DNA analysis, they demonstrated that capillary electrophoresis with UV detection can be used for DNA analysis starting from clinical sample without purification. After PCR reaction using cheek cell, blood or HIV-1 gag DNA, the reaction mixtures was injected into the capillary either on-line or off-line by base stacking. The protocol was also applied to capillary array electrophoresis. The use of cheaper detection, and the elimination of purification of DNA sample before or after PCR reaction, will make this approach an

  18. Hepatitis B virus DNA quantification with the three-in-one (3io) method allows accurate single-step differentiation of total HBV DNA and cccDNA in biopsy-size liver samples.

    Science.gov (United States)

    Taranta, Andrzej; Tien Sy, Bui; Zacher, Behrend Johan; Rogalska-Taranta, Magdalena; Manns, Michael Peter; Bock, Claus Thomas; Wursthorn, Karsten

    2014-08-01

    Hepatitis B virus (HBV) replicates via reverse transcription converting its partially double stranded genome into the covalently closed circular DNA (cccDNA). The long-lasting cccDNA serves as a replication intermediate in the nuclei of hepatocytes. It is an excellent, though evasive, parameter for monitoring the course of liver disease and treatment efficiency. To develop and test a new approach for HBV DNA quantification in serum and small-size liver samples. The p3io plasmid contains an HBV fragment and human β-actin gene (hACTB) as a standard. Respective TaqMan probes were labeled with different fluorescent dyes. A triplex real-time PCR for simultaneous quantification of total HBV DNA, cccDNA and hACTB could be established. Three-in-one method allows simultaneous analysis of 3 targets with a lower limit of quantification of 48 copies per 20 μl PCR reaction and a wide range of linearity (R(2)>0.99, pDNA samples from HBV infected patients. Total HBV DNA and cccDNA could be quantified in 32 and 22 of 33 FFPE preserved liver specimens, respectively. Total HBV DNA concentrations quantified by the 3io method remained comparable with Cobas TaqMan HBV Test v2.0. The three-in-one protocol allows the single step quantification of viral DNA in samples from different sources. Therefore lower sample input, faster data acquisition, a lowered error and significantly lower costs are the advantages of the method. Copyright © 2014 Elsevier B.V. All rights reserved.

  19. The impact of small-scale mining activities on the levels of mercury in the environment. The case of Prestea and its environs

    International Nuclear Information System (INIS)

    Serfor-Armah, Y.; Adotey, D.K.; Nyarko, B.J.B.; Akaho, E.H.K.; Adomako, D.

    2004-01-01

    To obtain the baseline information of mercury pollution due to gold mining activities in Prestea and its environs total mercury (T-Hg) concentrations were measured in water and stream sediment. The samples were analyzed by instrumental neutron activation analysis (INAA). They were irradiated and counted without any preconcentration. Higher levels of T-Hg concentration were found in samples at the sites with extensive small-scale 'galamsey' gold mining activities than at the sites with low small-scale 'galamsey' activities. Concentrations varied between 6.80-19.82 mg/l for water and 28.90-84.30 mg/kg in sediment at sites with extensive small-scale mining activities. At low small-scale mining sites concentration levels for T-Hg varied between 0.50-9.10 mg/l and 1.20-22.75 mg/kg in water and sediment, respectively. The concentration levels of T-Hg in water from all the sampling sites are in excess of the WHO tolerable limit of 0.001 mg/l for drinking water. (author)

  20. Reef-associated crustacean fauna: biodiversity estimates using semi-quantitative sampling and DNA barcoding

    Science.gov (United States)

    Plaisance, L.; Knowlton, N.; Paulay, G.; Meyer, C.

    2009-12-01

    The cryptofauna associated with coral reefs accounts for a major part of the biodiversity in these ecosystems but has been largely overlooked in biodiversity estimates because the organisms are hard to collect and identify. We combine a semi-quantitative sampling design and a DNA barcoding approach to provide metrics for the diversity of reef-associated crustacean. Twenty-two similar-sized dead heads of Pocillopora were sampled at 10 m depth from five central Pacific Ocean localities (four atolls in the Northern Line Islands and in Moorea, French Polynesia). All crustaceans were removed, and partial cytochrome oxidase subunit I was sequenced from 403 individuals, yielding 135 distinct taxa using a species-level criterion of 5% similarity. Most crustacean species were rare; 44% of the OTUs were represented by a single individual, and an additional 33% were represented by several specimens found only in one of the five localities. The Northern Line Islands and Moorea shared only 11 OTUs. Total numbers estimated by species richness statistics (Chao1 and ACE) suggest at least 90 species of crustaceans in Moorea and 150 in the Northern Line Islands for this habitat type. However, rarefaction curves for each region failed to approach an asymptote, and Chao1 and ACE estimators did not stabilize after sampling eight heads in Moorea, so even these diversity figures are underestimates. Nevertheless, even this modest sampling effort from a very limited habitat resulted in surprisingly high species numbers.

  1. [On the use of FTA technology for collection, archieving, and molecular analysis of microsporidia dna from clinical stool samples].

    Science.gov (United States)

    Sokolova, O I; Dem'ianov, A V; Bovers, L S; Did'e, E S; Sokolova, Iu Ia

    2011-01-01

    The FTA technology was applied for sampling, archiving, and molecular analysis of the DNA isolated from stool samples to diagnose and identify microsporidia, the intracellular opportunistic parasites which induce malabsortion syndrome in immunosuppressed humans, particularly in patients with AIDS. Microsporidia DNA was successfully amplified in 6 of 50 stool samples of HIV-positive patients of the S. P. Botkin Memorial Infectious Disease Hospital (St. Petersburg) applied to FTA cards (FTA-Cars, Whatman Inc. Florham Park, NJ, USA). Amplicons (the fragments of rDNA) were directly sequenced, and microsporidia species--Encephalitozoon intestinalis, E. cuniculi, E. hellem, and Enterocytozoon bieneusi--were identified in Genbank by NCBI BLAST program. The FTA method of DNA immobilization is especially promising for epidemiological and field population studies which involve genotyping of microsporidia species and isolates.

  2. Experimental evidence for convergent evolution of maternal care heuristics in industrialized and small-scale populations.

