High-throughput quantitative analysis by desorption electrospray ionization mass spectrometry.

PubMed

Manicke, Nicholas E; Kistler, Thomas; Ifa, Demian R; Cooks, R Graham; Ouyang, Zheng

2009-02-01

A newly developed high-throughput desorption electrospray ionization (DESI) source was characterized in terms of its performance in quantitative analysis. A 96-sample array, containing pharmaceuticals in various matrices, was analyzed in a single run with a total analysis time of 3 min. These solution-phase samples were examined from a hydrophobic PTFE ink printed on glass. The quantitative accuracy, precision, and limit of detection (LOD) were characterized. Chemical background-free samples of propranolol (PRN) with PRN-d(7) as internal standard (IS) and carbamazepine (CBZ) with CBZ-d(10) as IS were examined. So were two other sample sets consisting of PRN/PRN-d(7) at varying concentration in a biological milieu of 10% urine or porcine brain total lipid extract, total lipid concentration 250 ng/microL. The background-free samples, examined in a total analysis time of 1.5 s/sample, showed good quantitative accuracy and precision, with a relative error (RE) and relative standard deviation (RSD) generally less than 3% and 5%, respectively. The samples in urine and the lipid extract required a longer analysis time (2.5 s/sample) and showed RSD values of around 10% for the samples in urine and 4% for the lipid extract samples and RE values of less than 3% for both sets. The LOD for PRN and CBZ when analyzed without chemical background was 10 and 30 fmol, respectively. The LOD of PRN increased to 400 fmol analyzed in 10% urine, and 200 fmol when analyzed in the brain lipid extract.

Analysis Of Condensate Samples In Support Of The Antifoam Degradation Study

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hay, M.; Martino, C.

2016-01-12

The degradation of Antifoam 747 to form flammable decomposition products has resulted in declaration of a Potential Inadequacy in the Safety Analysis (PISA) for the Defense Waste Processing Facility (DWPF). Savannah River National Laboratory (SRNL) testing with simulants showed that hexamethyldisiloxane (HMDSO), trimethylsilanol (TMS), and 1-propanal are formed in the offgas from the decomposition of the antifoam. A total of ten DWPF condensate samples from Batch 735 and 736 were analyzed by SRNL for three degradation products and additional analytes. All of the samples were analyzed to determine the concentrations of HMDSO, TMS, and propanal. The results of the organicmore » analysis found concentrations for propanal and HMDSO near or below the detection limits for the analysis. The TMS concentrations ranged from below detection to 11 mg/L. The samples from Batch 736 were also analyzed for formate and oxalate anions, total organic carbon, and aluminum, iron, manganese, and silicon. Most of the samples contained low levels of formate and therefore low levels of organic carbon. These two values for each sample show reasonable agreement in most cases. Low levels of all the metals (Al, Fe, Mn, and Si) were present in most of the samples.« less

ANALYSIS OF CONDENSATE SAMPLES IN SUPPORT OF THE ANTIFOAM DEGRADATION STUDY

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hay, M.; Martino, C.

2016-02-29

The degradation of Antifoam 747 to form flammable decomposition products has resulted in declaration of a Potential Inadequacy in the Safety Analysis (PISA) for the Defense Waste Processing Facility (DWPF). Savannah River National Laboratory (SRNL) testing with simulants showed that hexamethyldisiloxane (HMDSO), trimethylsilanol (TMS), and 1-propanal are formed in the offgas from the decomposition of the antifoam. A total of ten DWPF condensate samples from Batch 735 and 736 were analyzed by SRNL for three degradation products and additional analytes. All of the samples were analyzed to determine the concentrations of HMDSO, TMS, and propanal. The results of the organicmore » analysis found concentrations for propanal and HMDSO near or below the detection limits for the analysis. The TMS concentrations ranged from below detection to 11 mg/L. The samples from Batch 736 were also analyzed for formate and oxalate anions, total organic carbon, and aluminum, iron, manganese, and silicon. Most of the samples contained low levels of formate and therefore low levels of organic carbon. These two values for each sample show reasonable agreement in most cases. Low levels of all the metals (Al, Fe, Mn, and Si) were present in most of the samples.« less

Point-of-care mobile digital microscopy and deep learning for the detection of soil-transmitted helminths and Schistosoma haematobium.

PubMed

Holmström, Oscar; Linder, Nina; Ngasala, Billy; Mårtensson, Andreas; Linder, Ewert; Lundin, Mikael; Moilanen, Hannu; Suutala, Antti; Diwan, Vinod; Lundin, Johan

2017-06-01

Microscopy remains the gold standard in the diagnosis of neglected tropical diseases. As resource limited, rural areas often lack laboratory equipment and trained personnel, new diagnostic techniques are needed. Low-cost, point-of-care imaging devices show potential in the diagnosis of these diseases. Novel, digital image analysis algorithms can be utilized to automate sample analysis. Evaluation of the imaging performance of a miniature digital microscopy scanner for the diagnosis of soil-transmitted helminths and Schistosoma haematobium, and training of a deep learning-based image analysis algorithm for automated detection of soil-transmitted helminths in the captured images. A total of 13 iodine-stained stool samples containing Ascaris lumbricoides, Trichuris trichiura and hookworm eggs and 4 urine samples containing Schistosoma haematobium were digitized using a reference whole slide-scanner and the mobile microscopy scanner. Parasites in the images were identified by visual examination and by analysis with a deep learning-based image analysis algorithm in the stool samples. Results were compared between the digital and visual analysis of the images showing helminth eggs. Parasite identification by visual analysis of digital slides captured with the mobile microscope was feasible for all analyzed parasites. Although the spatial resolution of the reference slide-scanner is higher, the resolution of the mobile microscope is sufficient for reliable identification and classification of all parasites studied. Digital image analysis of stool sample images captured with the mobile microscope showed high sensitivity for detection of all helminths studied (range of sensitivity = 83.3-100%) in the test set (n = 217) of manually labeled helminth eggs. In this proof-of-concept study, the imaging performance of a mobile, digital microscope was sufficient for visual detection of soil-transmitted helminths and Schistosoma haematobium. Furthermore, we show that deep learning-based image analysis can be utilized for the automated detection and classification of helminths in the captured images.

Point-of-care mobile digital microscopy and deep learning for the detection of soil-transmitted helminths and Schistosoma haematobium

PubMed Central

Holmström, Oscar; Linder, Nina; Ngasala, Billy; Mårtensson, Andreas; Linder, Ewert; Lundin, Mikael; Moilanen, Hannu; Suutala, Antti; Diwan, Vinod; Lundin, Johan

2017-01-01

ABSTRACT Background: Microscopy remains the gold standard in the diagnosis of neglected tropical diseases. As resource limited, rural areas often lack laboratory equipment and trained personnel, new diagnostic techniques are needed. Low-cost, point-of-care imaging devices show potential in the diagnosis of these diseases. Novel, digital image analysis algorithms can be utilized to automate sample analysis. Objective: Evaluation of the imaging performance of a miniature digital microscopy scanner for the diagnosis of soil-transmitted helminths and Schistosoma haematobium, and training of a deep learning-based image analysis algorithm for automated detection of soil-transmitted helminths in the captured images. Methods: A total of 13 iodine-stained stool samples containing Ascaris lumbricoides, Trichuris trichiura and hookworm eggs and 4 urine samples containing Schistosoma haematobium were digitized using a reference whole slide-scanner and the mobile microscopy scanner. Parasites in the images were identified by visual examination and by analysis with a deep learning-based image analysis algorithm in the stool samples. Results were compared between the digital and visual analysis of the images showing helminth eggs. Results: Parasite identification by visual analysis of digital slides captured with the mobile microscope was feasible for all analyzed parasites. Although the spatial resolution of the reference slide-scanner is higher, the resolution of the mobile microscope is sufficient for reliable identification and classification of all parasites studied. Digital image analysis of stool sample images captured with the mobile microscope showed high sensitivity for detection of all helminths studied (range of sensitivity = 83.3–100%) in the test set (n = 217) of manually labeled helminth eggs. Conclusions: In this proof-of-concept study, the imaging performance of a mobile, digital microscope was sufficient for visual detection of soil-transmitted helminths and Schistosoma haematobium. Furthermore, we show that deep learning-based image analysis can be utilized for the automated detection and classification of helminths in the captured images. PMID:28838305

Searching for signatures across microbial communities: Metagenomic analysis of soil samples from mangrove and other ecosystems.

PubMed

Imchen, Madangchanok; Kumavath, Ranjith; Barh, Debmalya; Azevedo, Vasco; Ghosh, Preetam; Viana, Marcus; Wattam, Alice R

2017-08-18

In this study, we categorize the microbial community in mangrove sediment samples from four different locations within a vast mangrove system in Kerala, India. We compared this data to other samples taken from the other known mangrove data, a tropical rainforest, and ocean sediment. An examination of the microbial communities from a large mangrove forest that stretches across southwestern India showed strong similarities across the higher taxonomic levels. When ocean sediment and a single isolate from a tropical rain forest were included in the analysis, a strong pattern emerged with Bacteria from the phylum Proteobacteria being the prominent taxon among the forest samples. The ocean samples were predominantly Archaea, with Euryarchaeota as the dominant phylum. Principal component and functional analyses grouped the samples isolated from forests, including those from disparate mangrove forests and the tropical rain forest, from the ocean. Our findings show similar patterns in samples were isolated from forests, and these were distinct from the ocean sediment isolates. The taxonomic structure was maintained to the level of class, and functional analysis of the genes present also displayed these similarities. Our report for the first time shows the richness of microbial diversity in the Kerala coast and its differences with tropical rain forest and ocean microbiome.

Importance of the efficiency of double-stranded DNA formation in cDNA synthesis for the imprecision of microarray expression analysis.

PubMed

Thormar, Hans G; Gudmundsson, Bjarki; Eiriksdottir, Freyja; Kil, Siyoen; Gunnarsson, Gudmundur H; Magnusson, Magnus Karl; Hsu, Jason C; Jonsson, Jon J

2013-04-01

The causes of imprecision in microarray expression analysis are poorly understood, limiting the use of this technology in molecular diagnostics. Two-dimensional strandness-dependent electrophoresis (2D-SDE) separates nucleic acid molecules on the basis of length and strandness, i.e., double-stranded DNA (dsDNA), single-stranded DNA (ssDNA), and RNA·DNA hybrids. We used 2D-SDE to measure the efficiency of cDNA synthesis and its importance for the imprecision of an in vitro transcription-based microarray expression analysis. The relative amount of double-stranded cDNA formed in replicate experiments that used the same RNA sample template was highly variable, ranging between 0% and 72% of the total DNA. Microarray experiments showed an inverse relationship between the difference between sample pairs in probe variance and the relative amount of dsDNA. Approximately 15% of probes showed between-sample variation (P < 0.05) when the dsDNA percentage was between 12% and 35%. In contrast, only 3% of probes showed between-sample variation when the dsDNA percentage was 69% and 72%. Replication experiments of the 35% dsDNA and 72% dsDNA samples were used to separate sample variation from probe replication variation. The estimated SD of the sample-to-sample variation and of the probe replicates was lower in 72% dsDNA samples than in 35% dsDNA samples. Variation in the relative amount of double-stranded cDNA synthesized can be an important component of the imprecision in T7 RNA polymerase-based microarray expression analysis. © 2013 American Association for Clinical Chemistry

Drinking water quality assessment.

PubMed

Aryal, J; Gautam, B; Sapkota, N

2012-09-01

Drinking water quality is the great public health concern because it is a major risk factor for high incidence of diarrheal diseases in Nepal. In the recent years, the prevalence rate of diarrhoea has been found the highest in Myagdi district. This study was carried out to assess the quality of drinking water from different natural sources, reservoirs and collection taps at Arthunge VDC of Myagdi district. A cross-sectional study was carried out using random sampling method in Arthunge VDC of Myagdi district from January to June,2010. 84 water samples representing natural sources, reservoirs and collection taps from the study area were collected. The physico-chemical and microbiological analysis was performed following standards technique set by APHA 1998 and statistical analysis was carried out using SPSS 11.5. The result was also compared with national and WHO guidelines. Out of 84 water samples (from natural source, reservoirs and tap water) analyzed, drinking water quality parameters (except arsenic and total coliform) of all water samples was found to be within the WHO standards and national standards.15.48% of water samples showed pH (13) higher than the WHO permissible guideline values. Similarly, 85.71% of water samples showed higher Arsenic value (72) than WHO value. Further, the statistical analysis showed no significant difference (P<0.05) of physico-chemical parameters and total coliform count of drinking water for collection taps water samples of winter (January, 2010) and summer (June, 2010). The microbiological examination of water samples revealed the presence of total coliform in 86.90% of water samples. The results obtained from physico-chemical analysis of water samples were within national standard and WHO standards except arsenic. The study also found the coliform contamination to be the key problem with drinking water.

Forensic Comparison of Soil Samples Using Nondestructive Elemental Analysis.

PubMed

Uitdehaag, Stefan; Wiarda, Wim; Donders, Timme; Kuiper, Irene

2017-07-01

Soil can play an important role in forensic cases in linking suspects or objects to a crime scene by comparing samples from the crime scene with samples derived from items. This study uses an adapted ED-XRF analysis (sieving instead of grinding to prevent destruction of microfossils) to produce elemental composition data of 20 elements. Different data processing techniques and statistical distances were evaluated using data from 50 samples and the log-LR cost (C llr ). The best performing combination, Canberra distance, relative data, and square root values, is used to construct a discriminative model. Examples of the spatial resolution of the method in crime scenes are shown for three locations, and sampling strategy is discussed. Twelve test cases were analyzed, and results showed that the method is applicable. The study shows how the combination of an analysis technique, a database, and a discriminative model can be used to compare multiple soil samples quickly. © 2016 American Academy of Forensic Sciences.

Chemical analyses of provided samples

NASA Technical Reports Server (NTRS)

Becker, Christopher H.

1993-01-01

A batch of four samples were received and chemical analysis was performed of the surface and near surface regions of the samples by the surface analysis by laser ionization (SALI) method. The samples included four one-inch diameter optics labeled windows no. PR14 and PR17 and MgF2 mirrors 9-93 PPPC exp. and control DMES 26-92. The analyses emphasized surface contamination or modification. In these studies, pulsed desorption by 355 nm laser light and single-photon ionization (SPI) above the sample by coherent 118 nm radiation (at approximately 5 x 10(exp 5) W/cm(sup 2)) were used, emphasizing organic analysis. For the two windows with an apparent yellowish contaminant film, higher desorption laser power was needed to provide substantial signals, indicating a less volatile contamination than for the two mirrors. Window PR14 and the 9-93 mirror showed more hydrocarbon components than the other two samples. The mass spectra, which show considerable complexity, are discussed in terms of various potential chemical assignments.

Zooanthroponotic transmission of rotavirus in Haryana State of Northern India.

PubMed

Choudhary, P; Minakshi, P; Ranjan, K; Basanti, B

Rotaviruses are the major cause of severe gastroenteritis and mortality in young children and animals. Due to segmented nature of dsRNA genome and wide host range, vast genetic and antigenic diversity exists amongst different isolates of rotaviruses. A total of 230 fecal ovine and caprine samples collected from organized farms and villages in Haryana were screened for rotavirus detection. Samples were screened by latex agglutination test and RNA-PAGE followed by RT-PCR and nucleic acid sequencing. The latex agglutination test showed 25 newborn lamb and 4 kid fecal samples positive for rotavirus. However, RNA-PAGE showed only 9 lamb fecal samples positive for rotavirus. All the samples were subjected to RT-PCR employing vp4 and vp7 gene specific primers of group A rotavirus of ovine, bovine and human origin. Only two samples from lamb (Sheep18/Hisar/2013 and Sheep22/Hisar/2013) showed vp4 and vp7 gene specific amplification with human group A rotavirus (GAR) specific primer. However, they did not show any amplification with ovine and bovine rotavirus specific primers. The nucleotide as well as deduced amino acid sequence analysis of vp4 gene of these isolates showed >98/97% and vp7 gene >95/94% nt/aa identity with human GAR from different regions of the world. Based on nucleotide similarity search, Sheep18/Hisar/2013 and Sheep22/Hisar/2013 isolates were genotyped as G1P[8] and G1P[4]. Phylogenetic analysis also confirmed that these isolates were clustered closely with human rotaviruses from different regions of the world. Earlier, higher prevalence of human rotaviruses was reported from the sample collecting area. The amplification of ovine samples with human rotavirus gene specific primers, sequence identity and phylogenetic analysis strongly suggests the zoonotic transmission of human GAR to sheep.

Isolation of Canine parvovirus with a view to identify the prevalent serotype on the basis of partial sequence analysis.

PubMed

Kaur, Gurpreet; Chandra, Mudit; Dwivedi, P N; Sharma, N S

2015-01-01

The aim of this study was to isolate Canine parvovirus (CPV) from suspected dogs on madin darby canine kidney (MDCK) cell line and its confirmation by polymerase chain reaction (PCR) and nested PCR (NPCR). Further, VP2 gene of the CPV isolates was amplified and sequenced to determine prevailing antigenic type. A total of 60 rectal swabs were collected from dogs showing signs of gastroenteritis, processed and subjected to isolation in MDCK cell line. The samples showing cytopathic effects (CPE) were confirmed by PCR and NPCR. These samples were subjected to PCR for amplification of VP2 gene of CPV, sequenced and analyzed to study the prevailing antigenic types of CPV. Out of the 60 samples subjected to isolation in MDCK cell line five samples showed CPE in the form of rounding of cells, clumping of cells and finally detachment of the cells. When these samples and the two commercially available vaccines were subjected to PCR for amplification of VP2 gene, a 1710 bp product was amplified. The sequence analysis revealed that the vaccines belonged to the CPV-2 type and the samples were of CPV-2b type. It can be concluded from the present study that out of a total of 60 samples 5 samples exhibited CPE as observed in MDCK cell line. Sequence analysis of the VP2 gene among the samples and vaccine strains revealed that samples belonged to CPV-2b type and vaccines belonging to CPV-2.

Getting Ready for Sampling on Mars

NASA Image and Video Library

2012-09-12

This image from NASA Curiosity rover shows the cover on an inlet that will receive powdered rock and soil samples for analysis. The image also shows sand and angular and rounded pebbles that were deposited on the rover deck when it landed.

Grain size statistics and depositional pattern of the Ecca Group sandstones, Karoo Supergroup in the Eastern Cape Province, South Africa

NASA Astrophysics Data System (ADS)

Baiyegunhi, Christopher; Liu, Kuiwu; Gwavava, Oswald

2017-11-01

Grain size analysis is a vital sedimentological tool used to unravel the hydrodynamic conditions, mode of transportation and deposition of detrital sediments. In this study, detailed grain-size analysis was carried out on thirty-five sandstone samples from the Ecca Group in the Eastern Cape Province of South Africa. Grain-size statistical parameters, bivariate analysis, linear discriminate functions, Passega diagrams and log-probability curves were used to reveal the depositional processes, sedimentation mechanisms, hydrodynamic energy conditions and to discriminate different depositional environments. The grain-size parameters show that most of the sandstones are very fine to fine grained, moderately well sorted, mostly near-symmetrical and mesokurtic in nature. The abundance of very fine to fine grained sandstones indicate the dominance of low energy environment. The bivariate plots show that the samples are mostly grouped, except for the Prince Albert samples that show scattered trend, which is due to the either mixture of two modes in equal proportion in bimodal sediments or good sorting in unimodal sediments. The linear discriminant function analysis is dominantly indicative of turbidity current deposits under shallow marine environments for samples from the Prince Albert, Collingham and Ripon Formations, while those samples from the Fort Brown Formation are lacustrine or deltaic deposits. The C-M plots indicated that the sediments were deposited mainly by suspension and saltation, and graded suspension. Visher diagrams show that saltation is the major process of transportation, followed by suspension.

The use of multicomponent statistical analysis in hydrogeological environmental research.

PubMed

Lambrakis, Nicolaos; Antonakos, Andreas; Panagopoulos, George

2004-04-01

The present article examines the possibilities of investigating NO(3)(-) spread in aquifers by applying multicomponent statistical methods (factor, cluster and discriminant analysis) on hydrogeological, hydrochemical, and environmental parameters. A 4-R-Mode factor model determined from the analysis showed its useful role in investigating hydrogeological parameters affecting NO(3)(-) concentration, such as its dilution by upcoming groundwater of the recharge areas. The relationship between NO(3)(-) concentration and agricultural activities can be determined sufficiently by the first factor which relies on NO(3)(-) and SO(4)(2-) of the same origin-that of agricultural fertilizers. The other three factors of R-Mode analysis are not connected directly to the NO(3)(-) problem. They do however, by extracting the role of the unsaturated zone, show an interesting relationship between organic matter content, thickness and saturated hydraulic conductivity. The application of Hirerarchical Cluster Analysis, based on all possible combinations of classification method, showed two main groups of samples. The first group comprises samples from the edges and the second from the central part of the study area. By the application of Discriminant Analysis it was shown that NO(3)(-) and SO(4)(2-) ions are the most significant variables in the discriminant function. Therefore, the first group is considered to comprise all samples from areas not influenced by fertilizers lying on the edges of contaminating activities such as crop cultivation, while the second comprises all the other samples.

A quarter of a century of the DBQ: some supplementary notes on its validity with regard to accidents.

PubMed

de Winter, Joost C F; Dodou, Dimitra; Stanton, Neville A

2015-01-01

This article synthesises the latest information on the relationship between the Driver Behaviour Questionnaire (DBQ) and accidents. We show by means of computer simulation that correlations with accidents are necessarily small because accidents are rare events. An updated meta-analysis on the zero-order correlations between the DBQ and self-reported accidents yielded an overall r of .13 (fixed-effect and random-effects models) for violations (57,480 participants; 67 samples) and .09 (fixed-effect and random-effects models) for errors (66,028 participants; 56 samples). An analysis of a previously published DBQ dataset (975 participants) showed that by aggregating across four measurement occasions, the correlation coefficient with self-reported accidents increased from .14 to .24 for violations and from .11 to .19 for errors. Our meta-analysis also showed that DBQ violations (r = .24; 6353 participants; 20 samples) but not DBQ errors (r = - .08; 1086 participants; 16 samples) correlated with recorded vehicle speed. Practitioner Summary: The DBQ is probably the most widely used self-report questionnaire in driver behaviour research. This study shows that DBQ violations and errors correlate moderately with self-reported traffic accidents.

Determination of total sulfur in lichens and plants by combustion-infrared analysis

USGS Publications Warehouse

Jackson, L.L.; Engleman, E.E.; Peard, J.L.

1985-01-01

Sulfur was determined in plants and lichens by combustion of the sample and infrared detection of evolved sulfur dioxide using an automated sulfur analyzer. Vanadium pentaoxide was used as a combustion accelerator. Pelletization of the sample prior to combustion was not found to be advantageous. Washing studies showed that leaching of sulfur was not a major factor in the sample preparation. The combustion-IR analysis usually gave higher sulfur content than the turbidimetric analysis as well as shorter analysis time. Relative standard deviations of less than 7% were obtained by the combustion-IR technique when sulfur levels in plant material ranged from 0.05 to 0.70%. Determination of sulfur in National Bureau of Standards botanical reference materials showed good agreement between the combustion-IR technique and other instrumental procedures. Seven NBS botanical reference materials were analyzed.

Comparison of vacuum and non-vacuum urine tubes for urinary sediment analysis.

PubMed

Topcuoglu, Canan; Sezer, Sevilay; Kosem, Arzu; Ercan, Mujgan; Turhan, Turan

2017-12-01

Urine collection systems with aspiration system for vacuum tubes are becoming increasingly common for urinalysis, especially for microscopic examination of the urine. In this study, we aimed to examine whether vacuum aspiration of the urine sample has any adverse effect on sediment analysis by comparing results from vacuum and non-vacuum urine tubes. The study included totally 213 urine samples obtained from inpatients and outpatients in our hospital. Urine samples were collected to containers with aspiration system for vacuum tubes. Each sample was aliquoted to both vacuum and non-vacuum urine tubes. Urinary sediment analysis was performed using manual microscope. Results were evaluated using chi-square test. Comparison of the sediment analysis results from vacuum and non-vacuum urine tubes showed that results were highly concordant for erythrocyte, leukocyte and epithelial cells (gamma values 1, 0.997, and 0.994, respectively; p < .001). Results were also concordant for urinary casts, crystals and yeast (kappa values 0.815, 0.945 and 1, respectively; p < .001). The results show that in urinary sediment analysis, vacuum aspiration has no adverse effect on the cellular components except on casts.

Isolation of Canine parvovirus with a view to identify the prevalent serotype on the basis of partial sequence analysis

PubMed Central

Kaur, Gurpreet; Chandra, Mudit; Dwivedi, P. N.; Sharma, N. S.

2015-01-01

Aim: The aim of this study was to isolate Canine parvovirus (CPV) from suspected dogs on madin darby canine kidney (MDCK) cell line and its confirmation by polymerase chain reaction (PCR) and nested PCR (NPCR). Further, VP2 gene of the CPV isolates was amplified and sequenced to determine prevailing antigenic type. Materials and Methods: A total of 60 rectal swabs were collected from dogs showing signs of gastroenteritis, processed and subjected to isolation in MDCK cell line. The samples showing cytopathic effects (CPE) were confirmed by PCR and NPCR. These samples were subjected to PCR for amplification of VP2 gene of CPV, sequenced and analyzed to study the prevailing antigenic types of CPV. Results: Out of the 60 samples subjected to isolation in MDCK cell line five samples showed CPE in the form of rounding of cells, clumping of cells and finally detachment of the cells. When these samples and the two commercially available vaccines were subjected to PCR for amplification of VP2 gene, a 1710 bp product was amplified. The sequence analysis revealed that the vaccines belonged to the CPV-2 type and the samples were of CPV-2b type. Conclusion: It can be concluded from the present study that out of a total of 60 samples 5 samples exhibited CPE as observed in MDCK cell line. Sequence analysis of the VP2 gene among the samples and vaccine strains revealed that samples belonged to CPV-2b type and vaccines belonging to CPV-2. PMID:27046996

Breakdown Characteristic Analysis of Paper- Oil Insulation under AC and DC Voltage

NASA Astrophysics Data System (ADS)

Anuar, N. F.; Jamail, N. A. M.; Rahman, R. A.; Kamarudin, M. S.

2017-08-01

This paper presents the study of breakdown characteristic of Kraft paper insulated with two different types of insulating fluid, which are Palm oil and Coconut oil. Palm oil and Coconut oil are chosen as the alternative fluid to the transformer oil because it has high potential and environmentally-friendly. The Segezha Kraft papers with various thicknesses (65.5 gsm, 75 gsm, 85gsm, 90 gsm) have been used in this research. High Voltage Direct Current (HVDC), High Voltage Alternating Current (HVAC) and carbon track and severity analysis is conducted to observe the sample of aging Kraft paper. These samples have been immersed using Palm oil and Coconut oil up to 90 days to observe the absorption rate. All samples started to reach saturation level at 70 days of immersion. HVDC and HVAC breakdown experiments have been done after the samples had reached the saturation level based on normal condition, immersed in Palm oil and immersed in Coconut oil. All samples immersed in liquid show different breakdown voltage reading compared to normal condition. The analysis of carbon track and severity on surface has been done using Analytical Scanning Electron Microscope (SEM) Analysis. The results of the experiment show that the sample of Kraft paper immersed in Palm oil was better than Coconut oil immersed sample. Therefore the sample condition was the main factor that determines the value of breakdown voltage test. Introduction

Fingerprint analysis of Hibiscus mutabilis L. leaves based on ultra performance liquid chromatography with photodiode array detector combined with similarity analysis and hierarchical clustering analysis methods

PubMed Central

Liang, Xianrui; Ma, Meiling; Su, Weike

2013-01-01

Background: A method for chemical fingerprint analysis of Hibiscus mutabilis L. leaves was developed based on ultra performance liquid chromatography with photodiode array detector (UPLC-PAD) combined with similarity analysis (SA) and hierarchical clustering analysis (HCA). Materials and Methods: 10 batches of Hibiscus mutabilis L. leaves samples were collected from different regions of China. UPLC-PAD was employed to collect chemical fingerprints of Hibiscus mutabilis L. leaves. Results: The relative standard deviations (RSDs) of the relative retention times (RRT) and relative peak areas (RPA) of 10 characteristic peaks (one of them was identified as rutin) in precision, repeatability and stability test were less than 3%, and the method of fingerprint analysis was validated to be suitable for the Hibiscus mutabilis L. leaves. Conclusions: The chromatographic fingerprints showed abundant diversity of chemical constituents qualitatively in the 10 batches of Hibiscus mutabilis L. leaves samples from different locations by similarity analysis on basis of calculating the correlation coefficients between each two fingerprints. Moreover, the HCA method clustered the samples into four classes, and the HCA dendrogram showed the close or distant relations among the 10 samples, which was consistent to the SA result to some extent. PMID:23930008

The Effect of Postmastectomy Radiation Therapy on Breast Implants: Material Analysis on Silicone and Polyurethane Prosthesis.

PubMed

Lo Torto, Federico; Relucenti, Michela; Familiari, Giuseppe; Vaia, Nicola; Casella, Donato; Matassa, Roberto; Miglietta, Selenia; Marinozzi, Franco; Bini, Fabiano; Fratoddi, Ilaria; Sciubba, Fabio; Cassese, Raffaele; Tombolini, Vincenzo; Ribuffo, Diego

2018-05-17

The pathogenic mechanism underlying capsular contracture is still unknown. It is certainly a multifactorial process, resulting from human body reaction, biofilm activation, bacteremic seeding, or silicone exposure. The scope of the present article is to investigate the effect of hypofractionated radiotherapy protocol (2.66 Gy × 16 sessions) both on silicone and polyurethane breast implants. Silicone implants and polyurethane underwent irradiation according to a hypofractionated radiotherapy protocol for the treatment of breast cancer. After irradiation implant shells underwent mechanical, chemical, and microstructural evaluation by means of tensile testing, infrared spectra in attenuated total reflectance mode, nuclear magnetic resonance, and field emission scanning electron microscopy. At superficial analysis, irradiated silicone samples show several visible secondary and tertiary blebs. Polyurethane implants showed an open cell structure, which closely resembles a sponge. Morphological observation of struts from treated polyurethane sample shows a more compact structure, with significantly shorter and thicker struts compared with untreated sample. The infrared spectra in attenuated total reflectance mode spectra of irradiated and control samples were compared either for silicon and polyurethane samples. In the case of silicone-based membranes, treated and control specimens showed similar bands, with little differences in the treated one. Nuclear magnetic resonance spectra on the fraction soluble in CDCl3 support these observations. Tensile tests on silicone samples showed a softer behavior of the treated ones. Tensile tests on Polyurethane samples showed no significant differences. Polyurethane implants seem to be more resistant to radiotherapy damage, whereas silicone prosthesis showed more structural, mechanical, and chemical modifications.

Mars Rock Analysis Briefing

NASA Image and Video Library

2013-03-12

Paul Mahaffy, principal investigator for Curiosity's Sample Analysis at Mars (SAM) investigation at NASA's Goddard Space Flight Center in Maryland, answer's a reporters question at a news conference, Tuesday, March 12, 2013 at NASA Headquarters in Washington. The news conference covered the findings that the analysis of the rock sample collected shows ancient Mars could have supported living microbes. Photo Credit: (NASA/Carla Cioffi)

High resolution DNA melting analysis: an application for prenatal control of alpha-thalassemia.

PubMed

Sirichotiyakul, Supatra; Wanapirak, Chanane; Saetung, Rattika; Sanguansermsri, Torpong

2010-04-01

To report the use of real-time gap-PCR using SYTO9 with high-resolution melting analysis (HRMA) in prenatal diagnosis of alpha-thalassemia 1. Real-time gap-PCR using SYTO9 with HRMA was performed in 33 DNA samples from chorionic villi sampling (8 normal, 16 heterozygous, and 9 homozygous) to determine the alpha-thalassemia 1 gene [normal and Southeast Asia (-SEA) allele]. The dissociation curve analysis in normal and - SEA allele gave a peak of T(m) at 91.80 +/- 0.14 degrees C and 88.67 +/- 0.08 degrees C, respectively. Normal genotype and homozygous alpha-thalassemia 1 showed a single peak of T(m) that corresponded to their alleles. The heterozygotes gave both peaks with higher normal peak and smaller - SEA peak. Thirty one samples showed consistent results with the conventional gap-PCR. Two samples with ambiguous results were confirmed to be maternal DNA contamination on real-time quantitative PCR and microsatellite assay. HRMA from both samples showed similar pattern to that of heterozygotes. However, they showed much smaller normal peak compared with the - SEA peak, which is in contrast to those of heterozygotes and can readily be distinguished. HRMA with SYTO9 is feasible for prenatal diagnosis of alpha-thalassemia. It had potential advantage of prompt detection maternal DNA contamination. Copyright (c) 2010 John Wiley & Sons, Ltd.

Analysis of imidacloprid residues in fruits, vegetables, cereals, fruit juices, and baby foods, and daily intake estimation in and around Lucknow, India.

PubMed

Kapoor, Upasana; Srivastava, M K; Srivastava, Ashutosh Kumar; Patel, D K; Garg, Veena; Srivastava, L P

2013-03-01

A total of 250 samples-including fruits, fruit juices, and baby foods (50 samples each), vegetables (70 samples), and cereals (30 samples)-were collected from Lucknow, India, and analyzed for the presence of imidacloprid residues. The QuEChERS (quick, easy, cheap, effective, rugged, and safe) method of extraction coupled with high-performance liquid chromatographic analysis were carried out, and imidacloprid residues were qualitatively confirmed by liquid chromatography-mass spectrometry. Imidacloprid was not detected in samples of fruit juices and baby foods. It was, however, detected in 38 samples of fruits, vegetables, and cereals, which is about 15.20% of the total samples. Of samples of fruits, 22% showed the presence of imidacloprid, and 2% of samples showed residues above the maximal residue limit. Although imidacloprid was detected in 24% of vegetable samples, only 5.71% showed the presence of imidacloprid above the maximal residue limit. However, 33% of cereal samples showed the presence of imidacloprid, and about 3% of samples were above the maximal residue limit. The calculated estimated daily intake ranged between 0.004 and 0.131 µg/kg body weight, and the hazard indices ranged from 0.007 to 0.218 for these food commodities. It is therefore indicated that lifetime consumption of vegetables, fruits, fruit juices, baby foods, wheat, rice, and pulses may not pose a health hazard for the population of Lucknow because the hazard indices for imidacloprid residues were below one. Copyright © 2012 SETAC.

Comparative forensic soil analysis of New Jersey state parks using a combination of simple techniques with multivariate statistics.

PubMed

Bonetti, Jennifer; Quarino, Lawrence

2014-05-01

This study has shown that the combination of simple techniques with the use of multivariate statistics offers the potential for the comparative analysis of soil samples. Five samples were obtained from each of twelve state parks across New Jersey in both the summer and fall seasons. Each sample was examined using particle-size distribution, pH analysis in both water and 1 M CaCl2 , and a loss on ignition technique. Data from each of the techniques were combined, and principal component analysis (PCA) and canonical discriminant analysis (CDA) were used for multivariate data transformation. Samples from different locations could be visually differentiated from one another using these multivariate plots. Hold-one-out cross-validation analysis showed error rates as low as 3.33%. Ten blind study samples were analyzed resulting in no misclassifications using Mahalanobis distance calculations and visual examinations of multivariate plots. Seasonal variation was minimal between corresponding samples, suggesting potential success in forensic applications. © 2014 American Academy of Forensic Sciences.

An overview on forensic analysis devoted to analytical chemists.

PubMed

Castillo-Peinado, L S; Luque de Castro, M D

2017-05-15

The present article has as main aim to show analytical chemists interested in forensic analysis the world they will face if decision in favor of being a forensic analytical chemist is adopted. With this purpose, the most outstanding aspects of forensic analysis in dealing with sampling (involving both bodily and no bodily samples), sample preparation, and analytical equipment used in detection, identification and quantitation of key sample components are critically discussed. The role of the great omics in forensic analysis, and the growing role of the youngest of the great omics -metabolomics- are also discussed. The foreseeable role of integrative omics is also outlined. Copyright © 2017 Elsevier B.V. All rights reserved.

Chemometric techniques on the analysis of Raman spectra of serum blood samples of breast cancer patients

NASA Astrophysics Data System (ADS)

Rocha-Osornio, L. N.; Pichardo-Molina, J. L.; Barbosa-Garcia, O.; Frausto-Reyes, C.; Araujo-Andrade, C.; Huerta-Franco, R.; Gutiérrez-Juárez, G.

2008-02-01

Raman spectroscopy and Multivariate methods were used to study serum blood samples of control and breast cancer patients. Blood samples were obtained from 11 patients and 12 controls from the central region of Mexico. Our results show that principal component analysis is able to discriminate serum sample of breast cancer patients from those of control group, also the loading vectors of PCA plotted as a function of Raman shift shown which bands permitted to make the maximum discrimination between both groups of samples.

Effects of orbital exposure on Halar during the LDEF mission

NASA Technical Reports Server (NTRS)

Brower, William E., Jr.; Holla, Harish; Bauer, Robert A.

1992-01-01

Thermomechanical Analysis (TMA), Differential Scanning Calorimetry (DSC), and Thermogravimetric Analysis (TGA) were performed on samples of Halar exposed on the LDEF Mission for 6 years in orbit and unexposed Halar control samples. Sections 10-100 microns thick were removed from the exposed surface down to a depth of 1,000 microns through the 3 mm thick samples. The TMA and DSC results, which arise from the entire slice and not just its surface, showed no differences between the LDEF and the control samples. TMA scans were run from ambient to 300 C; results were compared by a tabulation of the glass transition temperatures. DSC scans were run from ambient to 700 C; the enthalpy of melting was compared for the samples as a function of section depth with the sample. The TGA results, which arise from the surface of the sample initially, showed a sharp increase in the topmost 50 micron section (the exposed, discolored side) in the weight loss of 170 C in oxygen. This weight loss dropped to bulk values in the range of depth of 50-200 microns. The control sample showed only a slight increase in weight loss as the top surface was approached. The LDEF Halar sample appears to be mechanically undamaged, with a surface layer which oxidizes faster as a result of orbital exposure.

Synthesis and characterization of Zn-Mg ferrite

NASA Astrophysics Data System (ADS)

Singh, Shailndra; Barbar, S. K.; Ram, Sahi

2018-05-01

The Zn-Mg ferrite sample of general formula Zn0.5Mg0.5Fe2O4 have been prepared by standard solid state reaction technique using high purity oxides. X-ray diffraction analysis shows the formation of a zinc-magnesium ferrite cubic phase at room temperature with space group Fd3m. FTIR spectra show two significant absorption bands first at 665.15 cm-1 corresponding to tetrahedral (A) and second band at 434 cm-1 corresponding to octahedral (B) sites of the spinel. Morphology of the sample determined by the SEM measurement and EDS analysis has confirmed the composition of atoms in the sample.

Applying glass ionomer cement to MTA flow™ and biodentine™ and its effects on the interface layer

NASA Astrophysics Data System (ADS)

Savitri, D.; Suprastiwi, E.; Margono, A.

2017-08-01

This study compared the interface layer formation between Glass Ionomer Cement (GIC) with Biodentine™ and between GIC with MTA Flow™. There were 10 samples in each group. Biodentine™ and MTA Flow™ were filled with GIC in plastic molds then incubated at a temperature of 37 °C with 100% humidity for 24 hours. Samples were sectioned vertically with diamond discs and examined using a scanning electron microscope. The statistical analysis was performed using the Mann-Whitney Test. In group 1, 80% of the samples showed a score of 1 and 20% of the samples showed a score of 2. In group 2, 30% of the samples showed a score of 2 and 70% of the samples showed a score of 3. This clinical trial showed that the formation of interface layers in Biodentine™ and MTA Flow™ were significantly different.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jackson, L.L.; Engleman, E.E.; Peard, J.L.

Sulfur was determined in plants and lichens by combustion of the sample and infrared detection of evolved sulfur dioxide using an automated sulfur analyzer. Vanadium pentaoxide was used as a combustion accelerator. Pelletization of the sample prior to combustion was not found to be advantageous. Washing studies showed that leaching of sulfur was not a major factor in the sample preparation. The combustion-IR analysis usually gave higher sulfur content than the turbidimetric analysis as well as shorter analysis time. Relative standard deviations of less than 7% were obtained by the combustion-IR technique when sulfur levels in plant material range frommore » 0.05 to 0.70%. Determination of sulfur in National Bureau of Standards botanical reference materials showed good agreement between the combustion-IR technique and other instrumental procedures. Seven NBS botanical reference materials were analyzed.« less

Detection of caffeine in tea, instant coffee, green tea beverage, and soft drink by direct analysis in real time (DART) source coupled to single-quadrupole mass spectrometry.

PubMed

Wang, Lei; Zhao, Pengyue; Zhang, Fengzu; Bai, Aijuan; Pan, Canping

2013-01-01

Ambient ionization direct analysis in real time (DART) coupled to single-quadrupole MS (DART-MS) was evaluated for rapid detection of caffeine in commercial samples without chromatographic separation or sample preparation. Four commercial samples were examined: tea, instant coffee, green tea beverage, and soft drink. The response-related parameters were optimized for the DART temperature and MS fragmentor. Under optimal conditions, the molecular ion (M+H)+ was the major ion for identification of caffeine. The results showed that DART-MS is a promising tool for the quick analysis of important marker molecules in commercial samples. Furthermore, this system has demonstrated significant potential for high sample throughput and real-time analysis.

Design and Field Procedures in the US National Comorbidity Survey Replication Adolescent Supplement (NCS-A)

PubMed Central

Kessler, Ronald C.; Avenevoli, Shelli; Costello, E. Jane; Green, Jennifer Greif; Gruber, Michael J.; Heeringa, Steven; Merikangas, Kathleen R.; Pennell, Beth-Ellen; Sampson, Nancy A.; Zaslavsky, Alan M.

2009-01-01

An overview is presented of the design and field procedures of the US National Comorbidity Survey Replication Adolescent Supplement (NCS-A), a US face-to-face household survey of the prevalence and correlates of DSM-IV mental disorders. The survey was based on a dual-frame design that included 904 adolescent residents of the households that participated in the US National Comorbidity Survey Replication (85.9% response rate) and 9,244 adolescent students selected from a nationally representative sample of 320 schools (74.7% response rate). After expositing the logic of dual-frame designs, comparisons are presented of sample and population distributions on Census socio-demographic variables and, in the school sample, school characteristics. These document only minor differences between the samples and the population. The results of statistical analysis of the bias-efficiency trade-off in weight trimming are then presented. These show that modest trimming meaningfully reduces mean squared error. Analysis of comparative sample efficiency shows that the household sample is more efficient than the school sample, leading to the household sample getting a higher weight relative to its size in the consolidated sample relative to the school sample. Taken together, these results show that the NCS-A is an efficient sample of the target population with good representativeness on a range of socio-demographic and geographic variables. PMID:19507169

Surface Enhanced Raman Spectroscopy (SERS) and multivariate analysis as a screening tool for detecting Sudan I dye in culinary spices

NASA Astrophysics Data System (ADS)

Di Anibal, Carolina V.; Marsal, Lluís F.; Callao, M. Pilar; Ruisánchez, Itziar

2012-02-01

Raman spectroscopy combined with multivariate analysis was evaluated as a tool for detecting Sudan I dye in culinary spices. Three Raman modalities were studied: normal Raman, FT-Raman and SERS. The results show that SERS is the most appropriate modality capable of providing a proper Raman signal when a complex matrix is analyzed. To get rid of the spectral noise and background, Savitzky-Golay smoothing with polynomial baseline correction and wavelet transform were applied. Finally, to check whether unadulterated samples can be differentiated from samples adulterated with Sudan I dye, an exploratory analysis such as principal component analysis (PCA) was applied to raw data and data processed with the two mentioned strategies. The results obtained by PCA show that Raman spectra need to be properly treated if useful information is to be obtained and both spectra treatments are appropriate for processing the Raman signal. The proposed methodology shows that SERS combined with appropriate spectra treatment can be used as a practical screening tool to distinguish samples suspicious to be adulterated with Sudan I dye.

A hierarchical and modular approach to the discovery of robust associations in genome-wide association studies from pooled DNA samples

PubMed Central

Sebastiani, Paola; Zhao, Zhenming; Abad-Grau, Maria M; Riva, Alberto; Hartley, Stephen W; Sedgewick, Amanda E; Doria, Alessandro; Montano, Monty; Melista, Efthymia; Terry, Dellara; Perls, Thomas T; Steinberg, Martin H; Baldwin, Clinton T

2008-01-01

Background One of the challenges of the analysis of pooling-based genome wide association studies is to identify authentic associations among potentially thousands of false positive associations. Results We present a hierarchical and modular approach to the analysis of genome wide genotype data that incorporates quality control, linkage disequilibrium, physical distance and gene ontology to identify authentic associations among those found by statistical association tests. The method is developed for the allelic association analysis of pooled DNA samples, but it can be easily generalized to the analysis of individually genotyped samples. We evaluate the approach using data sets from diverse genome wide association studies including fetal hemoglobin levels in sickle cell anemia and a sample of centenarians and show that the approach is highly reproducible and allows for discovery at different levels of synthesis. Conclusion Results from the integration of Bayesian tests and other machine learning techniques with linkage disequilibrium data suggest that we do not need to use too stringent thresholds to reduce the number of false positive associations. This method yields increased power even with relatively small samples. In fact, our evaluation shows that the method can reach almost 70% sensitivity with samples of only 100 subjects. PMID:18194558

Quantifying Antimicrobial Resistance at Veal Calf Farms

PubMed Central

Bosman, Angela B.; Wagenaar, Jaap; Stegeman, Arjan; Vernooij, Hans; Mevius, Dik

2012-01-01

This study was performed to determine a sampling strategy to quantify the prevalence of antimicrobial resistance on veal calf farms, based on the variation in antimicrobial resistance within and between calves on five farms. Faecal samples from 50 healthy calves (10 calves/farm) were collected. From each individual sample and one pooled faecal sample per farm, 90 selected Escherichia coli isolates were tested for their resistance against 25 mg/L amoxicillin, 25 mg/L tetracycline, 0.5 mg/L cefotaxime, 0.125 mg/L ciprofloxacin and 8/152 mg/L trimethoprim/sulfamethoxazole (tmp/s) by replica plating. From each faecal sample another 10 selected E. coli isolates were tested for their resistance by broth microdilution as a reference. Logistic regression analysis was performed to compare the odds of testing an isolate resistant between both test methods (replica plating vs. broth microdilution) and to evaluate the effect of pooling faecal samples. Bootstrap analysis was used to investigate the precision of the estimated prevalence of resistance to each antimicrobial obtained by several simulated sampling strategies. Replica plating showed similar odds of E. coli isolates tested resistant compared to broth microdilution, except for ciprofloxacin (OR 0.29, p≤0.05). Pooled samples showed in general lower odds of an isolate being resistant compared to individual samples, although these differences were not significant. Bootstrap analysis showed that within each antimicrobial the various compositions of a pooled sample provided consistent estimates for the mean proportion of resistant isolates. Sampling strategies should be based on the variation in resistance among isolates within faecal samples and between faecal samples, which may vary by antimicrobial. In our study, the optimal sampling strategy from the perspective of precision of the estimated levels of resistance and practicality consists of a pooled faecal sample from 20 individual animals, of which 90 isolates are tested for their susceptibility by replica plating. PMID:22970313

Impact of Oriented Clay Particles on X-Ray Spectroscopy Analysis

NASA Astrophysics Data System (ADS)

Lim, A. J. M. S.; Syazwani, R. N.; Wijeyesekera, D. C.