    Science.gov (United States)

    Kushnick, Geoff; Hanowell, Ben; Kim, Jun-Hong; Langstieh, Banrida; Magnano, Vittorio; Oláh, Katalin

    2015-06-01

    Maternal care decision rules should evolve responsiveness to factors impinging on the fitness pay-offs of care. Because the caretaking environments common in industrialized and small-scale societies vary in predictable ways, we hypothesize that heuristics guiding maternal behaviour will also differ between these two types of populations. We used a factorial vignette experiment to elicit third-party judgements about likely caretaking decisions of a hypothetical mother and her child when various fitness-relevant factors (maternal age and access to resources, and offspring age, sex and quality) were varied systematically in seven populations-three industrialized and four small-scale. Despite considerable variation in responses, we found that three of five main effects, and the two severity effects, exhibited statistically significant industrialized/ small-scale population differences. All differences could be explained as adaptive solutions to industrialized versus small-scale caretaking environments. Further, we found gradients in the relationship between the population-specific estimates and national-level socio-economic indicators, further implicating important aspects of the variation in industrialized and small-scale caretaking environments in shaping heuristics. Although there is mounting evidence for a genetic component to human maternal behaviour, there is no current evidence for interpopulation variation in candidate genes. We nonetheless suggest that heuristics guiding maternal behaviour in diverse societies emerge via convergent evolution in response to similar selective pressures.

  3. Seismic detection method for small-scale discontinuities based on dictionary learning and sparse representation

    Science.gov (United States)

    Yu, Caixia; Zhao, Jingtao; Wang, Yanfei

    2017-02-01

    Studying small-scale geologic discontinuities, such as faults, cavities and fractures, plays a vital role in analyzing the inner conditions of reservoirs, as these geologic structures and elements can provide storage spaces and migration pathways for petroleum. However, these geologic discontinuities have weak energy and are easily contaminated with noises, and therefore effectively extracting them from seismic data becomes a challenging problem. In this paper, a method for detecting small-scale discontinuities using dictionary learning and sparse representation is proposed that can dig up high-resolution information by sparse coding. A K-SVD (K-means clustering via Singular Value Decomposition) sparse representation model that contains two stage of iteration procedure: sparse coding and dictionary updating, is suggested for mathematically expressing these seismic small-scale discontinuities. Generally, the orthogonal matching pursuit (OMP) algorithm is employed for sparse coding. However, the method can only update one dictionary atom at one time. In order to improve calculation efficiency, a regularized version of OMP algorithm is presented for simultaneously updating a number of atoms at one time. Two numerical experiments demonstrate the validity of the developed method for clarifying and enhancing small-scale discontinuities. The field example of carbonate reservoirs further demonstrates its effectiveness in revealing masked tiny faults and small-scale cavities.

  4. GENDER DIFFERENTIALS IN FACTORS AFFECTING PERFORMANCE OF SMALL-SCALE ENTERPRISES IN LAGOS STATE – NIGERIA

    Directory of Open Access Journals (Sweden)

    Yusuff Olabisi Sherifat

    2013-05-01

    Full Text Available There is a lack of empirical data segregation on factors affecting gender as the variable of interest. However, previous research had indicated several factors that affect business performances among small-scale enterprise owners. Using feminist theory and a descriptive survey research design, data were collected from fifty (50 small-scale enterprise owners that were purposively chosen across the study area. The findings show that the factors that were significant for female were significantly different from male. For female small scale enterprise owners, marital status (64% Age of Children (68%, Role Model/ advisors (58% were significant factors that affect their business performance. For male small-scale enterprise owners, Friends (70%, a lack of Government support (80%, inability to display innovativeness (78% and Risk-Taking (84% were significant for male. Lack of availability of capital and finances were significant for the two. Other factors that affect performance include friends, inadequate training and business location. Adequate knowledge of factors that affect gender enterprise performance will go a long way in alleviating these problems. Small-scale enterprises should be supported for poverty alleviation, especially among women and for the nation’s economic development

  5. Assessing the Efficiency of Small-Scale and Bottom Trawler Vessels in Greece

    Directory of Open Access Journals (Sweden)

    Dario Pinello

    2016-07-01

    Full Text Available This study explores the technical and scale efficiency of two types of Greek fishing vessels, small-scale vessels and bottom trawlers, using a bias-corrected input-oriented Data Envelopment Analysis model. Moreover, the associations between efficiency scores and vessel’s and skipper’s characteristics are also explored. The results indicate that small-scale vessels achieve a very low average technical efficiency score (0.42 but a much higher scale efficiency score (0.81. Conversely, bottom trawlers achieve lower scale but higher technical efficiency scores (0.68 and 0.73, respectively. One important finding of this study is that the technical efficiency of small-scale vessels, in contrast to trawlers, is positively associated with the experience of the skipper. In a looser context, it can be said that small-scale fisheries mainly rely on skill, whereas bottom trawlers rely more on technology. This study concludes that there is space for improvement in efficiency, mainly for small-scale vessels, which could allow the achievement of the same level of output by using reduced inputs.

  6. Incidence of Listeria monocytogenes and Listeria spp. in a small-scale mushroom production facility.

    Science.gov (United States)

    Viswanath, Prema; Murugesan, Latha; Knabel, Stephen J; Verghese, Bindhu; Chikthimmah, Naveen; Laborde, Luke F

    2013-04-01

    Listeria monocytogenes is a foodborne pathogen of significant concern to the agricultural and food processing industry because of its ability to grow and persist in cool and moist environments and its association with listeriosis, a disease with a very high mortality rate. Although there have been no listeriosis outbreaks attributed to fresh mushrooms in the United States, retail surveys and recalls are evidence that L. monocytogenes contamination of mushrooms (Agaricus bisporus) can occur. The objective of this study was to determine the prevalence of Listeria spp., including L. monocytogenes, in a small-scale mushroom production facility on the campus of the Pennsylvania State University in the United States. Of 184 samples taken from five production zones within the facility, 29 (15.8%) samples were positive for Listeria spp. Among the Listeria spp. isolates, L. innocua was most prevalent (10.3%) followed by L. welshimeri (3.3%), L. monocytogenes (1.6%), and L. grayi (0.5%). L. monocytogenes was recovered only from the phase I raw material composting area. Isolates of L. monocytogenes were confirmed and serotyped by multiplex PCR. The epidemiological relatedness of the three L. monocytogenes isolates to those serotypes or lineages frequently encountered in listeriosis infections was determined by multi-virulence-locus sequence typing using six virulence genes, namely, prfA, inlB, inlC, dal, clpP, and lisR. The phylogenetic positions of the three isolates in the dendrogram prepared with data from other isolates of L. monocytogenes showed that all isolates were grouped with serotype 4a, lineage IIIA. To date, this serotype has rarely been reported in foodborne disease outbreaks.

  7. Evaluation on the effects of ageing factor, sampling and preservation methods on Asiatic black bear (Ursus thibetanus noninvasive DNA amplification

    Directory of Open Access Journals (Sweden)

    Chih-Chin SHIH

    2017-11-01

    Full Text Available Noninvasive genetic sampling allows studying wildlife without having to catch, handle or even observe individuals. In this study, factors which may affect the quality of noninvasive samples of Asiatic black bear (Ursus thibetanus in the subtropical areas were identified. We collected hair and faecal samples from captive Asiatic black bears and quantitatively evaluated the effects of hair age (from fresh to 60 days, faeces age (from fresh to 14 days, faeces sampling locations (i.e. sample collected from either the surface, inside or a mixture of both the surface and inside of faeces, and faeces preservation methods (frozen or kept at room temperature in 95% ethanol on amplification success rates of mitochondrial DNA fragments of different sizes (450bp, 900bp, and 1600bp. The results showed that the amplification success rates decreased with sample age and amplicon size in both hair and faecal DNA. In subtropical environment, there was no significant difference between amplification success of DNA extracted from fresh and 7-day-old samples of either the hair or faeces. The amplification success rates were not influenced by sampling location of faeces. For faeces preserved in 95% ethanol, the amplification success appeared unaffected by frozen at -20 °C or kept at room temperature in shorter mtDNA fragments, but was significantly influenced when amplicon size was 1600bp. The results of this study will reinforce the optimization of noninvasive sampling approaches in Asiatic black bear research, especially in the subtropics.

  8. Distribution and Prevalence of Myxobolus cerebralis in Postfire Areas of Plumas National Forest: Utility of Environmental DNA Sampling.

    Science.gov (United States)

    Richey, Christine A; Kenelty, Kirsten V; Van Stone Hopkins, Kristina; Stevens, Brittany N; Martínez-López, Beatriz; Barnum, Samantha M; Hallett, Sascha L; Atkinson, Stephen D; Bartholomew, Jerri L; Soto, Esteban

    2018-04-30

    Myxobolus cerebralis is a myxozoan parasite and the etiological agent of whirling disease in salmonids. The parasite's life cycle involves waterborne spores and requires both a salmonid fish and the benthic freshwater oligochaete worm Tubifex tubifex (Oligochaeta: Tubificidae). Wildfires can lead to the erosion of fine sediments into stream channels and have been implicated as promoting environmental conditions that are suitable for the survival and success of T. tubifex, whose presence in turn can affect the prevalence of M. cerebralis. Analysis of environmental DNA (eDNA) has the potential to be a powerful tool for evaluating the presence of microorganisms, for which direct observation is impossible. We investigated the presence of M. cerebraliseDNA in river water and river sediment samples collected from areas affected by recent fire activity in Plumas National Forest, California. We compared eDNA loads in the environment to M. cerebralis infection in T. tubifex and sentinel-exposed Rainbow Trout Oncorhynchus mykiss and the presence of T. tubifex lineages in the same environment. For the latter, we developed a multiplex quantitative PCR assay for detection of T. tubifex lineages I, III, and V. Lineage IIIT. tubifex and M. cerebralis (eDNA as well as DNA extracted from fish and worm tissues) were detected only in samples obtained from areas affected by the Moonlight wildfire. The association between M. cerebralis infection in sentinel-exposed fish and eDNA detection in environmental samples only approached significance at a P-value of 0.056. However, given the difference in relative effort between the two sampling methods (host versus nonhost environment), our data suggest that eDNA sampling of water and substrate is a promising approach for surveillance of myxozoan fish parasites. © 2018 American Fisheries Society.

  9. Development of a Novel Self-Enclosed Sample Preparation Device for DNA/RNA Isolation in Space

    Science.gov (United States)

    Zhang, Ye; Mehta, Satish K.; Pensinger, Stuart J.; Pickering, Karen D.

    2011-01-01

    Modern biology techniques present potentials for a wide range of molecular, cellular, and biochemistry applications in space, including detection of infectious pathogens and environmental contaminations, monitoring of drug-resistant microbial and dangerous mutations, identification of new phenotypes of microbial and new life species. However, one of the major technological blockades in enabling these technologies in space is a lack of devices for sample preparation in the space environment. To overcome such an obstacle, we constructed a prototype of a DNA/RNA isolation device based on our novel designs documented in the NASA New Technology Reporting System (MSC-24811-1/3-1). This device is self-enclosed and pipette free, purposely designed for use in the absence of gravity. Our design can also be modified easily for preparing samples in space for other applications, such as flowcytometry, immunostaining, cell separation, sample purification and separation according to its size and charges, sample chemical labeling, and sample purification. The prototype of our DNA/RNA isolation device was tested for efficiencies of DNA and RNA isolation from various cell types for PCR analysis. The purity and integrity of purified DNA and RNA were determined as well. Results showed that our developed DNA/RNA isolation device offers similar efficiency and quality in comparison to the samples prepared using the standard protocol in the laboratory.

  10. SPIDIA-DNA: An External Quality Assessment for the pre-analytical phase of blood samples used for DNA-based analyses

    Czech Academy of Sciences Publication Activity Database

    Malentacchi, F.; Pazzagli, M.; Simi, L.; Orlando, C.; Wyrich, R.; Hartmann, C.C.; Verderio, P.; Pizzamiglio, S.; Ciniselli, C.M.; Tichopád, Aleš; Kubista, Mikael; Gelmini, S.

    -, č. 424 (2013), s. 274-286 ISSN 0009-8981 Institutional research plan: CEZ:AV0Z50520701 Keywords : Pre-analytical phase * DNA quality * Blood samples Subject RIV: EB - Genetics ; Molecular Biology Impact factor: 2.764, year: 2013

  11. Small-scale field-aligned currents observed by the AKEBONO (EXOS-D) satellite

    International Nuclear Information System (INIS)

    Fukunishi, H.; Oya, H.; Kokubun, S.; Tohyama, F.; Mukai, T.; Fujii, R.