2016-07-01

Understanding the engineering properties of the mineralogy and microfabic of clayey soils is very complex and thus very difficult for soil characterization. Micromechanics of soils recognize that the micro structure and mineralogy of clay have a significant influence on its engineering behaviour. To achieve a more reliable quantitative evaluation of clay mineralogy, a proper sample preparation technique for quantitative clay mineral analysis is necessary. This paper presents the quantitative evaluation of elemental analysis and chemical characterization of oriented and random oriented clay particles using X-ray spectroscopy. Three different types of clays namely marine clay, bentonite and kaolin clay were studied. The oriented samples were prepared by placing the dispersed clay in water and left to settle on porous ceramic tiles by applying a relatively weak suction through a vacuum pump. Images form a Scanning Electron Microscope (SEM) was also used to show the comparison between the orientation patterns of both the sample preparation techniques. From the quantitative analysis of the X-ray spectroscopy, oriented sampling method showed more accuracy in identifying mineral deposits, because it produced better peak intensity on the spectrum and more mineral content can be identified compared to randomly oriented samples.

Rapid Analysis of Carbohydrates in Bioprocess Samples: An Evaluation of the CarboPac SA10 for HPAE-PAD Analysis by Interlaboratory Comparison

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sevcik, R. S.; Hyman, D. A.; Basumallich, L.

2013-01-01

A technique for carbohydrate analysis for bioprocess samples has been developed, providing reduced analysis time compared to current practice in the biofuels R&D community. The Thermofisher CarboPac SA10 anion-exchange column enables isocratic separation of monosaccharides, sucrose and cellobiose in approximately 7 minutes. Additionally, use of a low-volume (0.2 mL) injection valve in combination with a high-volume detection cell minimizes the extent of sample dilution required to bring sugar concentrations into the linear range of the pulsed amperometric detector (PAD). Three laboratories, representing academia, industry, and government, participated in an interlaboratory study which analyzed twenty-one opportunistic samples representing biomass pretreatment, enzymaticmore » saccharification, and fermentation samples. The technique's robustness, linearity, and interlaboratory reproducibility were evaluated and showed excellent-to-acceptable characteristics. Additionally, quantitation by the CarboPac SA10/PAD was compared with the current practice method utilizing a HPX-87P/RID. While these two methods showed good agreement a statistical comparison found significant quantitation difference between them, highlighting the difference between selective and universal detection modes.« less

Partitioning behavior of heavy metals and persistent organic pollutants among feto-maternal bloods and tissues.

PubMed

Kim, Jun-Tae; Son, Min-Hui; Lee, Duk-Hee; Seong, Won Joon; Han, Seunghee; Chang, Yoon-Seok

2015-06-16

Heavy metals and persistent organic pollutants (POPs), including Pb, Cd, T-Hg, MeHg, PCDD/Fs, PCBs, PBDEs, PCNs, and PBDD/Fs, were analyzed in 20 paired samples of cord blood, maternal blood, maternal urine, and placenta. The samples were collected from pregnant mothers and neonates from South Korea in 2010. The distribution of heavy metals among the samples varied with their physicochemical characteristics. The concentrations of Pb and Hg in the maternal and the cord blood samples were significantly correlated each other, implying efficient transplacental transport (TPT). Cd and Hg were accumulated in the placenta, forming protein conjugates, and T-Hg was higher in the cord blood samples than the maternal blood samples due to the binding affinity of Hg with fetal proteins. POPs generally showed the highest concentrations in the maternal serum samples, and the POPs levels in the cord serum and the placenta samples were dependent on the degree of halogenation. The TPT of POPs was seemingly related to lipoprotein transportation. Some PBDE congeners, however, showed their highest concentrations in the cord serum samples, suggesting an additional TPT mechanism. This is the first study to detect PCNs and PBDD/Fs in the cord serum samples, showing that the PCN levels were comparable to other POPs. According to the principal component analysis (PCA) results of the contaminant levels, POPs and heavy metals showed significantly different characteristics, whereas PBDEs had an intermediate attribute. Despite the limited number of participants, the comprehensive analysis of trace contaminants in the paired sample sets enabled us to infer the distribution and TPT mechanism of various contaminants.

A Two-Stage Method to Determine Optimal Product Sampling considering Dynamic Potential Market

PubMed Central

Hu, Zhineng; Lu, Wei; Han, Bing

2015-01-01

This paper develops an optimization model for the diffusion effects of free samples under dynamic changes in potential market based on the characteristics of independent product and presents a two-stage method to figure out the sampling level. The impact analysis of the key factors on the sampling level shows that the increase of the external coefficient or internal coefficient has a negative influence on the sampling level. And the changing rate of the potential market has no significant influence on the sampling level whereas the repeat purchase has a positive one. Using logistic analysis and regression analysis, the global sensitivity analysis gives a whole analysis of the interaction of all parameters, which provides a two-stage method to estimate the impact of the relevant parameters in the case of inaccuracy of the parameters and to be able to construct a 95% confidence interval for the predicted sampling level. Finally, the paper provides the operational steps to improve the accuracy of the parameter estimation and an innovational way to estimate the sampling level. PMID:25821847

Is High Resolution Melting Analysis (HRMA) Accurate for Detection of Human Disease-Associated Mutations? A Meta Analysis

PubMed Central

Ma, Feng-Li; Jiang, Bo; Song, Xiao-Xiao; Xu, An-Gao

2011-01-01

Background High Resolution Melting Analysis (HRMA) is becoming the preferred method for mutation detection. However, its accuracy in the individual clinical diagnostic setting is variable. To assess the diagnostic accuracy of HRMA for human mutations in comparison to DNA sequencing in different routine clinical settings, we have conducted a meta-analysis of published reports. Methodology/Principal Findings Out of 195 publications obtained from the initial search criteria, thirty-four studies assessing the accuracy of HRMA were included in the meta-analysis. We found that HRMA was a highly sensitive test for detecting disease-associated mutations in humans. Overall, the summary sensitivity was 97.5% (95% confidence interval (CI): 96.8–98.5; I2 = 27.0%). Subgroup analysis showed even higher sensitivity for non-HR-1 instruments (sensitivity 98.7% (95%CI: 97.7–99.3; I2 = 0.0%)) and an eligible sample size subgroup (sensitivity 99.3% (95%CI: 98.1–99.8; I2 = 0.0%)). HRMA specificity showed considerable heterogeneity between studies. Sensitivity of the techniques was influenced by sample size and instrument type but by not sample source or dye type. Conclusions/Significance These findings show that HRMA is a highly sensitive, simple and low-cost test to detect human disease-associated mutations, especially for samples with mutations of low incidence. The burden on DNA sequencing could be significantly reduced by the implementation of HRMA, but it should be recognized that its sensitivity varies according to the number of samples with/without mutations, and positive results require DNA sequencing for confirmation. PMID:22194806

Effect of DMMP on the pyrolysis products of polyurethane foam materials in the gaseous phase

NASA Astrophysics Data System (ADS)

Liu, W.; Li, F.; Ge, X. G.; Zhang, Z. J.; He, J.; Gao, N.

2016-07-01

Dimethyl methylphosphonate (DMMP) has been used as a flame retardant containing phosphorus to decrease the flammability of the polyurethane foam material (PUF). Flame retardancy and thermal degradation of PUF samples have been investigated by the LOI tests and thermal analysis. The results show that LOI values of all PUF/DMMP samples are higher than that of the neat PUF sample and the LOI value of the samples increases with both DMMP concentration and the %P value. Thermal analysis indicates that flame retardant PUF shows a dominant condensed flame retardant activity during combustion. Thermogravimetric analysis-infrared spectrometry (TG-FTIR) has been used to study the influence of DMMP on the pyrolysis products in the gaseous phase during the thermal degradation of the PUF sample. Fourier transform infrared spectrometry (FTIR) spectra of the PUF sample at the maximum evolution rates and the generated trends of water and the products containing -NCO have been examined to obtain more information about the pyrolysis product evolutions of the samples at high temperature. These results reveal that although DMMP could improve the thermal stability of PUF samples through the formation of the residual char layer between fire and the decomposed materials, the influence of DMMP on the gaseous phase can be also observed during the thermal degradation process of materials.

Carbon ions irradiation on nano- and microcrystalline CaSO4 : Dy

NASA Astrophysics Data System (ADS)

Salah, Numan

2008-08-01

Nanoparticles of CaSO4 : Dy phosphor with a particle size of around 30 nm have been prepared by the chemical co-precipitation technique. Pellet samples of the nanomaterials were irradiated by a 75 MeV C6+ ion beam at the fluence range 1 × 109-1 × 1013 ions cm-2. Thermoluminescence (TL) glow curves of the irradiated samples were recorded and studied. The microcrystalline form of this sample is also included in the study with the aim of reporting a comparative measurement. The TL analysis shows that the glow curve of the nanomaterial has two peaks at around 166 and 210 °C. These peaks are similar to those induced in the microcrystalline sample with a slight difference in their TL response. The second peak is more prominent in the case of the microcrystalline sample at low fluences, while the first one dominates in the nanostructured sample mainly at higher fluences. The TRIM code based on Monte Carlo simulation was also used for calculating some ion beam parameters. Dosimetric properties of the carbon ion beam irradiated materials show that the nanostructure material has excellent features such as a simple glow curve structure and a linear TL response over a wider range than the corresponding microcrystalline sample. These results show that the nanostructure form of CaSO4 : Dy might be useful for detecting the high doses of carbon ions used in radiotherapy. Thermal analysis of the prepared nano- and microcrystalline materials was also done in the range 50-500 °C using thermogravimetry analysis and differential thermal analysis. No phase transitions within this range of heating for both the materials are observed.

Detection of anabolic androgenic steroid abuse in doping control using mammalian reporter gene bioassays.

PubMed

Houtman, Corine J; Sterk, Saskia S; van de Heijning, Monique P M; Brouwer, Abraham; Stephany, Rainer W; van der Burg, Bart; Sonneveld, Edwin

2009-04-01

Anabolic androgenic steroids (AAS) are a class of steroid hormones related to the male hormone testosterone. They are frequently detected as drugs in sport doping control. Being similar to or derived from natural male hormones, AAS share the activation of the androgen receptor (AR) as common mechanism of action. The mammalian androgen responsive reporter gene assay (AR CALUX bioassay), measuring compounds interacting with the AR can be used for the analysis of AAS without the necessity of knowing their chemical structure beforehand, whereas current chemical-analytical approaches may have difficulty in detecting compounds with unknown structures, such as designer steroids. This study demonstrated that AAS prohibited in sports and potential designer AAS can be detected with this AR reporter gene assay, but that also additional steroid activities of AAS could be found using additional mammalian bioassays for other types of steroid hormones. Mixtures of AAS were found to behave additively in the AR reporter gene assay showing that it is possible to use this method for complex mixtures as are found in doping control samples, including mixtures that are a result of multi drug use. To test if mammalian reporter gene assays could be used for the detection of AAS in urine samples, background steroidal activities were measured. AAS-spiked urine samples, mimicking doping positive samples, showed significantly higher androgenic activities than unspiked samples. GC-MS analysis of endogenous androgens and AR reporter gene assay analysis of urine samples showed how a combined chemical-analytical and bioassay approach can be used to identify samples containing AAS. The results indicate that the AR reporter gene assay, in addition to chemical-analytical methods, can be a valuable tool for the analysis of AAS for doping control purposes.

Synthesis, characterization and catalytic activity of indium substituted nanocrystalline Mobil Five (MFI) zeolite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shah, Kishor Kr.; Nandi, Mithun; Talukdar, Anup K., E-mail: anup_t@sify.com

2015-06-15

Highlights: • In situ modification of the MFI zeolite by incorporation of indium. • The samples were characterized by XRD, FTIR, TGA, UV–vis (DRS), SAA, EDX and SEM. • The incorporation of indium was confirmed by XRD, FT-IR, UV–vis (DRS), EDX and TGA. • Hydroxylation of phenol reaction was studied on the synthesized catalysts. - Abstract: A series of indium doped Mobil Five (MFI) zeolite were synthesized hydrothermally with silicon to aluminium and indium molar ratio of 100 and with aluminium to indium molar ratios of 1:1, 2:1 and 3:1. The MFI zeolite phase was identified by XRD and FT-IRmore » analysis. In XRD analysis the prominent peaks were observed at 2θ values of around 6.5° and 23° with a few additional shoulder peaks in case of all the indium incorporated samples suggesting formation of pure phase of the MFI zeolite. All the samples under the present investigation were found to exhibit high crystallinity (∼92%). The crystallite sizes of the samples were found to vary from about 49 to 55 nm. IR results confirmed the formation of MFI zeolite in all cases showing distinct absorbance bands near 1080, 790, 540, 450 and 990 cm{sup −1}. TG analysis of In-MFI zeolites showed mass losses in three different steps which are attributed to the loss due to adsorbed water molecules and the two types TPA{sup +} cations. Further, the UV–vis (DRS) studies reflected the position of the indium metal in the zeolite framework. Surface area analysis of the synthesized samples was carried out to characterize the synthesized samples The analysis showed that the specific surface area ranged from ∼357 to ∼361 m{sup 2} g{sup −1} and the pore volume of the synthesized samples ranged from 0.177 to 0.182 cm{sup 3} g{sup −1}. The scanning electron microscopy studies showed the structure of the samples to be rectangular and twinned rectangular shaped. The EDX analysis was carried out for confirmation of Si, Al and In in zeolite frame work. The catalytic activities of the synthesized samples were investigated with respect to hydroxylation of phenol, in which catechol and hydroquinone were found to be the major products. It is observed that under all reaction conditions catechol selectivity was higher than the hydroquinone selectivity. In-MFI zeolites were successfully synthesized and were used as an effective catalyst for the hydroxylation of phenol to synthesize catechol and hydroquinone as the major product.« less

Occurrence of brominated diphenyl ethers, dibenzo-p-dioxins and dibenzofurans in foam materials in scrapped car seats from 1985 to 2012.

PubMed

Redin, L; Niinipuu, M; Jansson, S

2017-03-01

The purpose of this study was to evaluate the occurrence of polybrominated diphenyl ethers (PBDEs), dibenzo-p-dioxins (PBDDs) and dibenzofurans (PBDFs) in polyurethane foam (PUF) from car seats of end-of-life vehicles (ELVs) and compare the concentrations of PBDEs with the stipulated regulations in the POP Directive. The method comprised screening by X-ray fluorescence (XRF) and GG-MS analysis. Of 59 tested samples from ELVs, 17 samples showed lines above limit of detection (LOD) levels when screening by XRF. Those samples were selected as replicates and for further analysis by GC-MS. The majority of the studied samples showed low or non-detectable concentrations of PBDEs and PBDD/Fs, but two samples showed concentrations of Σ Te-HpBDEs close to the regulated level for Te-HpBDEs in waste (1000mgkg -1 ); one was slightly higher (1390mgkg -1 ) and the other slightly lower (570mgkg -1 ). It was concluded that brominated pollutants such as Te-HpBDEs occur in low levels in automotive applications in scrapped cars produced in years when brominated flame retardants were used. However, two of the 59 samples tested showed levels close to those stipulated by regulations concerning POPs in waste. Copyright © 2016 Elsevier Ltd. All rights reserved.

Measurements of 55Fe activity in activated steel samples with GEMPix

NASA Astrophysics Data System (ADS)

Curioni, A.; Dinar, N.; La Torre, F. P.; Leidner, J.; Murtas, F.; Puddu, S.; Silari, M.

2017-03-01

In this paper we present a novel method, based on the recently developed GEMPix detector, to measure the 55Fe content in samples of metallic material activated during operation of CERN accelerators and experimental facilities. The GEMPix, a gas detector with highly pixelated read-out, has been obtained by coupling a triple Gas Electron Multiplier (GEM) to a quad Timepix ASIC. Sample preparation, measurements performed on 45 samples and data analysis are described. The calibration factor (counts per second per unit specific activity) has been obtained via measurements of the 55Fe activity determined by radiochemical analysis of the same samples. Detection limit and sensitivity to the current Swiss exemption limit are calculated. Comparison with radiochemical analysis shows inconsistency for the sensitivity for only two samples, most likely due to underestimated uncertainties of the GEMPix analysis. An operative test phase of this technique is already planned at CERN.

Sensory characteristics and consumer preference for chicken meat in Guinea.

PubMed

Sow, T M A; Grongnet, J F

2010-10-01

This study identified the sensory characteristics and consumer preference for chicken meat in Guinea. Five chicken samples [live village chicken, live broiler, live spent laying hen, ready-to-cook broiler, and ready-to-cook broiler (imported)] bought from different locations were assessed by 10 trained panelists using 19 sensory attributes. The ANOVA results showed that 3 chicken appearance attributes (brown, yellow, and white), 5 chicken odor attributes (oily, intense, medicine smell, roasted, and mouth persistent), 3 chicken flavor attributes (sweet, bitter, and astringent), and 8 chicken texture attributes (firm, tender, juicy, chew, smooth, springy, hard, and fibrous) were significantly discriminating between the chicken samples (P<0.05). Principal component analysis of the sensory data showed that the first 2 principal components explained 84% of the sensory data variance. The principal component analysis results showed that the live village chicken, the live spent laying hen, and the ready-to-cook broiler (imported) were very well represented and clearly distinguished from the live broiler and the ready-to-cook broiler. One hundred twenty consumers expressed their preferences for the chicken samples using a 5-point Likert scale. The hierarchical cluster analysis of the preference data identified 4 homogenous consumer clusters. The hierarchical cluster analysis results showed that the live village chicken was the most preferred chicken sample, whereas the ready-to-cook broiler was the least preferred one. The partial least squares regression (PLSR) type 1 showed that 72% of the sensory data for the first 2 principal components explained 83% of the chicken preference. The PLSR1 identified that the sensory characteristics juicy, oily, sweet, hard, mouth persistent, and yellow were the most relevant sensory drivers of the Guinean chicken preference. The PLSR2 (with multiple responses) identified the relationship between the chicken samples, their sensory attributes, and the consumer clusters. Our results showed that there was not a chicken category that was exclusively preferred from the other chicken samples and therefore highlight the existence of place for development of all chicken categories in the local market.

Molecular analysis of partial VP-2 gene amplified from rectal swab samples of diarrheic dogs in Pakistan confirms the circulation of canine parvovirus genetic variant CPV-2a and detects sequences of feline panleukopenia virus (FPV).

PubMed

Ahmed, Nisar; Riaz, Adeel; Zubair, Zahra; Saqib, Muhammad; Ijaz, Sehrish; Nawaz-Ul-Rehman, Muhammad Shah; Al-Qahtani, Ahmed; Mubin, Muhammad

2018-03-15

The infection in dogs due to canine parvovirus (CPV), is a highly contagious one with high mortality rate. The present study was undertaken for a detailed genetic analysis of partial VP2 gene i.e., 630 bp isolated from rectal swab samples of infected domestic and stray dogs from all areas of district Faisalabad. Monitoring of viruses is important, as continuous prevalence of viral infection might be associated with emergence of new virulent strains. In the present study, 40 rectal swab samples were collected from diarrheic dogs from different areas of district Faisalabad, Pakistan, in 2014-15 and screened for the presence of CPV by immunochromatography. Most of these dogs were stray dogs showing symptoms of diarrhea. Viral DNA was isolated and partial VP2 gene was amplified using gene specific primer pair Hfor/Hrev through PCR. Amplified fragments were cloned in pTZ57R/T (Fermentas) and completely sequenced. Sequences were analyzed and assembled by the Lasergene DNA analysis package (v8; DNAStar Inc., Madison, WI, USA). The results with immunochromatography showed that 33/40 (82%) of dogs were positive for CPV. We were able to amplify a fragment of 630 bp from 25 samples. In 25 samples the sequences of CPV-2a were detected showing the amino acid substitution Ser297Ala and presence of amino acid (426-Asn) in partial VP2 protein. Interestingly the BLAST analysis showed the of feline panleukopenia virus (FPV) sequences in 3 samples which were already positive for new CPV-2a, with 99% sequence homology to other FPV sequences present in GenBank. Phylogenetic analysis showed clustering of partial CPV-VP-2 gene with viruses from China, India, Japan and Uruguay identifying a new variant, whereas the 3 FPV sequences showed immediate ancestral relationship with viruses from Portugal, South Africa and USA. Interesting observation was that CPV are clustering away from the commercial vaccine strains. In this work we provide a better understanding of CPV prevailing in Pakistan at molecular level. The detection of FPV could be a case of real co-infection or a case of dual presence, due to ingestion of contaminated food.

[Quantitative surface analysis of Pt-Co, Cu-Au and Cu-Ag alloy films by XPS and AES].

PubMed

Li, Lian-Zhong; Zhuo, Shang-Jun; Shen, Ru-Xiang; Qian, Rong; Gao, Jie

2013-11-01

In order to improve the quantitative analysis accuracy of AES, We associated XPS with AES and studied the method to reduce the error of AES quantitative analysis, selected Pt-Co, Cu-Au and Cu-Ag binary alloy thin-films as the samples, used XPS to correct AES quantitative analysis results by changing the auger sensitivity factors to make their quantitative analysis results more similar. Then we verified the accuracy of the quantitative analysis of AES when using the revised sensitivity factors by other samples with different composition ratio, and the results showed that the corrected relative sensitivity factors can reduce the error in quantitative analysis of AES to less than 10%. Peak defining is difficult in the form of the integral spectrum of AES analysis since choosing the starting point and ending point when determining the characteristic auger peak intensity area with great uncertainty, and to make analysis easier, we also processed data in the form of the differential spectrum, made quantitative analysis on the basis of peak to peak height instead of peak area, corrected the relative sensitivity factors, and verified the accuracy of quantitative analysis by the other samples with different composition ratio. The result showed that the analytical error in quantitative analysis of AES reduced to less than 9%. It showed that the accuracy of AES quantitative analysis can be highly improved by the way of associating XPS with AES to correct the auger sensitivity factors since the matrix effects are taken into account. Good consistency was presented, proving the feasibility of this method.

Analyzing small data sets using Bayesian estimation: the case of posttraumatic stress symptoms following mechanical ventilation in burn survivors

PubMed Central

van de Schoot, Rens; Broere, Joris J.; Perryck, Koen H.; Zondervan-Zwijnenburg, Mariëlle; van Loey, Nancy E.

2015-01-01

Background The analysis of small data sets in longitudinal studies can lead to power issues and often suffers from biased parameter values. These issues can be solved by using Bayesian estimation in conjunction with informative prior distributions. By means of a simulation study and an empirical example concerning posttraumatic stress symptoms (PTSS) following mechanical ventilation in burn survivors, we demonstrate the advantages and potential pitfalls of using Bayesian estimation. Methods First, we show how to specify prior distributions and by means of a sensitivity analysis we demonstrate how to check the exact influence of the prior (mis-) specification. Thereafter, we show by means of a simulation the situations in which the Bayesian approach outperforms the default, maximum likelihood and approach. Finally, we re-analyze empirical data on burn survivors which provided preliminary evidence of an aversive influence of a period of mechanical ventilation on the course of PTSS following burns. Results Not suprisingly, maximum likelihood estimation showed insufficient coverage as well as power with very small samples. Only when Bayesian analysis, in conjunction with informative priors, was used power increased to acceptable levels. As expected, we showed that the smaller the sample size the more the results rely on the prior specification. Conclusion We show that two issues often encountered during analysis of small samples, power and biased parameters, can be solved by including prior information into Bayesian analysis. We argue that the use of informative priors should always be reported together with a sensitivity analysis. PMID:25765534

Analyzing small data sets using Bayesian estimation: the case of posttraumatic stress symptoms following mechanical ventilation in burn survivors.

PubMed

van de Schoot, Rens; Broere, Joris J; Perryck, Koen H; Zondervan-Zwijnenburg, Mariëlle; van Loey, Nancy E

2015-01-01

Background : The analysis of small data sets in longitudinal studies can lead to power issues and often suffers from biased parameter values. These issues can be solved by using Bayesian estimation in conjunction with informative prior distributions. By means of a simulation study and an empirical example concerning posttraumatic stress symptoms (PTSS) following mechanical ventilation in burn survivors, we demonstrate the advantages and potential pitfalls of using Bayesian estimation. Methods : First, we show how to specify prior distributions and by means of a sensitivity analysis we demonstrate how to check the exact influence of the prior (mis-) specification. Thereafter, we show by means of a simulation the situations in which the Bayesian approach outperforms the default, maximum likelihood and approach. Finally, we re-analyze empirical data on burn survivors which provided preliminary evidence of an aversive influence of a period of mechanical ventilation on the course of PTSS following burns. Results : Not suprisingly, maximum likelihood estimation showed insufficient coverage as well as power with very small samples. Only when Bayesian analysis, in conjunction with informative priors, was used power increased to acceptable levels. As expected, we showed that the smaller the sample size the more the results rely on the prior specification. Conclusion : We show that two issues often encountered during analysis of small samples, power and biased parameters, can be solved by including prior information into Bayesian analysis. We argue that the use of informative priors should always be reported together with a sensitivity analysis.

RAPD study on some common species of Porphyra in China

NASA Astrophysics Data System (ADS)

Kuang, Mei; Wang, Su-Juan; Li, Yao; Shen, Da-Leng; Zeng, Cheng-Kui

1998-03-01

RAPD analysis of seven samples of five Porphyra species, P haitanensis (three samples of cultured population), P. katadai var. hemiphylla, P. oligospermatangia, P. suborbiculata and P. yezoensis, showed the closest relationship existing among the three cultured populations of P. haitanensis. The genetic distance between P. haitanensis and P. oligospermatangia was the same as that between P. haitanensis and P. suborbiculata, both were 0.9. The genetic distances, among the other species of Porphyra ranged from 0.7 to 0.8. UPGMA analysis showed P. suborbiculata and P. yezoensis belong to another lineage. Results of this study suggests that RAPD analysis is effective at population level.

[Influence of sample surface roughness on mathematical model of NIR quantitative analysis of wood density].

PubMed

Huang, An-Min; Fei, Ben-Hua; Jiang, Ze-Hui; Hse, Chung-Yun

2007-09-01

Near infrared spectroscopy is widely used as a quantitative method, and the main multivariate techniques consist of regression methods used to build prediction models, however, the accuracy of analysis results will be affected by many factors. In the present paper, the influence of different sample roughness on the mathematical model of NIR quantitative analysis of wood density was studied. The result of experiments showed that if the roughness of predicted samples was consistent with that of calibrated samples, the result was good, otherwise the error would be much higher. The roughness-mixed model was more flexible and adaptable to different sample roughness. The prediction ability of the roughness-mixed model was much better than that of the single-roughness model.

Validity of Bioelectrical Impedance Analysis to Estimation Fat-Free Mass in the Army Cadets.

PubMed

Langer, Raquel D; Borges, Juliano H; Pascoa, Mauro A; Cirolini, Vagner X; Guerra-Júnior, Gil; Gonçalves, Ezequiel M

2016-03-11

Bioelectrical Impedance Analysis (BIA) is a fast, practical, non-invasive, and frequently used method for fat-free mass (FFM) estimation. The aims of this study were to validate predictive equations of BIA to FFM estimation in Army cadets and to develop and validate a specific BIA equation for this population. A total of 396 males, Brazilian Army cadets, aged 17-24 years were included. The study used eight published predictive BIA equations, a specific equation in FFM estimation, and dual-energy X-ray absorptiometry (DXA) as a reference method. Student's t-test (for paired sample), linear regression analysis, and Bland-Altman method were used to test the validity of the BIA equations. Predictive BIA equations showed significant differences in FFM compared to DXA (p < 0.05) and large limits of agreement by Bland-Altman. Predictive BIA equations explained 68% to 88% of FFM variance. Specific BIA equations showed no significant differences in FFM, compared to DXA values. Published BIA predictive equations showed poor accuracy in this sample. The specific BIA equations, developed in this study, demonstrated validity for this sample, although should be used with caution in samples with a large range of FFM.

Solid-state stability studies of 13-cis-retinoic acid and all-trans-retinoic acid using microcalorimetry and HPLC analysis.

PubMed

Tan, X; Meltzer, N; Lindebaum, S

1992-09-01

The solid-state stabilities of 13-cis-retinoic acid and all-trans-retinoic acid in the presence and absence of oxygen were investigated. The samples were first evaluated using microcalorimetry. The rate laws of different samples under different conditions were deduced from the shapes of the heat flow curves, and the activation energies of the reactions were determined from Arrhenius plots. Under an air atmosphere, the decomposition of 13-cis-retinoic acid is an autocatalytic reaction, while all-trans-retinoic acid undergoes a zero-order process. The degradation of the two compounds at a selected elevated temperature was also determined utilizing HPLC analysis. This technique confirmed the decomposition kinetics. Hence, their half-lives and shelf lives at room temperature could be calculated. Under a nitrogen atmosphere, the microcalorimetric experiment showed a first-order phenomenon for both samples, but HPLC analysis showed no degradation, suggesting that the two samples, in the absence of oxygen, undergo only a physical change.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Young, J.; Ajo, H.; Brown, L.

Analysis of the recent WIPP samples are summarized in this report; WIPP Cam Filters 4, 6, 9 (3, 7, 11 were analyzed with FAS-118 in a separate campaign); WIPP Drum Lip R16 C4; WIPP Standard Waste Box R15 C5; WIPP MgO R16 C2; WIPP MgO R16 C4; WIPP MgO R16 C6; LANL swipes of parent drum; LANL parent drum debris; LANL parent drum; IAEA Swipe; Unused “undeployed” Swheat; Unused “undeployed” MgO; and Masselin cloth “smears”. Analysis showed that the MgO samples were very pure with low carbonate and water content. Other samples showed the expected dominant presence of Mg, Namore » and Pb. Parent drum debris sample was mildly acidic. Interpretation of results is not provided in this document, but rather to present and preserve the analytical work that was performed. The WIPP Technical Analysis Team is responsible for result interpretation which will be written separately.« less

Neutron activation analysis of certified samples by the absolute method

NASA Astrophysics Data System (ADS)

Kadem, F.; Belouadah, N.; Idiri, Z.

2015-07-01

The nuclear reactions analysis technique is mainly based on the relative method or the use of activation cross sections. In order to validate nuclear data for the calculated cross section evaluated from systematic studies, we used the neutron activation analysis technique (NAA) to determine the various constituent concentrations of certified samples for animal blood, milk and hay. In this analysis, the absolute method is used. The neutron activation technique involves irradiating the sample and subsequently performing a measurement of the activity of the sample. The fundamental equation of the activation connects several physical parameters including the cross section that is essential for the quantitative determination of the different elements composing the sample without resorting to the use of standard sample. Called the absolute method, it allows a measurement as accurate as the relative method. The results obtained by the absolute method showed that the values are as precise as the relative method requiring the use of standard sample for each element to be quantified.

Robust gene selection methods using weighting schemes for microarray data analysis.

PubMed

Kang, Suyeon; Song, Jongwoo

2017-09-02

A common task in microarray data analysis is to identify informative genes that are differentially expressed between two different states. Owing to the high-dimensional nature of microarray data, identification of significant genes has been essential in analyzing the data. However, the performances of many gene selection techniques are highly dependent on the experimental conditions, such as the presence of measurement error or a limited number of sample replicates. We have proposed new filter-based gene selection techniques, by applying a simple modification to significance analysis of microarrays (SAM). To prove the effectiveness of the proposed method, we considered a series of synthetic datasets with different noise levels and sample sizes along with two real datasets. The following findings were made. First, our proposed methods outperform conventional methods for all simulation set-ups. In particular, our methods are much better when the given data are noisy and sample size is small. They showed relatively robust performance regardless of noise level and sample size, whereas the performance of SAM became significantly worse as the noise level became high or sample size decreased. When sufficient sample replicates were available, SAM and our methods showed similar performance. Finally, our proposed methods are competitive with traditional methods in classification tasks for microarrays. The results of simulation study and real data analysis have demonstrated that our proposed methods are effective for detecting significant genes and classification tasks, especially when the given data are noisy or have few sample replicates. By employing weighting schemes, we can obtain robust and reliable results for microarray data analysis.

On the incidence of Mg II absorbers along the blazar sightlines

NASA Astrophysics Data System (ADS)

Mishra, S.; Chand, H.; Krishna, Gopal-; Joshi, R.; Shchekinov, Y. A.; Fatkhullin, T. A.

2018-02-01

It is widely believed that the cool gas clouds traced by Mg II absorption, within a velocity offset of 5000 km s-1 relative to the background quasar are mostly associated with the quasar itself, whereas the absorbers seen at larger velocity offsets towards us are intervening absorber systems and hence their existence is completely independent of the background quasar. Recent evidence by Bergeron et al. (hereinafter BBM) has seriously questioned this paradigm, by showing that the number density of intervening Mg II absorbers towards the 45 blazars in their sample is nearly two times the expectation based on the Mg II absorption systems seen towards normal quasars (QSOs). Given its serious implications, it becomes important to revisit this finding, by enlarging the blazar sample and subjecting it to an independent analysis. Here, we first report the outcome of our re-analysis of the available spectroscopic data for the BBM sample itself. Our analysis of the BBM sample reproduces their claimed factor of 2 excess of dN/dz along blazar sightlines, vis-à-vis normal QSOs. We have also assembled an approxmately three times larger sample of blazars, albeit with moderately sensitive optical spectra. Using this sample together with the BBM sample, our analysis shows that the dN/dz of the Mg II absorbers statistically matches that known for normal QSO sightlines. Further, the analysis indicates that associated absorbers might be contributing significantly to the estimated dN/dz up to offset speeds Δv ∼ 0.2c relative to the blazar.

Effect of annealing temperature on the size and magnetic properties of CoFe2O4 nanoparticle

NASA Astrophysics Data System (ADS)

Sunny, Annrose; Akshay, V. R.; Vasundhara, M.

2018-05-01

CoFe2O4 (CFO) nanoparticles (NPs) are synthesized using sol gel method and are annealed at 400, 600 and 800 °C for 4h. The crystal structure and morphology of the NPs are investigated through XRD and TEM analysis. The X- ray diffraction analysis shows that all the samples are well formed and attain a cubic structure with Fd-3m space group. The morphology of the material is found to be polygonal and the particle size of the NPs is increased with increase of annealing temperature as 400, 600 and 800 to be 20 nm, 30 nm and 70 nm respectively. The magnetic properties of the NPs are investigated using VSM and observed that the curie temperature for 400, 600 and 800 °C annealing temperature are 762 K, 780 K, 769 K respectively. The Ms of 600 sample is 80 emu/g. The 400 and 800 sample shows lower Ms value this is due to poor crystalanity and exaggerated grain growth at the respective temperatures. The coercivity of the sample shows linear dependence with particle size of the material the highest coercivity is obtained for 400 sample and low value for 800 sample.

Evaluation of needle trap micro-extraction and automatic alveolar sampling for point-of-care breath analysis.

PubMed

Trefz, Phillip; Rösner, Lisa; Hein, Dietmar; Schubert, Jochen K; Miekisch, Wolfram

2013-04-01

Needle trap devices (NTDs) have shown many advantages such as improved detection limits, reduced sampling time and volume, improved stability, and reproducibility if compared with other techniques used in breath analysis such as solid-phase extraction and solid-phase micro-extraction. Effects of sampling flow (2-30 ml/min) and volume (10-100 ml) were investigated in dry gas standards containing hydrocarbons, aldehydes, and aromatic compounds and in humid breath samples. NTDs contained (single-bed) polymer packing and (triple-bed) combinations of divinylbenzene/Carbopack X/Carboxen 1000. Substances were desorbed from the NTDs by means of thermal expansion and analyzed by gas chromatography-mass spectrometry. An automated CO2-controlled sampling device for direct alveolar sampling at the point-of-care was developed and tested in pilot experiments. Adsorption efficiency for small volatile organic compounds decreased and breakthrough increased when sampling was done with polymer needles from a water-saturated matrix (breath) instead from dry gas. Humidity did not affect analysis with triple-bed NTDs. These NTDs showed only small dependencies on sampling flow and low breakthrough from 1-5 %. The new sampling device was able to control crucial parameters such as sampling flow and volume. With triple-bed NTDs, substance amounts increased linearly with increasing sample volume when alveolar breath was pre-concentrated automatically. When compared with manual sampling, automatic sampling showed comparable or better results. Thorough control of sampling and adequate choice of adsorption material is mandatory for application of needle trap micro-extraction in vivo. The new CO2-controlled sampling device allows direct alveolar sampling at the point-of-care without the need of any additional sampling, storage, or pre-concentration steps.

Spectroscopic analysis of the role of extractives on heat-induced discoloration of black locust (Robinia pseudoacacia)

Treesearch

Yao Chen; Yongming Fan; Jianmin Gao; Mandla A. Tshabalala; Nicole M. Stark

2012-01-01

To investigate the role of extractives on heat-induced discoloration of wood, samples of black locust (Robinia pseudoacacia) wood flour were extracted with various solvents prior to heat-treatment. Analysis of their color parameters and chromophoric structures showed that the chroma value of the unextracted sample decreased while that of the...

Mars Rock Analysis Briefing

NASA Image and Video Library

2013-03-12

David Blake, principal investigator for Curiosity's Chemistry and Mineralogy investigation at NASA's Ames Research Center in Calif., speaks at a news conference presenting findings of the Curiosity rover's analysis of the first sample of rock powder collected on Mars, Tuesday, March 12, 2013 in Washington. The rock sample collected shows ancient Mars could have supported living microbes. Photo Credit: (NASA/Carla Cioffi)

The Association of Attitude to Reading and Reading Achievement among a Representative Sample of Nine Year Olds in Ireland

ERIC Educational Resources Information Center

Fives, Allyn

2016-01-01

This study explored the association between reading self-belief and reading achievement among a representative sample of nine year old children in the Republic of Ireland. Results from analysis of variance and simple effects analysis showed a positive linear association between reading achievement and "attitude to reading." The…

Understanding and comparisons of different sampling approaches for the Fourier Amplitudes Sensitivity Test (FAST)

PubMed Central

Xu, Chonggang; Gertner, George

2013-01-01

Fourier Amplitude Sensitivity Test (FAST) is one of the most popular uncertainty and sensitivity analysis techniques. It uses a periodic sampling approach and a Fourier transformation to decompose the variance of a model output into partial variances contributed by different model parameters. Until now, the FAST analysis is mainly confined to the estimation of partial variances contributed by the main effects of model parameters, but does not allow for those contributed by specific interactions among parameters. In this paper, we theoretically show that FAST analysis can be used to estimate partial variances contributed by both main effects and interaction effects of model parameters using different sampling approaches (i.e., traditional search-curve based sampling, simple random sampling and random balance design sampling). We also analytically calculate the potential errors and biases in the estimation of partial variances. Hypothesis tests are constructed to reduce the effect of sampling errors on the estimation of partial variances. Our results show that compared to simple random sampling and random balance design sampling, sensitivity indices (ratios of partial variances to variance of a specific model output) estimated by search-curve based sampling generally have higher precision but larger underestimations. Compared to simple random sampling, random balance design sampling generally provides higher estimation precision for partial variances contributed by the main effects of parameters. The theoretical derivation of partial variances contributed by higher-order interactions and the calculation of their corresponding estimation errors in different sampling schemes can help us better understand the FAST method and provide a fundamental basis for FAST applications and further improvements. PMID:24143037

Understanding and comparisons of different sampling approaches for the Fourier Amplitudes Sensitivity Test (FAST).

PubMed

Xu, Chonggang; Gertner, George

2011-01-01

Fourier Amplitude Sensitivity Test (FAST) is one of the most popular uncertainty and sensitivity analysis techniques. It uses a periodic sampling approach and a Fourier transformation to decompose the variance of a model output into partial variances contributed by different model parameters. Until now, the FAST analysis is mainly confined to the estimation of partial variances contributed by the main effects of model parameters, but does not allow for those contributed by specific interactions among parameters. In this paper, we theoretically show that FAST analysis can be used to estimate partial variances contributed by both main effects and interaction effects of model parameters using different sampling approaches (i.e., traditional search-curve based sampling, simple random sampling and random balance design sampling). We also analytically calculate the potential errors and biases in the estimation of partial variances. Hypothesis tests are constructed to reduce the effect of sampling errors on the estimation of partial variances. Our results show that compared to simple random sampling and random balance design sampling, sensitivity indices (ratios of partial variances to variance of a specific model output) estimated by search-curve based sampling generally have higher precision but larger underestimations. Compared to simple random sampling, random balance design sampling generally provides higher estimation precision for partial variances contributed by the main effects of parameters. The theoretical derivation of partial variances contributed by higher-order interactions and the calculation of their corresponding estimation errors in different sampling schemes can help us better understand the FAST method and provide a fundamental basis for FAST applications and further improvements.

Influence of Capping Ligand and Synthesis Method on Structure and Morphology of Aqueous Phase Synthesized CuInSe2 Nanoparticles

NASA Astrophysics Data System (ADS)

Ram Kumar, J.; Ananthakumar, S.; Moorthy Babu, S.

2017-01-01

A facile route to synthesize copper indium diselenide (CuInSe2) nanoparticles in aqueous medium was developed using mercaptoacetic acid (MAA) as capping agent. Two different mole ratios (5 and 10) of MAA were used to synthesize CuInSe2 nanoparticles at room temperature, as well as hydrothermal (high temperature) method. Powder x-ray diffraction analysis reveals that the nanoparticles exhibit chalcopyrite phase and the crystallinity increases with increasing the capping ratio. Raman analysis shows a strong band at 233 cm-1 due to the combination of B2 (E) modes. Broad absorption spectra were observed for the synthesized CuInSe2 nanoparticles. The effective surface capping by MAA on the nanoparticles surface was confirmed through attenuated total reflection-Fourier transform infrared spectral analysis. The thermal stability of the synthesized samples was analyzed through thermogravimetric analysis-differential scanning calorimetry. The change in morphology of the synthesized samples was analyzed through scanning electron microscope and it shows that the samples prepared at room temperature are spherical in shape, whereas hydrothermally synthesized samples were found to have nanorod- and nanoflake-like structures. Transmission electron microscope analysis further indicates larger grains for the hydrothermally prepared samples with 10 mol ratio of MAA. Comparative analyses were made for synthesizing CuInSe2 nanoparticles by two different methods to explore the role of ligand and influence of temperature.

Small-Noise Analysis and Symmetrization of Implicit Monte Carlo Samplers

DOE PAGES

Goodman, Jonathan; Lin, Kevin K.; Morzfeld, Matthias

2015-07-06

Implicit samplers are algorithms for producing independent, weighted samples from multivariate probability distributions. These are often applied in Bayesian data assimilation algorithms. We use Laplace asymptotic expansions to analyze two implicit samplers in the small noise regime. Our analysis suggests a symmetrization of the algorithms that leads to improved implicit sampling schemes at a relatively small additional cost. Here, computational experiments confirm the theory and show that symmetrization is effective for small noise sampling problems.

Large genetic differentiation and low variation in vector competence for dengue and yellow fever viruses of Aedes albopictus from Brazil, the United States, and the Cayman Islands.

PubMed

Lourenço de Oliveira, Ricardo; Vazeille, Marie; de Filippis, Ana Maria Bispo; Failloux, Anna-Bella

2003-07-01

We conducted a population genetic analysis of Aedes albopictus collected from 20 sites in Brazil, the United States (Florida, Georgia, and Illinois), and the Cayman Islands. Using isoenzyme analysis, we examined genetic diversity and patterns of gene flow. High genetic differentiation was found among Brazilian samples, and between them and North American samples. Regression analysis of genetic differentiation according to geographic distances indicated that Ae. albopictus samples from Florida were genetically isolated by distance. Infection rates with dengue and yellow fever viruses showed greater differences between two Brazilian samples than between the two North American samples or between a Brazilian sample and a North American sample. Introductions and establishments of new Ae. albopictus populations in the Americas are still in progress, shaping population genetic composition and potentially modifying both dengue and yellow fever transmission patterns.

Analysis of spreadable cheese by Raman spectroscopy and chemometric tools.

PubMed

Oliveira, Kamila de Sá; Callegaro, Layce de Souza; Stephani, Rodrigo; Almeida, Mariana Ramos; de Oliveira, Luiz Fernando Cappa

2016-03-01

In this work, FT-Raman spectroscopy was explored to evaluate spreadable cheese samples. A partial least squares discriminant analysis was employed to identify the spreadable cheese samples containing starch. To build the models, two types of samples were used: commercial samples and samples manufactured in local industries. The method of supervised classification PLS-DA was employed to classify the samples as adulterated or without starch. Multivariate regression was performed using the partial least squares method to quantify the starch in the spreadable cheese. The limit of detection obtained for the model was 0.34% (w/w) and the limit of quantification was 1.14% (w/w). The reliability of the models was evaluated by determining the confidence interval, which was calculated using the bootstrap re-sampling technique. The results show that the classification models can be used to complement classical analysis and as screening methods. Copyright © 2015 Elsevier Ltd. All rights reserved.

Study of morphological changes in scattering and optically anisotropic medium through correlation images

NASA Astrophysics Data System (ADS)

Jain, Neha; Shukla, Prashant; Singh, Jai

2018-05-01

Correlation images are very useful in determining the morphological changes. We have investigated the correlation image analysis on depolarization and retardance matrices of polystyrene and gelatine samples respectively. We observed that that correlation images have a potential to show a significant variation with change in the concentration of samples (polystyrene and gelatine). For polystyrene microspheres the correlation value decreases with increasing scattering coefficient. In gelatine samples the correlation also decreases with sample concentration. This variation in correlation for retardance shows the change in a birefringence property of gelatine solution.

Integrative genome-wide analysis of the determinants of RNA splicing in kidney renal clear cell carcinoma.

PubMed

Lehmann, Kjong-Van; Kahles, André; Kandoth, Cyriac; Lee, William; Schultz, Nikolaus; Stegle, Oliver; Rätsch, Gunnar

2015-01-01

We present a genome-wide analysis of splicing patterns of 282 kidney renal clear cell carcinoma patients in which we integrate data from whole-exome sequencing of tumor and normal samples, RNA-seq and copy number variation. We proposed a scoring mechanism to compare splicing patterns in tumor samples to normal samples in order to rank and detect tumor-specific isoforms that have a potential for new biomarkers. We identified a subset of genes that show introns only observable in tumor but not in normal samples, ENCODE and GEUVADIS samples. In order to improve our understanding of the underlying genetic mechanisms of splicing variation we performed a large-scale association analysis to find links between somatic or germline variants with alternative splicing events. We identified 915 cis- and trans-splicing quantitative trait loci (sQTL) associated with changes in splicing patterns. Some of these sQTL have previously been associated with being susceptibility loci for cancer and other diseases. Our analysis also allowed us to identify the function of several COSMIC variants showing significant association with changes in alternative splicing. This demonstrates the potential significance of variants affecting alternative splicing events and yields insights into the mechanisms related to an array of disease phenotypes.

Dielectric Spectroscopy Analysis of Aged EVOH films with Application to Deterioration of Food Packaging Materials

NASA Astrophysics Data System (ADS)

Hoeller, Timothy

2007-06-01

Samples of EVOH films from compositions of 29 - 44 mol% ethylene content were exposed to thermal aging with and without light exposure. The results of Dielectric Spectroscopy on select samples showed Cole-Cole plots of skewed dielectric constant indicating multiple distributions of dipole relaxation times. The onset for decreases in dielectric response occurs earlier in samples exposed to elevated temperature under light exposure. Lower permittivity is exhibited in samples of higher ethylene content. Results from heat exposed samples are presented. Colorimetric analysis indicates only a slight film yellowing in one case. Raman spectroscopy on untreated films discerns changes in the C-C-O stretch associated with the alcohol. The effects of aging on microstructure may cause hindrance of molecular motion from moisture desorption. Slight material degradation occurs from film hardening presumably due to crosslinking. An electrical circuit model of the conduction processes associated with the EVOH films is presented. Dielectric analysis shows promise for monitoring material changes related to deterioration. We are also using these methods to understand Fluorescence Imaging which has been recently released for paper and plastic materials analysis. Future work may include refinement of these techniques for identification of changes in material properties correlated to packaging material barrier resistance.