    1991-01-01

    The EXOS-D fluxgate magnetometer data obtained at 3,000-10,000 km altitude have shown that small-scale field-aligned currents always exist in large-scale region 1, region 2, cusp and polar cap current systems. Assuming that these small-scale field-aligned currents have current sheet structure, the width of current sheet is estimated to be 5-20 km at ionospheric altitude. By comparing the magnetometer data with charged particle and high frequency plasma wave data simultaneously obtained from EXOS-D, it is found that small-scale currents have one-to-one correspondence with localized electron precipitation events characterized by flux enhancement over a wide energy range from 10 eV to several keV and broadband electrostatic bursts occasionally extending above local plasma frequencies or electron cyclotron frequencies

  12. Thermodynamic modeling of small scale biomass gasifiers: Development and assessment of the ''Multi-Box'' approach.

    Science.gov (United States)

    Vakalis, Stergios; Patuzzi, Francesco; Baratieri, Marco

    2016-04-01

    Modeling can be a powerful tool for designing and optimizing gasification systems. Modeling applications for small scale/fixed bed biomass gasifiers have been interesting due to their increased commercial practices. Fixed bed gasifiers are characterized by a wide range of operational conditions and are multi-zoned processes. The reactants are distributed in different phases and the products from each zone influence the following process steps and thus the composition of the final products. The present study aims to improve the conventional 'Black-Box' thermodynamic modeling by means of developing multiple intermediate 'boxes' that calculate two phase (solid-vapor) equilibriums in small scale gasifiers. Therefore the model is named ''Multi-Box''. Experimental data from a small scale gasifier have been used for the validation of the model. The returned results are significantly closer with the actual case study measurements in comparison to single-stage thermodynamic modeling. Copyright © 2016 Elsevier Ltd. All rights reserved.

  13. Responding to the challenge of artisanal and small-scale mining. How can knowledge networks help?

    Energy Technology Data Exchange (ETDEWEB)

    Buxton, Abbi

    2013-02-15

    This paper reviews what is known about the problems and structural challenges facing the 20-30 million artisanal and small-scale miners and their communities worldwide. Better understanding of these structural challenges is needed to improve policies and policy implementation to further sustainable development opportunities for the sector. The paper explores the current gaps in knowledge to achieve policy change from researchers, practitioners and artisanal and small-scale miners themselves. It explores how a 'knowledge intermediary', which acts to link knowledge with policy, could address these gaps and includes case studies of IIED’s work on knowledge networks and programmes. The paper concludes by proposing a way forward for designing a knowledge programme to meet the particular needs of the artisanal and small-scale mining (ASM) sector, and by inviting ASM sector stakeholders to share their views on the options outlined.

  14. Responding to the challenge of artisanal and small-scale mining. How can knowledge networks help?

    Energy Technology Data Exchange (ETDEWEB)

    Buxton, Abbi

    2013-02-15

    This paper reviews what is known about the problems and structural challenges facing the 20-30 million artisanal and small-scale miners and their communities worldwide. Better understanding of these structural challenges is needed to improve policies and policy implementation to further sustainable development opportunities for the sector. The paper explores the current gaps in knowledge to achieve policy change from researchers, practitioners and artisanal and small-scale miners themselves. It explores how a 'knowledge intermediary', which acts to link knowledge with policy, could address these gaps and includes case studies of IIED’s work on knowledge networks and programmes. The paper concludes by proposing a way forward for designing a knowledge programme to meet the particular needs of the artisanal and small-scale mining (ASM) sector, and by inviting ASM sector stakeholders to share their views on the options outlined.

  15. A novel method of selective removal of human DNA improves PCR sensitivity for detection of Salmonella Typhi in blood samples.

    Science.gov (United States)

    Zhou, Liqing; Pollard, Andrew J

    2012-07-27

    Enteric fever is a major public health problem, causing an estimated 21million new cases and 216,000 or more deaths every year. Current diagnosis of the disease is inadequate. Blood culture only identifies 45 to 70% of the cases and is time-consuming. Serological tests have very low sensitivity and specificity. Clinical samples obtained for diagnosis of enteric fever in the field generally have blood, so that even PCR-based methods, widely used for detection of other infectious diseases, are not a straightforward option in typhoid diagnosis. We developed a novel method to enrich target bacterial DNA by selective removal of human DNA from blood samples, enhancing the sensitivity of PCR tests. This method offers the possibility of improving PCR assays directly using clinical specimens for diagnosis of this globally important infectious disease. Blood samples were mixed with ox bile for selective lysis of human blood cells and the released human DNA was then digested with addition of bile resistant micrococcal nuclease. The intact Salmonella Typhi bacteria were collected from the specimen by centrifugation and the DNA extracted with QIAamp DNA mini kit. The presence of Salmonella Typhi bacteria in blood samples was detected by PCR with the fliC-d gene of Salmonella Typhi as the target. Micrococcal nuclease retained activity against human blood DNA in the presence of up to 9% ox bile. Background human DNA was dramatically removed from blood samples through the use of ox bile lysis and micrococcal nuclease for removal of mammalian DNA. Consequently target Salmonella Typhi DNA was enriched in DNA preparations and the PCR sensitivity for detection of Salmonella Typhi in spiked blood samples was enhanced by 1,000 fold. Use of a combination of selective ox-bile blood cell lysis and removal of human DNA with micrococcal nuclease significantly improves PCR sensitivity and offers a better option for improved typhoid PCR assays directly using clinical specimens in diagnosis of

  16. Estimating the “Forgone” ESVs for Small-Scale Gold Mining Using Historical Image Data

    Directory of Open Access Journals (Sweden)

    Ernest Frimpong Asamoah

    2017-10-01

    Full Text Available Ghana’s economic development relies largely on the mining industry, but the ecological cost is very high, particularly for the small-scale sector. To ascertain and give an account of the ecological pressures from the small-scale gold mining sector, we quantified and appraised the ecosystems (land cover types degradation due to mining land use along portions of the renowned Pra River basin of Ghana. The study classified and analysed high-quality Landsat image data (1986–2016 to monitor processes and changes in the river basin and adopted the Ecosystem Service Value (ESV model to quantify the forgone value in monetary term. The results revealed that the initial ESV of 17.69 million US$ in 1986 increased to 18.40 million US$ in 2002 for the study landscape with the small-scale mining sector accounting for 8.4% of the trade-off costs. The expansion of forest areas and its higher value coefficient (VC was, however, prevalent and this resulted in a net positive change during this period. However, in 2016, out of the total ESV of 14.63 million US$ obtained, the small-scale mining activities accounted for 36.8% of the trade-off costs. The substantial increase in trade-off costs with a subsequent decrease in ESV in the study landscape, following the intensification of small-scale gold mining, indicates that their activities have been degrading the watershed ecosystem and are, therefore, unsustainable. The study affirms the need for policymakers/government to review the laws, particularly on post-mining monitoring schemes to deter illegal miners and support the registered small-scale miners who are willing to implement land rehabilitation activities.

  17. Public involvement in pharmacogenomics research: a national survey on patients' attitudes towards pharmacogenomics research and the willingness to donate DNA samples to a DNA bank in Japan.

    Science.gov (United States)

    Kobayashi, Eriko; Sakurada, Tomoya; Ueda, Shiro; Satoh, Nobunori

    2011-05-01

    To assess the attitude of Japanese patients towards pharmacogenomics research and a DNA bank for identifying genomic markers associated with adverse drug reactions (ADRs) and their willingness to donate DNA samples, we conducted a survey of 550 male and female patients. The majority of the respondents showed a positive attitude towards pharmacogenomics research (87.6%) and a DNA bank (75.1%). The willingness to donate DNA samples when experiencing severe ADRs (55.8%) was higher than when taking medications (40.4%). Positive attitudes towards a DNA bank and organ donation were significantly associated with an increased willingness to donate. Though the level of positive attitude in the patient population was higher than that in the general public in our former study (81.0 and 70.4%, respectively), the level of the willingness of patients to donate was 40.4% when taking medications and 55.8% when experiencing severe ADRs which was lower than that of the general public in our former study (45.3 and 61.7%). The results suggested that the level of true willingness in the patient population was lower than that of the general public considering the fictitious situation presented to the public (to suppose that they were patients receiving medication). It is important to assess the willingness of patients who are true potential donors, not the general public.

  18. Rapid colorimetric assay for detection of Listeria monocytogenes in food samples using LAMP formation of DNA concatemers and gold nanoparticle-DNA probe complex

    Science.gov (United States)

    Wachiralurpan, Sirirat; Sriyapai, Thayat; Areekit, Supatra; Sriyapai, Pichapak; Augkarawaritsawong, Suphitcha; Santiwatanakul, Somchai; Chansiri, Kosum

    2018-04-01

    ABSTRACT Listeria monocytogenes is a major foodborne pathogen of global health concern. Herein, the rapid diagnosis of L. monocytogenes has been achieved using loop-mediated isothermal amplification (LAMP) based on the phosphatidylcholine-phospholipase C gene (plcB). Colorimetric detection was then performed through the formation of DNA concatemers and a gold nanoparticle/DNA probe complex (GNP/DNA probe). The overall detection process was accomplished within approximately 1 h with no need for complicated equipment. The limits of detection for L. monocytogenes in the forms of purified genomic DNA and pure culture were 800 fg and 2.82 CFU mL-1, respectively. No cross reactions were observed from closely related bacteria species. The LAMP-GNP/DNA probe assay was applied to the detection of 200 raw chicken meat samples and compared to routine standard methods. The data revealed that the specificity, sensitivity and accuracy were 100%, 90.20% and 97.50%, respectively. The present assay was 100% in conformity with LAMP-agarose gel electrophoresis assay. Five samples that were negative by both assays appeared to have the pathogen at below the level of detection. The assay can be applied as a rapid direct screening method for L. monocytogenes.

  19. Public involvement in pharmacogenomics research: a national survey on public attitudes towards pharmacogenomics research and the willingness to donate DNA samples to a DNA bank in Japan.

    Science.gov (United States)

    Kobayashi, Eriko; Satoh, Nobunori

    2009-11-01

    To assess the attitudes of the Japanese general public towards pharmacogenomics research and a DNA bank for identifying genomic markers associated with ADRs and their willingness to donate DNA samples, we conducted a national survey for 1,103 Japanese adults from the general public, not a patient population. The response rate was 36.8%. The majority of the respondents showed a positive attitude towards pharmacogenomics research (81.0%) and a DNA bank (70.4%). Considering fictitious clinical situations such as taking medications and experiencing ADRs, the willingness to donate DNA samples when experiencing ADRs (61.7%) was higher than when taking medications (45.3%). Older generations were significantly associated with a decreased willingness to donate (OR = 0.45, CI 0.28-0.72 in 50s. OR = 0.49, CI: 0.31-0.77 in 60s). Positive attitudes towards pharmacogenomics research, a DNA bank, blood/bone marrow/organ donation were significantly associated with an increased willingness. However, the respondents had the following concerns regarding a DNA bank: the confidentiality of their personal information, the manner by which research results were utilized and simply the use of their own DNA for research. In order to attain public understanding to overcome these concerns, a process of public awareness should be put into place to emphasize the beneficial aspects of identifying genomic markers associated with ADRs and to address these concerns raised in our study. Further study is needed to assess the willingness of actual patients taking medications in real situations, since the respondents in our study were from the general public, not a patient population, and their willingness was assessed on the condition of assuming that they were patients taking medications.

  20. Validity of thermally-driven small-scale ventilated filling box models

    Science.gov (United States)

    Partridge, Jamie L.; Linden, P. F.

    2013-11-01

    The majority of previous work studying building ventilation flows at laboratory scale have used saline plumes in water. The production of buoyancy forces using salinity variations in water allows dynamic similarity between the small-scale models and the full-scale flows. However, in some situations, such as including the effects of non-adiabatic boundaries, the use of a thermal plume is desirable. The efficacy of using temperature differences to produce buoyancy-driven flows representing natural ventilation of a building in a small-scale model is examined here, with comparison between previous theoretical and new, heat-based, experiments.

  1. ITER baffle module small-scale mock-ups: first wall thermo-mechanical testing results

    International Nuclear Information System (INIS)

    Severi, Y.; Giancarli, L.; Poitevin, Y.; Salavy, J.F.; Le Marois, G.; Roedig, M.; Vieider, G.