Prevalence of bacteria and absence of anisakid parasites in raw and prepared fish and seafood dishes in Spanish restaurants.

PubMed

Sospedra, I; Rubert, J; Soriano, J M; Mañes, J; Fuentes, M V

2015-03-01

This study evaluated the presence of bacteria and anisakid parasites in 45 samples of raw anchovies in vinegar, a dish widely eaten in Spain, and in 227 samples of cooked fish and cephalopods served in Spanish food service establishments. Our analysis showed that, according to European and Spanish regulation, 14 to 30% of the prepared fish and cephalopod dishes exceeded the maximum allowable level for mesophilic aerobic counts, and 10 to 40% of these samples exceeded the allowable levels for Enterobacteriaceae. None of the studied samples showed evidence of anisakid parasites, Escherichia coli, Staphylococcus aureus, Salmonella, or Listeria monocytogenes. These results indicate that application of hazard analysis and critical control points, food safety training courses, and routine inspections in compliance with current European and Spanish legislation help protect consumer health.

Thermal behaviour and microanalysis of coal subbituminus

NASA Astrophysics Data System (ADS)

Heriyanti; Prendika, W.; Ashyar, R.; Sutrisno

2018-04-01

Differential scanning calorimetry (DSC) and X-ray powder diffraction (XRD) is used to study the thermal behaviour of sub-bituminous coal. The DSC experiment was performed in air atmosphere up to 125 °C at a heating rate of 25 °C min1. The DSC curve showed that the distinct transitional stages in the coal samples studied. Thermal heating temperature intervals, peak and dissociation energy of the coal samples were also determined. The XRD analysis was used to evaluate the diffraction pattern and crystal structure of the compounds in the coal sample at various temperatures (25-350 °C). The XRD analysis of various temperatures obtained compounds from the coal sample, dominated by quartz (SiO2) and corundum (Al2O3). The increase in temperature of the thermal treatment showed a better crystal formation.

Pituitary gland volumes in bipolar disorder.

PubMed

Clark, Ian A; Mackay, Clare E; Goodwin, Guy M

2014-12-01

Bipolar disorder has been associated with increased Hypothalamic-Pituitary-Adrenal axis function. The mechanism is not well understood, but there may be associated increases in pituitary gland volume (PGV) and these small increases may be functionally significant. However, research investigating PGV in bipolar disorder reports mixed results. The aim of the current study was twofold. First, to assess PGV in two novel samples of patients with bipolar disorder and matched healthy controls. Second, to perform a meta-analysis comparing PGV across a larger sample of patients and matched controls. Sample 1 consisted of 23 established patients and 32 matched controls. Sample 2 consisted of 39 medication-naïve patients and 42 matched controls. PGV was measured on structural MRI scans. Seven further studies were identified comparing PGV between patients and matched controls (total n; 244 patients, 308 controls). Both novel samples showed a small (approximately 20mm(3) or 4%), but non-significant, increase in PGV in patients. Combining the two novel samples showed a significant association of age and PGV. Meta-analysis showed a trend towards a larger pituitary gland in patients (effect size: .23, CI: -.14, .59). While results suggest a possible small difference in pituitary gland volume between patients and matched controls, larger mega-analyses with sample sizes greater even than those used in the current meta-analysis are still required. There is a small but potentially functionally significant increase in PGV in patients with bipolar disorder compared to controls. Results demonstrate the difficulty of finding potentially important but small effects in functional brain disorders. Copyright © 2014 Elsevier B.V. All rights reserved.

Hydrogeochemical processes and isotopes analysis. Study case: "La Línea Tunnel", Colombia

NASA Astrophysics Data System (ADS)

Piña, Adriana; Donado, Leonardo; Cramer, Thomas

2017-04-01

Hydrogeochemical and stable isotopes analyses have been widely used to identify recharge and discharge zones, flowpaths, type, origin and age of water, chemical processes between minerals and groundwater as well as effects caused by anthropogenic or natural pollution. In this paper we analyze the interactions between groundwater and surface water using as laboratory the tunnels located at the La Línea Massif in the Cordillera Central of the Colombian Andes. The massif is formed by two igneous-metamorphic fractured complexes (Cajamarca and Quebradagrande group) plus andesithic porphyry rocks from the tertiary period. There, eight main fault zones related to surface creeks were identified and main inflows inside the tunnels were reported. 60 water samples were collected in surface and inside the tunnel in fault zones in two different years, 2010 and 2015. To classify water samples, a multivariate statistical analysis combining Factor Analysis (FA) with Hierarchical Cluster Analysis (HCA) was performed. Then, analyses of the major chemical elements and water isotopes (18O, 2H and 3H) were used to define the origin of dissolved components and to analyse the evolution in time. Most samples were classified as bicarbonate calcite water or bicarbonate magnesium water type. Isotopic analyses show a characteristic behavior for east and west watershed and each geologic group. According to the FA and HCA, obtained factors and clusters are first related to the location of the samples (surface or tunnel samples) followed by the geology. Surface samples behave according to the Colombian meteoric line as inflows related to permeable faults while less permeable faults show hydrothermal processes. Finally, water evolution in time shows a decrease of pH, conductivity and Mg2+ related to silicate weathering or precipitation/dissolution processes that affect the spacing in fractures and consequently, the hydraulic properties.

Occurrence and sources of antibiotics and their metabolites in river water, WWTPs, and swine wastewater in Jiulongjiang River basin, south China.

PubMed

Jiang, Hongyou; Zhang, Dandan; Xiao, Shichang; Geng, Chunnv; Zhang, Xian

2013-12-01

In this study, the occurrence and sources of five cataloged antibiotics and metabolites were studied in Jiulongjiang River basin, south China. Nineteen antibiotics and 13 metabolites were detected in water samples from 16 river sampling sites, wastewater from 5 swine-raising facilities, and effluent from 5 wastewater treatment plants (WWTPs). The results showed that 12 antibiotics and 6 metabolites were detected in river water samples. Sulfonamides (SAs) and their metabolites were detected at high concentrations (8.59-158.94 ng/L). Tetracyclines (TCs) and their metabolites were frequently detected in swine wastewater, and the maximum concentration was up to the level in milligram per liter. Macrolides (MLs) and β-lactams (β-Ls) were found in all WWTP effluent samples and some river samples, while they were never found in any of the swine wastewater samples. SAs and quinolones (QNs) were detected in all samples. Hierarchical cluster analysis of 16 surface water samples was applied to achieve the spatial distribution characteristics of antibiotics in the Jiulongjiang River. As a result, two categories were obviously obtained. Principal component analysis and redundancy analysis showed that TCs and SAs as well as their metabolites were the major antibiotics in Jiulongjiang River, and they mainly originated from swine wastewater, while the QNs, MLs, and β-Ls in the Jiulongjiang River came from WWTP effluent.

Modulation of flyash-induced genotoxicity in Vicia faba by vermicomposting.

PubMed

Jain, Kavindra; Singh, Jitendra; Chauhan, L K S; Murthy, R C; Gupta, S K

2004-09-01

Cytogenetic effects of pre- and postvermicomposted flyash samples were evaluated on the root meristem cells of Vicia faba. Seedlings of V. faba were directly sown in flyash and cow dung-soil mixtures (20%, 40%, 60%, and 80%) and the lateral roots grown in these test mixtures were sampled at 5 days. Negative control was run parallel in cow dung-soil (CS) mixture alone. One set of flyash-cow dung-soil (FCS) mixture was subjected to vermicomposting by introducing Eisenia foetida species of earthworms for 30 days and the cytogenetic effects were reinvestigated through V. faba root meristems. Chemical analysis carried out prior to vermicomposting revealed high concentrations of heavy metals such as Cr, Cu, Pb, Zn, and Ni in FCS samples. CS samples also showed the presence of these metals. Cytogenetic examinations of root meristems exposed to the FCS mixtures showed significant inhibition of mitotic index (MI), induction of chromosome aberrations (CA), and a significantly increased frequency of mitotic aberrations (MA). The increase of the aberrations was dependent on the flyash concentrations. Roots grown in CS samples also showed chromosomal and MAs; however, the percentage was lower than that observed with FCS and also statistically nonsignificant. Cytogenetic analysis of vermicomposted samples of FCS revealed a 15-45% decline in the aberration frequencies whereas chemical analysis showed a 10-50% decline in the metal concentrations, viz. Cr, Cu, Pb, Zn, and Ni, which indicates E. foetida a potential accumulator of heavy metals and the decline in metal concentrations may be the cause of the decrease in aberration frequencies. The present study indicates the genotoxicity potential of flyash and also the feasibility of vermicomposting for cleanup of metal-contaminated soil to mitigate the toxicity/genotoxicity. Copyright 2004 Elsevier Inc.

[Identification of Dendrobium varieties by infrared spectroscopy].

PubMed

Liu, Fei; Wang, Yuan-Zhong; Yang, Chun-Yan; Jin, Hang

2014-11-01

The difference of Dendrobium varieties were analyzed by Fourier transform infrared (FTIR) spectroscopy. The infrared spectra of 206 stems from 30 Dendrobium varieties were obtained, and showed that polysaccharides, especially fiber, were the main components in Dendrobium plants. FTIR combined with Wilks' Lambda stepwise discriminative analysis was used to identify Dendrobium varieties. The effects of spectral range and number of training samples on the discrimination results were also analysed. Two hundred eighty seven variables in the spectral range of 1 800-1 250 cm(-1) were studied, and showed that the return discrimination is 100% correct when the training samples number of each species was 2, 3, 4, 5, and 6, respectively, whereas for the remaining samples the correct rates of identification were equal to 79.4%, 91.3%, 93.0%, 98.2%, and 100%, respectively. The same discriminative analyses on five different training samples in the spectral range of 1 800-1 500, 1 500-1 250, 1 250-600, 1 250-950 and 950-650 cm(-1) were compared, which showed that the variables in the range of 1 800-1 250, 1 800-1 500 and 950-600 cm(-1) were more suitable for variety identification, and one can obtain the satisfactory result for discriminative analysis when the training sample is more than 3. Our results indicate that FTIR combined with stepwise discriminative analysis is an effective way to distinguish different Dendrobium varieties.

Distribution and Taxonomic Significance of Secondary Metabolites Occurring in the Methanol Extracts of the Stonecrops (Sedum L., Crassulaceae) from the Central Balkan Peninsula.

PubMed

Stojanovic, Gordana S; Jovanović, Snežana C; Zlatković, Bojan K

2015-06-01

The present study is engaged in the chemical composition of methanol extracts of Sedum taxa from the central part of the Balkan Peninsula, and representatives from other genera of Crassulaceae (Crassula, Echeveria and Kalanchoe) considered as out-groups. The chemical composition of extracts was determined by HPLC analysis, according to retention time of standards and characteristic absorption spectra of components. Identified components were considered as original variables with possible chemotaxonomic significance. Relationships of examined plant samples were investigated by agglomerative hierarchical cluster analysis (AHC). The obtained results showed how the distribution of methanol extract components (mostly phenolics) affected grouping of the examined samples. The obtained clustering showed satisfactory grouping of the examined samples, among which some representatives of the Sedum series, Rupestria and Magellensia, are the most remote. The out-group samples were not clearly singled out with regard to Sedum samples as expected; this especially applies to samples of Crassula ovata and Echeveria lilacina, while Kalanchoe daigremontiana was more separated from most of the Sedum samples.

Pyrolysis-mass spectrometry/pattern recognition on a well-characterized suite of humic samples

USGS Publications Warehouse

MacCarthy, P.; DeLuca, S.J.; Voorhees, K.J.; Malcolm, R.L.; Thurman, E.M.

1985-01-01

A suite of well-characterized humic and fulvic acids of freshwater, soil and plant origin was subjected to pyrolysis-mass spectrometry and the resulting data were analyzed by pattern recognition and factor analysis. A factor analysis plot of the data shows that the humic acids and fulvic acids can be segregated into two distinct classes. Carbohydrate and phenolic components are more pronounced in the pyrolysis products of the fulvic acids, and saturated and unsaturated hydrocarbons contribute more to the humic acid pyrolysis products. A second factor analysis plot shows a separation which appears to be based primarily on whether the samples are of aquatic or soil origin. ?? 1985.

Identification of multiple mRNA and DNA sequences from small tissue samples isolated by laser-assisted microdissection.

PubMed

Bernsen, M R; Dijkman, H B; de Vries, E; Figdor, C G; Ruiter, D J; Adema, G J; van Muijen, G N

1998-10-01

Molecular analysis of small tissue samples has become increasingly important in biomedical studies. Using a laser dissection microscope and modified nucleic acid isolation protocols, we demonstrate that multiple mRNA as well as DNA sequences can be identified from a single-cell sample. In addition, we show that the specificity of procurement of tissue samples is not compromised by smear contamination resulting from scraping of the microtome knife during sectioning of lesions. The procedures described herein thus allow for efficient RT-PCR or PCR analysis of multiple nucleic acid sequences from small tissue samples obtained by laser-assisted microdissection.

A comparison of sample unit designs in the national inventory of the U.S.

Treesearch

B. E. Borders; G. H. Brister; N. Grahl; B. D. Shiver; C. J. Cieszewski

2000-01-01

The Forest Inventory and Analysis (FIA) program of the USDA Forest Service has adopted a new sampling unit for the national forest inventory of the U.S. We compared this new sampling unit with five other sampling units. Data from natural loblolly pine (Pinus taeda L.) stands in the Georgia piedmont show that all sample units produce reasonable...

Scanning Electron Microscopy Investigation of a Sample Depth Profile Through the Martian Meteorite Nakhla

NASA Technical Reports Server (NTRS)

Toporski, Jan; Steele, Andrew; Westall, Frances; McKay, David S.

2000-01-01

The ongoing scientific debate as to whether or not the Martian meteorite ALH84001 contained evidence of possible biogenic activities showed the need to establish consistent methods to ascertain the origin of such evidence. To distinguish between terrestrial organic material/microbial contaminants and possible indigenous microbiota within meteorites is therefore crucial. With this in mind a depth profile consisting of four samples from a new sample allocation of Martian meteorite Nakhla was investigated using scanning electron microscopy (SEM) and energy dispersive X-ray analysis. SEM imaging of freshly broken fractured chips revealed structures strongly recent terrestrial microorganisms, in some cases showing evidence of active growth. This conclusion was supported by EDX analysis, which showed the presence of carbon associated with these structures, we concluded that these structures represent recent terrestrial contaminants rather than structures indigenous to the meteorite. Page

Detection of Organic Constituents Including Chloromethylpropene in the Analyses of the ROCKNEST Drift by Sample Analysis at Mars (SAM)

NASA Technical Reports Server (NTRS)

Eigenbrode, J. L.; Glavin, D.; Coll, P.; Summons, R. E.; Mahaffy, P.; Archer, D.; Brunner, A.; Conrad, P.; Freissinet, C.; Martin, M.;

Quasi-closed phase forward-backward linear prediction analysis of speech for accurate formant detection and estimation.

PubMed

Gowda, Dhananjaya; Airaksinen, Manu; Alku, Paavo

2017-09-01

Recently, a quasi-closed phase (QCP) analysis of speech signals for accurate glottal inverse filtering was proposed. However, the QCP analysis which belongs to the family of temporally weighted linear prediction (WLP) methods uses the conventional forward type of sample prediction. This may not be the best choice especially in computing WLP models with a hard-limiting weighting function. A sample selective minimization of the prediction error in WLP reduces the effective number of samples available within a given window frame. To counter this problem, a modified quasi-closed phase forward-backward (QCP-FB) analysis is proposed, wherein each sample is predicted based on its past as well as future samples thereby utilizing the available number of samples more effectively. Formant detection and estimation experiments on synthetic vowels generated using a physical modeling approach as well as natural speech utterances show that the proposed QCP-FB method yields statistically significant improvements over the conventional linear prediction and QCP methods.

HPLC fingerprint analysis combined with chemometrics for pattern recognition of ginger.

PubMed

Feng, Xu; Kong, Weijun; Wei, Jianhe; Ou-Yang, Zhen; Yang, Meihua

2014-03-01

Ginger, the fresh rhizome of Zingiber officinale Rosc. (Zingiberaceae), has been used worldwide; however, for a long time, there has been no standard approbated internationally for its quality control. To establish an efficacious and combinational method and pattern recognition technique for quality control of ginger. A simple, accurate and reliable method based on high-performance liquid chromatography with photodiode array (HPLC-PDA) detection was developed for establishing the chemical fingerprints of 10 batches of ginger from different markets in China. The method was validated in terms of precision, reproducibility and stability; and the relative standard deviations were all less than 1.57%. On the basis of this method, the fingerprints of 10 batches of ginger samples were obtained, which showed 16 common peaks. Coupled with similarity evaluation software, the similarities between each fingerprint of the sample and the simulative mean chromatogram were in the range of 0.998-1.000. Then, the chemometric techniques, including similarity analysis, hierarchical clustering analysis and principal component analysis were applied to classify the ginger samples. Consistent results were obtained to show that ginger samples could be successfully classified into two groups. This study revealed that HPLC-PDA method was simple, sensitive and reliable for fingerprint analysis, and moreover, for pattern recognition and quality control of ginger.

Geochemical characterisation of pyrite oxidation and environmental problems related to release and transport of metals from a coal washing low-grade waste dump, Shahrood, northeast Iran.

PubMed

Doulati Ardejani, Faramarz; Jodieri Shokri, Behshad; Moradzadeh, Ali; Shafaei, Seyed Ziadin; Kakaei, Reza

2011-12-01

Pyrite oxidation and release of the oxidation products from a low-grade coal waste dump to stream, groundwater and soil was investigated by geochemical and hydrogeochemical techniques at Alborz Sharghi coal washing plant, Shahrood, northeast Iran. Hydrogeochemical analysis of water samples indicates that the metal concentrations in the stream waters were low. Moreover, the pH of the water showed no considerable change. The analysis of the stream water samples shows that except the physical changes, pyrite oxidation process within the coal washing waste dump has not affected the quality of the stream water. Water type was determined to be calcium sulphate. The results of the analysis of groundwater samples indicate that the pH varies from 7.41 to 7.51. The concentrations of the toxic metals were low. The concentration of SO4 is slightly above than its standard concentration in potable water. It seems that the groundwater less affected by the coal washing operation in the study area. Geochemical analysis of the sediment samples shows that Fe concentration decreases gradually downstream the waste dump with pH rising. SO(4) decreases rapidly downstream direction. Copper, Zn and Co concentrations decrease with distance from the waste dump due to a dilution effect by the mixing of uncontaminated sediments. These elements, in particular, Zn are considerably elevated in sediment sample collected at the nearest distance to the waste dump. There is no doubt that such investigations can help to develop an appropriate water remediation plan.

Standoff spectroscopic interrogation of samples irradiated by high energy lasers

NASA Astrophysics Data System (ADS)

Daigle, Jean-François; Pudo, Dominik; Théberge, Francis

2017-10-01

We report on a novel method that shows the potential to provide real-time, standoff forensic analysis of samples being irradiated by a high energy laser (HEL). The interaction of the HEL beam with matter produces specific optical signatures that can be detected from the location of the HEL system. A spectroscopic analysis of these signals can then provide useful information to the operator including the impact the laser has on the sample as well as providing data about the its structure and composition.

Characterization and forensic analysis of soil samples using laser-induced breakdown spectroscopy (LIBS).

PubMed

Jantzi, Sarah C; Almirall, José R

2011-07-01

A method for the quantitative elemental analysis of surface soil samples using laser-induced breakdown spectroscopy (LIBS) was developed and applied to the analysis of bulk soil samples for discrimination between specimens. The use of a 266 nm laser for LIBS analysis is reported for the first time in forensic soil analysis. Optimization of the LIBS method is discussed, and the results compared favorably to a laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS) method previously developed. Precision for both methods was <10% for most elements. LIBS limits of detection were <33 ppm and bias <40% for most elements. In a proof of principle study, the LIBS method successfully discriminated samples from two different sites in Dade County, FL. Analysis of variance, Tukey's post hoc test and Student's t test resulted in 100% discrimination with no type I or type II errors. Principal components analysis (PCA) resulted in clear groupings of the two sites. A correct classification rate of 99.4% was obtained with linear discriminant analysis using leave-one-out validation. Similar results were obtained when the same samples were analyzed by LA-ICP-MS, showing that LIBS can provide similar information to LA-ICP-MS. In a forensic sampling/spatial heterogeneity study, the variation between sites, between sub-plots, between samples and within samples was examined on three similar Dade sites. The closer the sampling locations, the closer the grouping on a PCA plot and the higher the misclassification rate. These results underscore the importance of careful sampling for geographic site characterization.

Identification and molecular analysis of infectious bursal disease in broiler farms in the Kurdistan Regional Government of Iraq.

PubMed

Amin, Oumed Gerjis M; Jackwood, Daral J

2014-10-01

The present study was undertaken to characterize field isolates of infectious bursal disease virus (IBDV). The identification was done using reverse transcription-polymerase chain reaction (RT-PCR) and partial sequencing of the VP2 gene. Pooled bursal samples were collected from commercial broiler farms located in the Kurdistan Regional Government (KRG) of Iraq. The genetic material of the IBDV was detected in 10 out of 29 field samples. Sequences of the hypervariable VP2 region were determined for 10 of these viruses. Molecular analysis of the VP2 gene of five IBDVs showed amino acid sequences consistent with the very virulent (vv) IBDV. Two samples were identified as classic vaccine viruses, and three samples were classic vaccine viruses that appear to have mutated during replication in the field. Phylogenetic analysis showed that all five field IBDV strains of the present study were closely related to each other. On the basis of nucleotide sequencing and phylogenetic analysis, it is very likely that IBD-causing viruses in this part of Iraq are of the very virulent type. These IBDVs appear to be evolving relative to their type strains.

Evaluation of micro-organism-detaching efficacy from meat samples by spindle or stomacher treatment and quality analysis of suspensions.

PubMed

Kim, S-J; Kim, D-K; Kang, D-H

2016-04-01

We investigated and compared the efficacy of a new apparatus for detaching micro-organisms from meat samples. The efficacy of Spindle and stomacher in detaching micro-organisms from meat samples was evaluated. Also, evaluation of appropriateness of suspensions generated by both methods for carrying out molecular biological analysis was implemented. A nearly identical correlation and high R(2) were obtained between Spindle and stomacher in Aerobic Plate Count (APC), and no significant differences were observed in detachment of three major foodborne pathogens. The suspension generated by the Spindle showed lower turbidity and total protein concentration. Also, significantly different threshold cycles were observed in Real-time PCR analysis using suspensions generated by both methods. The Spindle shows nearly identical efficacy with stomacher treatment in detaching micro-organisms from meat samples. Furthermore, the high quality of suspensions generated by the Spindle, in terms of turbidity and total protein assay, allows for a lower threshold cycle than stomached suspension in Real-time PCR. The Spindle could be an alternative method for detaching micro-organisms, yielding a higher quality of suspensions which may be better suited for further molecular microbiological analysis. © 2016 The Society for Applied Microbiology.

Étude de la variation spatio-temporelle des paramètres physico-chimiques caractérisant la qualité des eaux d'une lagune côtière et ses zonations écologiques : cas de Moulay Bousselham, Maroc

NASA Astrophysics Data System (ADS)

Labbardi, Hanane; Ettahiri, Omar; Lazar, Said; Massik, Zakia; El Antri, Said

2005-04-01

Our interest is related to the hydrological characteristics of the Moulay Bousselham lagoon. Water samples were taken monthly from July 2001 to June 2002 in 15 stations distributed along the lagoon. The various measured hydrological parameters (temperature, salinity, suspended matter, chlorophyll a) showed significant monthly variations ( p<0.001), whereas spatially among all sampled stations, only the salinity showed significant variations. The variability analysis approached by the analysis of the normalized principal components combined with discriminate analysis showed very small inter-stations variability. Its percentage is 11% and 9% of the total variance during high and low tide, respectively. To cite this article: H. Labbardi et al., C. R. Geoscience 337 (2005).

Amino Acid profile as a feasible tool for determination of the authenticity of fruit juices.

PubMed

Asadpoor, Mostafa; Ansarin, Masoud; Nemati, Mahboob

2014-12-01

Fruit juice is a nutrient rich food product with a direct connection to public health. The purpose of this research was to determine the amino acid profile of juices and provide a quick and accurate indicator for determining their authenticity. The method of analysis was HPLC with fluorescence detector and pre-column derivatization by orthophtaldialdehyde (OPA). Sixty-six samples of fruit juices were analyzed, and fourteen amino acids were identified and determined in the sampled fruit juices. The fruit samples used for this analysis were apples, oranges, cherry, pineapple, mango, apricot, pomegranate, peach and grapes. The results showed that 32% of samples tested in this study had a lower concentrate percentage as compared to that of their labels and/or other possible authenticity problems in the manufacturing process. The following samples showed probable adulteration: four cherry juice samples, two pomegranate juice samples, one mango, three grape, four peach, seven orange, two apple and one apricot juice samples. In general, determining the amount of amino acids and comparing sample amino acids profiles with the standard values seems to be an indicator for quality control. This method can provide the regulatory agencies with a tool, to help produce a healthier juice. The aim of this study is the analytical control of the fruit juice composition is becoming an important issue, and HPLC can provide an important and essential tool for more accurate research as well as for routine analysis.

Demographic characteristics, social competence, and behavior problems in children with gender identity disorder: a cross-national, cross-clinic comparative analysis.

PubMed

Cohen-Kettenis, Peggy T; Owen, Allison; Kaijser, Vanessa G; Bradley, Susan J; Zucker, Kenneth J

2003-02-01

This study examined demographic characteristics, social competence, and behavior problems in clinic-referred children with gender identity problems in Toronto, Canada (N = 358), and Utrecht, The Netherlands (N = 130). The Toronto sample was, on average, about a year younger than the Utrecht sample at referral, had a higher percentage of boys, had a higher mean IQ, and was less likely to be living with both parents. On the Child Behavior Checklist (CBCL), both groups showed, on average, clinical range scores in both social competence and behavior problems. A CBCL-derived measure of poor peer relations showed that boys in both clinics had worse ratings than did the girls. A multiple regression analysis showed that poor peer relations were the strongest predictor of behavior problems in both samples. This study-the first cross-national, cross-clinic comparative analysis of children with gender identity disorder-found far more similarities than differences in both social competence and behavior problems. The most salient demographic difference was age at referral. Cross-national differences in factors that might influence referral patterns are discussed.

Extractive electrospray ionization mass spectrometry toward in situ analysis without sample pretreatment.

PubMed

Li, Ming; Hu, Bin; Li, Jianqiang; Chen, Rong; Zhang, Xie; Chen, Huanwen

2009-09-15

A homemade novel nanoextractive electrospray ionization (nanoEESI) source has been characterized for in situ mass spectrometric analysis of ambient samples without sample pretreatment. The primary ions generated using a nanospray emitter interact with the neutral sample plume created by manually nebulizing liquid samples, allowing production of the analyte ions in the spatial cross section of the nanoEESI source. The performance of nanoEESI is experimentally investigated by coupling the nanoEESI source to a commercial LTQ mass spectrometer for rapid analysis of various ambient samples using positive/negative ion detection modes. Compounds of interest in actual samples such as aerosol drug preparations, beverages, milk suspensions, farmland water, and groundwater were unambiguously detected using tandem nanoEESI ion trap mass spectrometry. The limit of detection was low picogram per milliliter levels for the compounds tested. Acceptable relative standard deviation (RSD) values (5-10%) were obtained for direct measurement of analytes in complex matrixes, providing linear dynamic signal responses using manual sample introduction. A single sample analysis was completed within 1.2 s. Requiring no sheath gas for either primary ion production or neutral sample introduction, the nanoEESI has advantages including readiness for miniaturization and integration, simple maintenance, easy operation, and low cost. The experimental data demonstrate that the nanoEESI is a promising tool for high-throughput, sensitive, quantitative, in situ analysis of ambient complex samples, showing potential applications for in situ analysis in multiple disciplines including but not limited to pharmaceutical analysis, food quality control, pesticides residue detection, and homeland security.

Methods to increase reproducibility in differential gene expression via meta-analysis

PubMed Central

Sweeney, Timothy E.; Haynes, Winston A.; Vallania, Francesco; Ioannidis, John P.; Khatri, Purvesh

2017-01-01

Findings from clinical and biological studies are often not reproducible when tested in independent cohorts. Due to the testing of a large number of hypotheses and relatively small sample sizes, results from whole-genome expression studies in particular are often not reproducible. Compared to single-study analysis, gene expression meta-analysis can improve reproducibility by integrating data from multiple studies. However, there are multiple choices in designing and carrying out a meta-analysis. Yet, clear guidelines on best practices are scarce. Here, we hypothesized that studying subsets of very large meta-analyses would allow for systematic identification of best practices to improve reproducibility. We therefore constructed three very large gene expression meta-analyses from clinical samples, and then examined meta-analyses of subsets of the datasets (all combinations of datasets with up to N/2 samples and K/2 datasets) compared to a ‘silver standard’ of differentially expressed genes found in the entire cohort. We tested three random-effects meta-analysis models using this procedure. We showed relatively greater reproducibility with more-stringent effect size thresholds with relaxed significance thresholds; relatively lower reproducibility when imposing extraneous constraints on residual heterogeneity; and an underestimation of actual false positive rate by Benjamini–Hochberg correction. In addition, multivariate regression showed that the accuracy of a meta-analysis increased significantly with more included datasets even when controlling for sample size. PMID:27634930

Single hair analysis of small molecules using MALDI-triple quadrupole MS imaging and LC-MS/MS: investigations on opportunities and pitfalls.

PubMed

Poetzsch, Michael; Steuer, Andrea E; Roemmelt, Andreas T; Baumgartner, Markus R; Kraemer, Thomas

2014-12-02

Single hair analysis normally requires extensive sample preparation microscale protocols including time-consuming steps like segmentation and extraction. Matrix assisted laser desorption and ionization mass spectrometric imaging (MALDI-MSI) was shown to be an alternative tool in single hair analysis, but still, questions remain. Therefore, an investigation of MALDI-MSI in single hair analysis concerning the extraction process, usage of internal standard (IS), and influences on the ionization processes were systematically investigated to enable the reliable application to hair analysis. Furthermore, single dose detection, quantitative correlation to a single hair, and hair strand LC-MS/MS results were performed, and the performance was compared to LC-MS/MS single hair monitoring. The MALDI process was shown to be independent from natural hair color and not influenced by the presence of melanin. Ionization was shown to be reproducible along and in between different hair samples. MALDI image intensities in single hair and hair snippets showed good semiquantitative correlation to zolpidem hair concentrations obtained from validated routine LC-MS/MS methods. MALDI-MSI is superior to LC-MS/MS analysis when a fast, easy, and cheap sample preparation is necessary, whereas LC-MS/MS showed higher sensitivity with the ability of single dose detection for zolpidem. MALDI-MSI and LC-MS/MS segmental single hair analysis showed good correlation, and both are suitable for consumption monitoring of drugs of abuse with a high time resolution.

Comparison of Ion Personal Genome Machine Platforms for the Detection of Variants in BRCA1 and BRCA2.

PubMed

Hwang, Sang Mee; Lee, Ki Chan; Lee, Min Seob; Park, Kyoung Un

2018-01-01

Transition to next generation sequencing (NGS) for BRCA1 / BRCA2 analysis in clinical laboratories is ongoing but different platforms and/or data analysis pipelines give different results resulting in difficulties in implementation. We have evaluated the Ion Personal Genome Machine (PGM) Platforms (Ion PGM, Ion PGM Dx, Thermo Fisher Scientific) for the analysis of BRCA1 /2. The results of Ion PGM with OTG-snpcaller, a pipeline based on Torrent mapping alignment program and Genome Analysis Toolkit, from 75 clinical samples and 14 reference DNA samples were compared with Sanger sequencing for BRCA1 / BRCA2 . Ten clinical samples and 14 reference DNA samples were additionally sequenced by Ion PGM Dx with Torrent Suite. Fifty types of variants including 18 pathogenic or variants of unknown significance were identified from 75 clinical samples and known variants of the reference samples were confirmed by Sanger sequencing and/or NGS. One false-negative results were present for Ion PGM/OTG-snpcaller for an indel variant misidentified as a single nucleotide variant. However, eight discordant results were present for Ion PGM Dx/Torrent Suite with both false-positive and -negative results. A 40-bp deletion, a 4-bp deletion and a 1-bp deletion variant was not called and a false-positive deletion was identified. Four other variants were misidentified as another variant. Ion PGM/OTG-snpcaller showed acceptable performance with good concordance with Sanger sequencing. However, Ion PGM Dx/Torrent Suite showed many discrepant results not suitable for use in a clinical laboratory, requiring further optimization of the data analysis for calling variants.

Haplotype data for 23 Y-chromosome markers in a reference sample from Bosnia and Herzegovina.

PubMed

Kovačević, Lejla; Fatur-Cerić, Vera; Hadzic, Negra; Čakar, Jasmina; Primorac, Dragan; Marjanović, Damir

2013-06-01

To detect polymorphisms of 23 Y-chromosomal short tandem repeat (STR) loci, including 6 new loci, in a reference database of male population of Bosnia and Herzegovina, as well as to assess the importance of increasing the number of Y-STR loci utilized in forensic DNA analysis. The reference sample consisted of 100 healthy, unrelated men originating from Bosnia and Herzegovina. Sample collection using buccal swabs was performed in all geographical regions of Bosnia and Herzegovina in the period from 2010 to 2011. DNA samples were typed for 23 Y STR loci, including 6 new loci: DYS576, DYS481, DYS549, DYS533, DYS570, and DYS643, which are included in the new PowerPlex® Y 23 amplification kit. The absolute frequency of generated haplotypes was calculated and results showed that 98 samples had unique Y 23 haplotypes, and that only two samples shared the same haplotype. The most polymorphic locus was DYS418, with 14 detected alleles and the least polymorphic loci were DYS389I, DYS391, DYS437, and DYS393. This study showed that by increasing the number of highly polymorphic Y STR markers, to include those tested in our analysis, leads to a reduction of repeating haplotypes, which is very important in the application of forensic DNA analysis.

Task 2 Report: Algorithm Development and Performance Analysis

DTIC Science & Technology

1993-07-01

separated peaks ............................................. 39 7-16 Example ILGC data for schedule 3 phosphites showing an analysis method which integrates...more closely follows the baseline ................. 40 7-18 Example R.GC data for schedule 3 phosphites showing an analysis method resulting in unwanted...much of the ambiguity that can arise in GC/MS with trace environmental samples, for example. Correlated chromatography, on the other hand, separates the

Characterization of Malaysian coals for carbon dioxide sequestration

NASA Astrophysics Data System (ADS)

Abunowara, M.; Bustam, M. A.; Sufian, S.; Eldemerdash, U.

2016-06-01

Coal samples from Mukah-Balingian and Merit-Pila coal mines were characterized with ultimate, approximate, petrographic analysis, FT-IR spectra patterns, FESEM images and BET measurements to obtain information on the chemical composition and chemical structure in the samples. Two coal samples were obtained from Merit-Pila coal mine namely sample1 (S1) and sample2 (S2). The other two coal samples were obtained from Mukah-Balingian coal mine namely sample3 (S3) and sample4 (S4), Sarawak, Malaysia. The results of ultimate analysis show that coal S1 has the highest carbon percentage by 54.47%, the highest hydrogen percentage by 10.56% and the lowest sulfur percentage by 0.19% and the coal S4 has the highest moisture content by 31.5%. The coal S1 has the highest fixed carbon percentage by 42.6%. The coal S4 has BET surface area by 2.39 m2/g and Langmuir surface area by 3.0684 m2/g respectively. Fourier-Transform Infrared (FT-IR) spectroscopy analysis of all coal samples shows a presence of oxygen containing functional groups which considered are as active sites on coal surface. The oxygen functional groups are mainly carboxyl (-COOH), hydroxyl (-OH), alkyl (-CH, -CH2, -CH3), aliphatic (C-O-C stretching associated with -OH), amino (-NH stretching vibrations), (-NH stretching vibrations), aromatic (C=C), vinylic (C=C) and clay minerals. In all FE-SEM images of coal samples matrix, it can be seen that there are luminous and as non luminous features which refer to the existence of various minerals types distributed in the coal organic matrix. The bright luminosity is due to the presence of sodium, potassium or aluminium. According to petrographic analysis, all coal sample samples are range in vitrinite reflectance from 0.38% to 56% (VRr) are sub-bituminous coals.

Discrimination of whisky brands and counterfeit identification by UV-Vis spectroscopy and multivariate data analysis.

PubMed

Martins, Angélica Rocha; Talhavini, Márcio; Vieira, Maurício Leite; Zacca, Jorge Jardim; Braga, Jez Willian Batista

2017-08-15

The discrimination of whisky brands and counterfeit identification were performed by UV-Vis spectroscopy combined with partial least squares for discriminant analysis (PLS-DA). In the proposed method all spectra were obtained with no sample preparation. The discrimination models were built with the employment of seven whisky brands: Red Label, Black Label, White Horse, Chivas Regal (12years), Ballantine's Finest, Old Parr and Natu Nobilis. The method was validated with an independent test set of authentic samples belonging to the seven selected brands and another eleven brands not included in the training samples. Furthermore, seventy-three counterfeit samples were also used to validate the method. Results showed correct classification rates for genuine and false samples over 98.6% and 93.1%, respectively, indicating that the method can be helpful for the forensic analysis of whisky samples. Copyright © 2017 Elsevier Ltd. All rights reserved.

The Use of Thermal Analysis and Photoacoustic Spectroscopy in the Evaluation of Maltodextrin Microencapsulation of Anthocyanins from Juçara Palm Fruit (Euterpe edulis Mart.) and Their Application in Food

PubMed Central

Paula da Silva dos Passos, Ana; Madrona, Grasiele Scaramal; Marcolino, Vanessa Aparecida; Baesso, Mauro Luciano

2015-01-01

Summary Anthocyanins extracted from the pulp of the fruit of juçara palm (Euterpe edulis Mart.) were microencapsulated with maltodextrin in order to stabilise them. Photoacoustic spectroscopy was used to investigate the photostability of the microencapsulated samples. Complementary differential scanning calorimetry and scanning electron microscopy measurements were also performed. Lyophilised extract had 14 340.2 mg/L of total anthocyanins, and the microencapsulation efficiency of 93.6%. Temperature analysis showed that maltodextrin conferred protection up to 70 °C for 120 min. Scanning electron microscopy showed that the microencapsulated particles had a flake-like morphology with a smooth surface, characteristic of lyophilisation processes. In addition, when added to yogurt, a red colourant was predominant in the samples at pH from 1.5 up to 5.0. Thermal analysis showed a weak interaction between the sample and the encapsulating agent, and photoacoustic data indicated the photostability of the matrix when exposed to light. Yogurts containing microencapsulated anthocyanins showed a more intense pink colour than yogurts treated with pure dye, and sensory analysis demonstrated that they can have good acceptance on the market. Microencapsulation enabled the innovative application of anthocyanins from juçara palm fruit, and complementary techniques allied to the photoacoustic spectroscopy were effective tools for its evaluation. PMID:27904373

The Use of Thermal Analysis and Photoacoustic Spectroscopy in the Evaluation of Maltodextrin Microencapsulation of Anthocyanins from Juçara Palm Fruit (Euterpe edulis Mart.) and Their Application in Food.

PubMed

Paula da Silva Dos Passos, Ana; Madrona, Grasiele Scaramal; Marcolino, Vanessa Aparecida; Baesso, Mauro Luciano; Matioli, Graciette

2015-12-01

Anthocyanins extracted from the pulp of the fruit of juçara palm ( Euterpe edulis Mart.) were microencapsulated with maltodextrin in order to stabilise them. Photoacoustic spectroscopy was used to investigate the photostability of the microencapsulated samples. Complementary differential scanning calorimetry and scanning electron microscopy measurements were also performed. Lyophilised extract had 14 340.2 mg/L of total anthocyanins, and the microencapsulation efficiency of 93.6%. Temperature analysis showed that maltodextrin conferred protection up to 70 °C for 120 min. Scanning electron microscopy showed that the microencapsulated particles had a flake-like morphology with a smooth surface, characteristic of lyophilisation processes. In addition, when added to yogurt, a red colourant was predominant in the samples at pH from 1.5 up to 5.0. Thermal analysis showed a weak interaction between the sample and the encapsulating agent, and photoacoustic data indicated the photostability of the matrix when exposed to light. Yogurts containing microencapsulated anthocyanins showed a more intense pink colour than yogurts treated with pure dye, and sensory analysis demonstrated that they can have good acceptance on the market. Microencapsulation enabled the innovative application of anthocyanins from juçara palm fruit, and complementary techniques allied to the photoacoustic spectroscopy were effective tools for its evaluation.

The effect of acidity of electrolyte on the porosity and the nanostructure morphology of electrolytic manganese dioxide

NASA Astrophysics Data System (ADS)

Adelkhani, H.

2012-06-01

The effects of acidity of electrolyte (pH) on the hysteresis behavior, the specific surface area, and nanostructure morphology of electrolytic manganese dioxides (EMDs) have been studied by using the Barrett-Joyner-Halenda (BJH) analysis, X-ray diffraction (XRD) and scanning electron microscopy (SEM) images analysis. EMD samples are electrodeposited at a variable pH (6 to 1) and many fixed pH (2, 3, 4, 5, and 6). Results indicate that pH play key roles in the characteristics of EMD. The samples obtained at low pH (2 and 3) show multi-branched morphology and represent a H4 hysteresis loop. At pH 4 and 5, a uniform and dense structure of MnO2 is obtained without hysteresis behavior. The sample electrodeposited at pH 6 shows a regular reticulate, that its adsorption-desorption isotherm show hysteresis behavior. By electrodeposition at a variable pH, the sample shows a cauliflower-like and multi-branched form. From the viewpoint of classification of isotherm, pH strongly affects on Type of isotherm. The results show that γ-MnO2 is as main-product of electrodeposition and α-MnO2 and β-MnO2 were obtained as side-product at low and high pH, respectively.

Interaction of Soil Heavy Metal Pollution with Industrialisation and the Landscape Pattern in Taiyuan City, China

PubMed Central

Liu, Yong; Su, Chao; Zhang, Hong; Li, Xiaoting; Pei, Jingfei

2014-01-01

Many studies indicated that industrialization and urbanization caused serious soil heavy metal pollution from industrialized age. However, fewer previous studies have conducted a combined analysis of the landscape pattern, urbanization, industrialization, and heavy metal pollution. This paper was aimed at exploring the relationships of heavy metals in the soil (Pb, Cu, Ni, As, Cd, Cr, Hg, and Zn) with landscape pattern, industrialisation, urbanisation in Taiyuan city using multivariate analysis. The multivariate analysis included correlation analysis, analysis of variance (ANOVA), independent-sample T test, and principal component analysis (PCA). Geographic information system (GIS) was also applied to determine the spatial distribution of the heavy metals. The spatial distribution maps showed that the heavy metal pollution of the soil was more serious in the centre of the study area. The results of the multivariate analysis indicated that the correlations among heavy metals were significant, and industrialisation could significantly affect the concentrations of some heavy metals. Landscape diversity showed a significant negative correlation with the heavy metal concentrations. The PCA showed that a two-factor model for heavy metal pollution, industrialisation, and the landscape pattern could effectively demonstrate the relationships between these variables. The model explained 86.71% of the total variance of the data. Moreover, the first factor was mainly loaded with the comprehensive pollution index (P), and the second factor was primarily loaded with landscape diversity and dominance (H and D). An ordination of 80 samples could show the pollution pattern of all the samples. The results revealed that local industrialisation caused heavy metal pollution of the soil, but such pollution could respond negatively to the landscape pattern. The results of the study could provide a basis for agricultural, suburban, and urban planning. PMID:25251460

Interaction of soil heavy metal pollution with industrialisation and the landscape pattern in Taiyuan city, China.

PubMed

Liu, Yong; Su, Chao; Zhang, Hong; Li, Xiaoting; Pei, Jingfei

2014-01-01

Many studies indicated that industrialization and urbanization caused serious soil heavy metal pollution from industrialized age. However, fewer previous studies have conducted a combined analysis of the landscape pattern, urbanization, industrialization, and heavy metal pollution. This paper was aimed at exploring the relationships of heavy metals in the soil (Pb, Cu, Ni, As, Cd, Cr, Hg, and Zn) with landscape pattern, industrialisation, urbanisation in Taiyuan city using multivariate analysis. The multivariate analysis included correlation analysis, analysis of variance (ANOVA), independent-sample T test, and principal component analysis (PCA). Geographic information system (GIS) was also applied to determine the spatial distribution of the heavy metals. The spatial distribution maps showed that the heavy metal pollution of the soil was more serious in the centre of the study area. The results of the multivariate analysis indicated that the correlations among heavy metals were significant, and industrialisation could significantly affect the concentrations of some heavy metals. Landscape diversity showed a significant negative correlation with the heavy metal concentrations. The PCA showed that a two-factor model for heavy metal pollution, industrialisation, and the landscape pattern could effectively demonstrate the relationships between these variables. The model explained 86.71% of the total variance of the data. Moreover, the first factor was mainly loaded with the comprehensive pollution index (P), and the second factor was primarily loaded with landscape diversity and dominance (H and D). An ordination of 80 samples could show the pollution pattern of all the samples. The results revealed that local industrialisation caused heavy metal pollution of the soil, but such pollution could respond negatively to the landscape pattern. The results of the study could provide a basis for agricultural, suburban, and urban planning.

Determination of element composition and extraterrestrial material occurrence in moss and lichen samples from King George Island (Antarctica) using reactor neutron activation analysis and SEM microscopy.

PubMed

Mróz, Tomasz; Szufa, Katarzyna; Frontasyeva, Marina V; Tselmovich, Vladimir; Ostrovnaya, Tatiana; Kornaś, Andrzej; Olech, Maria A; Mietelski, Jerzy W; Brudecki, Kamil

2018-01-01

Seven lichens (Usnea antarctica and U. aurantiacoatra) and nine moss samples (Sanionia uncinata) collected in King George Island were analyzed using instrumental neutron activation analysis, and concentration of major and trace elements was calculated. For some elements, the concentrations observed in moss samples were higher than corresponding values reported from other sites in the Antarctica, but in the lichens, these were in the same range of concentrations. Scanning electron microscopy (SEM) and statistical analysis showed large influence of volcanic-origin particles. Also, the interplanetary cosmic particles (ICP) were observed in investigated samples, as mosses and lichens are good collectors of ICP and micrometeorites.