    1998-01-01

    The EU-home team is in charge of the R and D related to the ITER baffle first wall. Five small-scale mock-ups, using Be, CFC and W tiles and different armour/heat-sink material joints under development, have been fabricated and thermomechanically tested in FE200 (Le Creusot) and JUDITH (Juelich) electron beam facilities. The small-scale mock-ups have been submitted to thermo-mechanical fatigue tests (up to failure using accelerating techniques). The objective was to determine the performances of the armour material joints under high heat flux cycles. (orig.)

  2. Notes on a Dramaturgical Analysis of Unequal Small-Scale Corruption Experiences

    Directory of Open Access Journals (Sweden)

    Edgar Daniel Manchinelly Mota

    2017-10-01

    Full Text Available In the last two decades, corruption has emerged as a relevant subject on a worldwide scale, because of its negative effects on the economy and State institutions, among other things. Research has focused on the macro aspects of corruption, emphasizing its causes and consequences. However, small-scale corruption has not been studied in such detail. This document proposes a theoretical-methodological framework for a dramaturgical analysis of small-scale corruption, with the aim of demonstrating that it is a stratified interaction. In this sense, corruption is an unequal experience for citizens, which depends on individuals’ social position.

  3. A review of mercury exposure among artisanal small-scale gold miners in developing countries

    DEFF Research Database (Denmark)

    Kristensen, Anders Kasper Bruun; Thomsen, Jane Frølund; Mikkelsen, Sigurd

    2014-01-01

    Extraction of gold using mercury has been a way out of poverty for millions of people in developing countries. Artisanal small-scale gold mining (ASGM) has expanded during the last decades and is often carried out under primitive conditions. Thus, workers in this industry may be exposed to high...... levels of mercury and suffer from toxic effects from mercury exposure. The objective of this review was to provide an outline of the studies available on elemental mercury exposure among artisanal small-scale gold miners....

  4. Small-scale biomass CHP using gasa turbines: a scoping study

    International Nuclear Information System (INIS)

    James, D.W.; Landen, R.

    1996-01-01

    Various options for small-scale (up to 250 KWe) Combined Heat and Power (CHP) plants evaluated in this scoping study. Plants using small gas turbines, and able to use biomass fuels when available are included. Three detailed case studies of small-scale biomass CHP plants are compared to match specific technical options with customer requirements. The commercial development of such biomass-fired CHP units, using gas turbines, is shown to be economically viable depending on fuel costs and the continuation of existing financial incentives. (UK)

  5. Air emissions of small-scale (< 10 MW) biomass boilers. Review of three field tests

    International Nuclear Information System (INIS)

    Autret, E.

    2011-01-01

    Objectives of greenhouse gases emission reduction, which encourages bio-energy development for heat purposes, are compatible with air-quality policies if the concept of clean biomass combustion is applied. This paper presents actual emission levels of atmospheric pollutants of small-scale ( 2 , NO x , fine particulate matters, metallic compounds. Installation design (power, flue-gas cleaning techno logy) also has a major impact on organic pollutants and fine particulate matter emissions. A large majority of boilers have very low emission levels. Guidelines are finally stated to keep on promoting small-scale biomass boilers in order to be air-quality compatible and efficient to fight climate change. (author)

  6. Small-scale fluctuations in the microwave background radiation and multiple gravitational lensing

    International Nuclear Information System (INIS)

    Kashlinsky, A.

    1988-01-01

    It is shown that multiple gravitational lensing of the microwave background radiation (MBR) by static compact objects significantly attenuates small-scale fluctuations in the MBR. Gravitational lensing, by altering trajectories of MBR photons reaching an observer, leads to (phase) mixing of photons from regions with different initial fluctuations. As a result of this diffusion process the original fluctuations are damped on scales up to several arcmin. An equation that describes this process and its general solution are given. It is concluded that the present upper limits on the amplitude of the MBR fluctuations on small scales cannot constrain theories of galaxy formation. 25 references

  7. Exploring the role of small-scale livestock keepers for national biosecurity-The pig case.

    Science.gov (United States)

    Correia-Gomes, Carla; Henry, Madeleine K; Auty, Harriet K; Gunn, George J

    2017-09-15

    Small-scale keepers are less likely to engage with production organisations and may therefore be less aware of legislation, rules and biosecurity practices which are implemented in the livestock sector. Their role in the transmission of endemic and exotic diseases is not well studied, but is believed to be important. The authors use small-scale pig keepers in Scotland as an example of how important small-scale livestock keepers might be for national biosecurity. In Scotland more than two thirds of pig producers report that they keep less than 10 pigs, meaning that biosecurity practices and pig health status on a substantial number of holdings are largely unknown; it is considered important to fill this knowledge gap. A questionnaire was designed and implemented in order to gather some of this information. The questionnaire comprised a total of 37 questions divided into seven sections (location of the enterprise, interest in pigs, details about the pig enterprise, marketing of pigs, transport of pigs, pig husbandry, and pig health/biosecurity). Over 610 questionnaires were sent through the post and the questionnaire was also available online. The questionnaire was implemented from June to October 2013 and 135 questionnaires were returned by target respondents. The responses for each question are discussed in detail in this paper. Overall, our results suggest that the level of disease identified by small-scale pig keepers is low but the majority of the small-scale pig keepers are mixed farms, with associated increased risk for disease transmission between species. Almost all respondents implemented at least one biosecurity measure, although the measures taken were not comprehensive in the majority of cases. Overall as interaction between small-scale keepers and commercial producers exists in Scotland the former can pose a risk for commercial production. This investigation fills gaps in knowledge which will allow industry stakeholders and policy makers to adapt their

  8. Determination of DNA profiling of siwak and toothbrush samples used in Kingdom of Saudi Arabia

    Directory of Open Access Journals (Sweden)

    Nagy Alfadaly

    2016-10-01

    Conclusion: Siwak contains enough quantity of DNA, and retained good DNA profiling; and when compared to toothbrushes, siwak is a reasonable source of DNA profiling when found at the scene of crime. In addition, time of storage up to 4 months had no or little effects on results.

  9. Identification of eukaryotic open reading frames in metagenomic cDNA libraries made from environmental samples.

    Science.gov (United States)

    Grant, Susan; Grant, William D; Cowan, Don A; Jones, Brian E; Ma, Yanhe; Ventosa, Antonio; Heaphy, Shaun

    2006-01-01

    Here we describe the application of metagenomic technologies to construct cDNA libraries from RNA isolated from environmental samples. RNAlater (Ambion) was shown to stabilize RNA in environmental samples for periods of at least 3 months at -20 degrees C. Protocols for library construction were established on total RNA extracted from Acanthamoeba polyphaga trophozoites. The methodology was then used on algal mats from geothermal hot springs in Tengchong county, Yunnan Province, People's Republic of China, and activated sludge from a sewage treatment plant in Leicestershire, United Kingdom. The Tenchong libraries were dominated by RNA from prokaryotes, reflecting the mainly prokaryote microbial composition. The majority of these clones resulted from rRNA; only a few appeared to be derived from mRNA. In contrast, many clones from the activated sludge library had significant similarity to eukaryote mRNA-encoded protein sequences. A library was also made using polyadenylated RNA isolated from total RNA from activated sludge; many more clones in this library were related to eukaryotic mRNA sequences and proteins. Open reading frames (ORFs) up to 378 amino acids in size could be identified. Some resembled known proteins over their full length, e.g., 36% match to cystatin, 49% match to ribosomal protein L32, 63% match to ribosomal protein S16, 70% to CPC2 protein. The methodology described here permits the polyadenylated transcriptome to be isolated from environmental samples with no knowledge of the identity of the microorganisms in the sample or the necessity to culture them. It has many uses, including the identification of novel eukaryotic ORFs encoding proteins and enzymes.

  10. Performance of a Small-scale Treatment Wetland for Treatment of Landscaping Wash Water

    Science.gov (United States)

    Thompson, R. J.; Fayed, E.; Fish, W.

    2011-12-01

    A large number of lawn mowers and related equipment must be cleaned each day by commercial landscaping operations and state and local highway maintenance crews. Washing these devices produces wastewater that contains high amounts of organic matter and potentially problematic nutrients, as well as oil and grease and other chemicals and metals that come from the machinery itself. Dirty water washes off the mowers, flows off the pavement and into nearby storm drains without any kind of treatment. A better idea would be to collect such wastewater, retain it in an appropriate catchment such as an engineered wetland where natural processes could break down any pollutants in the wash water, and allow the water to naturally evaporate or percolate into the soil where it could recharge ground water resources safely. This research examines the performance of a small-scale treatment wetland tailored to remove nitrogen from landscaping wash water by incorporating both aerobic and anaerobic phases. Contaminants are analyzed through physical and chemical methods. Both methods involve collection of samples, followed by standardized, validated analytical laboratory tests for measuring total solids, total kjeldahl nitrogen, nitrates, total and dissolved phosphorus, COD, BOD, oil and grease, and metals (Zn and Cu). High levels of total solids, total kjeldahl nitrogen, nitrates, total and dissolved phosphorus, COD, BOD, oil and grease are found. Zinc and copper levels are low. Wetland treatment removes 99% total solids, 77% total kjeldahl nitrogen, 100% nitrates, 94% total phosphorus, 86% dissolved phosphorus, 94% COD, 97% BOD, and 76% oil and grease. The results will be a critical step towards developing a sustainable low-energy system for treating such wastewater that could be used by private landscaping companies and government agencies.

  11. Small scale structure of magnetospheric electron density through on-line tracking of plasma resonances

    International Nuclear Information System (INIS)

    Higel, B.

    1978-01-01

    The plasma resonance phenomena observed at fsub(pe), nfsub(ce), and fsub(qn) by the GEOS-1 S-301 relaxation sounder are identified through a pattern recognition software process implemented in a mini-computer which receives on-line the compressed data. First, this processing system distributes in real time fsub(pe) and fsub(ce) measurements to the ground media. Second, it drives and controls automatically the S-301 on-board experiment by sending appropriate telecommands: the tracking of resonances is performed by shortening the frequency sweeps to a narrow range centered on the resonance location. Examples of such tracking sequences are presented, exhibiting sampling rates of the electron density measurements from once every 22s (slowest rate) to once every 86 ms (highest rate available). The results give evidence of the existence of very small scale structures in the magnetospheric density, having characteristic sizes of the order of a few 10 2 m or/and a few 10 -1 s. The relative amplitude of these density fluctuations is typically 1%. Because of satellite spinning, fixed frequency sounding sequences allow to measure in a few seconds the directivity features of the plasma resonance signals. Examples of directional patterns in the plane perpendicular to the geomagnetic field are presented: the electrostatic nature of the waves received at fsub(pe), nfsub(ce), and fsub(qn) being consistent with these patterns, the corresponding k vector orientations become available. The Bernstein modes properties are used to interpret the nfsub(ce) and fsub(qn) results. (Auth.)

  12. Extraction of Total DNA and RNA from Marine Filter Samples and Generation of a cDNA as Universal Template for Marker Gene Studies.

    Science.gov (United States)

    Schneider, Dominik; Wemheuer, Franziska; Pfeiffer, Birgit; Wemheuer, Bernd

    2017-01-01

    Microbial communities play an important role in marine ecosystem processes. Although the number of studies targeting marker genes such as the 16S rRNA gene has been increased in the last few years, the vast majority of marine diversity is rather unexplored. Moreover, most studies focused on the entire bacterial community and thus disregarded active microbial community players. Here, we describe a detailed protocol for the simultaneous extraction of DNA and RNA from marine water samples and for the generation of cDNA from the isolated RNA which can be used as a universal template in various marker gene studies.

  13. Evaluating sampling strategy for DNA barcoding study of coastal and inland halo-tolerant Poaceae and Chenopodiaceae: A case study for increased sample size.

    Directory of Open Access Journals (Sweden)

    Peng-Cheng Yao

    Full Text Available Environmental conditions in coastal salt marsh habitats have led to the development of specialist genetic adaptations. We evaluated six DNA barcode loci of the 53 species of Poaceae and 15 species of Chenopodiaceae from China's coastal salt marsh area and inland area. Our results indicate that the optimum DNA barcode was ITS for coastal salt-tolerant Poaceae and matK for the Chenopodiaceae. Sampling strategies for ten common species of Poaceae and Chenopodiaceae were analyzed according to optimum barcode. We found that by increasing the number of samples collected from the coastal salt marsh area on the basis of inland samples, the number of haplotypes of Arundinella hirta, Digitaria ciliaris, Eleusine indica, Imperata cylindrica, Setaria viridis, and Chenopodium glaucum increased, with a principal coordinate plot clearly showing increased distribution points. The results of a Mann-Whitney test showed that for Digitaria ciliaris, Eleusine indica, Imperata cylindrica, and Setaria viridis, the distribution of intraspecific genetic distances was significantly different when samples from the coastal salt marsh area were included (P < 0.01. These results suggest that increasing the sample size in specialist habitats can improve measurements of intraspecific genetic diversity, and will have a positive effect on the application of the DNA barcodes in widely distributed species. The results of random sampling showed that when sample size reached 11 for Chloris virgata, Chenopodium glaucum, and Dysphania ambrosioides, 13 for Setaria viridis, and 15 for Eleusine indica, Imperata cylindrica and Chenopodium album, average intraspecific distance tended to reach stability. These results indicate that the sample size for DNA barcode of globally distributed species should be increased to 11-15.