Effect Of Neodymium Substitution In Structural Characteristics Of Magnesium Ferrite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Thankachan, Smitha; Binu, P. J.; Xavier, Sheena

2011-10-20

The effect of Nd{sup 3+} substitution on the structural properties of Magnesium ferrite was studied in the series MgNd{sub x}Fe{sub 2-x}O{sub 4}, where x = 0 to 0.3 in steps of 0.05. The series was prepared by sol-gel technique which is one of the novel technique to prepare nanosized samples. Structural characterization was done using X-ray diffractometer and Fourier Transform Infrared Spectrometer. XRD analysis reveals the prepared samples are single phasic till x = 0.2. From x0 = .25, a secondary phase of iron neodymium oxide appears along with the spinel phase. Particle size calculation shows the prepared samples aremore » in the 9nm to 11 nm regime. Lattice parameter was found to increase with concentration of Nd. XRD and FTIR analysis confirmed spinel structure of the prepared samples. XRF result shows the expected composition of prepared samples. The frequency dependence of the dielectric constant in the range 100 Hz--120MHz was also studied« less

Application of GeO2 nanoparticle as electrically erasable memory and its photo catalytic behaviour

NASA Astrophysics Data System (ADS)

Seal, M.; Bose, N.; Mukherjee, S.

2018-06-01

Germanium oxide nanoparticle is synthesized from bulk GeO2 powder through hydrothermal technique. The structural characterization of the prepared sample is performed with x-ray Diffraction and Transmission Electron Microscope. From the PL emission spectra and x-ray photoelectron spectra, the existence of oxygen defects inside the sample is confirmed. Thermogravimetric (TG) analysis of the sample shows that there is no weight loss with increase in temperature instead of a very little weight gain. An estimation of Oxygen vacancy concentration is made from the amount of weight gain as measured during TG analysis. The sample is also characterized with PE loop tracer, which indicates that GeO2 nanoparticle is able to show hysteresis loop regarding variation of Polarization with electric field. Such phenomenon implies that the sample can be used as electrically erasable memory device. Further, GeO2 nanoparticle is also exploited as photo catalyst to degrade Methylene Blue (MB) solution in the presence of ultraviolet ray. This phenomenon is also explained with oxygen vacancy.

Analysis of simulated high burnup nuclear fuel by laser induced breakdown spectroscopy

NASA Astrophysics Data System (ADS)

Singh, Manjeet; Sarkar, Arnab; Banerjee, Joydipta; Bhagat, R. K.

2017-06-01

Advanced Heavy Water Reactor (AHWR) grade (Th-U)O2 fuel sample and Simulated High Burn-Up Nuclear Fuels (SIMFUEL) samples mimicking the 28 and 43 GWd/Te irradiated burn-up fuel were studied using laser-induced breakdown spectroscopy (LIBS) setup in a simulated hot-cell environment from a distance of > 1.5 m. Resolution of < 38 pm has been used to record the complex spectra of the SIMFUEL samples. By using spectrum comparison and database matching > 60 emission lines of fission products was identified. Among them only a few emission lines were found to generate calibration curves. The study demonstrates the possibility to investigate impurities at concentrations around hundreds of ppm, rapidly at atmospheric pressure without any sample preparation. The results of Ba and Mo showed the advantage of LIBS analysis over traditional methods involving sample dissolution, which introduces possible elemental loss. Limits of detections (LOD) under Ar atmosphere shows significant improvement, which is shown to be due to the formation of stable plasma.

Performance evaluation of the Abbott CELL-DYN Emerald for use as a bench-top analyzer in a research setting.

PubMed

Khoo, T-L; Xiros, N; Guan, F; Orellana, D; Holst, J; Joshua, D E; Rasko, J E J

2013-08-01

The CELL-DYN Emerald is a compact bench-top hematology analyzer that can be used for a three-part white cell differential analysis. To determine its utility for analysis of human and mouse samples, we evaluated this machine against the larger CELL-DYN Sapphire and Sysmex XT2000iV hematology analyzers. 120 human (normal and abnormal) and 30 mouse (normal and abnormal) samples were analyzed on both the CELL-DYN Emerald and CELL-DYN Sapphire or Sysmex XT2000iV analyzers. For mouse samples, the CELL-DYN Emerald analyzer required manual recalibration based on the histogram populations. Analysis of the CELL-DYN Emerald showed excellent precision, within accepted ranges (white cell count CV% = 2.09%; hemoglobin CV% = 1.68%; platelets CV% = 4.13%). Linearity was excellent (R² ≥ 0.99), carryover was minimal (<1%), and overall interinstrument agreement was acceptable for both human and mouse samples. Comparison between the CELL-DYN Emerald and Sapphire analyzers for human samples or Sysmex XT2000iV analyzer for mouse samples showed excellent correlation for all parameters. The CELL-DYN Emerald was generally comparable to the larger reference analyzer for both human and mouse samples. It would be suitable for use in satellite research laboratories or as a backup system in larger laboratories. © 2012 John Wiley & Sons Ltd.

A summary of phase analysis on Apollo 14 samples

NASA Technical Reports Server (NTRS)

Fredriksson, K.; Nelen, J.; Noonan, A.; Kraut, F.

1971-01-01

The results of an analysis of lunar samples from Apollo 14 are presented. The large number of breccias returned from the Fra Mauro formation show that impact events are an important rock forming mechanism on the moon. Larger rocks as well as micro breccias bear structural resemblance to brecciated chondrites and terrestrial impactites. Many show evidence of repetitious events of break-up and accumulation welding. The surface of the regolith has become thoroughly mixed by this process. Most components however appear locally derived from basalts rich in feldspar and Kreep components, similar to rocks such as 14310.

Spectral analysis software improves confidence in plant and soil water stable isotope analyses performed by isotope ratio infrared spectroscopy (IRIS).

PubMed

West, A G; Goldsmith, G R; Matimati, I; Dawson, T E

2011-08-30

Previous studies have demonstrated the potential for large errors to occur when analyzing waters containing organic contaminants using isotope ratio infrared spectroscopy (IRIS). In an attempt to address this problem, IRIS manufacturers now provide post-processing spectral analysis software capable of identifying samples with the types of spectral interference that compromises their stable isotope analysis. Here we report two independent tests of this post-processing spectral analysis software on two IRIS systems, OA-ICOS (Los Gatos Research Inc.) and WS-CRDS (Picarro Inc.). Following a similar methodology to a previous study, we cryogenically extracted plant leaf water and soil water and measured the δ(2)H and δ(18)O values of identical samples by isotope ratio mass spectrometry (IRMS) and IRIS. As an additional test, we analyzed plant stem waters and tap waters by IRMS and IRIS in an independent laboratory. For all tests we assumed that the IRMS value represented the "true" value against which we could compare the stable isotope results from the IRIS methods. Samples showing significant deviations from the IRMS value (>2σ) were considered to be contaminated and representative of spectral interference in the IRIS measurement. Over the two studies, 83% of plant species were considered contaminated on OA-ICOS and 58% on WS-CRDS. Post-analysis, spectra were analyzed using the manufacturer's spectral analysis software, in order to see if the software correctly identified contaminated samples. In our tests the software performed well, identifying all the samples with major errors. However, some false negatives indicate that user evaluation and testing of the software are necessary. Repeat sampling of plants showed considerable variation in the discrepancies between IRIS and IRMS. As such, we recommend that spectral analysis of IRIS data must be incorporated into standard post-processing routines. Furthermore, we suggest that the results from spectral analysis be included when reporting stable isotope data from IRIS. Copyright © 2011 John Wiley & Sons, Ltd.

Reproducibility of NMR Analysis of Urine Samples: Impact of Sample Preparation, Storage Conditions, and Animal Health Status

PubMed Central

Schreier, Christina; Kremer, Werner; Huber, Fritz; Neumann, Sindy; Pagel, Philipp; Lienemann, Kai; Pestel, Sabine

2013-01-01

Introduction. Spectroscopic analysis of urine samples from laboratory animals can be used to predict the efficacy and side effects of drugs. This employs methods combining 1H NMR spectroscopy with quantification of biomarkers or with multivariate data analysis. The most critical steps in data evaluation are analytical reproducibility of NMR data (collection, storage, and processing) and the health status of the animals, which may influence urine pH and osmolarity. Methods. We treated rats with a solvent, a diuretic, or a nephrotoxicant and collected urine samples. Samples were titrated to pH 3 to 9, or salt concentrations increased up to 20-fold. The effects of storage conditions and freeze-thaw cycles were monitored. Selected metabolites and multivariate data analysis were evaluated after 1H NMR spectroscopy. Results. We showed that variation of pH from 3 to 9 and increases in osmolarity up to 6-fold had no effect on the quantification of the metabolites or on multivariate data analysis. Storage led to changes after 14 days at 4°C or after 12 months at −20°C, independent of sample composition. Multiple freeze-thaw cycles did not affect data analysis. Conclusion. Reproducibility of NMR measurements is not dependent on sample composition under physiological or pathological conditions. PMID:23865070

Reproducibility of NMR analysis of urine samples: impact of sample preparation, storage conditions, and animal health status.

PubMed

Schreier, Christina; Kremer, Werner; Huber, Fritz; Neumann, Sindy; Pagel, Philipp; Lienemann, Kai; Pestel, Sabine

2013-01-01

Spectroscopic analysis of urine samples from laboratory animals can be used to predict the efficacy and side effects of drugs. This employs methods combining (1)H NMR spectroscopy with quantification of biomarkers or with multivariate data analysis. The most critical steps in data evaluation are analytical reproducibility of NMR data (collection, storage, and processing) and the health status of the animals, which may influence urine pH and osmolarity. We treated rats with a solvent, a diuretic, or a nephrotoxicant and collected urine samples. Samples were titrated to pH 3 to 9, or salt concentrations increased up to 20-fold. The effects of storage conditions and freeze-thaw cycles were monitored. Selected metabolites and multivariate data analysis were evaluated after (1)H NMR spectroscopy. We showed that variation of pH from 3 to 9 and increases in osmolarity up to 6-fold had no effect on the quantification of the metabolites or on multivariate data analysis. Storage led to changes after 14 days at 4°C or after 12 months at -20°C, independent of sample composition. Multiple freeze-thaw cycles did not affect data analysis. Reproducibility of NMR measurements is not dependent on sample composition under physiological or pathological conditions.

Statistical analysis of arsenic contamination in drinking water in a city of Iran and its modeling using GIS.

PubMed

Sadeghi, Fatemeh; Nasseri, Simin; Mosaferi, Mohammad; Nabizadeh, Ramin; Yunesian, Masud; Mesdaghinia, Alireza

2017-05-01

In this research, probable arsenic contamination in drinking water in the city of Ardabil was studied in 163 samples during four seasons. In each season, sampling was carried out randomly in the study area. Results were analyzed statistically applying SPSS 19 software, and the data was also modeled by Arc GIS 10.1 software. The maximum permissible arsenic concentration in drinking water defined by the World Health Organization and Iranian national standard is 10 μg/L. Statistical analysis showed 75, 88, 47, and 69% of samples in autumn, winter, spring, and summer, respectively, had concentrations higher than the national standard. The mean concentrations of arsenic in autumn, winter, spring, and summer were 19.89, 15.9, 10.87, and 14.6 μg/L, respectively, and the overall average in all samples through the year was 15.32 μg/L. Although GIS outputs indicated that the concentration distribution profiles changed in four consecutive seasons, variance analysis of the results showed that statistically there is no significant difference in arsenic levels in four seasons.

Controls on the chemistry of runoff from an upland peat catchment

NASA Astrophysics Data System (ADS)

Worrall, Fred; Burt, Tim; Adamson, John

2003-07-01

This study uses 2 years of data from a detailed weekly water sampling programme in a 11·4 km2 upland peat catchment in the Northern Pennines, UK. The sampling comprised precipitation, soil-water samples and a number of streams, including the basin outlet. Samples were analysed for: pH, conductivity, alkalinity, Na, K, Ca, Mg, Fe, Al, Total N, SO4, Cl and colour. Principal component analysis (PCA) was used to identify end-members and compositional trends in order to identify controls on the development of water composition. The study showed that the direct use of PCA had several advantages over the use of end-member mixing analysis (EMMA) as it combines an analysis of mixing and evolving waters without the assumption of having to know the compositional sources of the water. In its application to an upland peat catchment, the study supports the view that shallow throughflow at the catotelm/acrotelm boundary is responsible for storm runoff generation and shows that baseflow is controlled by cation exchange in the catotelm and mixing with a base-rich groundwater.

[Spatiotemporal variation characteristics of heavy metals pollution in the water, soil and sediments environment of the Lean River-Poyang Lake Wetland].

PubMed

Jian, Min-Fei; Li, Ling-Yu; Xu, Peng-Fei; Chen, Pu-Qing; Xiong, Jian-Qiu; Zhou, Xue-Ling

2014-05-01

Overlying water, sediments, surface soils in the typical wetland areas of Lean River and Poyang Lake which were rich in non-ferrous metal mineral resources on both sides of the river, were chosen for monitoring heavy metals including copper, lead and cadmium of base flow in average season, flood season, and dry season in 2012. Statistical analysis methods were coupled to characterize the spatiotemporal variation of heavy metals pollution and identify the main sources. The results indicated that the concentrations of copper were the highest in all samples of each sampling sites in the Lean River-Poyang Lake wetland. And the content values of copper, lead and cadmium in different samples of different sampling sites also showed that the content values of copper were higher than those of lead, and the content values of lead were also higher than those of cadmium. The results also showed that the heavy metals pollution of copper, lead and cadmium in flood season was the heaviest whereas the heavy metals pollution in dry season was comparatively light. The results of the contents of the three kinds of heavy metals elements in different sampling sites of the watersheds of lean River showed that the contents of copper in the samples from the upstream sampling sites of Lean River were higher than those of other samples from other sites. And the contents of lead in the samples from the downstream sampling sites of Lean River were higher than those of other samples from other sampling sites. The contents of cadmium in the samples from the midstream sampling sites of Lean River were higher than those of other samples from other sites. The first principal component representing copper pollution explained 36. 99% of the total variance of water quality. The second principal component concerning representing lead pollution explained 30. 12% of the total variance. The correlation analysis results showed that there were significant positive correlations among the contents of copper in sediments and the contents of copper in overlying water. And there was also significant positive correlation between the contents of copper in sediments and the contents of copper in the surface soils. And the correlation analysis showed that there were significant positive correlations among the contents of cadmium in sediments and the contents of cadmium in surface soils. The above results reflected that the copper pollution or cadmium sources of water, soil and sediments were consistent, which were mainly from heavy metal acidic waste of mining emissions. The correlations between other components were not very obvious, which reflected the sources of pollutants were different.

High Strength and Ductility of Additively Manufactured 316L Stainless Steel Explained

NASA Astrophysics Data System (ADS)

Shamsujjoha, Md.; Agnew, Sean R.; Fitz-Gerald, James M.; Moore, William R.; Newman, Tabitha A.

2018-04-01

Structure-property relationships of an additively manufactured 316L stainless steel were explored. A scanning electron microscope and electron backscattered diffraction (EBSD) analysis revealed a fine cellular-dendritic (0.5 to 2 μm) substructure inside large irregularly shaped grains ( 100 μm). The cellular structure grows along the <100> crystallographic directions. However, texture analysis revealed that the main <100> texture component is inclined by 15 deg from the building direction. X-ray diffraction line profile analysis indicated a high dislocation density of 1 × 1015 m-2 in the as-built material, which correlates well with the observed EBSD microstructure and high-yield strength, via the traditional Taylor hardening equation. Significant variations in strain hardening behavior and ductility were observed for the horizontal (HB) and vertical (VB) built samples. Ductility of HB and VB samples measured 49 and 77 pct, respectively. The initial growth texture and subsequent texture evolution during tensile deformation are held responsible for the observed anisotropy. Notably, EBSD analysis of deformed samples showed deformation twins, which predominately form in the grains with <111> aligned parallel to the loading direction. The VB samples showed higher twinning activity, higher strain hardening rates at high strain, and therefore, higher ductility. Analysis of annealed samples revealed that the observed microstructures and properties are thermally stable, with only a moderate decrease in strength and very similar levels of ductility and anisotropy, compared with the as-built condition.

High Strength and Ductility of Additively Manufactured 316L Stainless Steel Explained

NASA Astrophysics Data System (ADS)

Shamsujjoha, Md.; Agnew, Sean R.; Fitz-Gerald, James M.; Moore, William R.; Newman, Tabitha A.

2018-07-01

Structure-property relationships of an additively manufactured 316L stainless steel were explored. A scanning electron microscope and electron backscattered diffraction (EBSD) analysis revealed a fine cellular-dendritic (0.5 to 2 μm) substructure inside large irregularly shaped grains ( 100 μm). The cellular structure grows along the <100> crystallographic directions. However, texture analysis revealed that the main <100> texture component is inclined by 15 deg from the building direction. X-ray diffraction line profile analysis indicated a high dislocation density of 1 × 1015 m-2 in the as-built material, which correlates well with the observed EBSD microstructure and high-yield strength, via the traditional Taylor hardening equation. Significant variations in strain hardening behavior and ductility were observed for the horizontal (HB) and vertical (VB) built samples. Ductility of HB and VB samples measured 49 and 77 pct, respectively. The initial growth texture and subsequent texture evolution during tensile deformation are held responsible for the observed anisotropy. Notably, EBSD analysis of deformed samples showed deformation twins, which predominately form in the grains with <111> aligned parallel to the loading direction. The VB samples showed higher twinning activity, higher strain hardening rates at high strain, and therefore, higher ductility. Analysis of annealed samples revealed that the observed microstructures and properties are thermally stable, with only a moderate decrease in strength and very similar levels of ductility and anisotropy, compared with the as-built condition.

Temporal variability of coastal Planctomycetes clades at Kabeltonne station, North Sea.

PubMed

Pizzetti, Ilaria; Fuchs, Bernhard M; Gerdts, Gunnar; Wichels, Antje; Wiltshire, Karen H; Amann, Rudolf

2011-07-01

Members of the bacterial phylum Planctomycetes are reported in marine water samples worldwide, but quantitative information is scarce. Here we investigated the phylogenetic diversity, abundance, and distribution of Planctomycetes in surface waters off the German North Sea island Helgoland during different seasons by 16S rRNA gene analysis and catalyzed reporter deposition fluorescence in situ hybridization (CARD-FISH). Generally Planctomycetes are more abundant in samples collected in summer and autumn than in samples collected in winter and spring. Statistical analysis revealed that Planctomycetes abundance was correlated to the Centrales diatom bloom in spring 2007. The analysis of size-fractionated seawater samples and of macroaggregates showed that ~90% of the Planctomycetes reside in the >3-μm size fraction. Comparative sequence analysis of 184 almost full-length 16S rRNA genes revealed three dominant clades. The clades, named Planctomyces-related group A, uncultured Planctomycetes group B, and Pirellula-related group D, were monitored by CARD-FISH using newly developed oligonucleotide probes. All three clades showed recurrent abundance patterns during two annual sampling campaigns. Uncultured Planctomycetes group B was most abundant in autumn samples, while Planctomyces-related group A was present in high numbers only during late autumn and winter. The levels of Pirellula-related group D were more constant throughout the year, with elevated counts in summer. Our analyses suggest that the seasonal succession of the Planctomycetes is correlated with algal blooms. We hypothesize that the niche partitioning of the different clades might be caused by their algal substrates.

Preliminary characterization of IL32 in basal-like/triple negative compared to other types of breast cell lines and tissues

PubMed Central

2014-01-01

Background Triple negative breast cancer (TNBC) and often basal-like cancers are defined as negative for estrogen receptor, progesterone receptor and Her2 gene expression. Over the past few years an incredible amount of data has been generated defining the molecular characteristics of both cancers. The aim of these studies is to better understand the cancers and identify genes and molecular pathways that might be useful as targeted therapies. In an attempt to contribute to the understanding of basal-like/TNBC, we examined the Gene Expression Omnibus (GEO) public datasets in search of genes that might define basal-like/TNBC. The Il32 gene was identified as a candidate. Findings Analysis of several GEO datasets showed differential expression of IL32 in patient samples previously designated as basal and/or TNBC compared to normal and luminal breast samples. As validation of the GEO results, RNA and protein expression levels were examined using MCF7 and MDA MB231 cell lines and tissue microarrays (TMAs). IL32 gene expression levels were higher in MDA MB231 compared to MCF7. Analysis of TMAs showed 42% of TNBC tissues and 25% of the non-TNBC were positive for IL32, while non-malignant patient samples and all but one hyperplastic tissue sample demonstrated lower levels of IL32 protein expression. Conclusion Data obtained from several publically available GEO datasets showed overexpression of IL32 gene in basal-like/TNBC samples compared to normal and luminal samples. In support of these data, analysis of TMA clinical samples demonstrated a particular pattern of IL32 differential expression. Considered together, these data suggest IL32 is a candidate suitable for further study. PMID:25100201

Thermal Decomposition Study on CuInSe2 Single Crystals

NASA Astrophysics Data System (ADS)

Chauhan, Sanjaysinh M.; Chaki, Sunil H.; Deshpande, M. P.; Malek, Tasmira J.; Tailor, J. P.

2018-01-01

The thermal analysis of the chemical vapor transport (CVT)-grown CuInSe2 single crystals was carried out by recording the thermogravimetric, differential thermogravimetric and differential thermal analysis curves. All the three thermo-curves were recorded simultaneously by thermal analyzer in the temperature range of ambient to 1080 K in inert nitrogen atmosphere. The thermo-curves were recorded for four heating rates of 5 K \\cdot min^{-1}, 10 K \\cdot min^{-1}, 15 K \\cdot min^{-1} and 20 K \\cdot min^{-1}. The TG curve analysis showed negligible mass loss in the temperature range of ambient to 600 K, stating the sample material to be thermally stable in this temperature range. Above 601 K to the temperature of 1080 K, the sample showed continuous mass loss. The DTG curves showed two peaks in the temperature range of 601 K to 1080 K. The corresponding DTA showed initial minor exothermic nature followed by endothermic nature up to nearly 750 K and above it showed exothermic nature. The initial exothermic nature is due to absorbed water converting to water vapor, whereas the endothermic nature states the absorption of heat by the sample up to nearly 950 K. Above nearly 950 K the exothermic nature is due to the decomposition of sample material. The absorption of heat in the endothermic region is substantiated by corresponding weight loss in TG. The thermal kinetic parameters of the CVT-grown CuInSe2 single crystals were determined employing the non-mechanistic Kissinger relation. The determined kinetic parameters support the observations of the thermo-curves.

Alginate coating as carrier of oligofructose and inulin and to maintain the quality of fresh-cut apples.

PubMed

Rössle, Christian; Brunton, Nigel; Gormley, Ronan T; Wouters, Rudy; Butler, Francis

2011-01-01

The aim of this study was to apply an edible coating containing prebiotics such as oligofructose and inulin to fresh-cut apple wedges. An assessment of the quality, sensory, polyphenol, and volatile attributes of coated and uncoated fresh-cut apple wedges was also undertaken. Fructan analysis showed that all prebiotics remained stable over the 14-d storage period and an intake of 100 g of apple supplies 1 to 3 g of prebiotics. Browning index, firmness, acidity remained stable throughout the 14 d compared to the control while applying prebiotic coatings resulted in an increase in soluble solids. Sensory and visual assessment indicated acceptable quality of apple wedges coated with prebiotics. HPLC analysis showed that levels of polyphenolic compounds were more stable in coated apple wedges (without prebiotic inclusions) than in uncoated control apples. No difference was found between O(2) and CO(2) headspace concentration of coated and uncoated samples. Significant differences (P < 0.001) were found for headspace volatile production between the samples. Most coated samples showed lower volatile production in the headspace than uncoated samples.

Evolutionary-inspired probabilistic search for enhancing sampling of local minima in the protein energy surface

PubMed Central

2012-01-01

Background Despite computational challenges, elucidating conformations that a protein system assumes under physiologic conditions for the purpose of biological activity is a central problem in computational structural biology. While these conformations are associated with low energies in the energy surface that underlies the protein conformational space, few existing conformational search algorithms focus on explicitly sampling low-energy local minima in the protein energy surface. Methods This work proposes a novel probabilistic search framework, PLOW, that explicitly samples low-energy local minima in the protein energy surface. The framework combines algorithmic ingredients from evolutionary computation and computational structural biology to effectively explore the subspace of local minima. A greedy local search maps a conformation sampled in conformational space to a nearby local minimum. A perturbation move jumps out of a local minimum to obtain a new starting conformation for the greedy local search. The process repeats in an iterative fashion, resulting in a trajectory-based exploration of the subspace of local minima. Results and conclusions The analysis of PLOW's performance shows that, by navigating only the subspace of local minima, PLOW is able to sample conformations near a protein's native structure, either more effectively or as well as state-of-the-art methods that focus on reproducing the native structure for a protein system. Analysis of the actual subspace of local minima shows that PLOW samples this subspace more effectively that a naive sampling approach. Additional theoretical analysis reveals that the perturbation function employed by PLOW is key to its ability to sample a diverse set of low-energy conformations. This analysis also suggests directions for further research and novel applications for the proposed framework. PMID:22759582

Distribution of Paenibacillus larvae spores inside honey bee colonies and its relevance for diagnosis.

PubMed

Gillard, M; Charriere, J D; Belloy, L

2008-09-01

One of the most important factors affecting the development of honey bee colonies is infectious diseases such as American foulbrood (AFB) caused by the spore forming Gram-positive bacterium Paenibacillus larvae. Colony inspections for AFB clinical symptoms are time consuming. Moreover, diseased cells in the early stages of the infection may easily be overlooked. In this study, we investigated whether it is possible to determine the sanitary status of a colony based on analyses of different materials collected from the hive. We analysed 237 bee samples and 67 honey samples originating from 71 colonies situated in 13 apiaries with clinical AFB occurrences. We tested whether a difference in spore load among bees inside the whole hive exists and which sample material related to its location inside the hive was the most appropriate for an early AFB diagnosis based on the culture method. Results indicated that diagnostics based on analysis of honey samples and bees collected at the hive entrance are of limited value as only 86% and 83%, respectively, of samples from AFB-symptomatic colonies were positive. Analysis of bee samples collected from the brood nest, honey chamber, and edge frame allowed the detection of all colonies showing AFB clinical symptoms. Microbiological analysis showed that more than one quarter of samples collected from colonies without AFB clinical symptoms were positive for P. larvae. Based on these results, we recommend investigating colonies by testing bee samples from the brood nest, edge frame or honey chamber for P. larvae spores.

Antibacterial properties of nano-silver coated PEEK prepared through magnetron sputtering.

PubMed

Liu, Xiuju; Gan, Kang; Liu, Hong; Song, Xiaoqing; Chen, Tianjie; Liu, Chenchen

2017-09-01

We aimed to investigate the cytotoxicity and antibacterial properties of nano-silver-coated polyetheretherketone (PEEK) produced through magnetron sputtering and provide a theoretical basis for its use in clinical applications. The surfaces of PEEKs were coated with nano-silver at varying thicknesses (3, 6, 9, and 12nm) through magnetron sputtering technology. The resulting coated PEEK samples were classified into the following groups according to the thickness of the nano-silver coating: PEEK-3 (3nm), PEEK-6 (6nm), PEEK-9 (9nm), PEEK-12 (12nm), and PEEK control group. The surface microstructure and composition of each sample were observed by scanning electron microscopy (SEM), atomic force microscopy (AFM), and energy dispersive spectrum (EDS) analysis. The water contact angle of each sample was then measured by contact angle meters. A cell counting kit (CCK-8) was used to analyze the cytotoxicity of the mouse fibroblast cells (L929) in the coated groups (n=5) and group test samples (n=6), negative control (polyethylene, PE) (n=6), and positive control group (phenol) (n=6). The antibacterial properties of the samples were tested by co-culturing Streptococcus mutans and Straphylococcus aureus. The bacteria that adhered to the surface of samples were observed by SEM. The antibacterial adhesion ability of each sample was then evaluated. SEM and AFM analysis results showed that the surfaces of control group samples were smooth but compact. Homogeneous silver nano-particles (AgNPs) and nano-silver coating were uniformly distributed on the surface of the coated group samples. Compared with the control samples, the nano-silver coated samples had a significant increase in surface roughness (P<0.05) as the thickness of their nano-silver coating increased. EDS analysis showed that not only C and O but also Ag were present on the surface of the coated samples. Moreover, the water contact angle of modified samples significantly increased after nano-silver coating modification (P<0.01). CCK-8 cytotoxicity test results showed that coated samples did not exhibit cytotoxicity. The antibacterial experimental results showed that the nano-silver coating can significantly improve the antibacterial activity and bacterial adhesion ability of the PEEK samples. The compact and homogeneous nano-silver coating was successfully prepared on the surface of PEEK through magnetron sputtering. The nano-silver coated PEEKs demonstrated enhanced antibacterial activities and bacterial adhesion abilities and had no cytotoxic effects. Copyright © 2017 The Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

Dried blood spot analysis for therapeutic drug monitoring of pazopanib.

PubMed

de Wit, Djoeke; den Hartigh, Jan; Gelderblom, Hans; Qian, Yanwen; den Hollander, Margret; Verheul, Henk; Guchelaar, Henk-Jan; van Erp, Nielka P

2015-12-01

Dried blood spot (DBS) sampling is potentially a more patient-friendly and flexible alternative to venous sampling of pazopanib. This study determined the agreement between pazopanib DBS and plasma concentrations to facilitate implementation of pazopanib DBS sampling into clinical practice. Paired DBS and plasma samples were collected in 12 patients. Pazopanib plasma concentrations were calculated from DBS concentrations using the formula: plasma concentration = DBSconcentration /(1 - hematocrit). Passing-Bablok and Bland-Altman analyses were used to determine the agreement between calculated and measured plasma concentrations. We predefined a clinical acceptance limit of 25% for the Bland-Altman analysis. Passing-Bablok analysis showed a small constant (intercept estimate, -8.53 [95%CI, -12.22 to -4.41]) and slightly proportional (slope estimate, 1.15 [95%CI, 1.04-1.24]) bias between calculated and measured concentrations. This bias was clinically nonrelevant, as shown by Bland-Altman analysis; the mean ratio of calculated to measured concentrations was 0.94 (95%CI, 0.65-1.23). The clinical acceptance limits were well within these 95% limits of agreement. More specifically, 92.6% of the data points were within the predefined acceptance limits. Pazopanib plasma concentrations can be accurately calculated from DBS concentrations. Although validation of DBS cards prepared by patients themselves is required, these results show that DBS sampling can be used to monitor pazopanib therapy in clinical practice. © 2015, The American College of Clinical Pharmacology.

Identification of a gamma-irradiated ingredient (garlic powder) in Korean barbeque sauce by thermoluminescence analysis.

PubMed

Ahn, Jae-Jun; Akram, Kashif; Lee, Jeongeun; Kim, Kyong-Su; Kwon, Joong-Ho

2012-04-01

Thermoluminescence (TL) analysis was applied to identify gamma-irradiated garlic powder in Korean barbeque sauce before and after pasteurization (85 °C, 30 min), when blended in different ratios (1%, 3%, and 5%). The sauce sample with nonirradiated garlic powder gave a background glow curve. However, the sample blended with irradiated ingredient (1 and 10 kGy) showed typical TL glow curves at temperatures of 150 to 200 °C. The identification properties of sauce samples were more influenced by blending ratios than by irradiation doses, showing that 3% and 5% added samples produced glow curves at 150 to 250 °C. After pasteurization of the samples containing the irradiated ingredient, TL glow intensity decreased but did not change its shape or temperature range. As a result, the pasteurization of Barbeque sauces containing irradiated ingredients had reduced TL glow intensity, but the shape and temperature range of glow curve were still able to provide information required for confirming irradiation treatment. To monitor the irradiated food in international market, thermoluminescence (TL) analysis is considered most promising identification technique because of its sensitivity and long-term stability. In this study the applicability of TL analysis to detect an irradiated ingredient (garlic powder) added in low quantity to a food matrix (sauce) was investigated. The effect of processing (pasteurization) on TL results was also evaluated. © 2012 Institute of Food Technologists®

Ultrasound extraction and thin layer chromatography-flame ionization detection analysis of the lipid fraction in marine mucilage samples.

PubMed

Mecozzi, M; Amici, M; Romanelli, G; Pietrantonio, E; Deluca, A

2002-07-19

This paper reports an analytical procedure based on ultrasound to extract lipids in marine mucilage samples. The experimental conditions of the ultrasound procedure (solvent and time) were identified by a FT-IR study performed on different standard samples of lipids and of a standard humic sample, before and after the sonication treatment. This study showed that diethyl ether was a more suitable solvent than methanol for the ultrasonic extraction of lipids from environmental samples because it allowed to minimize the possible oxidative modifications of lipids due to the acoustic cavitation phenomena. The optimized conditions were applied to the extraction of total lipid amount in marine mucilage samples and TLC-flame ionization detection analysis was used to identify the relevant lipid sub-fractions present in samples.

Statistical Analysis for Collision-free Boson Sampling.

PubMed

Huang, He-Liang; Zhong, Han-Sen; Li, Tan; Li, Feng-Guang; Fu, Xiang-Qun; Zhang, Shuo; Wang, Xiang; Bao, Wan-Su

2017-11-10

Boson sampling is strongly believed to be intractable for classical computers but solvable with photons in linear optics, which raises widespread concern as a rapid way to demonstrate the quantum supremacy. However, due to its solution is mathematically unverifiable, how to certify the experimental results becomes a major difficulty in the boson sampling experiment. Here, we develop a statistical analysis scheme to experimentally certify the collision-free boson sampling. Numerical simulations are performed to show the feasibility and practicability of our scheme, and the effects of realistic experimental conditions are also considered, demonstrating that our proposed scheme is experimentally friendly. Moreover, our broad approach is expected to be generally applied to investigate multi-particle coherent dynamics beyond the boson sampling.

Synthesis and characterization of biopolymer protected zinc sulphide nanoparticles

NASA Astrophysics Data System (ADS)

Senapati, U. S.; Sarkar, D.

2015-09-01

Zinc sulphide (ZnS) nanoparticles are prepared by a simple, economic and green synthesis route. X-ray diffraction patterns confirm zinc blend structure. ZnS formation is confirmed through chemical analysis by energy dispersive analysis of X-rays. Transmission electron microscopy reveals formation of nanosize with dimension in the range of 8-2 nm. Band gap of the nanocrystals is found to lie in the range of 4.51-4.65 eV. Photoluminescence study indicate defect like vacancies. The growth mechanism of ZnS nanoparticles is discussed with the help of Fourier transform infrared spectroscopy and thermogravimetric analysis. The materials show high dielectric constant compared to its bulk counterpart. The dielectric loss of the samples shows anomalous behaviour. The frequency dependent A.C. conductivity of the samples is discussed both in high and low frequency regimes. Current-voltage (I-V) characteristic performed under dark and under illumination, shows excellent light response of the material.

Microbiological Surveillance of Operation Theatres: Five Year Retrospective Analysis from a Tertiary Care Hospital in North India

PubMed Central

Najotra, Dipender Kaur; Malhotra, Aneeta Singh; Slathia, Poonam; Raina, Shivani; Dhar, Ashok

2017-01-01

Introduction: Microbiological contamination of air and environment in the operation theaters (OTs) are major risk factor for surgical site and other hospital-associated infections. Objectives: The aim was to identify bacterial colonization of surfaces and equipment and to determine the microbial contamination of air in the OTs of a tertiary care hospital. Materials and Methods: Five years (January 2010–December 2014) retrospective analysis of the data obtained from routine microbiological surveillance of the five OTs of the hospital was done. Surface samples were taken with wet swabs from different sites and equipment. Bacterial species were isolated and identified by conventional methods. Air quality surveillance of OTs was done by settle plate method. Results: A total of 4387 samples were collected from surfaces and articles of various OTs. Out of these only 195 (4.4%), samples showed bacterial growth and yielded 210 isolates. The predominant species isolated was Bacillus with 184 (87.6%) isolates followed by coagulase-negative Staphylococcus 17 (8.1%), Staphylococcus aureus 6 (2.9%), and Enteroccoccus spp. 3 (1.4%). Analysis of the OT air samples showed least colony forming unit (cfu) rate of air (27 cfu/m3) in ophthalmology OT and highest rate of 133 cfu/m3 in general surgery OT. Conclusion: The study shows that OTs of our hospital showed a very low bacterial contamination rate on surface swabbing and a cfu count per m3 of air well within permissible limits. PMID:28904915

Fluoride estimation and its correlation with other physicochemical parameters in drinking water of some areas of Balochistan, Pakistan.

PubMed

Chandio, Tasawar Ali; Khan, Muhammad Nasiruddin; Sarwar, Anila

2015-08-01

The fluoride level in drinking water is an important parameter and has to be controlled in order to prevent dental and skeletal fluorosis. The objective of this study is to assess fluoride content and other water quality parameters in the samples taken from open wells, tube wells, and karezes of Mastung, Mangochar, and Pringabad areas of Balochistan province. A total number of 96 drinking water samples out of 150 were found unfit for human consumption. Area-wise analysis show that the samples from 39 sites from Mastung, 12 from Mangochar, and 13 from Pringabad were found in the risk of dental fluorosis of mild to severe nature. However, 12 sampling sites from Mastung, 8 from Mangochar, and 2 from Pringabad were identified as the risks of mottling and skeletal fluorosis or other bone abnormalities. The highest concentration of F(-) has been observed as 14 mg L(-1) in Mastung. Correlation analysis show that fluoride solubility in drinking water is pH dependent; and the salts of Ca(2+), Na(+), K(+), Cl(-), and SO4(2-) contribute to attain the favorable pH for dissolution of fluoride compounds in drinking water. Principal component analysis shows that the geochemical composition of the rocks is only responsible for groundwater contamination. On the basis of the results, defloridation of the identified sampling sites and continuous monitoring of drinking water at regular basis is recommended at government level to avoid further fluorosis risks.

Application-Specific Graph Sampling for Frequent Subgraph Mining and Community Detection

DOE Office of Scientific and Technical Information (OSTI.GOV)

Purohit, Sumit; Choudhury, Sutanay; Holder, Lawrence B.

Graph mining is an important data analysis methodology, but struggles as the input graph size increases. The scalability and usability challenges posed by such large graphs make it imperative to sample the input graph and reduce its size. The critical challenge in sampling is to identify the appropriate algorithm to insure the resulting analysis does not suffer heavily from the data reduction. Predicting the expected performance degradation for a given graph and sampling algorithm is also useful. In this paper, we present different sampling approaches for graph mining applications such as Frequent Subgrpah Mining (FSM), and Community Detection (CD). Wemore » explore graph metrics such as PageRank, Triangles, and Diversity to sample a graph and conclude that for heterogeneous graphs Triangles and Diversity perform better than degree based metrics. We also present two new sampling variations for targeted graph mining applications. We present empirical results to show that knowledge of the target application, along with input graph properties can be used to select the best sampling algorithm. We also conclude that performance degradation is an abrupt, rather than gradual phenomena, as the sample size decreases. We present the empirical results to show that the performance degradation follows a logistic function.« less

Point-of-need simultaneous electrochemical detection of lead and cadmium using low-cost stencil-printed transparency electrodes.

PubMed

Martín-Yerga, Daniel; Álvarez-Martos, Isabel; Blanco-López, M Carmen; Henry, Charles S; Fernández-Abedul, M Teresa

2017-08-15

In this work, we report a simple and yet efficient stencil-printed electrochemical platform that can be integrated into the caps of sample containers and thus, allows in-field quantification of Cd(II) and Pb(II) in river water samples. The device exploits the low-cost features of carbon (as electrode material) and paper/polyester transparency sheets (as substrate). Electrochemical analysis of the working electrodes prepared on different substrates (polyester transparency sheets, chromatographic, tracing and office papers) with hexaammineruthenium(III) showed that their electroactive area and electron transfer kinetics are highly affected by the porosity of the material. Electrodes prepared on transparency substrates showed the best electroanalytical performance for the simultaneous determination of Cd(II) and Pb(II) by square-wave anodic stripping voltammetry. Interestingly, the temperature and time at which the carbon ink was cured had significant effect on the electrochemical response, especially the capacitive current. The amount of Cd and Pb on the electrode surface can be increased about 20% by in situ electrodeposition of bismuth. The electrochemical platform showed a linear range comprised between 1 and 200 μg/L for both metals, sensitivity of analysis of 0.22 and 0.087 μA/ppb and limits of detection of 0.2 and 0.3 μg/L for Cd(II) and Pb(II), respectively. The analysis of river water samples was done directly in the container where the sample was collected, which simplifies the procedure and approaches field analysis. The developed point-of-need detection system allowed simultaneous determination of Cd(II) and Pb(II) in those samples using the standard addition method with precise and accurate results. Copyright © 2017 Elsevier B.V. All rights reserved.

Expression of depressive symptoms in a nonclinical Brazilian adolescent sample.

PubMed

Gorenstein, Clarice; Andrade, Laura; Zanolo, Elaine; Artes, Rinaldo

2005-03-01

This study aimed to detect the prevalence of depressive symptomatology and its expression in a nonclinical Brazilian adolescent student sample. A sample of students from private and public schools (n = 1555, aged 13 to 17 years) answered the Beck Depression Inventory (BDI). We performed factor analysis of the BDI as an indicator of the expression of depressive symptomatology. The following cut-off scores defined nonclinical subgroups: "nondepressed," BDI < 15; "dysphoria," BDI 16 to 20; and "depressed," BDI > 20. We used discriminant analysis to test whether these subgroups could be separated by the depression-specific and nonspecific items. The point prevalence of depression was 7.6%, according to the BDI cut-off of 20. Girls had higher scores than boys in several items. Scores increased with age. Students from public schools had higher scores than did private school students. Factor analysis showed 2 common factors for the total sample and for each sex: the cognitive affective dimension and the somatic nonspecific dimension. In the adolescents showing clinical depression, items related to self-depreciation, sense of failure, guilty feelings, self-dislike, suicidal wishes, and distortion of body image were common components of BDI factors. Discriminant analysis showed that the BDI highly discriminates depressive symptomatology in adolescent students and also measures specific aspects of depression. The BDI is useful as a measure of specific aspects of depression in nonclinical adolescent samples; it was able to detect depression in approximately 7% of the surveyed population. The expression of depressive symptoms in a Brazilian adolescent population is compatible with international studies in this age group. Detecting depressive symptoms in a school population is a critical preventive strategy; to avoid damage to the learning process, it should be followed with further referral to treatment when needed.

Evaluation of seasonal variation of water quality using multivariate statistical analysis and irrigation parameter indices in Ajakanga area, Ibadan, Nigeria

NASA Astrophysics Data System (ADS)

Ganiyu, S. A.; Badmus, B. S.; Olurin, O. T.; Ojekunle, Z. O.

2018-03-01

The variation of groundwater quality across different regions is of great importance in the study of groundwater so as to ascertain the sources of contaminants to available water sources. Geochemical assessment of groundwater samples from hand-dug wells were done within the vicinity of Ajakanga dumpsite, Ibadan, Southwestern, Nigeria, with the aim of assessing their suitability for domestic and irrigation purposes. Ten groundwater samples were collected both in dry and wet seasons for analysis of physicochemical parameters such as: pH, EC, TDS, Na+, K+, Ca2+, Mg2+, HCO3^{ - } Cl-, SO4^{2 - }, NO3^{2 - } principal component analysis (PCA) and cluster analysis (CA) were used to determine probable sources of groundwater contamination. The results of the analyses showed the groundwater samples to be within permissible limits of WHO/NSDWQ, while elevated values of concentrations of most analyzed chemical constituents in water samples were noticed in S1 and S10 due to their nearness to the dumpsite and agricultural overflow, respectively. Groundwater in the study area is of hard, fresh and alkaline nature. There are very strong associations between EC and TDS, HCO3^{ - } and CO3^{2 - } in both seasons. PCA identified five and three major factors accounting for 95.7 and 88.7% of total variation in water quality for dry and wet seasons, respectively. PCA also identified factors influencing water quality as those probably related to mineral dissolution, groundwater-rock interaction, weathering process and anthropogenic activities from the dumpsite. Results of CA show groups based on similar water quality characteristics and on the extent of proximity to the dumpsite. Assessment for irrigation purpose showed that most of the water samples were suitable for agricultural purpose except in a few locations.

Trends in mercury concentrations in the hair of women of Nome, Alaska - Evidence of seafood consumption or abiotic absorption

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lasorsa, B.

1992-06-01

Eighty samples of hair from women of child-bearing age from Nome, Alaska, and seven control samples from women living in Sequim, Washington, were analyzed for mercury concentration by segmental analysis in an effort to determine whether seasonal fluctuations in mercury concentration in the hair samples can be correlated to seasonal seafood consumption. Full-length hair strands were analyzed in 1.1-cm segments representing 1 month's growth using a strong acid digestion and cold vapor atomic fluorescence analysis. It was assumed that the concentration of mercury in each segment is an indicator of the mercury body burden during the month in which themore » segment emerged from the scalp. Eighteen of the samples show seasonal variability, with five of the controls and one Nome resident showing winter highs while all Nome residents show summer highs. Twenty-six of the samples show an increase in mercury concentration toward the distal end of the strand regardless of month of growth. The trend of increasing mercury concentrations toward the distal end of the hair strand regardless of month of emergence, and the documented presence of elevated levels of elemental mercury in the Nome area suggest that these elevated levels may actually be due to external contamination of the hair strands by adsorption and not due to ingestion of contaminated foodstuffs such as seafood.« less

Trends in mercury concentrations in the hair of women of Nome, Alaska - Evidence of seafood consumption or abiotic absorption?

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lasorsa, B.

1992-06-01

Eighty samples of hair from women of child-bearing age from Nome, Alaska, and seven control samples from women living in Sequim, Washington, were analyzed for mercury concentration by segmental analysis in an effort to determine whether seasonal fluctuations in mercury concentration in the hair samples can be correlated to seasonal seafood consumption. Full-length hair strands were analyzed in 1.1-cm segments representing 1 month`s growth using a strong acid digestion and cold vapor atomic fluorescence analysis. It was assumed that the concentration of mercury in each segment is an indicator of the mercury body burden during the month in which themore » segment emerged from the scalp. Eighteen of the samples show seasonal variability, with five of the controls and one Nome resident showing winter highs while all Nome residents show summer highs. Twenty-six of the samples show an increase in mercury concentration toward the distal end of the strand regardless of month of growth. The trend of increasing mercury concentrations toward the distal end of the hair strand regardless of month of emergence, and the documented presence of elevated levels of elemental mercury in the Nome area suggest that these elevated levels may actually be due to external contamination of the hair strands by adsorption and not due to ingestion of contaminated foodstuffs such as seafood.« less

Characterization of monofloral honeys with multivariate analysis of their chemical profile and antioxidant activity.

PubMed

Sant'Ana, Luiza D'O; Sousa, Juliana P L M; Salgueiro, Fernanda B; Lorenzon, Maria Cristina Affonso; Castro, Rosane N

2012-01-01

Various bioactive chemical constituents were quantified for 21 honey samples obtained at Rio de Janeiro and Minas Gerais, Brazil. To evaluate their antioxidant activity, 3 different methods were used: the ferric reducing antioxidant power, the 1,1-diphenyl-2-picrylhydrazyl (DPPH) radical-scavenging activity, and the 2,2'-azinobis (3-ethylbenzothiazolin)-6-sulfonate (ABTS) assays. Correlations between the parameters were statistically significant (-0.6684 ≤ r ≤-0.8410, P < 0.05). Principal component analysis showed that honey samples from the same floral origins had more similar profiles, which made it possible to group the eucalyptus, morrão de candeia, and cambara honey samples in 3 distinct areas, while cluster analysis could separate the artificial honey from the floral honeys. This research might aid in the discrimination of honey floral origin, by using simple analytical methods in association with multivariate analysis, which could also show a great difference among floral honeys and artificial honey, indicating a possible way to help with the identification of artificial honeys. © 2011 Institute of Food Technologists®

[The present study situation and application prospect of nail analysis for abused drugs].