  14. Development and validation of a multi-locus DNA metabarcoding method to identify endangered species in complex samples.

    Science.gov (United States)

    Arulandhu, Alfred J; Staats, Martijn; Hagelaar, Rico; Voorhuijzen, Marleen M; Prins, Theo W; Scholtens, Ingrid; Costessi, Adalberto; Duijsings, Danny; Rechenmann, François; Gaspar, Frédéric B; Barreto Crespo, Maria Teresa; Holst-Jensen, Arne; Birck, Matthew; Burns, Malcolm; Haynes, Edward; Hochegger, Rupert; Klingl, Alexander; Lundberg, Lisa; Natale, Chiara; Niekamp, Hauke; Perri, Elena; Barbante, Alessandra; Rosec, Jean-Philippe; Seyfarth, Ralf; Sovová, Tereza; Van Moorleghem, Christoff; van Ruth, Saskia; Peelen, Tamara; Kok, Esther

    2017-10-01

    DNA metabarcoding provides great potential for species identification in complex samples such as food supplements and traditional medicines. Such a method would aid Convention on International Trade in Endangered Species of Wild Fauna and Flora (CITES) enforcement officers to combat wildlife crime by preventing illegal trade of endangered plant and animal species. The objective of this research was to develop a multi-locus DNA metabarcoding method for forensic wildlife species identification and to evaluate the applicability and reproducibility of this approach across different laboratories. A DNA metabarcoding method was developed that makes use of 12 DNA barcode markers that have demonstrated universal applicability across a wide range of plant and animal taxa and that facilitate the identification of species in samples containing degraded DNA. The DNA metabarcoding method was developed based on Illumina MiSeq amplicon sequencing of well-defined experimental mixtures, for which a bioinformatics pipeline with user-friendly web-interface was developed. The performance of the DNA metabarcoding method was assessed in an international validation trial by 16 laboratories, in which the method was found to be highly reproducible and sensitive enough to identify species present in a mixture at 1% dry weight content. The advanced multi-locus DNA metabarcoding method assessed in this study provides reliable and detailed data on the composition of complex food products, including information on the presence of CITES-listed species. The method can provide improved resolution for species identification, while verifying species with multiple DNA barcodes contributes to an enhanced quality assurance. © The Authors 2017. Published by Oxford University Press.

  15. Progress in generating fracture data base as a function of loading rate and temperature using small-scale tests

    International Nuclear Information System (INIS)

    Couque, H.; Hudak, S.J. Jr.

    1993-01-01

    Structural integrity assessment of nuclear pressure vessels requires small specimen fracture testing to generate data over a wide range of material loading, and temperature conditions. Small scale testing is employed since extensive testing is required including small radiation embrittled samples from nuclear surveillance capsules. However, current small scale technology does not provide the needed dynamic fracture toughness relevant to the crack arrest/reinitiation events that may occur during pressurized thermal shock transients following emergency shutdown. This paper addresses the generation of this much needed dynamic toughness data using a novel experimental-computational approach involving a coupled pressure bars (CPB) technique and a viscoplastic dynamic fracture code. CPB data have been generated to testing temperatures never before reached: 37 to 100 degrees C -- 60 to 123 degrees C above the nil ductility transition temperature. Fracture behavior of pressure vessel steel from lower shelf to upper shelf temperatures and previous toughness estimates for the 10 6 MPa√m s -1 loading rate regime are assessed in light of the new CPB data. 26 refs., 14 figs., 3 tabs

  16. Small-scale experimental contamination with diesel oil does not affect the recolonization of Sargassum (Fucales fronds by vagile macrofauna

    Directory of Open Access Journals (Sweden)

    Henrique Grande

    2012-04-01

    Full Text Available Coastal regions are subject to various forms of environmental impacts, such as spills of crude oil and associated products, with a wide range of effects on benthic biodiversity. This study characterized the patterns of recolonization of the macrofauna associated with the brown alga Sargassum cymosum(C. Agardh, on fronds contaminated by diesel oil in a small-scale field experiment. We collected 40 fronds of S. cymosum from an algal bed in southeastern Brazil and defaunated each frond by immersion in fresh water. Half of the fronds were then immersed in seawater (control group and the other half in a mixture of 50% diesel oil and 50% seawater (impacted group. The test fronds were returned to the algal bed, and natural recolonization took place over a period of 12 days. Samples of the vagile macrofauna were taken randomly at three-day intervals over the course of the recolonization period. No significant differences in the densities of most taxa were found between the impact treatment (IG and control treatment (CG. At the end of the recolonization period (day 12, the faunal composition of the treated fronds was very similar to the natural conditions, indicating a high rate of community recovery and suggesting that benthic associations can be rather resilient to diesel-oil impacts on a small scale.

  17. Role of small-scale independent providers in water and sanitation

    NARCIS (Netherlands)

    M.P. van Dijk (Meine Pieter)

    2008-01-01

    textabstractSmall-scale independent providers (SSIPs) and households are good for 10–69% of the household water supply and sometimes up to 95% of the sanitation solutions in cities in developing countries. Different types of SSIP can be distinguished. They could be allowed to make a more important

  18. The economic logic of persistent informality: Artisanal and small-scale mining in the Southern Philippines

    NARCIS (Netherlands)

    Verbrugge, B.L.P.

    2015-01-01

    This article critically evaluates existing causal explanations for the persistence of informality in artisanal and small-scale mining (ASM). These explanations share a legalistic focus on entry barriers and political impediments that prevent or discourage the formalization of poverty-driven ASM