PubMed

Chen, Hang; Xiang, Ping; Shen, Min

2010-10-01

In forensic toxicology analysis, various types of biological samples have their own special characteristics and scope of applications. In this article, the physiological structure of nails, methods for collecting and pre-processing samples, and for analyzing some poisons and drugs in the nails are reviewed with details. This paper introduces the influence factors of drug abuse of the nails. The prospects of its further applications are concluded based on the research results. Nails, as an unconventional bio-sample without general application, show great potential and advantages in forensic toxicology.

Cooperative investigation of precision and accuracy: In chemical analysis of silicate rocks

USGS Publications Warehouse

Schlecht, W.G.

1951-01-01

This is the preliminary report of the first extensive program ever organized to study the analysis of igneous rocks, a study sponsored by the United States Geological Survey, the Massachusetts Institute of Technology, and the Geophysical Laboratory of the Carnegie Institution of Washington. Large samples of two typical igneous rocks, a granite and a diabase, were carefully prepared and divided. Small samples (about 70 grams) of each were sent to 25 rock-analysis laboratories throughout the world; analyses of one or both samples were reported by 34 analysts in these laboratories. The results, which showed rather large discrepancies, are presented in histograms. The great discordance in results reflects the present unsatisfactory state of rock analysis. It is hoped that the ultimate establishment of standard samples and procedures will contribute to the improvement of quality of analyses. The two rock samples have also been thoroughly studied spectrographically and petrographically. Detailed reports of all the studies will be published.

Overcoming confounded controls in the analysis of gene expression data from microarray experiments.

PubMed

Bhattacharya, Soumyaroop; Long, Dang; Lyons-Weiler, James

2003-01-01

A potential limitation of data from microarray experiments exists when improper control samples are used. In cancer research, comparisons of tumour expression profiles to those from normal samples is challenging due to tissue heterogeneity (mixed cell populations). A specific example exists in a published colon cancer dataset, in which tissue heterogeneity was reported among the normal samples. In this paper, we show how to overcome or avoid the problem of using normal samples that do not derive from the same tissue of origin as the tumour. We advocate an exploratory unsupervised bootstrap analysis that can reveal unexpected and undesired, but strongly supported, clusters of samples that reflect tissue differences instead of tumour versus normal differences. All of the algorithms used in the analysis, including the maximum difference subset algorithm, unsupervised bootstrap analysis, pooled variance t-test for finding differentially expressed genes and the jackknife to reduce false positives, are incorporated into our online Gene Expression Data Analyzer ( http:// bioinformatics.upmc.edu/GE2/GEDA.html ).

Proton-Induced X-Ray Emission Analysis of Crematorium Emissions

NASA Astrophysics Data System (ADS)

Ali, Salina; Nadareski, Benjamin; Yoskowitz, Joshua; Labrake, Scott; Vineyard, Michael

2014-09-01

There has been considerable debate in recent years about possible mercury emissions from crematoria due to amalgam tooth restorations. We have performed a proton-induced X-ray emission (PIXE) analysis of aerosol and soil samples taken near the Vale Cemetery Crematorium in Schenectady, NY, to address this concern. The aerosol samples were collected on the roof of the crematorium using a nine-stage, cascade impactor that separates the particulate matter by aerodynamic diameter and deposits it onto thin Kapton foils. The soil samples were collected at several different distances from the crematorium and compressed into pellets with a hydraulic press. The Kapton foils containing the aerosol samples and the soil pellets were bombarded with 2.2-MeV protons from the 1.1-MV tandem Pelletron accelerator in the Union College Ion-Beam Analysis Laboratory. We measured significant concentrations of sulfur, phosphorus, potassium, calcium, and iron, but essentially no mercury in the aerosol samples. The lower limit of detection for airborne mercury in this experiment was approximately 0.2 ng / m3. The PIXE analysis of the soil samples showed the presence of elements commonly found in soil (Si, K, Ca, Ti, Mn, Fe), but no trace of mercury. There has been considerable debate in recent years about possible mercury emissions from crematoria due to amalgam tooth restorations. We have performed a proton-induced X-ray emission (PIXE) analysis of aerosol and soil samples taken near the Vale Cemetery Crematorium in Schenectady, NY, to address this concern. The aerosol samples were collected on the roof of the crematorium using a nine-stage, cascade impactor that separates the particulate matter by aerodynamic diameter and deposits it onto thin Kapton foils. The soil samples were collected at several different distances from the crematorium and compressed into pellets with a hydraulic press. The Kapton foils containing the aerosol samples and the soil pellets were bombarded with 2.2-MeV protons from the 1.1-MV tandem Pelletron accelerator in the Union College Ion-Beam Analysis Laboratory. We measured significant concentrations of sulfur, phosphorus, potassium, calcium, and iron, but essentially no mercury in the aerosol samples. The lower limit of detection for airborne mercury in this experiment was approximately 0.2 ng / m3. The PIXE analysis of the soil samples showed the presence of elements commonly found in soil (Si, K, Ca, Ti, Mn, Fe), but no trace of mercury. Union College Department of Physics and Astronomy.

Characterization of oily sludge from a Tehran oil refinery.

PubMed

Heidarzadeh, Nima; Gitipour, Saeid; Abdoli, Mohammad Ali

2010-10-01

In this study, oily sludge samples generated from a Tehran oil refinery (Pond I) were evaluated for their contamination levels and to propose an adequate remediation technique for the wastes. A simple, random, sampling method was used to collect the samples. The samples were analyzed to measure Total petroleum hydrocarbon (TPH), polyaromatic hydrocarbon (PAH) and heavy metal concentrations in the sludge. Statistical analysis showed that seven samples were adequate to assess the sludge with respect to TPH analyses. The mean concentration of TPHs in the samples was 265,600 mg kg⁻¹. A composite sample prepared from a mix of the seven samples was used to determine the sludge's additional characteristics. Composite sample analysis showed that there were no detectable amounts of PAHs in the sludge. In addition, mean concentrations of the selected heavy metals Ni, Pb, Cd and Zn were 2700, 850, 100, 6100 mg kg⁻¹, respectively. To assess the sludge contamination level, the results from the analysis above were compared with soil clean-up levels. Due to a lack of national standards for soil clean-up levels in Iran, sludge pollutant concentrations were compared with standards set in developed countries. According to these standards, the sludge was highly polluted with petroleum hydrocarbons. The results indicated that incineration, biological treatment and solidification/stabilization treatments would be the most appropriate methods for treatment of the sludges. In the case of solidification/stabilization, due to the high organic content of the sludge, it is recommended to use organophilic clays prior to treatment of the wastes.

Uncertainties in stormwater runoff data collection from a small urban catchment, Southeast China.

PubMed

Huang, Jinliang; Tu, Zhenshun; Du, Pengfei; Lin, Jie; Li, Qingsheng

2010-01-01

Monitoring data are often used to identify stormwater runoff characteristics and in stormwater runoff modelling without consideration of their inherent uncertainties. Integrated with discrete sample analysis and error propagation analysis, this study attempted to quantify the uncertainties of discrete chemical oxygen demand (COD), total suspended solids (TSS) concentration, stormwater flowrate, stormwater event volumes, COD event mean concentration (EMC), and COD event loads in terms of flow measurement, sample collection, storage and laboratory analysis. The results showed that the uncertainties due to sample collection, storage and laboratory analysis of COD from stormwater runoff are 13.99%, 19.48% and 12.28%. Meanwhile, flow measurement uncertainty was 12.82%, and the sample collection uncertainty of TSS from stormwater runoff was 31.63%. Based on the law of propagation of uncertainties, the uncertainties regarding event flow volume, COD EMC and COD event loads were quantified as 7.03%, 10.26% and 18.47%.

Conductive carbon tape used for support and mounting of both whole animal and fragile heat-treated tissue sections for MALDI MS imaging and quantitation.

PubMed

Goodwin, Richard J A; Nilsson, Anna; Borg, Daniel; Langridge-Smith, Pat R R; Harrison, David J; Mackay, C Logan; Iverson, Suzanne L; Andrén, Per E

2012-08-30

Analysis of whole animal tissue sections by MALDI MS imaging (MSI) requires effective sample collection and transfer methods to allow the highest quality of in situ analysis of small or hard to dissect tissues. We report on the use of double-sided adhesive conductive carbon tape during whole adult rat tissue sectioning of carboxymethyl cellulose (CMC) embedded animals, with samples mounted onto large format conductive glass and conductive plastic MALDI targets, enabling MSI analysis to be performed on both TOF and FT-ICR MALDI mass spectrometers. We show that mounting does not unduly affect small molecule MSI detection by analyzing tiotropium abundance and distribution in rat lung tissues, with direct on-tissue quantitation achieved. Significantly, we use the adhesive tape to provide support to embedded delicate heat-stabilized tissues, enabling sectioning and mounting to be performed that maintained tissue integrity on samples that had previously been impossible to adequately prepare section for MSI analysis. The mapping of larger peptidomic molecules was not hindered by tape mounting samples and we demonstrate this by mapping the distribution of PEP-19 in both native and heat-stabilized rat brains. Furthermore, we show that without heat stabilization PEP-19 degradation fragments can detected and identified directly by MALDI MSI analysis. Copyright © 2012 Elsevier B.V. All rights reserved.

Accuracy Enhancement of Raman Spectroscopy Using Complementary Laser-Induced Breakdown Spectroscopy (LIBS) with Geologically Mixed Samples.

PubMed

Choi, Soojin; Kim, Dongyoung; Yang, Junho; Yoh, Jack J

2017-04-01

Quantitative Raman analysis was carried out with geologically mixed samples that have various matrices. In order to compensate the matrix effect in Raman shift, laser-induced breakdown spectroscopy (LIBS) analysis was performed. Raman spectroscopy revealed the geological materials contained in the mixed samples. However, the analysis of a mixture containing different matrices was inaccurate due to the weak signal of the Raman shift, interference, and the strong matrix effect. On the other hand, the LIBS quantitative analysis of atomic carbon and calcium in mixed samples showed high accuracy. In the case of the calcite and gypsum mixture, the coefficient of determination of atomic carbon using LIBS was 0.99, while the signal using Raman was less than 0.9. Therefore, the geological composition of the mixed samples is first obtained using Raman and the LIBS-based quantitative analysis is then applied to the Raman outcome in order to construct highly accurate univariate calibration curves. The study also focuses on a method to overcome matrix effects through the two complementary spectroscopic techniques of Raman spectroscopy and LIBS.

Heterogenic Solid Biofuel Sampling Methodology and Uncertainty Associated with Prompt Analysis

PubMed Central

Pazó, Jose A.; Granada, Enrique; Saavedra, Ángeles; Patiño, David; Collazo, Joaquín

2010-01-01

Accurate determination of the properties of biomass is of particular interest in studies on biomass combustion or cofiring. The aim of this paper is to develop a methodology for prompt analysis of heterogeneous solid fuels with an acceptable degree of accuracy. Special care must be taken with the sampling procedure to achieve an acceptable degree of error and low statistical uncertainty. A sampling and error determination methodology for prompt analysis is presented and validated. Two approaches for the propagation of errors are also given and some comparisons are made in order to determine which may be better in this context. Results show in general low, acceptable levels of uncertainty, demonstrating that the samples obtained in the process are representative of the overall fuel composition. PMID:20559506

Combined radiogrammetry and texture analysis for early diagnosis of osteoporosis using Indian and Swiss data.

PubMed

Areeckal, Anu Shaju; Kamath, Jagannath; Zawadynski, Sophie; Kocher, Michel; S, Sumam David

2018-05-26

Osteoporosis is a bone disorder characterized by bone loss and decreased bone strength. The most widely used technique for detection of osteoporosis is the measurement of bone mineral density (BMD) using dual energy X-ray absorptiometry (DXA). But DXA scans are expensive and not widely available in low-income economies. In this paper, we propose a low cost pre-screening tool for the detection of low bone mass, using cortical radiogrammetry of third metacarpal bone and trabecular texture analysis of distal radius from hand and wrist radiographs. An automatic segmentation algorithm to automatically locate and segment the third metacarpal bone and distal radius region of interest (ROI) is proposed. Cortical measurements such as combined cortical thickness (CCT), cortical area (CA), percent cortical area (PCA) and Barnett Nordin index (BNI) were taken from the shaft of third metacarpal bone. Texture analysis of trabecular network at the distal radius was performed using features obtained from histogram, gray level Co-occurrence matrix (GLCM) and morphological gradient method (MGM). The significant cortical and texture features were selected using independent sample t-test and used to train classifiers to classify healthy subjects and people with low bone mass. The proposed pre-screening tool was validated on two ethnic groups, Indian sample population and Swiss sample population. Data of 134 subjects from Indian sample population and 65 subjects from Swiss sample population were analysed. The proposed automatic segmentation approach shows a detection accuracy of 86% in detecting the third metacarpal bone shaft and 90% in accurately locating the distal radius ROI. Comparison of the automatic radiogrammetry to the ground truth provided by experts show a mean absolute error of 0.04 mm for cortical width of healthy group, 0.12 mm for cortical width of low bone mass group, 0.22 mm for medullary width of healthy group, and 0.26 mm for medullary width of low bone mass group. Independent sample t-test was used to select the most discriminant features, to be used as input for training the classifiers. Pearson correlation analysis of the extracted features with DXA-BMD of lumbar spine (DXA-LS) shows significantly high correlation values. Classifiers were trained with the most significant features in the Indian and Swiss sample data. Weighted KNN classifier shows the best test accuracy of 78% for Indian sample data and 100% for Swiss sample data. Hence, combined automatic radiogrammetry and texture analysis is shown to be an effective low cost pre-screening tool for early diagnosis of osteoporosis. Copyright © 2018 Elsevier Ltd. All rights reserved.

Ecological tolerances of Miocene larger benthic foraminifera from Indonesia

NASA Astrophysics Data System (ADS)

Novak, Vibor; Renema, Willem

2018-01-01

To provide a comprehensive palaeoenvironmental reconstruction based on larger benthic foraminifera (LBF), a quantitative analysis of their assemblage composition is needed. Besides microfacies analysis which includes environmental preferences of foraminiferal taxa, statistical analyses should also be employed. Therefore, detrended correspondence analysis and cluster analysis were performed on relative abundance data of identified LBF assemblages deposited in mixed carbonate-siliciclastic (MCS) systems and blue-water (BW) settings. Studied MCS system localities include ten sections from the central part of the Kutai Basin in East Kalimantan, ranging from late Burdigalian to Serravallian age. The BW samples were collected from eleven sections of the Bulu Formation on Central Java, dated as Serravallian. Results from detrended correspondence analysis reveal significant differences between these two environmental settings. Cluster analysis produced five clusters of samples; clusters 1 and 2 comprise dominantly MCS samples, clusters 3 and 4 with dominance of BW samples, and cluster 5 showing a mixed composition with both MCS and BW samples. The results of cluster analysis were afterwards subjected to indicator species analysis resulting in the interpretation that generated three groups among LBF taxa: typical assemblage indicators, regularly occurring taxa and rare taxa. By interpreting the results of detrended correspondence analysis, cluster analysis and indicator species analysis, along with environmental preferences of identified LBF taxa, a palaeoenvironmental model is proposed for the distribution of LBF in Miocene MCS systems and adjacent BW settings of Indonesia.

Chemical Species, Micromorphology, and XRD Fingerprint Analysis of Tibetan Medicine Zuotai Containing Mercury

PubMed Central

Li, Cen; Yang, Hongxia; Xiao, Yuancan; Zhandui; Sanglao; Wang, Zhang; Ladan, Duojie; Bi, Hongtao

2016-01-01

Zuotai (gTso thal) is one of the famous drugs containing mercury in Tibetan medicine. However, little is known about the chemical substance basis of its pharmacodynamics and the intrinsic link of different samples sources so far. Given this, energy dispersive spectrometry of X-ray (EDX), scanning electron microscopy (SEM), atomic force microscopy (AFM), and powder X-ray diffraction (XRD) were used to assay the elements, micromorphology, and phase composition of nine Zuotai samples from different regions, respectively; the XRD fingerprint features of Zuotai were analyzed by multivariate statistical analysis. EDX result shows that Zuotai contains Hg, S, O, Fe, Al, Cu, and other elements. SEM and AFM observations suggest that Zuotai is a kind of ancient nanodrug. Its particles are mainly in the range of 100–800 nm, which commonly further aggregate into 1–30 μm loosely amorphous particles. XRD test shows that β-HgS, S8, and α-HgS are its main phase compositions. XRD fingerprint analysis indicates that the similarity degrees of nine samples are very high, and the results of multivariate statistical analysis are broadly consistent with sample sources. The present research has revealed the physicochemical characteristics of Zuotai, and it would play a positive role in interpreting this mysterious Tibetan drug. PMID:27738409

Chemical Species, Micromorphology, and XRD Fingerprint Analysis of Tibetan Medicine Zuotai Containing Mercury.

PubMed

Li, Cen; Yang, Hongxia; Du, Yuzhi; Xiao, Yuancan; Zhandui; Sanglao; Wang, Zhang; Ladan, Duojie; Bi, Hongtao; Wei, Lixin

2016-01-01

Zuotai ( gTso thal ) is one of the famous drugs containing mercury in Tibetan medicine. However, little is known about the chemical substance basis of its pharmacodynamics and the intrinsic link of different samples sources so far. Given this, energy dispersive spectrometry of X-ray (EDX), scanning electron microscopy (SEM), atomic force microscopy (AFM), and powder X-ray diffraction (XRD) were used to assay the elements, micromorphology, and phase composition of nine Zuotai samples from different regions, respectively; the XRD fingerprint features of Zuotai were analyzed by multivariate statistical analysis. EDX result shows that Zuotai contains Hg, S, O, Fe, Al, Cu, and other elements. SEM and AFM observations suggest that Zuotai is a kind of ancient nanodrug. Its particles are mainly in the range of 100-800 nm, which commonly further aggregate into 1-30  μ m loosely amorphous particles. XRD test shows that β -HgS, S 8 , and α -HgS are its main phase compositions. XRD fingerprint analysis indicates that the similarity degrees of nine samples are very high, and the results of multivariate statistical analysis are broadly consistent with sample sources. The present research has revealed the physicochemical characteristics of Zuotai , and it would play a positive role in interpreting this mysterious Tibetan drug.

Detection And Identification Of Inflammatory Bowel Disease Electronic Nose

NASA Astrophysics Data System (ADS)

Covington, J. A.; Ouaret, N.; Gardner, J. W.; Nwokolo, C.; Bardhan, K. D.; Arasaradnam, R. P.

2011-11-01

Inflammatory bowel disease (IBD) is an inflammation of the lining of the human bowel and a major health issue in Europe. IBD carries with it significant morbidity from toxic treatment, surgery and a risk of developing bowel cancer. Thus there is a need for early identification of the disease using non-invasive tests. Present diagnostic techniques are based around invasive tests (i.e. endoscopy) and laboratory culture; the latter is limited as only 50% of the gut bacteria can be identified. Here we explore the use of an e-nose as a tool to detect and identify two IBDs (i.e. Crohn's disease (CD) & Ulcerative Colitis (UC)) based on headspace analysis from urine samples. We believe that the gut bacterial flora is altered by disease (due to fermentation) that in-turn modulates the gas composition within urine samples. 24 samples (9 CD, 6 UC, 9 controls) were analysed with an in-house e-nose and an Owlstone IMS instrument. Data analysis was performed using linear discriminant analysis (LDA and principal components analysis (PCA). Using the e-nose, LDA separates both disease groups and control, whilst PCA shows a small overlap of classes. The IMS data are more complex but shows some disease/control separation. We are presently collecting further samples for a larger study using more advanced data processing methods.

Double sampling for stratification: a forest inventory application in the Interior West

Treesearch

David C. Chojnacky

1998-01-01

This paper documents the use of double sampling for Forest Inventory and Analysis (Forest Service, U.S. Department of Agriculture) inventories in the Interior West. Results show 18 equations describe the entire inventory summarization process for estimating population totals and means, and respective variances. Most equations are for standard use of double sampling,...

Physicochemical and antimicrobial properties of copaiba oil: implications on product quality control.

PubMed

Fonseca, Renata G; Barros, Francisco M; Apel, Miriam A; Poser, Gilsane L von; Andriolli, Jo O L; Filho, Pedro C Campos; Sousa, Dhierlate F; Lobo, Ivon P; Conceiç O, Aline O

2015-01-01

The copaiba oil is a common natural product used in cosmetic industry and as a nutraceutical product. However, lack of quality control and scarce knowledge about its antimicrobial activity is a point of concern. The proposal of this study was to investigate the physicochemical properties and the antimicrobial activity of five commercial brands of copaiba oil. Acidity and ester index, refractory index, solubility in alcohol, and thin layer chromatography were performed to verify the physicochemical properties of five commercial copaiba oils sold in local pharmacies. Ultra performance liquid chromatography coupled with diode-array detection and electrospray ionization quadrupole time-of-flight mass spectrometry (UPLC-DAD/ESI-Q-TOF-MS) was used to investigate diterpene acids while the volatile compounds were analysed by gas chromatography-mass spectrometry (GC-MS). Antibacterial and antifungal activities were also evaluated by agar diffusion technique; and minimal inhibitory concentration and maximal bactericidal concentration were defined for each sample and bacteria. The physical-chemical analysis revealed heterogeneity between all samples analysed. The A1 sample showed characteristics of copaiba oil and was mainly composed by hydrocarbon sesquiterpenes (29.95% β-bisabolene, 25.65% Z-α-bergamotene and 10.27% β-cariophyllene). Among diterpene acids, the UPLCDAD/ESI-Q-TOF-MS data are compatible with presence of copalic and/or kolavenic acid (m/z 305 [M + H]+). Candida albicans was sensitive to almost all samples at high concentration and Saccaromyces. Cerevisiae showed sensitivity to A1 sample at 100 mg/mL. Although variable, all samples showed antibacterial activity. Significant activity was seen for A3 (19.0 ±0 and 15.6 ±0.5 mm), A4 (16.6 ±0.5 and 15.6 ±0 mm), and A5 (17.1 ±0 and 17.1 ±0 mm) on Staphylococcus saprophyticus and S. aureus, respectively. All samples were active against Klebsiella pneumoniae showing ≥15 mm diameter halo inhibition; and only A2 was active against Eschirichia coli. Phytopatogens tested revealed resistance of Ralstonia solanacearum CGH12 to all samples and susceptibility of Xcv 112 strain of Xanthomonas campestris pv campestris to almost all samples. MIC and MMC showed bacteriostatic effect against clinical interest bacteria and bactericidal effect against phytopatogens. The results from physicochemical analysis reinforce the fact that it is imperative to include simple conventional methods in the analysis of oil products. The analysis of copaiba oil gives safe products and purity which ensure products with quality. Also, since copaiba oil is an over-the-counter product the results indicate that pharmacosurveillance must be improved by the governmental regulation agency to avoid microorganism resistance selection and to achieve better international quality products.

[Standard sample preparation method for quick determination of trace elements in plastic].

PubMed

Yao, Wen-Qing; Zong, Rui-Long; Zhu, Yong-Fa

2011-08-01

Reference sample was prepared by masterbatch method, containing heavy metals with known concentration of electronic information products (plastic), the repeatability and precision were determined, and reference sample preparation procedures were established. X-Ray fluorescence spectroscopy (XRF) analysis method was used to determine the repeatability and uncertainty in the analysis of the sample of heavy metals and bromine element. The working curve and the metrical methods for the reference sample were carried out. The results showed that the use of the method in the 200-2000 mg x kg(-1) concentration range for Hg, Pb, Cr and Br elements, and in the 20-200 mg x kg(-1) range for Cd elements, exhibited a very good linear relationship, and the repeatability of analysis methods for six times is good. In testing the circuit board ICB288G and ICB288 from the Mitsubishi Heavy Industry Company, results agreed with the recommended values.

Time Series Data Analysis of Wireless Sensor Network Measurements of Temperature.

PubMed

Bhandari, Siddhartha; Bergmann, Neil; Jurdak, Raja; Kusy, Branislav

2017-05-26

Wireless sensor networks have gained significant traction in environmental signal monitoring and analysis. The cost or lifetime of the system typically depends on the frequency at which environmental phenomena are monitored. If sampling rates are reduced, energy is saved. Using empirical datasets collected from environmental monitoring sensor networks, this work performs time series analyses of measured temperature time series. Unlike previous works which have concentrated on suppressing the transmission of some data samples by time-series analysis but still maintaining high sampling rates, this work investigates reducing the sampling rate (and sensor wake up rate) and looks at the effects on accuracy. Results show that the sampling period of the sensor can be increased up to one hour while still allowing intermediate and future states to be estimated with interpolation RMSE less than 0.2 °C and forecasting RMSE less than 1 °C.

NASA Aeronautics and Space Database for bibliometric analysis

NASA Technical Reports Server (NTRS)

Powers, R.; Rudman, R.

2004-01-01

The authors use the NASA Aeronautics and Space Database to perform bibliometric analysis of citations. This paper explains their research methodology and gives some sample results showing collaboration trends between NASA Centers and other institutions.

Characterization of Leaf Extracts of Schinus terebinthifolius Raddi by GC-MS and Chemometric Analysis

PubMed Central

Carneiro, Fabíola B.; Lopes, Pablo Q.; Ramalho, Ricardo C.; Scotti, Marcus T.; Santos, Sócrates G.; Soares, Luiz A. L.

2017-01-01

Background: Schinus terebinthifolius Raddi belongs to Anacardiacea family and is widely known as “aroeira.” This species originates from South America, and its extracts are used in folk medicine due to its therapeutic properties, which include antimicrobial, anti-inflammatory, and antipyretic effects. The complexity and variability of the chemical constitution of the herbal raw material establishes the quality of the respective herbal medicine products. Objective: Thus, the purpose of this study was to investigate the variability of the volatile compounds from leaves of S. terebinthifolius. Materials and Methods: The samples were collected from different states of the Northeast region of Brazil and analyzed with a gas chromatograph coupled to a mass spectrometer (GC-MS). The collected data were analyzed using multivariate data analysis. Results: The samples’ chromatograms, obtained by GC-MS, showed similar chemical profiles in a number of peaks, but some differences were observed in the intensity of these analytical markers. The chromatographic fingerprints obtained by GC-MS were suitable for discrimination of the samples; these results along with a statistical treatment (principal component analysis [PCA]) were used as a tool for comparative analysis between the different samples of S. terebinthifolius. Conclusion: The experimental data show that the PCA used in this study clustered the samples into groups with similar chemical profiles, which builds an appropriate approach to evaluate the similarity in the phytochemical pattern found in the different leaf samples. SUMMARY The leave extracts of Schinus terebinthifolius were obtained by turbo-extractionThe extracts were partitioned with hexane and analyzed by GC-MSThe chromatographic data were analyzed using the principal component analysis (PCA)The PCA plots showed the main compounds (phellandrene, limonene, and carene), which were used to group the samples from a different geographical location in accordance to their chemical similarity. Abbreviations used: AL: Alagoas, BA: Bahia, CE: Ceará, CPETEC: Center for Weather Forecasting and Climate Studies, GC-MS: Gas chromatograph coupled to a mass spectrometer, MA: Maranhão, MVA: Multivariate data analysis, PB: Paraíba, PC1: Direction that describes the maximum variance of the original data, PC2: Maximum direction variance of the data in the subspace orthogonal to PC1, PCA: Principal component analysis, PE: Pernambuco, PI: Piauí, RN: Rio Grande do Norte, SE: Sergipe. PMID:29142431

Haplotype data for 23 Y-chromosome markers in a reference sample from Bosnia and Herzegovina

PubMed Central

Kovačević, Lejla; Fatur-Cerić, Vera; Hadžić, Negra; Čakar, Jasmina; Primorac, Dragan; Marjanović, Damir

2013-01-01

Aim To detect polymorphisms of 23 Y-chromosomal short tandem repeat (STR) loci, including 6 new loci, in a reference database of male population of Bosnia and Herzegovina, as well as to assess the importance of increasing the number of Y-STR loci utilized in forensic DNA analysis. Methods The reference sample consisted of 100 healthy, unrelated men originating from Bosnia and Herzegovina. Sample collection using buccal swabs was performed in all geographical regions of Bosnia and Herzegovina in the period from 2010 to 2011. DNA samples were typed for 23 Y STR loci, including 6 new loci: DYS576, DYS481, DYS549, DYS533, DYS570, and DYS643, which are included in the new PowerPlex® Y 23 amplification kit. Results The absolute frequency of generated haplotypes was calculated and results showed that 98 samples had unique Y 23 haplotypes, and that only two samples shared the same haplotype. The most polymorphic locus was DYS418, with 14 detected alleles and the least polymorphic loci were DYS389I, DYS391, DYS437, and DYS393. Conclusion This study showed that by increasing the number of highly polymorphic Y STR markers, to include those tested in our analysis, leads to a reduction of repeating haplotypes, which is very important in the application of forensic DNA analysis. PMID:23771760

Statistical Symbolic Execution with Informed Sampling

NASA Technical Reports Server (NTRS)

Filieri, Antonio; Pasareanu, Corina S.; Visser, Willem; Geldenhuys, Jaco

2014-01-01

Symbolic execution techniques have been proposed recently for the probabilistic analysis of programs. These techniques seek to quantify the likelihood of reaching program events of interest, e.g., assert violations. They have many promising applications but have scalability issues due to high computational demand. To address this challenge, we propose a statistical symbolic execution technique that performs Monte Carlo sampling of the symbolic program paths and uses the obtained information for Bayesian estimation and hypothesis testing with respect to the probability of reaching the target events. To speed up the convergence of the statistical analysis, we propose Informed Sampling, an iterative symbolic execution that first explores the paths that have high statistical significance, prunes them from the state space and guides the execution towards less likely paths. The technique combines Bayesian estimation with a partial exact analysis for the pruned paths leading to provably improved convergence of the statistical analysis. We have implemented statistical symbolic execution with in- formed sampling in the Symbolic PathFinder tool. We show experimentally that the informed sampling obtains more precise results and converges faster than a purely statistical analysis and may also be more efficient than an exact symbolic analysis. When the latter does not terminate symbolic execution with informed sampling can give meaningful results under the same time and memory limits.

Analysis of Tank 38H (HTF-38-17-52, -53) and Tank 43H (HTF-43-17-54, -55) Samples for Support of the Enrichment Control and Corrosion Control Programs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hay, M.; Coleman, C.; Diprete, D.

SRNL analyzed samples from Tank 38H and Tank 43H to support ECP and CCP. The total uranium in the Tank 38H surface sample was 41.3 mg/L while the sub-surface sample was 43.5 mg/L. The Tank 43H samples contained total uranium concentrations of 28.5 mg/L in the surface sample and 28.1 mg/L in the sub-surface sample. The U-235 percentage ranged from 0.62% to 0.63% for the Tank 38H samples and Tank 43H samples. The total uranium and percent U-235 results in the table appear slightly lower than recent Tank 38H and Tank 43H uranium measurements. The plutonium results in the tablemore » show a large difference between the surface and sub-surface sample concentrations for Tank 38H. The Tank 43H plutonium results closely match the range of values measured on previous samples. The Cs-137 results for the Tank 38H surface and sub-surface samples show similar concentrations slightly higher than the concentrations measured in recent samples. The Cs-137 results for the two Tank 43H samples also show similar concentrations within the range of values measured on previous samples. The four samples show silicon concentrations somewhat lower than the previous samples with values ranging from 124 to 168 mg/L.« less

Analysis of Tank 38H (HTF-38-16-26, 27) and Tank 43H (HTF-43-16-28, 29) Samples for Support of the Enrichment Control and Corrosion Control Programs

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hay, M. S.

Savannah River National Laboratory analyzed samples from Tank 38H and Tank 43H to support Enrichment Control Program and Corrosion Control Program. The total uranium in the Tank 38H samples ranged from 20.5 to 34.0 mg/L while the Tank 43H samples ranged from 47.6 to 50.6 mg/L. The U-235 percentage ranged from 0.62% to 0.64% over the four samples. The total uranium and percent U-235 results appear consistent with previous Tank 38H and Tank 43H uranium measurements. The Tank 38H plutonium results show a large difference between the surface and sub-surface sample concentrations and a somewhat higher concentration than previous sub-surfacemore » samples. The two Tank 43H samples show similar plutonium concentrations and are within the range of values measured on previous samples. The plutonium results may be biased high due to the presence of plutonium contamination in the blank samples from the cell sample preparations. The four samples analyzed show silicon concentrations ranging from 47.9 to 105 mg/L.« less

Detection and phylogenetic analysis of hepatitis A virus and norovirus in marine recreational waters of Mexico.

PubMed

Félix, Josefina León; Fernandez, Yuridia Cháidez; Velarde-Félix, Jesús Salvador; Torres, Benigno Valdez; Cháidez, Cristobal

2010-06-01

An investigation was conducted to determine hepatitis A virus (HAV) and norovirus (NV) presence in marine recreational waters (MRWs) from two Mexican tourists beaches (Altata and Mazatlan), located at the northwestern state of Sinaloa, Mexico. Also, Binary Logistic Regression (BLR) analyses were conducted between physicochemical parameters (temperature, turbidity and salinity) and viral organisms (HAV and NV). A total of 32 MRWs samples were collected from April to July of 2006. Samples were processed according to the Environmental Protection Agency (EPA) adsorption-elution method. Overall, 18 MRWs samples (56.3%) were positive for HAV and NV; 4 (22.2%) were obtained from Altata and 14 (77.8%) from Mazatlan. HAV was detected in 3 MRWs samples (9.4%) and NV in 15 samples (46.8%). Phylogenetic analysis showed the presence of genotype I sub genotype B for HAV and NV genogroup II. BLR analysis showed significant correlations between NV and physicochemical parameters (temperature, turbidity and salinity) (p=0.017, p=0.08, p=0.048, respectively). No significant correlation between physicochemical parameters and HAV was observed. The results indicated that MRW quality of Sinaloa beaches is affected by human faecal pollution. Viral surveillance programs should be implemented to minimize health risks to bathers.

A method for the direct injection and analysis of small volume human blood spots and plasma extracts containing high concentrations of organic solvents using revered-phase 2D UPLC/MS.

PubMed

Rainville, Paul D; Simeone, Jennifer L; Root, Dan S; Mallet, Claude R; Wilson, Ian D; Plumb, Robert S

2015-03-21

The emergence of micro sampling techniques holds great potential to improve pharmacokinetic data quality, reduce animal usage, and save costs in safety assessment studies. The analysis of these samples presents new challenges for bioanalytical scientists, both in terms of sample processing and analytical sensitivity. The use of two dimensional LC/MS with, at-column-dilution for the direct analysis of highly organic extracts prepared from biological fluids such as dried blood spots and plasma is demonstrated. This technique negated the need to dry down and reconstitute, or dilute samples with water/aqueous buffer solutions, prior to injection onto a reversed-phase LC system. A mixture of model drugs, including bromhexine, triprolidine, enrofloxacin, and procaine were used to test the feasibility of the method. Finally an LC/MS assay for the probe pharmaceutical rosuvastatin was developed from dried blood spots and protein-precipitated plasma. The assays showed acceptable recovery, accuracy and precision according to US FDA guidelines. The resulting analytical method showed an increase in assay sensitivity of up to forty fold as compared to conventional methods by maximizing the amount loaded onto the system and the MS response for the probe pharmaceutical rosuvastatin from small volume samples.

Revisiting the incidence of Mg II absorbers along the blazar sightlines

NASA Astrophysics Data System (ADS)

Mishra, Sapna; Chand, Hum; Gopal-Krishna; Joshi, Ravi

2018-04-01

It is believed that the cool gas clouds traced by Mg II absorption, within a velocity offset of 5000 km/s from the background quasar, are associated with the quasar itself, whereas the absorbers seen at larger velocity offsets towards us are intervening systems and hence their existence is completely independent of the background quasar. Recent evidence by Bergeron et al. 2011 (hereafter BBM), however, seriously questions this canonical view, by showing that the number density of intervening Mg II absorbers along the sightlines towards 45 blazars is, on average, 2 times the expectation based on the Mg II absorption systems seen on the sightlines to normal QSOs. Given the serious implications of this finding, it becomes important to revisit this issue by enlarging the source sample and subjecting it to an independent analysis. Here, we first report our results based on a re-analysis of the spectroscopic data for the BBM sample; this has reproduced their factor 2 excess in dN/dz along blazar sightlines, vis-a-vis the normal QSOs. Next, we assemble a 6 times larger sample of blazar sightlines, albeit with lower SNR. Using this enlarged sample together with the BBM sample, our analysis shows that the dN/dz of Mg II absorbers statistically matches that known for normal QSO sightlines.

Mycotoxicological and palynological profiles of commercial brands of dried bee pollen.

PubMed

Deveza, Michele Valadares; Keller, Kelly Moura; Lorenzon, Maria Cristina Affonso; Nunes, Lucila Maria Teixeira; Sales, Érika Oliveira; Barth, Ortrud Monika

2015-01-01

Pollen is used in the human diet as a food supplement because of its high nutritional value; however, this product is prone to fungal contamination that could potentially generate toxins that are harmful to human health. This study aimed to verify the floral diversity of commercial brands of bee pollen and their mycotoxicological safety for human consumption. A total of 27 bee pollen samples were analyzed; these samples represented commercial brands, either showing an inspection seal or not, marketed in the State of Rio de Janeiro. The analyzed parameters included floral diversity through palynological analysis, water activity, fungal counts, identification and toxigenic profiles. The palynological analysis identified nine plant families, of which the Asteraceae was predominant. Analysis of hygienic quality based on fungal load showed that 92% of samples were reproved according to the commercial, sanitary, and food safety quality indicators. Aspergillus, Cladosporium and Penicillium were the most common genera. Toxigenic evaluation showed that 25% of the A. flavus strains produced aflatoxins. The high rate of contamination of products bearing an inspection seal emphasizes the need to monitor the entire procedure of bee pollen production, as well as to revise the current legislation to ensure safe commercialization of this product.

Investigation of Microstructure and Mechanical Properties of ECAP-Processed AM Series Magnesium Alloy

NASA Astrophysics Data System (ADS)

Gopi, K. R.; Nayaka, H. Shivananda; Sahu, Sandeep

2016-09-01

Magnesium alloy Mg-Al-Mn (AM70) was processed by equal channel angular pressing (ECAP) at 275 °C for up to 4 passes in order to produce ultrafine-grained microstructure and improve its mechanical properties. ECAP-processed samples were characterized for microstructural analysis using optical microscopy, scanning electron microscopy, and transmission electron microscopy. Microstructural analysis showed that, with an increase in the number of ECAP passes, grains refined and grain size reduced from an average of 45 to 1 µm. Electron backscatter diffraction analysis showed the transition from low angle grain boundaries to high angle grain boundaries in ECAP 4 pass sample as compared to as-cast sample. The strength and hardness values an showed increasing trend for the initial 2 passes of ECAP processing and then started decreasing with further increase in the number of ECAP passes, even though the grain size continued to decrease in all the successive ECAP passes. However, the strength and hardness values still remained quite high when compared to the initial condition. This behavior was found to be correlated with texture modification in the material as a result of ECAP processing.

Comparison of analytical methods for the determination of histamine in reference canned fish samples

NASA Astrophysics Data System (ADS)

Jakšić, S.; Baloš, M. Ž.; Mihaljev, Ž.; Prodanov Radulović, J.; Nešić, K.

2017-09-01

Two screening methods for histamine in canned fish, an enzymatic test and a competitive direct enzyme-linked immunosorbent assay (CD-ELISA), were compared with the reversed-phase liquid chromatography (RP-HPLC) standard method. For enzymatic and CD-ELISA methods, determination was conducted according to producers’ manuals. For RP-HPLC, histamine was derivatized with dansyl-chloride, followed by RP-HPLC and diode array detection. Results of analysis of canned fish, supplied as reference samples for proficiency testing, showed good agreement when histamine was present at higher concentrations (above 100 mg kg-1). At a lower level (16.95 mg kg-1), the enzymatic test produced some higher results. Generally, analysis of four reference samples according to CD-ELISA and RP-HPLC showed good agreement for histamine determination (r=0.977 in concentration range 16.95-216 mg kg-1) The results show that the applied enzymatic test and CD-ELISA appeared to be suitable screening methods for the determination of histamine in canned fish.

Structural characterization and evaluation of the antioxidant activities of polysaccharides extracted from Qingzhuan brick tea.

PubMed

Yang, Xinhe; Huang, Mingjun; Qin, Caiqin; Lv, Bangyu; Mao, Qingli; Liu, Zhonghua

2017-08-01

The crude tea polysaccharides (CTPS) from Qingzhuan brick tea(QZBT) were extracted and fractionated to afford two fractions, namely TPS-1 and TPS-2. Analyses were conducted concerning the structural characterization and antioxidant activities of these samples. Component analysis revealed that the carbohydrate, uronic acid, protein and polyphenol contents of these samples differed significantly. Fourier transform infrared analysis showed that these samples showed similar characteristic absorption peaks for polysaccharides. Ultraviolet-visible spectroscopy, circular dichroism, scanning electron microscopy and thermogravimetric analyses indicated that there were considerable differences in the presence of protein, surface features, conformational characteristics and thermodynamic behaviors. For antioxidant activities in vitro, CTPS, TPS-1 and TPS-2 exhibited concentration-dependent antioxidant activities, with TPS-2 showing significantly higher antioxidant activity than CTPS and TPS-1. These results provide a scientific and strong foundation for the use of tea polysaccharides(TPS) from QZBT and further research towards the relationships between the characteristics and antioxidant activities of TPS. Copyright © 2017 Elsevier B.V. All rights reserved.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Spangler, Lorenz R.; Most, Wm. A.

The Waste Isolation Pilot Plant (WIPP) Hazardous Waste Facility Permit (HWFP) limits the allowable emissions of volatile organic compounds (VOCs) from contact handled (CH) transuranic (TRU) waste. The environmental Performance standard within the HWFP, Module IV, Table IV.D.1, prescribes the allowed VOC emissions from the waste to ensure protection of human health and the environment. Compliance with the performance standard to ensure control of VOC emissions is based on VOC concentrations and monitoring in the underground. One of the mechanisms used to ensure compliance with the emissions standards is measuring the VOC concentration in the headspace gas of waste containersmore » prior to disposal. Headspace gas sampling and analysis is the waste characterization activity used to determine the concentration of VOCs in the headspace of waste containers. In addition to being used to demonstrate compliance with the emissions standards of Module IV, Table IV.D.1, the results of the headspace gas sampling and analysis are used to confirm the hazardous wastes identified in the acceptable knowledge (AK) process. Headspace gas sampling and analysis has been an ongoing part of the CH TRU waste characterization program and therefore data are now available concerning its use and applicability. The information from approved Waste Stream Profile Forms (WSPFs) and the headspace gas sampling and analysis results for over 16,000 containers of CH TRU waste were considered as part of this study. The headspace gas sampling and analysis results are based on data from the WIPP Waste Information System (WWIS). These results were evaluated to determine the usefulness of headspace gas sampling and analysis for confirming AK information. The evaluation shows that the reliability of using the results of headspace gas sampling and analysis to confirm AK information can be grouped by mixed and non-mixed waste streams. In general, for mixed waste streams due to VOCs (i.e., carrying VOC-related hazardous waste numbers), there is no reliable comparison that can be made for the detection of a particular target analyte and its associated hazardous waste number(s) based on the AK information on a compound by compound basis. However, for non-mixed waste streams, the results of headspace gas sampling and analysis show a better correlation to the AK information.« less

Composition and diversity of rhizosphere fungal community in Coptis chinensis Franch. continuous cropping fields

PubMed Central

Li, Longyun; Wu, Xiaoli; Wang, Yu

2018-01-01

In this study, effects of continuous cropping on soil properties, enzyme activities, and relative abundance, community composition and diversity of fungal taxa were investigated. Rhizosphere soil from field continuously cropped for one-year, three-year and five-year by Coptis chinensis Franch. was collected and analyzed. Illumina high-throughput sequencing analysis showed that continuous cropping of C. chinensis resulted in a significant and continuous decline in the richness and diversity of soil fungal population. Ascomycota, Zygomycota, Basidiomycota, and Glomeromycota were the dominant phyla of fungi detected in rhizosphere soil. Fungal genera such as Phoma, Volutella, Pachycudonia, Heterodermia, Gibberella, Cladosporium, Trichocladium, and Sporothrix, were more dominant in continuously cropped samples for three-year and five-year compared to that for one-year. By contrast, genera, such as Zygosaccharomyces, Pseudotaeniolina, Hydnum, Umbelopsis, Humicola, Crustoderma, Psilocybe, Coralloidiomyces, Mortierella, Polyporus, Pyrenula, and Monographella showed higher relative abundance in one-year samples than that in three-year and five-year samples. Cluster analysis of the fungal communities from three samples of rhizosphere soil from C. chinensis field revealed that the fungal community composition, diversity, and structure were significantly affected by the continuous cropping. Continuous cropping of C. chinensis also led to significant declines in soil pH, urease, and catalase activities. Redundancy analysis showed that the soil pH had the most significant effect on soil fungal population under continuous cropping of C. chinensis. PMID:29538438

Composition and diversity of rhizosphere fungal community in Coptis chinensis Franch. continuous cropping fields.

PubMed

Song, Xuhong; Pan, Yuan; Li, Longyun; Wu, Xiaoli; Wang, Yu

2018-01-01

In this study, effects of continuous cropping on soil properties, enzyme activities, and relative abundance, community composition and diversity of fungal taxa were investigated. Rhizosphere soil from field continuously cropped for one-year, three-year and five-year by Coptis chinensis Franch. was collected and analyzed. Illumina high-throughput sequencing analysis showed that continuous cropping of C. chinensis resulted in a significant and continuous decline in the richness and diversity of soil fungal population. Ascomycota, Zygomycota, Basidiomycota, and Glomeromycota were the dominant phyla of fungi detected in rhizosphere soil. Fungal genera such as Phoma, Volutella, Pachycudonia, Heterodermia, Gibberella, Cladosporium, Trichocladium, and Sporothrix, were more dominant in continuously cropped samples for three-year and five-year compared to that for one-year. By contrast, genera, such as Zygosaccharomyces, Pseudotaeniolina, Hydnum, Umbelopsis, Humicola, Crustoderma, Psilocybe, Coralloidiomyces, Mortierella, Polyporus, Pyrenula, and Monographella showed higher relative abundance in one-year samples than that in three-year and five-year samples. Cluster analysis of the fungal communities from three samples of rhizosphere soil from C. chinensis field revealed that the fungal community composition, diversity, and structure were significantly affected by the continuous cropping. Continuous cropping of C. chinensis also led to significant declines in soil pH, urease, and catalase activities. Redundancy analysis showed that the soil pH had the most significant effect on soil fungal population under continuous cropping of C. chinensis.

Sampling and analyte enrichment strategies for ambient mass spectrometry.

PubMed

Li, Xianjiang; Ma, Wen; Li, Hongmei; Ai, Wanpeng; Bai, Yu; Liu, Huwei

2018-01-01

Ambient mass spectrometry provides great convenience for fast screening, and has showed promising potential in analytical chemistry. However, its relatively low sensitivity seriously restricts its practical utility in trace compound analysis. In this review, we summarize the sampling and analyte enrichment strategies coupled with nine modes of representative ambient mass spectrometry (desorption electrospray ionization, paper vhspray ionization, wooden-tip spray ionization, probe electrospray ionization, coated blade spray ionization, direct analysis in real time, desorption corona beam ionization, dielectric barrier discharge ionization, and atmospheric-pressure solids analysis probe) that have dramatically increased the detection sensitivity. We believe that these advances will promote routine use of ambient mass spectrometry. Graphical abstract Scheme of sampling stretagies for ambient mass spectrometry.

Toolbox Approaches Using Molecular Markers and 16S rRNA Gene Amplicon Data Sets for Identification of Fecal Pollution in Surface Water

PubMed Central

Staley, C.; Sadowsky, M. J.; Gyawali, P.; Sidhu, J. P. S.; Palmer, A.; Beale, D. J.; Toze, S.

2015-01-01

In this study, host-associated molecular markers and bacterial 16S rRNA gene community analysis using high-throughput sequencing were used to identify the sources of fecal pollution in environmental waters in Brisbane, Australia. A total of 92 fecal and composite wastewater samples were collected from different host groups (cat, cattle, dog, horse, human, and kangaroo), and 18 water samples were collected from six sites (BR1 to BR6) along the Brisbane River in Queensland, Australia. Bacterial communities in the fecal, wastewater, and river water samples were sequenced. Water samples were also tested for the presence of bird-associated (GFD), cattle-associated (CowM3), horse-associated, and human-associated (HF183) molecular markers, to provide multiple lines of evidence regarding the possible presence of fecal pollution associated with specific hosts. Among the 18 water samples tested, 83%, 33%, 17%, and 17% were real-time PCR positive for the GFD, HF183, CowM3, and horse markers, respectively. Among the potential sources of fecal pollution in water samples from the river, DNA sequencing tended to show relatively small contributions from wastewater treatment plants (up to 13% of sequence reads). Contributions from other animal sources were rarely detected and were very small (<3% of sequence reads). Source contributions determined via sequence analysis versus detection of molecular markers showed variable agreement. A lack of relationships among fecal indicator bacteria, host-associated molecular markers, and 16S rRNA gene community analysis data was also observed. Nonetheless, we show that bacterial community and host-associated molecular marker analyses can be combined to identify potential sources of fecal pollution in an urban river. This study is a proof of concept, and based on the results, we recommend using bacterial community analysis (where possible) along with PCR detection or quantification of host-associated molecular markers to provide information on the sources of fecal pollution in waterways. PMID:26231650

A Note on Maximized Posttest Contrasts.

ERIC Educational Resources Information Center

Williams, John D.

1979-01-01

Hollingsworth recently showed a posttest contrast for analysis of variance situations that, for equal sample sizes, had several favorable qualities. However, for unequal sample sizes, the contrast fails to achieve status as a maximized contrast; thus, separate testing of the contrast is required. (Author/GSK)

The corrosion effect of ozonated seawater solution on titanium in polymer generated crevice environments

DOE Office of Scientific and Technical Information (OSTI.GOV)

Leveillee, S.Y.

1998-01-01

Two different tests were designed to evaluate the reaction of various polymers and grade-2 titanium in ozonated seawater in conjunction with a comparative analysis in an aerated seawater solution. The first was a weight loss test measuring the weight change of Polyvinyl chloride (PVC), Polyethylene and Teflon{trademark} in both ozonated and aerated artificial seawater baths. The second test was designed to induce crevice corrosion on the titanium test samples using various crevice generating materials in both ozonated and aerated solutions. The materials used to create the crevices were grade-2 titanium washers, PVC, Polyethylene, Saran and Teflon{trademark}. The weight loss testmore » showed that all three polymers lost weight in the ozonated bath. The results of the titanium washer crevice test provided no indication of corrosion or surface discoloration in either the ozonated or aerated solutions. Energy dispersive spectrometry (EDS) analysis found no fluorine, chlorine or other corrosion product. The PVC samples in the aerated bath also showed no signs of corrosion, but the PVC samples in the ozonated tank had light brown rings of surface discoloration. One of the ozonated PVC samples did show evidence of chlorine in the corrosion product. The outer circumference of the ozonated PVC washers exhibited the same type bleaching effect as in the weight loss samples, but the whitening of these samples were more pronounced. The polyethylene samples under aeration showed no discoloration or presence of fluorine or chlorine. The polyethylene crevice samples in the ozonated solution all exhibited the distinct brilliant blue color of titanium oxide. Fluorine was found in the corrosion product on only one of the samples. Chlorine was found on the surface of one of the other corrosion coupons. The results of the Teflon{trademark} crevice samples substantiated the previous Rensselaer study.« less

Physico-chemical analysis and antimicrobial potential of Apis dorsata, Apis mellifera and Ziziphus jujube honey samples from Pakistan

PubMed Central

Fahim, Hira; Dasti, Javid Iqbal; Ali, Ihsan; Ahmed, Safia; Nadeem, Muhammad

2014-01-01

Objective To evaluate physico-chemical properties and antimicrobial potential of indigenous honey samples against different reference strains including Escherichia coli ATCC 8739, Enterobacter aerogenes ATCC 13048, Pseudomonas aeroginosa ATCC 9027, Bacillus subtilis ATCC 6633, Staphylococcus aureus ATCC 25923, Salmonella typhi ATCC 14028, Klebsiella pneumonia ATCC 13883, Aspergillus niger ATCC 16404, Rhizopus oligosporus PCSIR1, Candida albicans ATCC 14053 and Candida utilis ATCC 9950. Methods By using standard methods samples were evaluated for their antimicrobial properties including additive effect of starch and non-peroxidase activity, antioxidative properties (phenol contents, flavonoid contents, 1,1-diphenyl-2-picrylhydrazyl radical scavenging activity). Prior to this evaluation, complete physico-chemical properties including pH, color, ash contents, protein contents, moisture contents, hydroxymethyl furfural contents, total sugar contents, reducing sugar and non-reducing sugar contents were analyzed. Results Relatively higher ash contents were found in the Siddar honey i.e. (0.590 0±0.033 6)% and small honey showed relatively higher protein contents i.e. (777.598±9.880) mg/kg. The moisture contents of tested honey samples ranged between 13.8%-16.6%, total sugar contents from 61.672%-72.420% and non-reducing sugar contents from 1.95%-3.93%. Presences of phenolic contents indicate higher antioxidant potential of these honey samples. All bacteria showed clear inhibition zones in response to tested honey samples whereas fungi and yeast showed inhibition at higher concentrations of these honey samples. For Escherichia coli, Bacillus subtilis, Salmonella typhi, Pseudomonas aeroginosa and Aspergillus niger, overall the small honey showed the higher activity than other honey samples. Conclusion Physico-chemical analysis of honey samples confirmed good quality of honey according to the standards set by European Union Commission and Codex Alimentarius Commission. Evaluation of these honey samples confirms antimicrobial potential of particular types of honeys indigenous to Pakistan. PMID:25183333

Structural and surface changes in glassy carbon due to strontium implantation and heat treatment

NASA Astrophysics Data System (ADS)

Odutemowo, O. S.; Malherbe, J. B.; Prinsloo, L. C.; Njoroge, E. G.; Erasmus, R.; Wendler, E.; Undisz, A.; Rettenmayr, M.

2018-01-01

There are still questions around the microstructure of glassy carbon (GC), like the observation of the micropores. These were proposed to explain the low density of GC. This paper explains the effect of ion bombardment (200 keV Sr+, 1 × 1016 Sr+/cm2 at RT) on the microstructure of GC. TEM and AFM show that micropores in pristine GC are destroyed leading to densification of GC from 1.42 g/cm3 to 2.03 g/cm3. The amorphisation of glassy carbon was also not complete with graphitic strands embedded within the GC. These were relatively few, as Raman analysis showed that the Sr implantation resulted in a typical amorphous Raman spectrum. Annealing of the sample at 900 °C only resulted in a slight recovery of the GC structure. AFM and SEM analysis showed that the surface of the sample became rougher after Sr implantation. The roughness increased after the sample was annealed at 600 °C due to segregation of Sr towards the surface of the GC. SEM measurements of a sample with both implanted and un-implanted edges after annealing at 900 °C, showed that the high temperature heat treatment did not affect the surface topography of un-irradiated GC.

Assessing the potential for racial bias in hair analysis for cocaine: examining the relative risk of positive outcomes when comparing urine samples to hair samples.

PubMed

Mieczkowski, Tom

2011-03-20

This article examines the conjecture that hair analysis, performed to detect cocaine use or exposure, is biased against African Americans. It does so by comparing the outcomes of 33,928 hair and 105,792 urine samples collected from both African American and white subjects. In making this comparison the analysis seeks to determine if there is a departure in rates of positive and negative outcomes when comparing the results of hair analysis for cocaine to the results from urinalysis for cocaine by racial group. It treats urine as an unbiased test. It compares both the relative ratios of positive outcomes when comparing the two groups and it calculates the relative risk of outcomes for each group for having positive or negative outcomes. The findings show that the ratios of each racial group are effectively same for hair and urine assays, and they also show that the relative risk and risk estimates for positive and negative outcomes are the same for both racial groups. Considering all samples, the cocaine positive risk estimate for the hair samples comparing the two racial groups is 3.28 and for urinalysis the risk estimate is 3.10 (Breslow-Day χ(2) .250, 1 df, p = 0.617) a non-significant difference in risk. For pre-employment samples, the cocaine positive risk estimate for the hair samples comparing the two racial groups is 3.10 and for urinalysis the risk estimate is 2.90 (Breslow-Day χ(2) .281, df = 1, p = 0.595), also a non-significant difference in risk. Copyright © 2010 Elsevier Ireland Ltd. All rights reserved.

Evaluation of the black light test for screening aflatoxin-contaminated maize in the Brazilian food industry.

PubMed

Gloria, E M; Fonseca, H; Calori-Domingues, M A; Souza, I M

1998-01-01

The results of the black light test for aflatoxin-contaminated maize carried out in a large food factory in the State of São Paulo was evaluated against bi-directional thin layer chromatography (TLC) analysis for 286 samples of maize. All 286 samples were accepted by the black light test (< 7 fluorescent points), however, the results from TLC analysis showed that 96 samples were contaminated and 14 showed aflatoxin B1 contamination levels higher than 20 micrograms/kg. There were 14 false negative results and no false positives and out of the 14 samples, six did not show visible fluorescent points. If the rejection criterion of one or more fluorescent points were applied, the six samples would be accepted by the black light test. But, in this case, 95 samples would be rejected and 87 results would be false positives because they did not have contamination levels over 20 micrograms/kg which is the acceptance limit of the black light test. The results indicate that the black light test, as utilized by this factory, was not able to indicate lots with possible contamination and the black light test, as recommended in the literature, would produce a high number of false positives. It is necessary to make more studies on the use of black light as a screening test for possible aflatoxin B1-contaminated maize.

Radiometric 81Kr dating identifies 120,000-year-old ice at Taylor Glacier, Antarctica

PubMed Central

Buizert, Christo; Baggenstos, Daniel; Jiang, Wei; Purtschert, Roland; Petrenko, Vasilii V.; Lu, Zheng-Tian; Müller, Peter; Kuhl, Tanner; Lee, James; Severinghaus, Jeffrey P.; Brook, Edward J.

2014-01-01

We present successful 81Kr-Kr radiometric dating of ancient polar ice. Krypton was extracted from the air bubbles in four ∼350-kg polar ice samples from Taylor Glacier in the McMurdo Dry Valleys, Antarctica, and dated using Atom Trap Trace Analysis (ATTA). The 81Kr radiometric ages agree with independent age estimates obtained from stratigraphic dating techniques with a mean absolute age offset of 6 ± 2.5 ka. Our experimental methods and sampling strategy are validated by (i) 85Kr and 39Ar analyses that show the samples to be free of modern air contamination and (ii) air content measurements that show the ice did not experience gas loss. We estimate the error in the 81Kr ages due to past geomagnetic variability to be below 3 ka. We show that ice from the previous interglacial period (Marine Isotope Stage 5e, 130–115 ka before present) can be found in abundance near the surface of Taylor Glacier. Our study paves the way for reliable radiometric dating of ancient ice in blue ice areas and margin sites where large samples are available, greatly enhancing their scientific value as archives of old ice and meteorites. At present, ATTA 81Kr analysis requires a 40–80-kg ice sample; as sample requirements continue to decrease, 81Kr dating of ice cores is a future possibility. PMID:24753606

Radiometric 81Kr dating identifies 120,000-year-old ice at Taylor Glacier, Antarctica.

PubMed

Buizert, Christo; Baggenstos, Daniel; Jiang, Wei; Purtschert, Roland; Petrenko, Vasilii V; Lu, Zheng-Tian; Müller, Peter; Kuhl, Tanner; Lee, James; Severinghaus, Jeffrey P; Brook, Edward J

2014-05-13

We present successful (81)Kr-Kr radiometric dating of ancient polar ice. Krypton was extracted from the air bubbles in four ∼350-kg polar ice samples from Taylor Glacier in the McMurdo Dry Valleys, Antarctica, and dated using Atom Trap Trace Analysis (ATTA). The (81)Kr radiometric ages agree with independent age estimates obtained from stratigraphic dating techniques with a mean absolute age offset of 6 ± 2.5 ka. Our experimental methods and sampling strategy are validated by (i) (85)Kr and (39)Ar analyses that show the samples to be free of modern air contamination and (ii) air content measurements that show the ice did not experience gas loss. We estimate the error in the (81)Kr ages due to past geomagnetic variability to be below 3 ka. We show that ice from the previous interglacial period (Marine Isotope Stage 5e, 130-115 ka before present) can be found in abundance near the surface of Taylor Glacier. Our study paves the way for reliable radiometric dating of ancient ice in blue ice areas and margin sites where large samples are available, greatly enhancing their scientific value as archives of old ice and meteorites. At present, ATTA (81)Kr analysis requires a 40-80-kg ice sample; as sample requirements continue to decrease, (81)Kr dating of ice cores is a future possibility.

Detection by denaturing gradient gel electrophoresis of ammonia-oxidizing bacteria in microcosms of crude oil-contaminated mangrove sediments.

PubMed

dos Santos, A C F; Marques, E L S; Gross, E; Souza, S S; Dias, J C T; Brendel, M; Rezende, R P

2012-01-27

Currently, the effect of crude oil on ammonia-oxidizing bacterium communities from mangrove sediments is little understood. We studied the diversity of ammonia-oxidizing bacteria in mangrove microcosm experiments using mangrove sediments contaminated with 0.1, 0.5, 1, 2, and 5% crude oil as well as non-contaminated control and landfarm soil from near an oil refinery in Camamu Bay in Bahia, Brazil. The evolution of CO(2) production in all crude oil-contaminated microcosms showed potential for mineralization. Cluster analysis of denaturing gradient gel electrophoresis-derived samples generated with primers for gene amoA, which encodes the functional enzyme ammonia monooxygenase, showed differences in the sample contaminated with 5% compared to the other samples. Principal component analysis showed divergence of the non-contaminated samples from the 5% crude oil-contaminated sediment. A Venn diagram generated from the banding pattern of PCR-denaturing gradient gel electrophoresis was used to look for operational taxonomic units (OTUs) in common. Eight OTUs were found in non-contaminated sediments and in samples contaminated with 0.5, 1, or 2% crude oil. A Jaccard similarity index of 50% was found for samples contaminated with 0.1, 0.5, 1, and 2% crude oil. This is the first study that focuses on the impact of crude oil on the ammonia-oxidizing bacterium community in mangrove sediments from Camamu Bay.

Confirmatory factor analysis and recommendations for improvement of the Autonomy-Preference-Index (API).

PubMed

Simon, Daniela; Kriston, Levente; Loh, Andreas; Spies, Claudia; Scheibler, Fueloep; Wills, Celia; Härter, Martin

2010-09-01

Validation of the German version of the Autonomy-Preference-Index (API), a measure of patients' preferences for decision making and information seeking. Stepwise confirmatory factor analysis was conducted on a sample of patients (n = 1592) treated in primary care for depression (n = 186), surgical and internal medicine inpatients (n = 811) and patients with minor trauma treated in an emergency department (n = 595). An initial test of the model was done on calculation and validation halves of the sample. Both local and global indexes-of-fit suggested modifications to the scale. The scale was modified and re-tested in the calculation sample and confirmed in the validation sample. Subgroup analyses for age, gender and type of treatment setting were also performed. The confirmatory analysis led to a modified version of the API with better local and global indexes-of-fit for samples of German-speaking patients. Two items of the sub-scale, 'preference for decision-making', and one item of the sub-scale, 'preference for information seeking', showed very low reliability scores and were deleted. Thus, several global indexes-of-fit clearly improved significantly. The modified scale was confirmed on the validation sample with acceptable to good indices of fit. Results of subgroup analyses indicated that no adaptations were necessary. This first confirmatory analysis for a German-speaking population showed that the API was improved by the removal of several items. There were theoretically plausible explanations for this improvement suggesting that the modifications might also be appropriate in English and other language versions.

Effects of temperature on microbial succession and metabolite change during saeu-jeot fermentation.

PubMed

Lee, Se Hee; Jung, Ji Young; Jeon, Che Ok

2014-04-01

To investigate the effects of temperature on saeu-jeot (shrimp) fermentation, four sets of saeu-jeot samples with approximately 25% (w/v) NaCl were fermented at 10 °C, 15 °C, 20 °C, and 25 °C. The pH values of the 10 °C and 15 °C samples were relatively constant during the entire fermentation period, whereas those of the 20 °C and 25 °C samples gradually decreased after 25 days of fermentation. Quantitative PCR showed that the maximum bacterial abundance was greater in higher temperature samples, and the bacterial abundance in the 10 °C samples steadily decreased during the entire fermentation period. Community analysis using pyrosequencing revealed that the initially dominant Proteobacteria including Pseudoalteromonas, Photobacterium, Vibrio, Aliivibrio, and Enterovibrio were replaced rapidly with Firmicutes such as Psychrobacter, Staphylococcus, Salimicrobium, Alkalibacillus, and Halanaerobium as the fermentation progressed. However, Vibrio, Photobacterium, Aliivibrio, and Enterovibrio, which may include potentially pathogenic strains, remained even after 215 days in the 10 °C samples. Metabolite analysis using (1)H NMR showed that amino acid profiles and initial quick increases of glucose and glycerol were similar and independent of bacterial growth in all temperature samples. After 25 days of fermentation, the levels of glucose, glycerol, and trimethylamine N-oxide decreased with the growth of Halanaerobium and the increase of acetate, butyrate, and methylamines in the 20 °C and 25 °C samples although the amino acid concentrations steadily increased until approximately 105 days of fermentation. Statistical triplot analysis showed that the bacterial successions occurred similarly regardless of the fermentation temperature, and Halanaerobium was likely responsible for the production of acetate, butyrate, and methylamines. This study suggests that around 15 °C might be the optimum temperature for the production of safe and tasty saeu-jeot. Copyright © 2013 Elsevier Ltd. All rights reserved.

Genetic variation in mitochondrial DNA among Enterobius vermicularis in Denmark.

PubMed

Ferrero, Mario Rodrıguez; Röser, Dennis; Nielsen, Henrik Vedel; Olsen, Annette; Nejsum, Peter

2013-01-01

Despite being the most prevalent nematode infections of man in Western Europe and North America, our knowledge of the genetic variability in Enterobius vermicularis is fragmented. We here report on a genetic study of pinworms in Denmark, performed using the cytochrome oxidase I (cox1) gene, with DNA extracted from individual eggs collected from clinical (human) samples. We collected cellophane-tape-test samples positive for pinworm eggs from 14 Departments of Clinical Microbiology in Denmark and surface-sterilized the eggs using a 1% hypochlorite solution before performing conventional PCR. Twenty-two haplotypes were identified from a total of 58 Danish patients. Cluster analysis showed that all Danish worms grouped together with human samples from Germany and Greece and with samples from Japanese chimpanzees designated as 'type B'. Analysis of molecular variance showed no significant difference or trends in geographical distribution of the pinworms in Denmark, and several haplotypes were identical or closely related to samples collected in Germany, Greece and Japan. However, worms from the 4 countries were found to belong to different populations, with Fst values in the range of 0·16 to 0·47. This study shows pinworms in Denmark to be a homogenous population, when analysed using the cox1 mitochondrial gene.

[The toxicity variation of organic extracts in drinking water treatment processes].

PubMed

Mei, M; Wei, S; Zijian, W; Wenhua, W; Baohua, Z; Suxia, Z

2001-01-01

Source water samples and outlet water samples from different treatment processes of the Beijing Ninth Water Works were concentrated in situ with XAD-2 filled columns. GC-MS analysis and toxic assessment including acute toxicity evaluation by luminescent bacterium bioassay(Q67 strains) and mutagenicity assessment by Ames test(TA98 and TA100 strains with and without S9 addition) were conducted on these samples. The results showed that prechlorination caused the direct and indirect frame shift mutagenicity as well as indirect base pair substitute mutagenicity. Addition of coagulant may increase the base pair substitute mutagenic effects greatly. Sand and coal filtration and granular activated carbon filtration could effectively remove most of the formed mutagens. The rechlorination do not obviously increase the mutagenic effects. No mutagenic effect was observed in tap water. Acute toxicity showed the same variation with that of mutagenicity during the treatment processes. Sample from flocculation treatment process was found to be the most toxic sample. Results of GC-MS analysis showed that water in this plant was not contaminated by PCB. Concentrations of toluene, naphthalene and phenol increased in flocculation treatment process and in tap water. However, the concentrations of these substances were at the level of microgram/L, therefore, were not high enough to cause mutagenicity.

Relationships between mercury concentration and food selectivity of many kinds of fishes in Minamata Bay

NASA Astrophysics Data System (ADS)

Mori, K.; Kanaya, G.

2016-02-01

Serious injuries occurred in residents who consumed fish and shellfishes in Minamata Bay polluted by high-concentration methyl-mercury in the 1950s. Pollution has fallen to a safe level because of the pollution prevention project (dredging etc.) carried out from 1977 to 1990. From 2010 we have been researching the bioaccumulation of mercury in several fishes in Minamata Bay and surrounding areas. We selected several sampling points that showed different environmental conditions, species composition and food web patterns. For the determination of feeding types of 60 species fishes (600 samples) sampled by gill net, we measured mercury levels of each sample and directly checked food items in gut, and distinguished carnivore, omnivore, herbivore and detritivore. At this time, we introduced a stable isotope analysis for checking the food history and feeding habits of dominant fish. In about 300 individuals of 30 species of dominant fish selected from the 600 samples, we measured the stable nitrogen and carbon isotope ratios (δ15N, δ13C) of each sample. Checking the food items in gut of fishes, more than 80% of fishes were carnivorous, and showed different selectivity of food items, such as fish, crustacean and so on. From the results of stable isotope ratios, benthic fish tended to show a higher ratio of δ13C. Usually benthic microalgae evidenced a higher ratio of δ13C than planktonic microalgae, and the ratio conservative through the food chain. In general, δ15N increases through the food chain with +3 to +4 ‰ enrichment per trophic step. In these data, carnivorous fishes of benthic and pelagic type showed medium and high ratios of δ15N. From comparing the stable isotope ratio to the mercury concentration of fishes, all of the high-mercury fishes belonged to benthic and carnivorous types. We consider the joint method of food web analysis and stable isotope analysis to be useful for understanding the mechanism of mercury bioaccumulation through the food web

Real-time polymerase chain reaction detection of parvovirus B19 DNA in blood donations using a commercial and an in-house assay.

PubMed

Koppelman, M H G M; van Swieten, P; Cuijpers, H T M

2011-06-01

European regulations require testing of manufacturing plasma for parvovirus B19 (B19) DNA to limit the load of this virus to a maximum acceptable level of 10 IU/µL. To meet this requirement, most manufacturers introduced a test algorithm to identify and eliminate high-load donations before making large manufacturing pools of plasma units. Sanquin screens all donations using a commercial assay from Roche and an in-house assay. Between 2006 and 2009, 6.2 million donations were screened using two different polymerase chain reaction (PCR) assays targeting B19 DNA. Donations with B19 DNA loads of greater than 1 × 10(6) IU/mL showing significant differences in viral load between the two assays were further analyzed by sequencing analysis. A total of 396 donations with B19 DNA loads of greater than 1 × 10(6) IU/mL were identified. Fifteen samples (3.8%) had discordant test results; 10 samples (2.5%) were underquantified by the Roche assay, two samples (0.5%) were underquantified by the in-house assay, and three samples (0.8%) were not detected by the Roche assay. Sequencing analysis revealed mismatches in primer and probe-binding regions. Phylogenetic analysis showed that 12 samples were B19 Genotype 1. The three samples not detected by the Roche assay were B19 Genotype 2. This study shows that 3.8% of the viremic B19 DNA-positive donations are not quantified correctly by the Roche or in-house B19 DNA assays. B19 Genotype 1 isolates showing incorrect test results are more common than B19 Genotype 2 or 3 isolates. Newly designed B19 PCR assays for blood screening should preferably have multiplexed formats targeting multiple regions of the B19 genome. © 2010 American Association of Blood Banks.

Infrared spectroscopy and upconversion luminescence behaviour of erbium doped yttrium (III) oxide phosphor

NASA Astrophysics Data System (ADS)

Dubey, Vikas; Tiwari, Ratnesh; Tamrakar, Raunak Kumar; Rathore, Gajendra Singh; Sharma, Chitrakant; Tiwari, Neha

2014-11-01

The paper reports upconversion luminescence behaviour and infra-red spectroscopic pattern of erbium doped yttrium (III) oxide phosphor. Sample was synthesized by solid state reaction method with variable concentration or erbium (0.5-2.5 mol%). The conventional solid state method is suitable for large scale production and eco-friendly method. The prepared sample was characterized by X-ray diffraction (XRD) technique. From structural analysis by XRD technique shows cubic structure of prepared sample with variable concentration of erbium and no impurity phase were found when increase the concentration of Er3+. Particle size was calculated by Scherer's formula and it varies from 67 nm to 120 nm. The surface morphology of prepared phosphor was determined by field emission gun scanning electron microscopy (FEGSEM) technique. The surface morphology of the sample shows good connectivity with grains as well as some agglomerates formation occurs in sample. The functional group analysis was done by Fourier transform infra-red technique (FTIR) analysis which confirm the formation of Y2O3:Er3+ phosphor was prepared. The results indicated that the Y2O3:Er3+ phosphors might have high upconversion efficiency because of their low vibrational energy. Under 980 nm laser excitation sample shows intense green emission at 555 nm and orange emission at 590 nm wavelength. For green emission transition occurs 2H11/2 → 4I15/2, 4S3/2 → 4I15/2 for upconversion emissions. Excited state absorption and energy transfer process were discussed as possible upconversion mechanisms. The near infrared luminescence spectra was recorded. The upconversion luminescence intensity increase with increasing the concentration or erbium up to 2 mol% after that luminescence intensity decreases due to concentration quenching occurs. Spectrophotometric determinations of peaks are evaluated by Commission Internationale de I'Eclairage (CIE) technique. From CIE technique the dominant peak of from PL spectra shows intense green emission so the prepared phosphor is may be useful for green light emitting diode (GLED) application.

Method of Analysis by the U.S. Geological Survey California District Sacramento Laboratory?Determination of Trihalomethane Formation Potential, Method Validation, and Quality-Control Practices

USGS Publications Warehouse

Crepeau, Kathryn L.; Fram, Miranda S.; Bush, Noel

2004-01-01

An analytical method for the determination of the trihalomethane formation potential of water samples has been developed. The trihalomethane formation potential is measured by dosing samples with chlorine under specified conditions of pH, temperature, incubation time, darkness, and residual-free chlorine, and then analyzing the resulting trihalomethanes by purge and trap/gas chromatography equipped with an electron capture detector. Detailed explanations of the method and quality-control practices are provided. Method validation experiments showed that the trihalomethane formation potential varies as a function of time between sample collection and analysis, residual-free chlorine concentration, method of sample dilution, and the concentration of bromide in the sample.

A sub-sampled approach to extremely low-dose STEM

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stevens, A.; Luzi, L.; Yang, H.

The inpainting of randomly sub-sampled images acquired by scanning transmission electron microscopy (STEM) is an attractive method for imaging under low-dose conditions (≤ 1 e -Å 2) without changing either the operation of the microscope or the physics of the imaging process. We show that 1) adaptive sub-sampling increases acquisition speed, resolution, and sensitivity; and 2) random (non-adaptive) sub-sampling is equivalent, but faster than, traditional low-dose techniques. Adaptive sub-sampling opens numerous possibilities for the analysis of beam sensitive materials and in-situ dynamic processes at the resolution limit of the aberration corrected microscope and is demonstrated here for the analysis ofmore » the node distribution in metal-organic frameworks (MOFs).« less

Sampling with poling-based flux balance analysis: optimal versus sub-optimal flux space analysis of Actinobacillus succinogenes.

PubMed

Binns, Michael; de Atauri, Pedro; Vlysidis, Anestis; Cascante, Marta; Theodoropoulos, Constantinos

2015-02-18

Flux balance analysis is traditionally implemented to identify the maximum theoretical flux for some specified reaction and a single distribution of flux values for all the reactions present which achieve this maximum value. However it is well known that the uncertainty in reaction networks due to branches, cycles and experimental errors results in a large number of combinations of internal reaction fluxes which can achieve the same optimal flux value. In this work, we have modified the applied linear objective of flux balance analysis to include a poling penalty function, which pushes each new set of reaction fluxes away from previous solutions generated. Repeated poling-based flux balance analysis generates a sample of different solutions (a characteristic set), which represents all the possible functionality of the reaction network. Compared to existing sampling methods, for the purpose of generating a relatively "small" characteristic set, our new method is shown to obtain a higher coverage than competing methods under most conditions. The influence of the linear objective function on the sampling (the linear bias) constrains optimisation results to a subspace of optimal solutions all producing the same maximal fluxes. Visualisation of reaction fluxes plotted against each other in 2 dimensions with and without the linear bias indicates the existence of correlations between fluxes. This method of sampling is applied to the organism Actinobacillus succinogenes for the production of succinic acid from glycerol. A new method of sampling for the generation of different flux distributions (sets of individual fluxes satisfying constraints on the steady-state mass balances of intermediates) has been developed using a relatively simple modification of flux balance analysis to include a poling penalty function inside the resulting optimisation objective function. This new methodology can achieve a high coverage of the possible flux space and can be used with and without linear bias to show optimal versus sub-optimal solution spaces. Basic analysis of the Actinobacillus succinogenes system using sampling shows that in order to achieve the maximal succinic acid production CO₂ must be taken into the system. Solutions involving release of CO₂ all give sub-optimal succinic acid production.

Field-based Evaluation of a Novel SPME-GC-MS Method for Investigation of Below-ground Interaction between Brassica Roots and Larvae of Cabbage Root Fly, Delia radicum L.

PubMed

Deasy, William; Shepherd, Tom; Alexander, Colin J; Birch, A Nicholas E; Evans, K Andrew

2016-11-01

Collection of volatiles from plant roots poses technical challenges due to difficulties accessing the soil environment without damaging the roots. To validate a new non-invasive method for passive sampling of root volatiles in situ, from plants grown under field conditions, using solid phase micro-extraction (SPME). SPME fibres were inserted into perforated polytetrafluoroethene (PTFE) tubes positioned in the soil next to broccoli plants for collection of root volatiles pre- and post-infestation with Delia radicum larvae. After sample analysis by gas chromatography-mass spectrometry (GC-MS), principal component analysis (PCA) was applied to determine differences in the profiles of volatiles between samples. GC-MS analysis revealed that this method can detect temporal changes in root volatiles emitted before and after Delia radicum damage. PCA showed that samples collected pre- and post-infestation were compositionally different due to the presence of root volatiles induced by D. radicum feeding. Sulphur containing compounds, in particular, accounted for the differences observed. Root volatiles emission patterns post-infestation are thought to follow the feeding and developmental progress of larvae. This study shows that volatiles released by broccoli roots can be collected in situ using SPME fibres within perforated PTFE tubes under field conditions. Plants damaged by Delia radicum larvae could be distinguished from plants sampled pre-infestation and soil controls on the basis of larval feeding-induced sulphur-containing volatiles. These results show that this new method is a powerful tool for non-invasive sampling of root volatiles below-ground. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

Automated SEM and TEM sample preparation applied to copper/low k materials

NASA Astrophysics Data System (ADS)

Reyes, R.; Shaapur, F.; Griffiths, D.; Diebold, A. C.; Foran, B.; Raz, E.

2001-01-01

We describe the use of automated microcleaving for preparation of both SEM and TEM samples as done by SELA's new MC500 and TEMstation tools. The MC500 is an automated microcleaving tool that is capable of producing cleaves with 0.25 μm accuracy resulting in SEM-ready samples. The TEMstation is capable of taking a sample output from the MC500 (or from SELA's earlier MC200 tool) and producing a FIB ready slice of 25±5 μm, mounted on a TEM-washer and ready for FIB thinning to electron transparency for TEM analysis. The materials selected for the tool set evaluation mainly included the Cu/TaN/HOSP low-k system. The paper is divided into three sections, experimental approach, SEM preparation and analysis of HOSP low-k, and TEM preparation and analysis of Cu/TaN/HOSP low-k samples. For the samples discussed, data is presented to show the quality of preparation provided by these new automated tools.

A Data Matrix Method for Improving the Quantification of Element Percentages of SEM/EDX Analysis

NASA Technical Reports Server (NTRS)

Lane, John

2009-01-01

A simple 2D M N matrix involving sample preparation enables the microanalyst to peer below the noise floor of element percentages reported by the SEM/EDX (scanning electron microscopy/ energy dispersive x-ray) analysis, thus yielding more meaningful data. Using the example of a 2 3 sample set, there are M = 2 concentration levels of the original mix under test: 10 percent ilmenite (90 percent silica) and 20 percent ilmenite (80 percent silica). For each of these M samples, N = 3 separate SEM/EDX samples were drawn. In this test, ilmenite is the element of interest. By plotting the linear trend of the M sample s known concentration versus the average of the N samples, a much higher resolution of elemental analysis can be performed. The resulting trend also shows how the noise is affecting the data, and at what point (of smaller concentrations) is it impractical to try to extract any further useful data.

Comparison of two headspace sampling techniques for the analysis of off-flavour volatiles from oat based products.

PubMed

Cognat, Claudine; Shepherd, Tom; Verrall, Susan R; Stewart, Derek

2012-10-01

Two different headspace sampling techniques were compared for analysis of aroma volatiles from freshly produced and aged plain oatcakes. Solid phase microextraction (SPME) using a Carboxen-Polydimethylsiloxane (PDMS) fibre and entrainment on Tenax TA within an adsorbent tube were used for collection of volatiles. The effects of variation in the sampling method were also considered using SPME. The data obtained using both techniques were processed by multivariate statistical analysis (PCA). Both techniques showed similar capacities to discriminate between the samples at different ages. Discrimination between fresh and rancid samples could be made on the basis of changes in the relative abundances of 14-15 of the constituents in the volatile profiles. A significant effect on the detection level of volatile compounds was observed when samples were crushed and analysed by SPME-GC-MS, in comparison to undisturbed product. The applicability and cost effectiveness of both methods were considered. Copyright © 2012 Elsevier Ltd. All rights reserved.

Intraoral laser welding: ultrastructural and mechanical analysis to compare laboratory laser and dental laser.

PubMed

Fornaini, Carlo; Passaretti, Francesca; Villa, Elena; Rocca, Jean-Paul; Merigo, Elisabetta; Vescovi, Paolo; Meleti, Marco; Manfredi, Maddalena; Nammour, Samir

2011-07-01

The Nd:YAG laser has been used since 1970 in dental laboratories to weld metals on dental prostheses. Recently in several clinical cases, we have suggested that the Nd:YAG laser device commonly utilized in the dental office could be used to repair broken fixed, removable and orthodontic prostheses and to weld metals directly in the mouth. The aim of this work was to evaluate, using scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDS) and dynamic mechanical analysis (DMA), the quality of the weld and its mechanical strength, comparing a device normally used in dental laboratory and a device normally used in the dental office for oral surgery, the same as that described for intraoral welding. Metal plates of a Co-Cr-Mo dental alloy and steel orthodontic wires were subjected to four welding procedures: welding without filler metal using the laboratory laser, welding with filler metal using the laboratory laser, welding without filler metal using the office laser, and welding with filler metal using the office laser. The welded materials were then analysed by SEM, EDS and DMA. SEM analysis did not show significant differences between the samples although the plates welded using the office laser without filler metal showed a greater number of fissures than the other samples. EDS microanalysis of the welding zone showed a homogeneous composition of the metals. Mechanical tests showed similar elastic behaviours of the samples, with minimal differences between the samples welded with the two devices. No wire broke even under the maximum force applied by the analyser. This study seems to demonstrate that the welds produced using the office Nd:YAG laser device and the laboratory Nd:YAG laser device, as analysed by SEM, EDS and DMA, showed minimal and nonsignificant differences, although these findings need to be confirmed using a greater number of samples.

Authoritarian Parenting and Asian Adolescent School Performance: Insights from the US and Taiwan

PubMed Central

Pong, Suet-ling; Johnston, Jamie; Chen, Vivien

2014-01-01

Our study re-examines the relationship between parenting and school performance among Asian students. We use two sources of data: wave I of the Adolescent Health Longitudinal Survey (Add Health), and waves I and II of the Taiwan Educational Panel Survey (TEPS). Analysis using Add Health reveals that the Asian-American/European-American difference in the parenting–school performance relationship is due largely to differential sample sizes. When we select a random sample of European-American students comparable to the sample size of Asian-American students, authoritarian parenting also shows no effect for European-American students. Furthermore, analysis of TEPS shows that authoritarian parenting is negatively associated with children's school achievement, while authoritative parenting is positively associated. This result for Taiwanese Chinese students is similar to previous results for European-American students in the US. PMID:24850978

Authoritarian Parenting and Asian Adolescent School Performance: Insights from the US and Taiwan.

PubMed

Pong, Suet-Ling; Johnston, Jamie; Chen, Vivien

2010-01-01

Our study re-examines the relationship between parenting and school performance among Asian students. We use two sources of data: wave I of the Adolescent Health Longitudinal Survey (Add Health), and waves I and II of the Taiwan Educational Panel Survey (TEPS). Analysis using Add Health reveals that the Asian-American/European-American difference in the parenting-school performance relationship is due largely to differential sample sizes. When we select a random sample of European-American students comparable to the sample size of Asian-American students, authoritarian parenting also shows no effect for European-American students. Furthermore, analysis of TEPS shows that authoritarian parenting is negatively associated with children's school achievement, while authoritative parenting is positively associated. This result for Taiwanese Chinese students is similar to previous results for European-American students in the US.

Solid-state characterization of nevirapine.

PubMed

Sarkar, Mahua; Perumal, O P; Panchagnula, R

2008-09-01

The purpose of this investigation is to characterize nevirapine from commercial samples and samples crystallized from different solvents under various conditions. The solid-state behavior of nevirapine samples was investigated using a variety of complementary techniques such as microscopy (optical, polarized, hot stage microscopy), differential scanning calorimeter, thermogravimetric analysis, Fourier transform infrared spectroscopy and powder X-ray diffractometry. The commercial samples of nevirapine had the same polymorphic crystalline form with an anhedral crystal habit. Intrinsic dissolution of nevirapine was similar for both the commercial batches. Powder dissolution showed pH dependency, with maximum dissolution in acidic pH and there was no significant effect of particle size. The samples recrystallized from different solvent systems with varying polarity yielded different crystal habits. Stirring and degrees of supersaturation influenced the size and shape of the crystals. The recrystallized samples did not produce any new polymorphic form, but weak solvates with varying crystal habit were produced. Recrystallized samples showed differences in the x-ray diffractograms. However, all the samples had the same internal crystal lattice as revealed from their similar melting points and heat of fusion. The intrinsic dissolution rate of recrystallized samples was lower than the commercial sample. It was found that the compression pressure resulted in desolvation and partial conversion of the crystal form. After compression, the recrystallized samples showed similar x-ray diffractograms to the commercial sample. Amorphous form showed slightly higher aqueous solubility than the commercial crystalline form.

Buccal Swabbing as a Noninvasive Method To Determine Bacterial, Archaeal, and Eukaryotic Microbial Community Structures in the Rumen

PubMed Central

Kirk, Michelle R.; Jonker, Arjan; McCulloch, Alan

2015-01-01

Analysis of rumen microbial community structure based on small-subunit rRNA marker genes in metagenomic DNA samples provides important insights into the dominant taxa present in the rumen and allows assessment of community differences between individuals or in response to treatments applied to ruminants. However, natural animal-to-animal variation in rumen microbial community composition can limit the power of a study considerably, especially when only subtle differences are expected between treatment groups. Thus, trials with large numbers of animals may be necessary to overcome this variation. Because ruminants pass large amounts of rumen material to their oral cavities when they chew their cud, oral samples may contain good representations of the rumen microbiota and be useful in lieu of rumen samples to study rumen microbial communities. We compared bacterial, archaeal, and eukaryotic community structures in DNAs extracted from buccal swabs to those in DNAs from samples collected directly from the rumen by use of a stomach tube for sheep on four different diets. After bioinformatic depletion of potential oral taxa from libraries of samples collected via buccal swabs, bacterial communities showed significant clustering by diet (R = 0.37; analysis of similarity [ANOSIM]) rather than by sampling method (R = 0.07). Archaeal, ciliate protozoal, and anaerobic fungal communities also showed significant clustering by diet rather than by sampling method, even without adjustment for potentially orally associated microorganisms. These findings indicate that buccal swabs may in future allow quick and noninvasive sampling for analysis of rumen microbial communities in large numbers of ruminants. PMID:26276109

Characterization of spatial distribution of Tetranychus urticae in peppermint in California and implication for improving sampling plan.

PubMed

Rijal, Jhalendra P; Wilson, Rob; Godfrey, Larry D

2016-02-01

Twospotted spider mite, Tetranychus urticae Koch, is an important pest of peppermint in California, USA. Spider mite feeding on peppermint leaves causes physiological changes in the plant, which coupling with the favorable environmental condition can lead to increased mite infestations. Significant yield loss can occur in absence of pest monitoring and timely management. Understating the within-field spatial distribution of T. urticae is critical for the development of reliable sampling plan. The study reported here aims to characterize the spatial distribution of mite infestation in four commercial peppermint fields in northern California using spatial techniques, variogram and Spatial Analysis by Distance IndicEs (SADIE). Variogram analysis revealed that there was a strong evidence for spatially dependent (aggregated) mite population in 13 of 17 sampling dates and the physical distance of the aggregation reached maximum to 7 m in peppermint fields. Using SADIE, 11 of 17 sampling dates showed aggregated distribution pattern of mite infestation. Combining results from variogram and SADIE analysis, the spatial aggregation of T. urticae was evident in all four fields for all 17 sampling dates evaluated. Comparing spatial association using SADIE, ca. 62% of the total sampling pairs showed a positive association of mite spatial distribution patterns between two consecutive sampling dates, which indicates a strong spatial and temporal stability of mite infestation in peppermint fields. These results are discussed in relation to behavior of spider mite distribution within field, and its implications for improving sampling guidelines that are essential for effective pest monitoring and management.

Impacts of a flash flood on drinking water quality: case study of areas most affected by the 2012 Beijing flood.

PubMed

Sun, Rubao; An, Daizhi; Lu, Wei; Shi, Yun; Wang, Lili; Zhang, Can; Zhang, Ping; Qi, Hongjuan; Wang, Qiang

2016-02-01

In this study, we present a method for identifying sources of water pollution and their relative contributions in pollution disasters. The method uses a combination of principal component analysis and factor analysis. We carried out a case study in three rural villages close to Beijing after torrential rain on July 21, 2012. Nine water samples were analyzed for eight parameters, namely turbidity, total hardness, total dissolved solids, sulfates, chlorides, nitrates, total bacterial count, and total coliform groups. All of the samples showed different degrees of pollution, and most were unsuitable for drinking water as concentrations of various parameters exceeded recommended thresholds. Principal component analysis and factor analysis showed that two factors, the degree of mineralization and agricultural runoff, and flood entrainment, explained 82.50% of the total variance. The case study demonstrates that this method is useful for evaluating and interpreting large, complex water-quality data sets.

Biomass, community structure and nutritional status attributes of the deep subsurface microbiota---at Idaho and Hanford sites

DOE Office of Scientific and Technical Information (OSTI.GOV)

White, D.C.; Ringelberg, D.B.

1991-10-28

The signature lipid biomarker technique based on phospholipid ester-linked fatty acid pattern analysis (PLFA) provides data on the total viable or potentially viable communities without the necessity of: (1) Quantitative recovery from the sediments or (2) The ability to culture the organisms. Analysis of PLFA provides evidence for the nutritional status (starvation and/or unbalanced growth) in situ. PLFA analysis of SSP samples from the INEL and PNL sites vadose zones showed higher biomass at the surface with prominent Actinomyces biomarkers with lower biomasses of stressed microbiota at progressively greater depth. The biomass and community diversity increased at the water tablemore » at both sites. Both these Western sites showed lower viable microbial biomasses than the WSRS samples. Cluster analysis of the total patterns from various sedimentary horizons showed three major consortia of microbes, with surface microbiota related at both sites, low viable biomass sites closely related at both sites, with anaerobic desaturase pathway being predominant at INEL and consortia utilizing predominantly branched saturated and the aerobic desaturase pathway at both sites. Preliminary examination of the consortia recovered from NTS show a clear relationship to water level.« less

Palynological Investigation of Mummified Human Remains.

PubMed

Reinhard, Karl J; Amaral, Marina Milanello do; Wall, Nicole

2018-01-01

Pollen analysis was applied to a mummified homicide victim in Nebraska, U.S.A., to determine the location of death. A control sample showed the normal ambient pollen in the garage crime scene. Ambient windborne types, common in the air of the region, dominated the control. Internal samples were analyzed from the sacrum, intestine, and diaphragm. Microfossils were recovered from the rehydrated intestine lumen. The intestinal sample was dominated by Brassica (broccoli). The sacrum sample was high in dietary types but with a showing of ambient types. The pollen from the diaphragm was dominated by ambient pollen similar to the control samples. The discovery of diverse pollen spectra from within a single mummy was unexpected. They show that ingested and inhaled pollen mixed in the corpse. The data linked the decedent to a specific crime scene in her Nebraska home in the southern tier of eastern counties on the border with Kansas. © 2017 American Academy of Forensic Sciences.

Magnetic measurements on human erythrocytes: Normal, beta thalassemia major, and sickle

NASA Astrophysics Data System (ADS)

Sakhnini, Lama

2003-05-01

In this article magnetic measurements were made on human erythrocytes at different hemoglobin states (normal and reduced hemoglobin). Different blood samples: normal, beta thalassemia major, and sickle were studied. Beta thalassemia major and sickle samples were taken from patients receiving lifelong blood transfusion treatment. All samples examined exhibited diamagnetic behavior. Beta thalassemia major and sickle samples showed higher diamagnetic susceptibilities than that for the normal, which was attributed to the increase of membrane to hemoglobin volume ratio of the abnormal cells. Magnetic measurements showed that the erythrocytes in the reduced state showed less diamagnetic response in comparison with erythrocytes in the normal state. Analysis of the paramagnetic component of magnetization curves gave an effective magnetic moment of μeff=7.6 μB per reduced hemoglobin molecule. The same procedure was applied to sickle and beta thalassemia major samples and values for μeff were found to be comparable to that of the normal erythrocytes.

RNA-Seq workflow: gene-level exploratory analysis and differential expression

PubMed Central

Love, Michael I.; Anders, Simon; Kim, Vladislav; Huber, Wolfgang

2015-01-01

Here we walk through an end-to-end gene-level RNA-Seq differential expression workflow using Bioconductor packages. We will start from the FASTQ files, show how these were aligned to the reference genome, and prepare a count matrix which tallies the number of RNA-seq reads/fragments within each gene for each sample. We will perform exploratory data analysis (EDA) for quality assessment and to explore the relationship between samples, perform differential gene expression analysis, and visually explore the results. PMID:26674615

Genetic diversity analysis of Jatropha curcas L. (Euphorbiaceae) based on methylation-sensitive amplification polymorphism.

PubMed

Kanchanaketu, T; Sangduen, N; Toojinda, T; Hongtrakul, V

2012-04-13

Genetic analysis of 56 samples of Jatropha curcas L. collected from Thailand and other countries was performed using the methylation-sensitive amplification polymorphism (MSAP) technique. Nine primer combinations were used to generate MSAP fingerprints. When the data were interpreted as amplified fragment length polymorphism (AFLP) markers, 471 markers were scored. All 56 samples were classified into three major groups: γ-irradiated, non-toxic and toxic accessions. Genetic similarity among the samples was extremely high, ranging from 0.95 to 1.00, which indicated very low genetic diversity in this species. The MSAP fingerprint was further analyzed for DNA methylation polymorphisms. The results revealed differences in the DNA methylation level among the samples. However, the samples collected from saline areas and some species hybrids showed specific DNA methylation patterns. AFLP data were used, together with methylation-sensitive AFLP (MS-AFLP) data, to construct a phylogenetic tree, resulting in higher efficiency to distinguish the samples. This combined analysis separated samples previously grouped in the AFLP analysis. This analysis also distinguished some hybrids. Principal component analysis was also performed; the results confirmed the separation in the phylogenetic tree. Some polymorphic bands, involving both nucleotide and DNA methylation polymorphism, that differed between toxic and non-toxic samples were identified, cloned and sequenced. BLAST analysis of these fragments revealed differences in DNA methylation in some known genes and nucleotide polymorphism in chloroplast DNA. We conclude that MSAP is a powerful technique for the study of genetic diversity for organisms that have a narrow genetic base.

Impurity profiling of trinitrotoluene using vacuum-outlet gas chromatography-mass spectrometry.

PubMed

Brust, Hanneke; Willemse, Sander; Zeng, Tuoyu; van Asten, Arian; Koeberg, Mattijs; van der Heijden, Antoine; Bolck, Annabel; Schoenmakers, Peter

2014-12-29

In this work, a reliable and robust vacuum-outlet gas chromatography-mass spectrometry (GC-MS) method is introduced for the identification and quantification of impurities in trinitrotoluene (TNT). Vacuum-outlet GC-MS allows for short analysis times; the analysis of impurities in TNT was performed in 4min. This study shows that impurity profiling of TNT can be used to investigate relations between TNT samples encountered in forensic casework. A wide variety of TNT samples were analyzed with the developed method. Dinitrobenzene, dinitrotoluene, trinitrotoluene and amino-dinitrotoluene isomers were detected at very low levels (<1wt.%) by applying the MS in selected-ion monitoring (SIM) mode. Limits of detection ranged from 6ng/mL for 2,6-dinitrotoluene to 43ng/mL for 4-amino-2,6-dinitrotoluene. Major impurities in TNT were 2,4-dinitrotoluene and 2,3,4-trinitrotoluene. Impurity profiles based on seven compounds showed to be useful to TNT samples from different sources. Statistical analysis of these impurity profiles using likelihood ratios demonstrated the potential to investigate whether two questioned TNT samples encountered in forensic casework are from the same source. Copyright © 2014 Elsevier B.V. All rights reserved.

Effect of vanadium doping on structural and magnetic properties of defective nano-nickel ferrite

NASA Astrophysics Data System (ADS)

Heiba, Zein K.; Mohamed, Mohamed Bakr; Wahba, Adel Maher; Almalowi, M. I.

2018-04-01

Nano-nickel ferrites defected by vanadium doping (NiV x Fe2-1.67 x O4, 0 ≤ x ≤ 0.25) were prepared using a simple sol gel method. Rietveld analysis revealed a nonmonotonic change in lattice parameter, oxygen parameter and magnetization upon doping with vanadium. Cation distributions suggested from either Rietveld analysis or from experimental magnetic moments were in a good agreement. For low doping values ( x = 0.05), vanadium was residing mainly in octahedral sites, while for samples with vanadium content ( x ≥ 0.1) a significant part of vanadium ions resided at tetrahedral sites; a result which has been confirmed by the analysis of Fourier-transform infrared (FTIR) spectrums obtained for the samples. The transmission electron microscope (TEM) image showed fine spherical particles with size of ˜ 11 nm. All samples showed a superparamagnetic nature with a nonmonotonic change of either magnetization ( M S) or coercivity (H C) with the content of nonmagnetic V5+. The cation occupancies indicated presence of an enormous number of vacancies through doping with high valence cation V5+, making present samples potential electrodes for Li- or Na-ion batteries.

National characteristics and variation in Arabic handwriting.

PubMed

Al-Hadhrami, Ahmed A N; Allen, Mike; Moffatt, Colin; Jones, Allison E

2015-02-01

From each of four Arabic countries; Morocco, Tunisia, Jordan and Oman, 150 participants produced handwriting samples which were examined to assess whether national characteristics were discernible. Ten characters, which have different configurations depending upon their position in the word, along with one short word, were classified into distinguishable forms, and these forms recorded for each handwriting sample. Tests of independence showed that character forms used were not independent of country (p<0.001) for all but one character-position (this was dropped from subsequent analyses). A correspondence analysis ordination plot and analysis of similarity (R=0.326, p=0.0002) showed that whole samples were discernibly grouped by country, and a tree analysis produced a classification which was 71% accurate for the original data and 83% accurate for 80 new handwriting samples that underwent 'blind' classification. When the countries were combined into two regions, North Africa and Middle East, the grouping was more marked. Thus, there appears to be some scope for narrowing down the nationality, and particularly the wider geographical region of an author based upon the character forms they use in Arabic handwriting. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Electrochemical Behavior Assessment of Micro- and Nano-Grained Commercial Pure Titanium in H2SO4 Solutions

NASA Astrophysics Data System (ADS)

Fattah-alhosseini, Arash; Ansari, Ali Reza; Mazaheri, Yousef; Karimi, Mohsen

2017-02-01

In this study, the electrochemical behavior of commercial pure titanium with both coarse-grained (annealed sample with the average grain size of about 45 µm) and nano-grained microstructure was compared by potentiodynamic polarization, electrochemical impedance spectroscopy (EIS), and Mott-Schottky analysis. Nano-grained Ti, which typically has a grain size of about 90 nm, is successfully made by six-cycle accumulative roll-bonding process at room temperature. Potentiodynamic polarization plots and impedance measurements revealed that as a result of grain refinement, the passive behavior of the nano-grained sample was improved compared to that of annealed pure Ti in H2SO4 solutions. Mott-Schottky analysis indicated that the passive films behaved as n-type semiconductors in H2SO4 solutions and grain refinement did not change the semiconductor type of passive films. Also, Mott-Schottky analysis showed that the donor densities decreased as the grain size of the samples reduced. Finally, all electrochemical tests showed that the electrochemical behavior of the nano-grained sample was improved compared to that of annealed pure Ti, mainly due to the formation of thicker and less defective oxide film.

Correlation between thermal behavior of clays and their chemical and mineralogical composition: a review

NASA Astrophysics Data System (ADS)

Dwi Yanti, Evi; Pratiwi, I.

2018-02-01

Clay's abundance has been widely used as industrial raw materials, especially ceramic and tile industries. Utilization of these minerals needs a thermal process for producing ceramic products. Two studies conducted by Septawander et al. and Chin C et al., showed the relationship between thermal behavior of clays and their chemical and mineralogical composition. Clays are characterized by XRD analysis and thermal analysis, ranging from 1100°C to 1200°C room temperature. Specimen of raw materials of clay which is used for the thermal treatment is taken from different geological conditions and formation. In raw material, Quartz is almost present in all samples. Halloysite, montmorillonite, and feldspar are present in Tanjung Morawa raw clay. KC and MC similar kaolinite and illite are present in the samples. The research illustrates the interrelationships of clay minerals and chemical composition with their heat behavior. As the temperature of combustion increases, the sample reduces a significant weight. The minerals which have undergone a transformation phase became mullite, cristobalite or illite and quartz. Under SEM analysis, the microstructures of the samples showed irregularity in shape; changes occurred due the increase of heat.

Obsidian sources characterized by neutron-activation analysis.

PubMed

Gordus, A A; Wright, G A; Griffin, J B

1968-07-26

Concentrations of elements such as manganese, scandium, lanthanum, rubidium, samarium, barium, and zirconium in obsidian samples from different flows show ranges of 1000 percent or more, whereas the variation in element content in obsidian samples from a single flow appears to be less than 40 percent. Neutron-activation analysis of these elements, as well as of sodium and iron, provides a means of identifying the geologic source of an archeological artifact of obsidian.

A METHOD FOR AUTOMATED ANALYSIS OF 10 ML WATER SAMPLES CONTAINING ACIDIC, BASIC, AND NEUTRAL SEMIVOLATILE COMPOUNDS LISTED IN USEPA METHOD 8270 BY SOLID PHASE EXTRACTION COUPLED IN-LINE TO LARGE VOLUME INJECTION GAS CHROMATOGRAPHY/MASS SPECTROMETRY

EPA Science Inventory

Data is presented showing the progress made towards the development of a new automated system combining solid phase extraction (SPE) with gas chromatography/mass spectrometry for the single run analysis of water samples containing a broad range of acid, base and neutral compounds...

Rapid analysis of Δ-9-tetrahydrocannabinol in hair using direct analysis in real time ambient ionization orbitrap mass spectrometry.

PubMed

Duvivier, Wilco F; van Beek, Teris A; Pennings, Ed J M; Nielen, Michel W F

2014-04-15

Forensic hair analysis methods are laborious, time-consuming and provide only a rough retrospective estimate of the time of drug intake. Recently, hair imaging methods using matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS) were reported, but these methods require the application of MALDI matrix and are performed under vacuum. Direct analysis of entire locks of hair without any sample pretreatment and with improved spatial resolution would thus address a need. Hair samples were attached to stainless steel mesh screens and scanned in the X-direction using direct analysis in real time (DART) ambient ionization orbitrap MS. The DART gas temperature and the accuracy of the probed hair zone were optimized using Δ-9-tetrahydrocannabinol (THC) as a model compound. Since external contamination is a major issue in forensic hair analysis, sub-samples were measured before and after dichloromethane decontamination. The relative intensity of the THC signal in spiked blank hair versus that of quinine as the internal standard showed good reproducibility (26% RSD) and linearity of the method (R(2)  = 0.991). With the DART hair scan THC could be detected in hair samples from different chronic cannabis users. The presence of THC was confirmed by quantitative liquid chromatography/tandem mass spectrometry. Zones with different THC content could be clearly distinguished, indicating that the method might be used for retrospective timeline assessments. Detection of THC in decontaminated drug user hair showed that the DART hair scan not only probes THC on the surface of hair, but penetrates deeply enough to measure incorporated THC. A new approach in forensic hair analysis has been developed by probing complete locks of hair using DART-MS. Longitudinal scanning enables detection of incorporated compounds and can be used as pre-screening for THC without sample preparation. The method could also be adjusted for the analysis of other drugs of abuse. Copyright © 2014 John Wiley & Sons, Ltd.

Mount Saint Helens aerosol evolution

NASA Technical Reports Server (NTRS)

Oberbeck, V. R.; Farlow, N. H.; Snetsinger, K. G.; Ferry, G. V.; Fong, W.; Hayes, D. M.

1982-01-01

Stratospheric aerosol samples were collected using a wire impactor during the year following the eruption of Mt. St. Helens. Analysis of samples shows that aerosol volume increased for 6 months due to gas-to-particle conversion and then decreased to background levels in the following 6 months.

Nutritional composition, bioactive compounds and volatile profile of cocoa beans from different regions of Cameroon.

PubMed

Caprioli, Giovanni; Fiorini, Dennis; Maggi, Filippo; Nicoletti, Marcello; Ricciutelli, Massimo; Toniolo, Chiara; Prosper, Biapa; Vittori, Sauro; Sagratini, Gianni

2016-06-01

Analysis of the complex composition of cocoa beans provides fundamental information for evaluating the quality and nutritional aspects of cocoa-based food products, nutraceuticals and supplements. Cameroon, the world's fourth largest producer of cocoa, has been defined as "Africa in miniature" because of the variety it habitats. In order to evaluate the nutritional characteristics of cocoa beans from five different regions of Cameroon, we studied their polyphenolic content, volatile compounds and fatty acids composition. The High Performance Thin Layer Chromatography (HPTLC) analysis showed that the Mbalmayo sample had the highest content of theobromine (11.6 mg/g) and caffeic acid (2.1 mg/g), while the Sanchou sample had the highest level of (-)-epicatechin (142.9 mg/g). Concerning fatty acids, the lowest level of stearic acid was found in the Mbalmayo sample while the Bertoua sample showed the highest content of oleic acid. Thus, we confirmed that geographical origin influences the quality and nutritional characteristics of cocoa from these regions of Cameroon.

New polyelectrolyte complex from pectin/chitosan and montmorillonite clay.

PubMed

da Costa, Marcia Parente Melo; de Mello Ferreira, Ivana Lourenço; de Macedo Cruz, Mauricio Tavares

2016-08-01

A new nanocomposite hydrogel was prepared by forming a crosslinked hybrid polymer network based on chitosan and pectin in the presence of montmorillonite clay. The influence of clay concentration (0.5 and 2% wt) as well as polymer ratios (1:1, 1:2 and 2:1) was investigated carefully. The samples were characterized by different techniques: transmission and scanning electron microscopy, X-ray diffraction, thermogravimetric analysis, infrared spectroscopy, swelling degree and compression test. Most samples presented swelling degree above 1000%, which permits characterizing them as superabsorbent material. Images obtained by transmission electron microscopy showed the presence of clay nanoparticles into hydrogel. The hydrogels' morphological properties were evaluated by scanning electron microscope in high and low-vacuum. The micrographs showed that the samples presented porous. The incorporation of clay produced hydrogels with differentiated morphology. Thermogravimetric analysis results revealed that the incorporation of clay in the samples provided greater thermal stability to the hydrogels. The compression resistance also increased with addition of clay. Copyright © 2016 Elsevier Ltd. All rights reserved.

Modulation in magnetic exchange interaction, core shell structure and Hopkinson's peak with chromium substitution into Ni0.75Co0.25Fe2O4 nano particles

NASA Astrophysics Data System (ADS)

Uday Bhasker, S.; Choudary, G. S. V. R. K.; Reddy, M. V. Ramana

2018-05-01

The ever growing applications and ever evolving challenges of magnetic nano particles has been motivating the researchers from various disciplines towards this area of magnetic nano particles. Cation substitutional effect on the magnetic structure of the nanoparticles forms a crucial aspect in their applications. Here the environmentally benign auto combustion method was employed to synthesize chromium substituted nickel cobalt ferrite (Ni0.75Co0.25Fe2-xCrxO4; x = 0, 0.10, 0.15) nano particles, from aqueous metal nitrate solutions. Chromium substitution has shown its effect on the structural, magnetic and electrical properties of Ni0.75Co0.25Fe2O4. Structural and phase analysis of the prepared samples show increased phase purity of ferrite sample with increasing Cr substitution. The TEM (Transmission Electron Microscope) image confirms the nano size of the particles, EDS (Energy dispersive X-ray Spectroscopy) has supported the stoichiometry of the prepared samples and FTIR (Fourier-transform infrared spectroscopic) analysis confirms the spinel structure and also suggests cation redistributions with chromium substitution. VSM (Vibrational Sample Magnetometer) is used to study the magnetic properties through magnetic hysteresis (M-H) loop and magnetic Hopkinson effect. All samples show hysteresis and show reduction in magnetic properties with increase in chromium content. The thermo magnetic study shows Hopkinson peak(s) in the magnetization vs. temperature (M-T) graph and also shows variation in the nature of Hopkinson peak with chromium substitution. Possible reasons for the changes in the nature of the peak are discussed.

Evaluation of magnetic nanoparticle samples made from biocompatible ferucarbotran by time-correlation magnetic particle imaging reconstruction method

PubMed Central

2013-01-01

Background Molecular imaging using magnetic nanoparticles (MNPs)—magnetic particle imaging (MPI)—has attracted interest for the early diagnosis of cancer and cardiovascular disease. However, because a steep local magnetic field distribution is required to obtain a defined image, sophisticated hardware is required. Therefore, it is desirable to realize excellent image quality even with low-performance hardware. In this study, the spatial resolution of MPI was evaluated using an image reconstruction method based on the correlation information of the magnetization signal in a time domain and by applying MNP samples made from biocompatible ferucarbotran that have adjusted particle diameters. Methods The magnetization characteristics and particle diameters of four types of MNP samples made from ferucarbotran were evaluated. A numerical analysis based on our proposed method that calculates the image intensity from correlation information between the magnetization signal generated from MNPs and the system function was attempted, and the obtained image quality was compared with that using the prototype in terms of image resolution and image artifacts. Results MNP samples obtained by adjusting ferucarbotran showed superior properties to conventional ferucarbotran samples, and numerical analysis showed that the same image quality could be obtained using a gradient magnetic field generator with 0.6 times the performance. However, because image blurring was included theoretically by the proposed method, an algorithm will be required to improve performance. Conclusions MNP samples obtained by adjusting ferucarbotran showed magnetizing properties superior to conventional ferucarbotran samples, and by using such samples, comparable image quality (spatial resolution) could be obtained with a lower gradient magnetic field intensity. PMID:23734917

[Principal component analysis and cluster analysis of inorganic elements in sea cucumber Apostichopus japonicus].

PubMed

Liu, Xiao-Fang; Xue, Chang-Hu; Wang, Yu-Ming; Li, Zhao-Jie; Xue, Yong; Xu, Jie

2011-11-01

The present study is to investigate the feasibility of multi-elements analysis in determination of the geographical origin of sea cucumber Apostichopus japonicus, and to make choice of the effective tracers in sea cucumber Apostichopus japonicus geographical origin assessment. The content of the elements such as Al, V, Cr, Mn, Fe, Co, Ni, Cu, Zn, As, Se, Mo, Cd, Hg and Pb in sea cucumber Apostichopus japonicus samples from seven places of geographical origin were determined by means of ICP-MS. The results were used for the development of elements database. Cluster analysis(CA) and principal component analysis (PCA) were applied to differentiate the sea cucumber Apostichopus japonicus geographical origin. Three principal components which accounted for over 89% of the total variance were extracted from the standardized data. The results of Q-type cluster analysis showed that the 26 samples could be clustered reasonably into five groups, the classification results were significantly associated with the marine distribution of the sea cucumber Apostichopus japonicus samples. The CA and PCA were the effective methods for elements analysis of sea cucumber Apostichopus japonicus samples. The content of the mineral elements in sea cucumber Apostichopus japonicus samples was good chemical descriptors for differentiating their geographical origins.

Pet fur or fake fur? A forensic approach

PubMed Central

2014-01-01

Background In forensic science there are many types of crime that involve animals. Therefore, the identification of the species has become an essential investigative tool. The exhibits obtained from such offences are very often a challenge for forensic experts. Indeed, most biological materials are traces, hair or tanned fur. With hair samples, a common forensic approach should proceed from morphological and structural microscopic examination to DNA analysis. However, the microscopy of hair requires a lot of experience and a suitable comparative database to be able to recognize with a high degree of accuracy that a sample comes from a particular species and then to determine whether it is a protected one. DNA analysis offers the best opportunity to answer the question, ‘What species is this?’ In our work, we analyzed different samples of fur coming from China used to make hats and collars. Initially, the samples were examined under a microscope, then the mitochondrial DNA was tested for species identification. For this purpose, the genetic markers used were the 12S and 16S ribosomal RNA, while the hypervariable segment I of the control region was analyzed afterwards, to determine whether samples belonged to the same individual. Results Microscopic examination showed that the fibres were of animal origin, although it was difficult to determine with a high degree of confidence which species they belonged to and if they came from a protected species. Therefore, DNA analysis was essential to try to clarify the species of these fur samples. Conclusions Macroscopic and microscopic analysis confirmed the hypothesis regarding the analyzed hair belonging to real animals, although it failed to prove with any kind of certainty which actual family it came from, therefore, the species remains unknown. Sequence data analysis and comparisons with the samples available in GenBank showed that the hair, in most cases, belonged to the Canidae family, and in one case only to Felidae. PMID:24991403

Comparative analysis of taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors by metagenomic sequencing and radioisotopic analysis.

PubMed

Luo, Gang; Fotidis, Ioannis A; Angelidaki, Irini

2016-01-01

Biogas production is a very complex process due to the high complexity in diversity and interactions of the microorganisms mediating it, and only limited and diffuse knowledge exists about the variation of taxonomic and functional patterns of microbiomes across different biogas reactors, and their relationships with the metabolic patterns. The present study used metagenomic sequencing and radioisotopic analysis to assess the taxonomic, functional, and metabolic patterns of microbiomes from 14 full-scale biogas reactors operated under various conditions treating either sludge or manure. The results from metagenomic analysis showed that the dominant methanogenic pathway revealed by radioisotopic analysis was not always correlated with the taxonomic and functional compositions. It was found by radioisotopic experiments that the aceticlastic methanogenic pathway was dominant, while metagenomics analysis showed higher relative abundance of hydrogenotrophic methanogens. Principal coordinates analysis showed the sludge-based samples were clearly distinct from the manure-based samples for both taxonomic and functional patterns, and canonical correspondence analysis showed that the both temperature and free ammonia were crucial environmental variables shaping the taxonomic and functional patterns. The study further the overall patterns of functional genes were strongly correlated with overall patterns of taxonomic composition across different biogas reactors. The discrepancy between the metabolic patterns determined by metagenomic analysis and metabolic pathways determined by radioisotopic analysis was found. Besides, a clear correlation between taxonomic and functional patterns was demonstrated for biogas reactors, and also the environmental factors that shaping both taxonomic and functional genes patterns were identified.

The use of Vacutainer tubes for collection of soil samples for helium analysis

USGS Publications Warehouse

Hinkle, Margaret E.; Kilburn, James E.

1979-01-01

Measurements of the helium concentration of soil samples collected and stored in Vacutainer-brand evacuated glass tubes show that Vacutainers are reliable containers for soil collection. Within the limits of reproducibility, helium content of soils appears to be independent of variations in soil temperature, barometric pressure, and quantity of soil moisture present in the sample.

Amino acid analyses of Apollo 14 samples.

NASA Technical Reports Server (NTRS)

Gehrke, C. W.; Zumwalt, R. W.; Kuo, K.; Aue, W. A.; Stalling, D. L.; Kvenvolden, K. A.; Ponnamperuma, C.

1972-01-01

Detection limits were between 300 pg and 1 ng for different amino acids, in an analysis by gas-liquid chromatography of water extracts from Apollo 14 lunar fines in which amino acids were converted to their N-trifluoro-acetyl-n-butyl esters. Initial analyses of water and HCl extracts of sample 14240 and 14298 samples showed no amino acids above background levels.

Sampling tree tops by helicopter...special pole pruner cuts branchlets

Treesearch

John F. Wear; Robert G. Winterfeld

1966-01-01

A new technique for sampling tops of tall Douglas-fir trees by using a special pole pruner from a helicopter has been developed and field-tested. Thee pole pruner cuts and holds a branchlet. Foliage samples collected will be compared by spectral analysis to show the type of aerial imagery that best differentiates healthy trees from those attacked by root rot.

Structural morphology, upconversion luminescence and optical thermometric sensing behavior of Y2O3:Er(3+)/Yb(3+) nano-crystalline phosphor.

PubMed

Joshi, C; Dwivedi, A; Rai, S B

2014-08-14

Infrared-to-visible upconverting rare earths Er(3+)/Yb(3+) co-doped Y2O3 nano-crystalline phosphor samples have been prepared by solution combustion method followed by post-heat treatment at higher temperatures. A slight increase in average crystallite size has been found on calcinations verified by X-ray analysis. Transmission electron microscopy (TEM) confirms the nano-crystalline nature of the as-prepared and calcinated samples. Fourier transform infrared (FTIR) analysis shows the structural changes in as-prepared and calcinated samples. Upconversion and downconversion emission recorded using 976 and 532 nm laser sources clearly demonstrates a better luminescence properties in the calcinated samples as compared to as-prepared sample. Upconversion emission has been quantified in terms of standard chromaticity diagram (CIE) showing a shift in overall upconversion emission of as-prepared and calcinated samples. Temperature sensing behaviour of this material has also been investigated by measurement of fluorescence intensity ratio (FIR) of various signals in green emission in the temperature range of 315 to 555 K under 976 nm laser excitation. Copyright © 2014 Elsevier B.V. All rights reserved.

Discrimination of cultivation ages and cultivars of ginseng leaves using Fourier transform infrared spectroscopy combined with multivariate analysis

PubMed Central

Kwon, Yong-Kook; Ahn, Myung Suk; Park, Jong Suk; Liu, Jang Ryol; In, Dong Su; Min, Byung Whan; Kim, Suk Weon

2013-01-01

To determine whether Fourier transform (FT)-IR spectral analysis combined with multivariate analysis of whole-cell extracts from ginseng leaves can be applied as a high-throughput discrimination system of cultivation ages and cultivars, a total of total 480 leaf samples belonging to 12 categories corresponding to four different cultivars (Yunpung, Kumpung, Chunpung, and an open-pollinated variety) and three different cultivation ages (1 yr, 2 yr, and 3 yr) were subjected to FT-IR. The spectral data were analyzed by principal component analysis and partial least squares-discriminant analysis. A dendrogram based on hierarchical clustering analysis of the FT-IR spectral data on ginseng leaves showed that leaf samples were initially segregated into three groups in a cultivation age-dependent manner. Then, within the same cultivation age group, leaf samples were clustered into four subgroups in a cultivar-dependent manner. The overall prediction accuracy for discrimination of cultivars and cultivation ages was 94.8% in a cross-validation test. These results clearly show that the FT-IR spectra combined with multivariate analysis from ginseng leaves can be applied as an alternative tool for discriminating of ginseng cultivars and cultivation ages. Therefore, we suggest that this result could be used as a rapid and reliable F1 hybrid seed-screening tool for accelerating the conventional breeding of ginseng. PMID:24558311

Geographical structuring of Trypanosoma cruzi populations from Chilean Triatoma infestans triatomines and their genetic relationship with other Latino American counterparts

PubMed Central

Venegas, J; Rojas, T; DÍaz, F; Miranda, S; Jercic, M I; González, C; Coñoepán, W; Pichuantes, S; RodrÍguez, J; Gajardo, M; Sánchez, G

2011-01-01

In order to obtain more information about the population structure of Chilean Trypanosoma cruzi, and their genetic relationship with other Latino American counterparts, we performed the study of T. cruzi samples detected in the midgut content of Triatoma infestans insects from three endemic regions of Chile. The genetic characteristics of these samples were analysed using microsatellite markers and PCR conditions that allow the detection of predominant T. cruzi clones directly in triatomine midgut content. Population genetic analyses using the Fisher’s exact method, analysis of molecular variance (AMOVA) and the determination of FST showed that the northern T. cruzi population sample was genetically differentiated from the two southern population counterparts. Further analysis showed that the cause of this genetic differentiation was the asymmetrical distribution of TcIII T. cruzi predominant clones. Considering all triatomines from the three regions, the most frequent predominant lineages were TcIII (38%), followed by TcI (34%) and hybrid (8%). No TcII lineage was observed along the predominant T. cruzi clones. The best phylogenetic reconstruction using the shared allelic genetic distance was concordant with the population genetic analysis and tree topology previously described studying foreign samples. The correlation studies showed that the lineage TcIII from the III region was genetically differentiated from the other two, and this differentiation was correlated with geographical distance including Chilean and mainly Brazilian samples. It will be interesting to investigate whether this geographical structure may be related with different clinical manifestation of Chagas disease. PMID:22325822

Analysis of YBCO high temperature superconductor doped with silver nanoparticles and carbon nanotubes using Williamson-Hall and size-strain plot

NASA Astrophysics Data System (ADS)

Dadras, Sedigheh; Davoudiniya, Masoumeh

2018-05-01

This paper sets out to investigate and compare the effects of Ag nanoparticles and carbon nanotubes (CNTs) doping on the mechanical properties of Y1Ba2Cu3O7-δ (YBCO) high temperature superconductor. For this purpose, the pure and doped YBCO samples were synthesized by sol-gel method. The microstructural analysis of the samples is performed using X-ray diffraction (XRD). The crystalline size, lattice strain and stress of the pure and doped YBCO samples were estimated by modified forms of Williamson-Hall analysis (W-H), namely, uniform deformation model (UDM), uniform deformation stress model (UDSM) and the size-strain plot method (SSP). These results show that the crystalline size, lattice strain and stress of the YBCO samples declined by Ag nanoparticles and CNTs doping.

Linear Combination Fitting (LCF)-XANES analysis of As speciation in selected mine-impacted materials

EPA Pesticide Factsheets

This table provides sample identification labels and classification of sample type (tailings, calcinated, grey slime). For each sample, total arsenic and iron concentrations determined by acid digestion and ICP analysis are provided along with arsenic in-vitro bioaccessibility (As IVBA) values to estimate arsenic risk. Lastly, the table provides linear combination fitting results from synchrotron XANES analysis showing the distribution of arsenic speciation phases present in each sample along with fitting error (R-factor).This dataset is associated with the following publication:Ollson, C., E. Smith, K. Scheckel, A. Betts, and A. Juhasz. Assessment of arsenic speciation and bioaccessibility in mine-impacted materials. Diana Aga, Wonyong Choi, Andrew Daugulis, Gianluca Li Puma, Gerasimos Lyberatos, and Joo Hwa Tay JOURNAL OF HAZARDOUS MATERIALS. Elsevier Science Ltd, New York, NY, USA, 313: 130-137, (2016).

Structural studies on the substitution of Ag, Na doped LCSMO CMR manganites

DOE Office of Scientific and Technical Information (OSTI.GOV)

Subhashini, P., E-mail: subhashinisvu@gmail.com; Krishnaiah, M.; Munirathinam, B.

2016-05-06

Synthesis and characterization of colossal magnetoresistance (CMR) materials has been a subject of scientific research due to the unique transport, magnetotransport, and magnetic properties. The single phase polycrystalline La{sub 0.7}Ca{sub 0.1}Sr{sub 0.1}M{sub 0.1}MnO{sub 3} (LCSMO) (M=Ag and Na) samples prepared using nitrate route method. The structural properties are studied at different dopants by X-ray diffraction. The surface morphology and elemental analysis of both samples were carried out by scanning electron microscopy (SEM) and energy dispersive X-ray technique (EDAX) respectively. The structural analysis shows that the LCSMO is crystallized in an orthorhombic perovskite structure belonging to Pnma space group. The crystalmore » size of the sample is calculated using Scherrer formula. The SEM images show that the polycrystalline grains are observed to be near spherical shape and uniform in size. EDAX spectra taken from the surface of the synthesized powders show a nominal composition near the desired one for M=Na sample where as some vacancies are present in the A-site in the case of Ag substitution as will be discussed in this paper.« less

Evaluating Composite Sampling Methods of Bacillus Spores at Low Concentrations

PubMed Central

Hess, Becky M.; Amidan, Brett G.; Anderson, Kevin K.; Hutchison, Janine R.

2016-01-01

Restoring all facility operations after the 2001 Amerithrax attacks took years to complete, highlighting the need to reduce remediation time. Some of the most time intensive tasks were environmental sampling and sample analyses. Composite sampling allows disparate samples to be combined, with only a single analysis needed, making it a promising method to reduce response times. We developed a statistical experimental design to test three different composite sampling methods: 1) single medium single pass composite (SM-SPC): a single cellulose sponge samples multiple coupons with a single pass across each coupon; 2) single medium multi-pass composite: a single cellulose sponge samples multiple coupons with multiple passes across each coupon (SM-MPC); and 3) multi-medium post-sample composite (MM-MPC): a single cellulose sponge samples a single surface, and then multiple sponges are combined during sample extraction. Five spore concentrations of Bacillus atrophaeus Nakamura spores were tested; concentrations ranged from 5 to 100 CFU/coupon (0.00775 to 0.155 CFU/cm2). Study variables included four clean surface materials (stainless steel, vinyl tile, ceramic tile, and painted dry wallboard) and three grime coated/dirty materials (stainless steel, vinyl tile, and ceramic tile). Analysis of variance for the clean study showed two significant factors: composite method (p< 0.0001) and coupon material (p = 0.0006). Recovery efficiency (RE) was higher overall using the MM-MPC method compared to the SM-SPC and SM-MPC methods. RE with the MM-MPC method for concentrations tested (10 to 100 CFU/coupon) was similar for ceramic tile, dry wall, and stainless steel for clean materials. RE was lowest for vinyl tile with both composite methods. Statistical tests for the dirty study showed RE was significantly higher for vinyl and stainless steel materials, but lower for ceramic tile. These results suggest post-sample compositing can be used to reduce sample analysis time when responding to a Bacillus anthracis contamination event of clean or dirty surfaces. PMID:27736999

Evaluating Composite Sampling Methods of Bacillus Spores at Low Concentrations.

PubMed

Hess, Becky M; Amidan, Brett G; Anderson, Kevin K; Hutchison, Janine R

2016-01-01

Restoring all facility operations after the 2001 Amerithrax attacks took years to complete, highlighting the need to reduce remediation time. Some of the most time intensive tasks were environmental sampling and sample analyses. Composite sampling allows disparate samples to be combined, with only a single analysis needed, making it a promising method to reduce response times. We developed a statistical experimental design to test three different composite sampling methods: 1) single medium single pass composite (SM-SPC): a single cellulose sponge samples multiple coupons with a single pass across each coupon; 2) single medium multi-pass composite: a single cellulose sponge samples multiple coupons with multiple passes across each coupon (SM-MPC); and 3) multi-medium post-sample composite (MM-MPC): a single cellulose sponge samples a single surface, and then multiple sponges are combined during sample extraction. Five spore concentrations of Bacillus atrophaeus Nakamura spores were tested; concentrations ranged from 5 to 100 CFU/coupon (0.00775 to 0.155 CFU/cm2). Study variables included four clean surface materials (stainless steel, vinyl tile, ceramic tile, and painted dry wallboard) and three grime coated/dirty materials (stainless steel, vinyl tile, and ceramic tile). Analysis of variance for the clean study showed two significant factors: composite method (p< 0.0001) and coupon material (p = 0.0006). Recovery efficiency (RE) was higher overall using the MM-MPC method compared to the SM-SPC and SM-MPC methods. RE with the MM-MPC method for concentrations tested (10 to 100 CFU/coupon) was similar for ceramic tile, dry wall, and stainless steel for clean materials. RE was lowest for vinyl tile with both composite methods. Statistical tests for the dirty study showed RE was significantly higher for vinyl and stainless steel materials, but lower for ceramic tile. These results suggest post-sample compositing can be used to reduce sample analysis time when responding to a Bacillus anthracis contamination event of clean or dirty surfaces.

Evaluating Composite Sampling Methods of Bacillus spores at Low Concentrations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hess, Becky M.; Amidan, Brett G.; Anderson, Kevin K.

Restoring facility operations after the 2001 Amerithrax attacks took over three months to complete, highlighting the need to reduce remediation time. The most time intensive tasks were environmental sampling and sample analyses. Composite sampling allows disparate samples to be combined, with only a single analysis needed, making it a promising method to reduce response times. We developed a statistical experimental design to test three different composite sampling methods: 1) single medium single pass composite: a single cellulose sponge samples multiple coupons; 2) single medium multi-pass composite: a single cellulose sponge is used to sample multiple coupons; and 3) multi-medium post-samplemore » composite: a single cellulose sponge samples a single surface, and then multiple sponges are combined during sample extraction. Five spore concentrations of Bacillus atrophaeus Nakamura spores were tested; concentrations ranged from 5 to 100 CFU/coupon (0.00775 to 0.155CFU/cm2, respectively). Study variables included four clean surface materials (stainless steel, vinyl tile, ceramic tile, and painted wallboard) and three grime coated/dirty materials (stainless steel, vinyl tile, and ceramic tile). Analysis of variance for the clean study showed two significant factors: composite method (p-value < 0.0001) and coupon material (p-value = 0.0008). Recovery efficiency (RE) was higher overall using the post-sample composite (PSC) method compared to single medium composite from both clean and grime coated materials. RE with the PSC method for concentrations tested (10 to 100 CFU/coupon) was similar for ceramic tile, painted wall board, and stainless steel for clean materials. RE was lowest for vinyl tile with both composite methods. Statistical tests for the dirty study showed RE was significantly higher for vinyl and stainless steel materials, but significantly lower for ceramic tile. These results suggest post-sample compositing can be used to reduce sample analysis time when responding to a Bacillus anthracis contamination event of clean or dirty surfaces.« less

Oil mist and vapour concentrations from drilling fluids: inter- and intra-laboratory comparison of chemical analyses.

PubMed

Galea, Karen S; Searl, Alison; Sánchez-Jiménez, Araceli; Woldbæk, Torill; Halgard, Kristin; Thorud, Syvert; Steinsvåg, Kjersti; Krüger, Kirsti; Maccalman, Laura; Cherrie, John W; van Tongeren, Martie

2012-01-01

There are no recognized analytical methods for measuring oil mist and vapours arising from drilling fluids used in offshore petroleum drilling industry. To inform the future development of improved methods of analysis for oil mist and vapours this study assessed the inter- and intra-laboratory variability in oil mist and vapour analysis. In addition, sample losses during transportation and storage were assessed. Replicate samples for oil mist and vapour were collected using the 37-mm Millipore closed cassette and charcoal tube assembly. Sampling was conducted in a simulated shale shaker room, similar to that found offshore for processing drilling fluids. Samples were analysed at two different laboratories, one in Norway and one in the UK. Oil mist samples were analysed using Fourier transform infrared spectroscopy (FTIR), while oil vapour samples were analysed by gas chromatography (GC). The comparison of replicate samples showed substantial within- and between-laboratory variability in reported oil mist concentrations. The variability in oil vapour results was considerably reduced compared to oil mist, provided that a common method of calibration and quantification was adopted. The study also showed that losses can occur during transportation and storage of samples. There is a need to develop a harmonized method for the quantification of oil mist on filter and oil vapour on charcoal supported by a suitable proficiency testing scheme for laboratories involved in the analysis of occupational hygiene samples for the petroleum industry. The uncertainties in oil mist and vapour measurement have substantial implications in relation to compliance with occupational exposure limits and also in the reliability of any exposure-response information reported in epidemiological studies.

Textbooks for Responsible Data Analysis in Excel

ERIC Educational Resources Information Center

Garrett, Nathan

2015-01-01

With 27 million users, Excel (Microsoft Corporation, Seattle, WA) is the most common business data analysis software. However, audits show that almost all complex spreadsheets have errors. The author examined textbooks to understand why responsible data analysis is taught. A purposeful sample of 10 textbooks was coded, and then compared against…

Performance Evaluation of the Operational Air Quality Monitor for Water Testing Aboard the International Space Station

NASA Technical Reports Server (NTRS)

Wallace, William T.; Limero, Thomas F.; Gazda, Daniel B.; Minton, John M.; Macatangay, Ariel V.; Dwivedi, Prabha; Fernandez, Facundo M.

2014-01-01

Real-time environmental monitoring on ISS is necessary to provide data in a timely fashion and to help ensure astronaut health. Current real-time water TOC monitoring provides high-quality trending information, but compound-specific data is needed. The combination of ETV with the AQM showed that compounds of interest could be liberated from water and analyzed in the same manner as air sampling. Calibration of the AQM using water samples allowed for the quantitative analysis of ISS archival samples. Some calibration issues remain, but the excellent accuracy of DMSD indicates that ETV holds promise for as a sample introduction method for water analysis in spaceflight.

Impact analysis of off-road-vehicle use on vegetation in the Grand Mere dune environment. [Lake Michigan

NASA Technical Reports Server (NTRS)

Schultink, G. (Principal Investigator)

1977-01-01

The author has identified the following significant results. A linear regression between percent nonvegetative land and the time variable was completed for the two sample areas. Sample area no. 1 showed an average vegetation loss of 1.901% per year, while the loss for sample area no. 2 amounted to 5.889% per year. Two basic reasons for the difference were assumed to play a role: the difference in access potential and the amount of already fragmented vegetation complexes in existence during the first year of the comparative analysis - 1970. Sample area no. 2 was located closer to potential access points and was more fragmented initially.

Q-controlled amplitude modulation atomic force microscopy in liquids: An analysis

NASA Astrophysics Data System (ADS)

Hölscher, H.; Schwarz, U. D.

2006-08-01

An analysis of amplitude modulation atomic force microscopy in liquids is presented with respect to the application of the Q-Control technique. The equation of motion is solved by numerical and analytic methods with and without Q-Control in the presence of a simple model interaction force adequate for many liquid environments. In addition, the authors give an explicit analytical formula for the tip-sample indentation showing that higher Q factors reduce the tip-sample force. It is found that Q-Control suppresses unwanted deformations of the sample surface, leading to the enhanced image quality reported in several experimental studies.

Analysis of the Enameled AISI 316LVM Stainless Steel

NASA Astrophysics Data System (ADS)

Bukovec, Mitja; Xhanari, Klodian; Lešer, Tadej; Petovar, Barbara; Finšgar, Matjaž

2018-03-01

In this work, four different enamels were coated on AISI 316LVM stainless steel and the corrosion resistance of these samples was tested in 5 wt.% NaCl solution at room temperature. The preparation procedure of the enamels was optimized in terms of firing temperature, time and composition. First the thermal expansion was measured using dilatometry followed by electrochemical analysis using chronopotentiometry, electrochemical impedance spectroscopy and cyclic polarization. The topography of the most resistant sample was obtained by 3D-profilometry. All samples coated with enamel showed significantly higher corrosion and dilatation resistance compared with the uncoated stainless steel material.

Inverse supercritical fluid extraction as a sample preparation method for the analysis of the nanoparticle content in sunscreen agents.

PubMed

Müller, David; Cattaneo, Stefano; Meier, Florian; Welz, Roland; de Vries, Tjerk; Portugal-Cohen, Meital; Antonio, Diana C; Cascio, Claudia; Calzolai, Luigi; Gilliland, Douglas; de Mello, Andrew

2016-04-01

We demonstrate the use of inverse supercritical carbon dioxide (scCO2) extraction as a novel method of sample preparation for the analysis of complex nanoparticle-containing samples, in our case a model sunscreen agent with titanium dioxide nanoparticles. The sample was prepared for analysis in a simplified process using a lab scale supercritical fluid extraction system. The residual material was easily dispersed in an aqueous solution and analyzed by Asymmetrical Flow Field-Flow Fractionation (AF4) hyphenated with UV- and Multi-Angle Light Scattering detection. The obtained results allowed an unambiguous determination of the presence of nanoparticles within the sample, with almost no background from the matrix itself, and showed that the size distribution of the nanoparticles is essentially maintained. These results are especially relevant in view of recently introduced regulatory requirements concerning the labeling of nanoparticle-containing products. The novel sample preparation method is potentially applicable to commercial sunscreens or other emulsion-based cosmetic products and has important ecological advantages over currently used sample preparation techniques involving organic solvents. Copyright © 2016 Elsevier B.V. All rights reserved.

Characterization of microbial communities in heavy crude oil from Saudi Arabia.

PubMed

Albokari, Majed; Mashhour, Ibrahim; Alshehri, Mohammed; Boothman, Chris; Al-Enezi, Mousa

The complete mineralization of crude oil into carbon dioxide, water, inorganic compounds and cellular constituents can be carried out as part of a bioremediation strategy. This involves the transformation of complex organic contaminants into simpler organic compounds by microbial communities, mainly bacteria. A crude oil sample and an oil sludge sample were obtained from Saudi ARAMCO Oil Company and investigated to identify the microbial communities present using PCR-based culture-independent techniques. In total, analysis of 177 clones yielded 30 distinct bacterial sequences. Clone library analysis of the oil sample was found to contain Bacillus , Clostridia and Gammaproteobacteria species while the sludge sample revealed the presence of members of the Alphaproteobacteria , Betaproteobacteria , Gammaproteobacteria , Clostridia , Spingobacteria and Flavobacteria . The dominant bacterial class identified in oil and sludge samples was found to be Bacilli and Flavobacteria , respectively. Phylogenetic analysis showed that the dominant bacterium in the oil sample has the closest sequence identity to Enterococcus aquimarinus and the dominant bacterium in the sludge sample is most closely related to the uncultured Bacteroidetes bacterium designated AH.KK.

Naturally acquired bovine besnoitiosis: Differential distribution of parasites in the skin of chronically infected cattle.

PubMed

Schares, G; Langenmayer, M C; Majzoub-Altweck, M; Scharr, J C; Gentile, A; Maksimov, A; Schares, S; Conraths, F J; Gollnick, N S

2016-01-30

Bovine besnoitiosis is caused by Besnoitia besnoiti, an apicomplexan parasite closely related to Toxoplasma gondii and Neospora caninum. In the acute stage of besnoitiosis, cattle suffer from pyrexia, swollen lymph nodes, anorexia and subcutaneous edema. In the chronic stage, tissue cysts are formed in a variety of tissues including the skin. Knowledge about the distribution of tissue cysts of different parts of the skin of infected animals is scarce. Four chronically infected cattle were euthanized and skin samples were taken from a total of 77 standardized cutaneous locations per animal. Portions of the dermis were taken, from which DNA was extracted and examined by real-time PCR. Cycle of transition (Ct) values reflecting the amount of parasite DNA in the samples were determined. For statistical analysis, samples were attributed to 11 larger skin regions ('OuterHindlegDistal', 'Rump, ForelegMiddle', 'NoseFrontEars', 'CheekEye', 'SideLowerPart', 'ForelegDistal', 'SideUpperPart', 'LegsInner', 'VentralHeadNeck', 'DorsalNeckWithersBackTail'). While all samples revealed a positive result in three female cattle, only 63.6% (49/77) of the samples of a bull showed positive results. For statistical analysis, a Ct value of 45 was assumed for samples with a negative result. The dams showed median Ct values of 16.1, 17.5 and 19.4, while in skin samples of the bull a median Ct value of 37.6 was observed. To determine the differences in DNA concentrations between different locations of the skin of the animals, a relative Ct (relCt) was determined by subtracting for each animal indv the MedianCtindv from each sample Ct. Analyses of the relCt values showed that the highest relative parasite DNA concentrations were observed in the categories 'OuterHindlegDistal', 'Rump', 'ForelegMiddle' and 'NoseFrontEars'. The relCt values in these categories differed statistically significantly from those determined for the categories 'VentralHeadNeck' and 'DorsalNeckWithersBackTail'. The analysis showed clear differences in the distribution and the detectability of parasite DNA in the skin of cattle infected with B. besnoiti. In all four animals, samples from the 'Rump' region (Regio fermoris) showed high parasite DNA concentrations. Because this region is also easily accessible for veterinarians, this skin location appears to be optimal for taking skin biopsies for detection or isolation of B. besnoiti. Copyright © 2015 Elsevier B.V. All rights reserved.

A Novel Approach to Detect Accelerated Aged and Surface-Mediated Degradation in Explosives by UPLC-ESI-MS.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Beppler, Christina L

2015-12-01

A new approach was created for studying energetic material degradation. This approach involved detecting and tentatively identifying non-volatile chemical species by liquid chromatography-mass spectrometry (LC-MS) with multivariate statistical data analysis that form as the CL-20 energetic material thermally degraded. Multivariate data analysis showed clear separation and clustering of samples based on sample group: either pristine or aged material. Further analysis showed counter-clockwise trends in the principal components analysis (PCA), a type of multivariate data analysis, Scores plots. These trends may indicate that there was a discrete shift in the chemical markers as the went from pristine to aged material, andmore » then again when the aged CL-20 mixed with a potentially incompatible material was thermally aged for 4, 6, or 9 months. This new approach to studying energetic material degradation should provide greater knowledge of potential degradation markers in these materials.« less

Qualitative Time-of-Flight Secondary Ion Mass Spectrometry Analysis of Root Dentin Irrigated with Sodium Hypochlorite, EDTA, or Chlorhexidine.

PubMed

Kolosowski, Kamil P; Sodhi, Rana N S; Kishen, Anil; Basrani, Bettina R

2015-10-01

Sodium hypochlorite (NaOCl), chelating agents, and chlorhexidine (CHX), which are commonly used irrigants during endodontic treatment, have the potential to alter the physical and chemical properties of the dentin structure. The aim of this study was to use time-of-flight secondary ion mass spectrometry to qualitatively evaluate the chemical characteristics of dentin surface and compare it with dentin exposed to NaOCl, EDTA, or CHX. Four blocks of dentin from a root of a human maxillary molar were embedded in resin and trimmed with a microtome to expose the dentin. Samples were randomly assigned to 4 treatment groups: (1) no irrigation treatment (sample A), (2) 2.5% NaOCl (sample B), (3) 17% EDTA (sample C), and (4) 2% CHX (sample D). Dentin surfaces were analyzed by time-of-flight secondary ion mass spectrometry, which allowed characterization of dentin surface chemistry by both imaging and mass spectroscopic analysis obtained in high mass and spatial resolution modes. Sample A revealed intense peaks characteristics of hydroxyapatite in addition to Na(+), K(+), CH4N(+), CN(-), CNO(-), Mg(+), F(-), and HCO2(-) peaks. Sample B showed severely decreased CH4N(+) and increased intensity of Cl(-). Sample C lacked Ca(+) and Mg(+) and showed decreased PO2(-) and PO3(-). Sample D exhibited a distinct presence of CHX. The spectral image of sample A displayed even distribution of Na(+) and Ca(+) on a smeared surface. The surfaces of samples B and D had patent dentinal tubules, whereas sample D showed an intense CHX signal. Sample C had some patent dentinal tubules and lacked Ca(+). NaOCl removed protein components from the dentin matrix, EDTA removed calcium and magnesium ions from the dentin, and CHX formed an adsorbed layer on the dentin surface. Copyright © 2015 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Overlap of Spoilage-Associated Microbiota between Meat and the Meat Processing Environment in Small-Scale and Large-Scale Retail Distributions

PubMed Central

Stellato, Giuseppina; La Storia, Antonietta; De Filippis, Francesca; Borriello, Giorgia; Villani, Francesco

2016-01-01

ABSTRACT Microbial contamination in food processing plants can play a fundamental role in food quality and safety. The aims of this study were to learn more about the possible influence of the meat processing environment on initial fresh meat contamination and to investigate the differences between small-scale retail distribution (SD) and large-scale retail distribution (LD) facilities. Samples were collected from butcheries (n = 20), including LD (n = 10) and SD (n = 10) facilities, over two sampling campaigns. Samples included fresh beef and pork cuts and swab samples from the knife, the chopping board, and the butcher's hand. The microbiota of both meat samples and environmental swabs were very complex, including more than 800 operational taxonomic units (OTUs) collapsed at the species level. The 16S rRNA sequencing analysis showed that core microbiota were shared by 80% of the samples and included Pseudomonas spp., Streptococcus spp., Brochothrix spp., Psychrobacter spp., and Acinetobacter spp. Hierarchical clustering of the samples based on the microbiota showed a certain separation between meat and environmental samples, with higher levels of Proteobacteria in meat. In particular, levels of Pseudomonas and several Enterobacteriaceae members were significantly higher in meat samples, while Brochothrix, Staphylococcus, lactic acid bacteria, and Psychrobacter prevailed in environmental swab samples. Consistent clustering was also observed when metabolic activities were considered by predictive metagenomic analysis of the samples. An increase in carbohydrate metabolism was predicted for the environmental swabs and was consistently linked to Firmicutes, while increases in pathways related to amino acid and lipid metabolism were predicted for the meat samples and were positively correlated with Proteobacteria. Our results highlighted the importance of the processing environment in contributing to the initial microbial levels of meat and clearly showed that the type of retail facility (LD or SD) did not apparently affect the contamination. IMPORTANCE The study provides an in-depth description of the microbiota of meat and meat processing environments. It highlights the importance of the environment as a contamination source of spoilage bacteria, and it shows that the size of the retail facility does not affect the level and type of contamination. PMID:27129965

Flow-cytometric identification of vinegars using a multi-parameter analysis optical detection module

NASA Astrophysics Data System (ADS)

Verschooten, T.; Ottevaere, H.; Vervaeke, M.; Van Erps, J.; Callewaert, M.; De Malsche, W.; Thienpont, H.

2015-09-01

We show a proof-of-concept demonstration of a multi-parameter analysis low-cost optical detection system for the flowcytometric identification of vinegars. This multi-parameter analysis system can simultaneously measure laser induced fluorescence, absorption and scattering excited by two time-multiplexed lasers of different wavelengths. To our knowledge no other polymer optofluidic chip based system offers more simultaneous measurements. The design of the optofluidic channels is aimed at countering the effects that viscous fingering, air bubbles, and emulsion samples can have on the correct operation of such a detection system. Unpredictable variations in viscosity and refractive index of the channel content can be turned into a source of information. The sample is excited by two laser diodes that are driven by custom made low-cost laser drivers. The optofluidic chip is built to be robust and easy to handle and is reproducible using hot embossing. We show a custom optomechanical holder for the optofluidic chip that ensures correct alignment and automatic connection to the external fluidic system. We show an experiment in which 92 samples of vinegar are measured. We are able to identify 9 different kinds of vinegar with an accuracy of 94%. Thus we show an alternative approach to the classic optical spectroscopy solution at a lowered. Furthermore, we have shown the possibility of predicting the viscosity and turbidity of vinegars with a goodness-of-fit R2 over 0.947.

Determining the optimal forensic DNA analysis procedure following investigation of sample quality.

PubMed

Hedell, Ronny; Hedman, Johannes; Mostad, Petter

2018-07-01

Crime scene traces of various types are routinely sent to forensic laboratories for analysis, generally with the aim of addressing questions about the source of the trace. The laboratory may choose to analyse the samples in different ways depending on the type and quality of the sample, the importance of the case and the cost and performance of the available analysis methods. Theoretically well-founded guidelines for the choice of analysis method are, however, lacking in most situations. In this paper, it is shown how such guidelines can be created using Bayesian decision theory. The theory is applied to forensic DNA analysis, showing how the information from the initial qPCR analysis can be utilized. It is assumed the alternatives for analysis are using a standard short tandem repeat (STR) DNA analysis assay, using the standard assay and a complementary assay, or the analysis may be cancelled following quantification. The decision is based on information about the DNA amount and level of DNA degradation of the forensic sample, as well as case circumstances and the cost for analysis. Semi-continuous electropherogram models are used for simulation of DNA profiles and for computation of likelihood ratios. It is shown how tables and graphs, prepared beforehand, can be used to quickly find the optimal decision in forensic casework.

Acute Toxic Neuropathy Mimicking Guillain Barre Syndrome

PubMed Central

Jalal, Muhammed Jasim Abdul; Fernandez, Shirley Joan; Menon, Murali Krishna

2015-01-01

Case: A 30 year old male presented with numbness of palms and soles followed by weakness of upper limbs and lower limbs of 5 days duration, which was ascending and progressive. Three months back he was treated for oral and genital ulcers with oral steroids. His ulcers improved and shifted to indigenous medication. His clinical examination showed polyneuropathy. CSF study did not show albuminocytological dissociation. Nerve conduction study showed demyelinating polyneuropathy. His blood samples and the ayurvedic drug samples were sent for toxicological analysis. Inference: Acute toxic neuropathy - Arsenic PMID:25811007

Characterization of porous nickel-titanium alloys for medical applications

NASA Astrophysics Data System (ADS)

Hernandez Tenorio, Rommy

The purpose of this study is to investigate the electrochemical behaviour of porous NiTi alloys provided by different sources. In order to achieve this goal, a systematic characterization of the physical and chemical properties by different techniques and new approaches were conducted. The martensite-austenite phase transition was determined by the use of the Differential scanning Calorimetry (DSC). The morphological characteristics (porosity and roughness) were measured with the Scanning Electron Microscopy (SEM). The surface chemical composition of the samples was identified by the use of X-ray Photoelectron Spectroscopy (XPS) and Auger Electron Spectroscopy (AES). In the case of porous material the biomechanical compatibility is closely related to the porosity distribution of the sample. To describe appropriately the influence of this parameter on the properties of NiTi, four types of materials provided by different sources were analyzed. The samples were produced by Self-propagating High-temperature Synthesis (SHS) procedure. A heat treatment was applied in order to release internal stress created during forming processes, one series of specimens from each type was submitted to an annealing process during 30 min at 550°C in an air atmosphere. Its influence on the properties of the materials was also evaluated. Our first results showed that despite the fact that all the materials present different pore size, all the samples exhibited an open and interconnected porosity that promotes a good fixation and bone ingrowth within their structure. The thermal analysis showed that the temperature of the inception of the martensite-austenite phase transition occurs at 60°C, which is greater than the body temperature by 20°C. The microscopic analysis for the samples revealed that the heat treatment did not generate any morphological changes. The XPS study indicated that the surface oxidation occurs after the heat treatment. This oxide layer has a different thickness for the materials in the range of 310--3990 A. The evaluation of the corrosion resistance of the four porous NiTi alloys showed a correlation between the chemical composition, pore size and the electrochemical behaviour. In particular it was found that the corrosion resistance is related to the surface chemical composition of the electrodes rather than to their surface morphology. First we observed that the impact of the annealing process varies with the type of sample. The non-treated samples showed higher breakdown potentials and also bigger pores. The materials with a pore size in the range of 80-120mum showed different behaviours, one material (B) showed no visible effect while the other two (A and C) exhibited a decrease of the breakdown potential value. The material with the smallest pore size 35-50mum showed an important improvement after the heat treatment. Therefore, we can conclude, that the surface treatment used in our investigations led to an improvement of the corrosion resistance for small pores whereas a decrease was observed for bigger pores. On the other hand the lower corrosion rates observed on treated samples are an indication of the high corrosion resistance compare to those non-treated. In this case we observed that the one material (B) exhibited the highest corrosion rate presented a difference in the chemical composition as shown by XPS analysis. Moreover, the absence of intermediate titanium oxides (Ti2+ and Ti3+) was observed. As these oxides were identified in the other materials (A, C and D) we conclude that the presence of intermediate titanium oxides on surface chemical composition of the samples results on better corrosion rates and improved corrosion resistance. The Spectroelectrochemistry evaluation showed that solid electropolished sample and solid mechanopolished samples exhibited a better corrosion resistance than porous mechanopolished samples. However the solid mechanopolished sample exhibits a higher corrosion rate almost as high as the one showed by the porous sample. On the other hand a higher breakdown potential was measured porous samples compared to previous studies. However this sample shows a higher susceptibility for pitting and crevice corrosion. This can be explained by the porous structure of the sample. The FTIR results showed the interactions between the solution and the samples. It can be observed that each sample exhibit a particular behaviour. The porous sample as well as the solid samples showed Ti-OH interactions. Moreover both solid samples exhibited another peak corresponding to the OTi(OH)CCH interaction, which is explained by the chemical composition of the electrolyte, in this case the Hank's solution that has a certain amount of glucose. However an inversion of the peak is observed in both samples, this direction change can be attributed to the surface treatment. The electropolished sample showed a more stable behaviour mean while the mechanopolished sample exhibited a change during the reverse scan. (Abstract shortened by UMI.)

Characterization of methane hydrate host sediments using synchrotron-computed microtomography (CMT)

USGS Publications Warehouse

Jones, K.W.; Feng, H.; Tomov, S.; Winters, W.J.; Prodanovic, M.; Mahajan, D.

2007-01-01

The hydrate-sediment interaction is an important aspect of gas hydrate studies that needs further examination. We describe here the applicability of the computed microtomography (CMT) technique that utilizes an intense X-ray synchrotron source to characterize sediment samples, two at various depths from the Blake Ridge area (a well-known hydrate-prone region) and one from Georges Bank, that once contained methane trapped as hydrates. Detailed results of the tomographic analysis performed on the deepest sample (667??m) from Blake Ridge are presented as 2-D and 3-D images which show several mineral constituents, the internal grain/pore microstructure, and, following segmentation into pore and grain space, a visualization of the connecting pathways through the pore-space of the sediment. Various parameters obtained from the analysis of the CMT data are presented for all three sediment samples. The micro-scale porosity values showed decreasing trend with increasing depth for all three samples that is consistent with the previously reported bulk porosity data. The 3-D morphology, pore-space pathways, porosity, and permeability values are also reported for all three samples. The application of CMT is now being expanded to the laboratory-formed samples of hydrate in sediments as well as field samples of methane hydrate bearing sediments.

Movement of Trace Elements During Residence in the Antarctic Ice: a Laboratory Simulation

NASA Technical Reports Server (NTRS)

Strait, Melissa M.

1991-01-01

Recent work has determined that differences in the trace element distribution between Antarctic eucrites and non-Antarctic eucrites may be due to weathering during residence in the ice, and samples that demonstrate trace element disturbances do not necessarily correspond to eucrites that appear badly weathered to the naked eye. This study constitutes a preliminary test of the idea that long-term residence in the ice is the cause of the trace element disturbances observed in the eucrites. Samples of a non-Antarctic eucrite were leached in water at room temperature conditions. Liquid samples were analyzed for rare earth element abundances using ion chromatography. The results for the short-term study showed little or no evidence that leaching had occurred. However, there were tantalizing hints that something may be happening. The residual solid samples are currently being analyzed for the unleached trace metals using instrumental neutron activation analysis and should show evidence of disturbance if the chromatography clues were real. In addition, another set of samples continues to be intermittently sampled for later analysis. The results should give us information about the movement of trace elements under our conditions and allow us to make some tentative extrapolations to what we observe in actual Antarctic eucrite samples.

ASTM clustering for improving coal analysis by near-infrared spectroscopy.

PubMed

Andrés, J M; Bona, M T

2006-11-15

Multivariate analysis techniques have been applied to near-infrared (NIR) spectra coals to investigate the relationship between nine coal properties (moisture (%), ash (%), volatile matter (%), fixed carbon (%), heating value (kcal/kg), carbon (%), hydrogen (%), nitrogen (%) and sulphur (%)) and the corresponding predictor variables. In this work, a whole set of coal samples was grouped into six more homogeneous clusters following the ASTM reference method for classification prior to the application of calibration methods to each coal set. The results obtained showed a considerable improvement of the error determination compared with the calibration for the whole sample set. For some groups, the established calibrations approached the quality required by the ASTM/ISO norms for laboratory analysis. To predict property values for a new coal sample it is necessary the assignation of that sample to its respective group. Thus, the discrimination and classification ability of coal samples by Diffuse Reflectance Infrared Fourier Transform Spectroscopy (DRIFTS) in the NIR range was also studied by applying Soft Independent Modelling of Class Analogy (SIMCA) and Linear Discriminant Analysis (LDA) techniques. Modelling of the groups by SIMCA led to overlapping models that cannot discriminate for unique classification. On the other hand, the application of Linear Discriminant Analysis improved the classification of the samples but not enough to be satisfactory for every group considered.

Sampling design for groundwater solute transport: Tests of methods and analysis of Cape Cod tracer test data

USGS Publications Warehouse

Knopman, Debra S.; Voss, Clifford I.; Garabedian, Stephen P.

1991-01-01

Tests of a one-dimensional sampling design methodology on measurements of bromide concentration collected during the natural gradient tracer test conducted by the U.S. Geological Survey on Cape Cod, Massachusetts, demonstrate its efficacy for field studies of solute transport in groundwater and the utility of one-dimensional analysis. The methodology was applied to design of sparse two-dimensional networks of fully screened wells typical of those often used in engineering practice. In one-dimensional analysis, designs consist of the downstream distances to rows of wells oriented perpendicular to the groundwater flow direction and the timing of sampling to be carried out on each row. The power of a sampling design is measured by its effectiveness in simultaneously meeting objectives of model discrimination, parameter estimation, and cost minimization. One-dimensional models of solute transport, differing in processes affecting the solute and assumptions about the structure of the flow field, were considered for description of tracer cloud migration. When fitting each model using nonlinear regression, additive and multiplicative error forms were allowed for the residuals which consist of both random and model errors. The one-dimensional single-layer model of a nonreactive solute with multiplicative error was judged to be the best of those tested. Results show the efficacy of the methodology in designing sparse but powerful sampling networks. Designs that sample five rows of wells at five or fewer times in any given row performed as well for model discrimination as the full set of samples taken up to eight times in a given row from as many as 89 rows. Also, designs for parameter estimation judged to be good by the methodology were as effective in reducing the variance of parameter estimates as arbitrary designs with many more samples. Results further showed that estimates of velocity and longitudinal dispersivity in one-dimensional models based on data from only five rows of fully screened wells each sampled five or fewer times were practically equivalent to values determined from moments analysis of the complete three-dimensional set of 29,285 samples taken during 16 sampling times.

Hydrogen concentration analysis in clinopyroxene using proton-proton scattering analysis

NASA Astrophysics Data System (ADS)

Weis, Franz A.; Ros, Linus; Reichart, Patrick; Skogby, Henrik; Kristiansson, Per; Dollinger, Günther

2018-02-01

Traditional methods to measure water in nominally anhydrous minerals (NAMs) are, for example, Fourier transformed infrared (FTIR) spectroscopy or secondary ion mass spectrometry (SIMS). Both well-established methods provide a low detection limit as well as high spatial resolution yet may require elaborate sample orientation or destructive sample preparation. Here we analyze the water content in erupted volcanic clinopyroxene phenocrysts by proton-proton scattering and reproduce water contents measured by FTIR spectroscopy. We show that this technique provides significant advantages over other methods as it can provide a three-dimensional distribution of hydrogen within a crystal, making the identification of potential inclusions possible as well as elimination of surface contamination. The sample analysis is also independent of crystal structure and orientation and independent of matrix effects other than sample density. The results are used to validate the accuracy of wavenumber-dependent vs. mineral-specific molar absorption coefficients in FTIR spectroscopy. In addition, we present a new method for the sample preparation of very thin crystals suitable for proton-proton scattering analysis using relatively low accelerator potentials.

Modeling of human operator dynamics in simple manual control utilizing time series analysis. [tracking (position)

NASA Technical Reports Server (NTRS)

Agarwal, G. C.; Osafo-Charles, F.; Oneill, W. D.; Gottlieb, G. L.

1982-01-01

Time series analysis is applied to model human operator dynamics in pursuit and compensatory tracking modes. The normalized residual criterion is used as a one-step analytical tool to encompass the processes of identification, estimation, and diagnostic checking. A parameter constraining technique is introduced to develop more reliable models of human operator dynamics. The human operator is adequately modeled by a second order dynamic system both in pursuit and compensatory tracking modes. In comparing the data sampling rates, 100 msec between samples is adequate and is shown to provide better results than 200 msec sampling. The residual power spectrum and eigenvalue analysis show that the human operator is not a generator of periodic characteristics.

Application of relativistic electrons for the quantitative analysis of trace elements

NASA Astrophysics Data System (ADS)

Hoffmann, D. H. H.; Brendel, C.; Genz, H.; Löw, W.; Richter, A.

1984-04-01

Particle induced X-ray emission methods (PIXE) have been extended to relativistic electrons to induce X-ray emission (REIXE) for quantitative trace-element analysis. The electron beam (20 ≤ E0≤ 70 MeV) was supplied by the Darmstadt electron linear accelerator DALINAC. Systematic measurements of absolute K-, L- and M-shell ionization cross sections revealed a scaling behaviour of inner-shell ionization cross sections from which X-ray production cross sections can be deduced for any element of interest for a quantitative sample investigation. Using a multielemental mineral monazite sample from Malaysia the sensitivity of REIXE is compared to well established methods of trace-element analysis like proton- and X-ray-induced X-ray fluorescence analysis. The achievable detection limit for very heavy elements amounts to about 100 ppm for the REIXE method. As an example of an application the investigation of a sample prepared from manganese nodules — picked up from the Pacific deep sea — is discussed, which showed the expected high mineral content of Fe, Ni, Cu and Ti, although the search for aliquots of Pt did not show any measurable content within an upper limit of 250 ppm.

Composite Sampling Approaches for Bacillus anthracis Surrogate Extracted from Soil

PubMed Central

France, Brian; Bell, William; Chang, Emily; Scholten, Trudy

2015-01-01

Any release of anthrax spores in the U.S. would require action to decontaminate the site and restore its use and operations as rapidly as possible. The remediation activity would require environmental sampling, both initially to determine the extent of contamination (hazard mapping) and post-decon to determine that the site is free of contamination (clearance sampling). Whether the spore contamination is within a building or outdoors, collecting and analyzing what could be thousands of samples can become the factor that limits the pace of restoring operations. To address this sampling and analysis bottleneck and decrease the time needed to recover from an anthrax contamination event, this study investigates the use of composite sampling. Pooling or compositing of samples is an established technique to reduce the number of analyses required, and its use for anthrax spore sampling has recently been investigated. However, use of composite sampling in an anthrax spore remediation event will require well-documented and accepted methods. In particular, previous composite sampling studies have focused on sampling from hard surfaces; data on soil sampling are required to extend the procedure to outdoor use. Further, we must consider whether combining liquid samples, thus increasing the volume, lowers the sensitivity of detection and produces false negatives. In this study, methods to composite bacterial spore samples from soil are demonstrated. B. subtilis spore suspensions were used as a surrogate for anthrax spores. Two soils (Arizona Test Dust and sterilized potting soil) were contaminated and spore recovery with composites was shown to match individual sample performance. Results show that dilution can be overcome by concentrating bacterial spores using standard filtration methods. This study shows that composite sampling can be a viable method of pooling samples to reduce the number of analysis that must be performed during anthrax spore remediation. PMID:26714315

Method for improving accuracy in full evaporation headspace analysis.

PubMed

Xie, Wei-Qi; Chai, Xin-Sheng

2017-05-01

We report a new headspace analytical method in which multiple headspace extraction is incorporated with the full evaporation technique. The pressure uncertainty caused by the solid content change in the samples has a great impact to the measurement accuracy in the conventional full evaporation headspace analysis. The results (using ethanol solution as the model sample) showed that the present technique is effective to minimize such a problem. The proposed full evaporation multiple headspace extraction analysis technique is also automated and practical, and which could greatly broaden the applications of the full-evaporation-based headspace analysis. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

On wiping the interior walls of 37-mm closed-face cassettes: an OSHA perspective.

PubMed

Hendricks, Warren; Stones, Fern; Lillquist, Dean

2009-12-01

As early as 1976, Occupational Safety and Health Administration (OSHA) methods for analyzing metal samples collected using 37-mm polystyrene closed-face cassettes specified that any loose dust be transferred from the cassette to the digestion vessel, that the cassette be rinsed, and that, if necessary, the cassette be wiped out to help ensure that all particles that enter the cassette are included along with the filter as part of the sample for analysis. OSHA analytical methods for metal analysis were recently revised to explicitly require cassette wiping for all metal samples. This change was based on policy that any material entering the collection device constitutes part of the sample and on OSHA Salt Lake Technical Center research showing that invisible residue on the cassette walls can significantly contribute to the total sample results reported. OSHA procedures are consistent with guidance given in the NIOSH Manual of Analytical Methods. This guidance concludes that internal deposits in sampling cassettes should be included in the analysis and that one way to accomplish this would be to wipe or wash the internal surfaces of the cassette and include the material along with the filter for analysis.

Bio-analytical applications of mid-infrared spectroscopy using silver halide fiber-optic probes1

NASA Astrophysics Data System (ADS)

Heise, H. M.; Küpper, L.; Butvina, L. N.

2002-10-01

Infrared-spectroscopy has proved to be a powerful method for the study of various biomedical samples, in particular for in-vitro analysis in the clinical laboratory and for non-invasive diagnostics. In general, the analysis of biofluids such as whole blood, urine, microdialysates and bioreactor broth media takes advantage of the fact that a multitude of analytes can be quantified simultaneously and rapidly without the need for reagents. Progress in the quality of infrared silver halide fibers enabled us to construct several flexible fiber-optic probes of different geometries, which are particularly suitable for the measurement of small biosamples. Recent trends show that dry film measurements by mid-infrared spectroscopy could revolutionize analytical tools in the clinical chemistry laboratory, and an example is given. Infrared diagnostic tools show a promising potential for patients, and minimal-invasive blood glucose assays or skin tissue pathology in particular cannot be left out using mid-infrared fiber-based probes. Other applications include the measurement of skin samples including penetration studies of vitamins and constituents of cosmetic cream formulations. A further field is the micro-domain analysis of biopsy samples from bog mummified corpses, and recent results on the chemistry of dermis and hair samples are reported. Another field of application, for which results are reported, is food analysis and bio-reactor monitoring.

Quantitative analysis of benzodiazepines in vitreous humor by high-performance liquid chromatography

PubMed Central

Bazmi, Elham; Behnoush, Behnam; Akhgari, Maryam; Bahmanabadi, Leila

2016-01-01

Objective: Benzodiazepines are frequently screened drugs in emergency toxicology, drugs of abuse testing, and in forensic cases. As the variations of benzodiazepines concentrations in biological samples during bleeding, postmortem changes, and redistribution could be biasing forensic medicine examinations, hence selecting a suitable sample and a validated accurate method is essential for the quantitative analysis of these main drug categories. The aim of this study was to develop a valid method for the determination of four benzodiazepines (flurazepam, lorazepam, alprazolam, and diazepam) in vitreous humor using liquid–liquid extraction and high-performance liquid chromatography. Methods: Sample preparation was carried out using liquid–liquid extraction with n-hexane: ethyl acetate and subsequent detection by high-performance liquid chromatography method coupled to diode array detector. This method was applied to quantify benzodiazepines in 21 authentic vitreous humor samples. Linear curve for each drug was obtained within the range of 30–3000 ng/mL with coefficient of correlation higher than 0.99. Results: The limit of detection and quantitation were 30 and 100 ng/mL respectively for four drugs. The method showed an appropriate intra- and inter-day precision (coefficient of variation < 10%). Benzodiazepines recoveries were estimated to be over 80%. The method showed high selectivity; no additional peak due to interfering substances in samples was observed. Conclusion: The present method was selective, sensitive, accurate, and precise for the quantitative analysis of benzodiazepines in vitreous humor samples in forensic toxicology laboratory. PMID:27635251

Development of methodology for identification the nature of the polyphenolic extracts by FTIR associated with multivariate analysis

NASA Astrophysics Data System (ADS)

Grasel, Fábio dos Santos; Ferrão, Marco Flôres; Wolf, Carlos Rodolfo

2016-01-01

Tannins are polyphenolic compounds of complex structures formed by secondary metabolism in several plants. These polyphenolic compounds have different applications, such as drugs, anti-corrosion agents, flocculants, and tanning agents. This study analyses six different type of polyphenolic extracts by Fourier transform infrared spectroscopy (FTIR) combined with multivariate analysis. Through both principal component analysis (PCA) and hierarchical cluster analysis (HCA), we observed well-defined separation between condensed (quebracho and black wattle) and hydrolysable (valonea, chestnut, myrobalan, and tara) tannins. For hydrolysable tannins, it was also possible to observe the formation of two different subgroups between samples of chestnut and valonea and between samples of tara and myrobalan. Among all samples analysed, the chestnut and valonea showed the greatest similarity, indicating that these extracts contain equivalent chemical compositions and structure and, therefore, similar properties.

Rapid fingerprinting and classification of extra virgin olive oil by microjet sampling and extractive electrospray ionization mass spectrometry.

PubMed

Law, Wai Siang; Chen, Huan Wen; Balabin, Roman; Berchtold, Christian; Meier, Lukas; Zenobi, Renato

2010-04-01

Microjet sampling in combination with extractive electrospray ionization (EESI) mass spectrometry (MS) was applied to the rapid characterization and classification of extra virgin olive oil (EVOO) without any sample pretreatment. When modifying the composition of the primary ESI spray solvent, mass spectra of an identical EVOO sample showed differences. This demonstrates the capability of this technique to extract molecules with varying polarities, hence generating rich molecular information of the EVOO. Moreover, with the aid of microjet sampling, compounds of different volatilities (e.g.E-2-hexenal, trans-trans-2,4-heptadienal, tyrosol and caffeic acid) could be sampled simultaneously. EVOO data was also compared with that of other edible oils. Principal Component Analysis (PCA) was performed to discriminate EVOO and EVOO adulterated with edible oils. Microjet sampling EESI-MS was found to be a simple, rapid (less than 2 min analysis time per sample) and powerful method to obtain MS fingerprints of EVOO without requiring any complicated sample pretreatment steps.

Distribution of the two-sample t-test statistic following blinded sample size re-estimation.

PubMed

Lu, Kaifeng

2016-05-01

We consider the blinded sample size re-estimation based on the simple one-sample variance estimator at an interim analysis. We characterize the exact distribution of the standard two-sample t-test statistic at the final analysis. We describe a simulation algorithm for the evaluation of the probability of rejecting the null hypothesis at given treatment effect. We compare the blinded sample size re-estimation method with two unblinded methods with respect to the empirical type I error, the empirical power, and the empirical distribution of the standard deviation estimator and final sample size. We characterize the type I error inflation across the range of standardized non-inferiority margin for non-inferiority trials, and derive the adjusted significance level to ensure type I error control for given sample size of the internal pilot study. We show that the adjusted significance level increases as the sample size of the internal pilot study increases. Copyright © 2016 John Wiley & Sons, Ltd. Copyright © 2016 John Wiley & Sons, Ltd.

A Genealogical Interpretation of Principal Components Analysis

PubMed Central

McVean, Gil

2009-01-01

Principal components analysis, PCA, is a statistical method commonly used in population genetics to identify structure in the distribution of genetic variation across geographical location and ethnic background. However, while the method is often used to inform about historical demographic processes, little is known about the relationship between fundamental demographic parameters and the projection of samples onto the primary axes. Here I show that for SNP data the projection of samples onto the principal components can be obtained directly from considering the average coalescent times between pairs of haploid genomes. The result provides a framework for interpreting PCA projections in terms of underlying processes, including migration, geographical isolation, and admixture. I also demonstrate a link between PCA and Wright's fst and show that SNP ascertainment has a largely simple and predictable effect on the projection of samples. Using examples from human genetics, I discuss the application of these results to empirical data and the implications for inference. PMID:19834557

Synthesis and characterization of nanocrystalline Co-Fe-Nb-Ta-B alloy

NASA Astrophysics Data System (ADS)

Raanaei, Hossein; Fakhraee, Morteza

2017-09-01

In this research work, structural and magnetic evolution of Co57Fe13Nb8Ta4B18 alloy, during mechanical alloying process, have been investigated by using, X-ray diffraction, scanning electron microscopy, transmission electron microscopy, electron dispersive X-ray spectroscopy, differential thermal analysis and also vibrating sample magnetometer. It is observed that at 120 milling time, the crystallite size reaches to about 7.8 nm. Structural analyses show that, the solid solution of the initial powder mixture occurs at160 h milling time. The coercivity behavior demonstrates a rise, up to 70 h followed by decreasing tendency up to final stage of milling process. Thermal analysis of 160 h milling time sample reveals two endothermic peaks. The characterization of annealed milled sample for 160 h milling time at 427 °C shows crystallite size growth accompanied by increasing in saturation magnetization.

Classification of 'Chemlali' accessions according to the geographical area using chemometric methods of phenolic profiles analysed by HPLC-ESI-TOF-MS.

PubMed

Taamalli, Amani; Arráez Román, David; Zarrouk, Mokhtar; Segura-Carretero, Antonio; Fernández-Gutiérrez, Alberto

2012-05-01

The present work describes a classification method of Tunisian 'Chemlali' olive oils based on their phenolic composition and geographical area. For this purpose, the data obtained by HPLC-ESI-TOF-MS from 13 samples of extra virgin olive oils, obtained from different production area throughout the country, were used for this study focusing in 23 phenolics compounds detected. The quantitative results showed a significant variability among the analysed oil samples. Factor analysis method using principal component was applied to the data in order to reduce the number of factors which explain the variability of the selected compounds. The data matrix constructed was subjected to a canonical discriminant analysis (CDA) in order to classify the oil samples. These results showed that 100% of cross-validated original group cases were correctly classified, which proves the usefulness of the selected variables. Copyright © 2011 Elsevier Ltd. All rights reserved.

Interpretation FTIR spectrum of seawater and sediment in the Ambon Bay (TAD)

NASA Astrophysics Data System (ADS)

Patty, Diana Julaidy; Loupatty, Grace; Sopalauw, Fitria

2017-01-01

Research has done to interpretated FTIR spectrum of seawaters and sediment of the Ambon Bay (TAD). Analysis of samples of sediment and seawater using FTIR spectroscopy. The results showed the sand sediment samples identified Stretch bond OH group (3600-3500 cm-1), N-H Stretch (3400-3300 cm-1), C≡N (2250 cm-1), and NH bending (1640 to 1550 cm-1). And for seawater samples identified bonding group that is N-H Stretch (3400-3350 cm-1), N-H bending (1640 to 1550 cm-1) and C=O (1670-1640 cm-1). The existence of functional groups, carbonyl (C=O), alcohol (OH), carboxyl (COOH) can cause the complexation of metal cations. And the results showed analysis group N-O bond-containing compounds Nitro indicate heavy metal content of Lead (Pb) and group N-H bond-containing compound Amina indicate heavy metal content of Cadmium (Cd).

Simultaneous saccharification and fermentation and economic evaluation of ultrasonic and jet cooking pretreatment of corn slurry.

PubMed

Montalbo-Lomboy, Melissa; Khanal, Samir Kumar; van Leeuwen, Johannes Hans; Raman, David Raj; Grewell, David

2011-01-01

The potential of ultrasonics to replace hydrocooking in corn-to-ethanol plants was examined in this study. Batch and continuous experiments were conducted on corn slurry with sonication at a frequency of 20 kHz. Batch mode used a catenoidal horn operated at an amplitude of 144 μm peak-to-peak (p–p) for 90 s. Continuous experiments used a donut horn operating at inner radius amplitude of 12 μm p–p. Jet-cooked samples from the same ethanol plant were compared with ultrasonicated samples. The highest starch-to-ethanol conversion was obtained by the jet-cooked samples with a yield of 74% of the theoretical yield. Batch and continuous sonication achieved 71.2% and 68% conversion, respectively, however, statistical analysis showed no significant difference between the jet cooking and ultrasonication. On the basis of the similar performance, an economic analysis was conducted comparing jet cooking and ultrasonic pretreatment. The analysis showed that the capital cost for the ultrasonics system was ~10 times higher compared to the capital cost of a hydrocooker. However,due to the large energy requirements of hydrocookers, the analysis showed lower total overall costs for continuous ultrasonication than that for jet cooking, assuming the current energy prices. Because of the high utility cost calculated for jet cooking, it is concluded that ultrasonication poses as a more economical option than jet cooking. Overall, the study shows that ultrasonics is a technically and economically viable alternative to jet cooking in dry-grind corn ethanol plant. © 2011 American Institute of Chemical Engineers

Epidemiological survey of swine influenza A virus in the wild boar population of two Italian provinces.

PubMed

Foni, Emanuela; Garbarino, Chiara; Chiapponi, Chiara; Baioni, Laura; Zanni, Irene; Cordioli, Paolo

2013-12-01

An epidemiological survey was carried out in order to obtain a better understanding of the role of wild boars in the epidemiology of the influenza virus. The samples were submitted to Real-Time PCR testing for gene M of the swine influenza virus (SIV), and virus isolation was performed from the positive PCR samples. Genome sequence analysis was performed on the isolates. Additionally, 1,977 boar sera samples were analyzed using ELISA and hemoagglutination inhibition. Over recent years, the wild boar population has greatly increased in Italy, including in areas of high-density industrial pig farming, where the influenza virus is widespread. From July to December 2012, wild boar lung samples were collected in the Parma and Piacenza area, in the Emilia Romagna region. 354 wild boar lung samples were collected. Wild-boar influenza A virus infection should be studied more broadly in order to obtain a better understanding of the epidemiological role played by this species. Three SIV strains were isolated out of 12 samples that resulted positive using PCR analysis and they were identified as avian-like SIV subtype H1N1. Phylogenetic analysis of the sequences obtained from isolate A/wild boar/291320/2012 showed that it clustered with recent Italian avian-like H1N1 SIVs isolated from domestic pigs. Sixty-eight sera samples showed a positive titer to the isolate A/wild boar/291320/2012. This study suggests that SIV actively circulates in the wild boar population in the investigated. area. © 2013 Blackwell Publishing Ltd.

Study of the Effect of Temporal Sampling Frequency on DSCOVR Observations Using the GEOS-5 Nature Run Results. Part II; Cloud Coverage

NASA Technical Reports Server (NTRS)

Holdaway, Daniel; Yang, Yuekui

2016-01-01

This is the second part of a study on how temporal sampling frequency affects satellite retrievals in support of the Deep Space Climate Observatory (DSCOVR) mission. Continuing from Part 1, which looked at Earth's radiation budget, this paper presents the effect of sampling frequency on DSCOVR-derived cloud fraction. The output from NASA's Goddard Earth Observing System version 5 (GEOS-5) Nature Run is used as the "truth". The effect of temporal resolution on potential DSCOVR observations is assessed by subsampling the full Nature Run data. A set of metrics, including uncertainty and absolute error in the subsampled time series, correlation between the original and the subsamples, and Fourier analysis have been used for this study. Results show that, for a given sampling frequency, the uncertainties in the annual mean cloud fraction of the sunlit half of the Earth are larger over land than over ocean. Analysis of correlation coefficients between the subsamples and the original time series demonstrates that even though sampling at certain longer time intervals may not increase the uncertainty in the mean, the subsampled time series is further and further away from the "truth" as the sampling interval becomes larger and larger. Fourier analysis shows that the simulated DSCOVR cloud fraction has underlying periodical features at certain time intervals, such as 8, 12, and 24 h. If the data is subsampled at these frequencies, the uncertainties in the mean cloud fraction are higher. These results provide helpful insights for the DSCOVR temporal sampling strategy.

The association between content of the elements S, Cl, K, Fe, Cu, Zn and Br in normal and cirrhotic liver tissue from Danes and Greenlandic Inuit examined by dual hierarchical clustering analysis.

PubMed

Laursen, Jens; Milman, Nils; Pind, Niels; Pedersen, Henrik; Mulvad, Gert

2014-01-01

Meta-analysis of previous studies evaluating associations between content of elements sulphur (S), chlorine (Cl), potassium (K), iron (Fe), copper (Cu), zinc (Zn) and bromine (Br) in normal and cirrhotic autopsy liver tissue samples. Normal liver samples from 45 Greenlandic Inuit, median age 60 years and from 71 Danes, median age 61 years. Cirrhotic liver samples from 27 Danes, median age 71 years. Element content was measured using X-ray fluorescence spectrometry. Dual hierarchical clustering analysis, creating a dual dendrogram, one clustering element contents according to calculated similarities, one clustering elements according to correlation coefficients between the element contents, both using Euclidian distance and Ward Procedure. One dendrogram separated subjects in 7 clusters showing no differences in ethnicity, gender or age. The analysis discriminated between elements in normal and cirrhotic livers. The other dendrogram clustered elements in four clusters: sulphur and chlorine; copper and bromine; potassium and zinc; iron. There were significant correlations between the elements in normal liver samples: S was associated with Cl, K, Br and Zn; Cl with S and Br; K with S, Br and Zn; Cu with Br. Zn with S and K. Br with S, Cl, K and Cu. Fe did not show significant associations with any other element. In contrast to simple statistical methods, which analyses content of elements separately one by one, dual hierarchical clustering analysis incorporates all elements at the same time and can be used to examine the linkage and interplay between multiple elements in tissue samples. Copyright © 2013 Elsevier GmbH. All rights reserved.

The Use and Effectiveness of Triple Multiplex System for Coding Region Single Nucleotide Polymorphism in Mitochondrial DNA Typing of Archaeologically Obtained Human Skeletons from Premodern Joseon Tombs of Korea

PubMed Central

Oh, Chang Seok; Lee, Soong Deok; Kim, Yi-Suk; Shin, Dong Hoon

2015-01-01

Previous study showed that East Asian mtDNA haplogroups, especially those of Koreans, could be successfully assigned by the coupled use of analyses on coding region SNP markers and control region mutation motifs. In this study, we tried to see if the same triple multiplex analysis for coding regions SNPs could be also applicable to ancient samples from East Asia as the complementation for sequence analysis of mtDNA control region. By the study on Joseon skeleton samples, we know that mtDNA haplogroup determined by coding region SNP markers successfully falls within the same haplogroup that sequence analysis on control region can assign. Considering that ancient samples in previous studies make no small number of errors in control region mtDNA sequencing, coding region SNP analysis can be used as good complimentary to the conventional haplogroup determination, especially of archaeological human bone samples buried underground over long periods. PMID:26345190

Molecularly imprinted membrane extraction combined with high-performance liquid chromatography for selective analysis of cloxacillin from shrimp samples.

PubMed

Du, Wei; Sun, Min; Guo, Pengqi; Chang, Chun; Fu, Qiang

2018-09-01

Nowadays, the abuse of antibiotics in aquaculture has generated considerable problems for food safety. Therefore, it is imperative to develop a simple and selective method for monitoring illegal use of antibiotics in aquatic products. In this study, a method combined molecularly imprinted membranes (MIMs) extraction and liquid chromatography was developed for the selective analysis of cloxacillin from shrimp samples. The MIMs was synthesized by UV photopolymerization, and characterized by scanning electron microscope, Fourier transform infrared spectra, thermo-gravimetric analysis and swelling test. The results showed that the MIMs exhibited excellent permselectivity, high adsorption capacity and fast adsorption rate for cloxacillin. Finally, the method was utilized to determine cloxacillin from shrimp samples, with good accuracies and acceptable relative standard deviation values for precision. The proposed method was a promising alternative for selective analysis of cloxacillin in shrimp samples, due to the easy-operation and excellent selectivity. Copyright © 2018. Published by Elsevier Ltd.

Water-quality assessment of the Trinity River Basin, Texas - Review and analysis of available pesticide information, 1968-91

USGS Publications Warehouse

Ulery, R.L.; Brown, M.F.

1995-01-01

Review of all available data showed that pesticides were detected to a substantial degree in various sample media over the time period covered by this report. The authors were able to locate little pesticide-sample data for ground water or for tributary streams because sampling efforts historically have been concentrated on the mainstem Trinity River.

Analysis of cannabis in oral fluid specimens by GC-MS with automatic SPE.

PubMed

Choi, Hyeyoung; Baeck, Seungkyung; Kim, Eunmi; Lee, Sooyeun; Jang, Moonhee; Lee, Juseon; Choi, Hwakyung; Chung, Heesun

2009-12-01

Methamphetamine (MA) is the most commonly abused drug in Korea, followed by cannabis. Traditionally, MA analysis is carried out on both urine and hair samples and cannabis analysis in urine samples only. Despite the fact that oral fluid has become increasingly popular as an alternative specimen in the field of driving under the influence of drugs (DUID) and work place drug testing, its application has not been expanded to drug analysis in Korea. Oral fluid is easy to collect and handle and can provide an indication of recent drug abuse. In this study, we present an analytical method using GC-MS to determine tetrahydrocannabinol (THC) and its main metabolite 11-nor-delta9-tetrahydrocannabinol-9-carboxylic acid (THC-COOH) in oral fluid. The validated method was applied to oral fluid samples collected from drug abuse suspects and the results were compared with those in urine. The stability of THC and THC-COOH in oral fluid stored in different containers was also investigated. Oral fluid specimens from 12 drug abuse suspects, submitted by the police, were collected by direct expectoration. The samples were screened with microplate ELISA. For confirmation they were extracted using automated SPE with mixed-mode cation exchange cartridge, derivatized and analyzed by GC-MS using selective ion monitoring (SIM). The concentrations ofTHC and THC-COOH in oral fluid showed a large variation and the results from oral fluid and urine samples from cannabis abusers did not show any correlation. Thus, detailed information about time interval between drug use and sample collection is needed to interpret the oral fluid results properly. In addition, further investigation about the detection time window ofTHC and THC-COOH in oral fluid is required to substitute oral fluid for urine in drug testing.

Triple Gene Analysis Using Samples Obtained by Endobronchial Ultrasound-guided Transbronchial Needle Aspiration

PubMed Central

Lee, Kyungjong; Um, Sang-Won; Jeong, Byeong-Ho; Yang, Jung Wook; Choi, Yoon-La; Han, Joungho; Kim, Hojoong; Kwon, O Jung

2016-01-01

Objective A mutational analysis of tumor tissue samples is an important part of advanced lung cancer treatment strategies. This study evaluated the efficacy of a triple gene analysis using samples obtained via endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA). Methods Either metastatic lymph nodes or primary lung mass samples obtained by EBUS-TBNA were collected between May 2011 and May 2013. We consecutively analyzed epidermal growth factor receptor (EGFR), V-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog (KRAS), and anaplastic lymphoma kinase (ALK) fusion genes using remnant tissue samples. Results A total of 109 patients were diagnosed with non-small cell lung cancer (NSCLC). Of these, 70% were adenocarcinoma, 27% squamous cell carcinoma with NSCLC, and 3% were related to other types of lung cancer. EGFR mutations were detected in 23 cases (21.1%), KRAS mutations in 13 cases (11.9%), and ALK fusion genes in 5 cases (4.9%). The ALK fusion genes could not be analyzed in four cases because of insufficient tissue samples remaining after routine histochemistry and an EGFR/KRAS mutation analysis. We found that small biopsy samples from EBUS-TBNA were adequate for performing a triple gene analysis in 97 patients (96%). ALK fusion protein immunohistochemistry (IHC) was 100% consistent with fluorescence in situ hybridization (FISH). Conclusion Small samples obtained by EBUS-TBNA were found to be sufficient for performing a triple gene analysis following routine histology and IHC. ALK IHC showed a very good concordance with FISH for detecting ALK fusion genes. PMID:27803402

Identification of Novel Prostate Cancer-Causitive Gene Mutations by Representational Difference Analysis of Microdissected Prostate Cancer

DTIC Science & Technology

2001-03-01

paired samples of microdissected benign and malignant prostate epithelium. The resulting subtraction products were cloned and screened in Southern blots... benign and malignant human prostate cancer. Data is given to show that microdissected tissue samples retain RNA of sufficient quality to perform gene

Digital PCR for Quantifying Norovirus in Oysters Implicated in Outbreaks, France.

PubMed

Polo, David; Schaeffer, Julien; Fournet, Nelly; Le Saux, Jean-Claude; Parnaudeau, Sylvain; McLeod, Catherine; Le Guyader, Françoise S

2016-12-01

Using samples from oysters clearly implicated in human disease, we quantified norovirus levels by using digital PCR. Concentrations varied from 43 to 1,170 RNA copies/oyster. The analysis of frozen samples from the production area showed the presence of norovirus 2 weeks before consumption.

An Experimental Study of Launch Vehicle Propellant Tank Fragmentation

NASA Technical Reports Server (NTRS)

Richardson, Erin; Jackson, Austin; Hays, Michael; Bangham, Mike; Blackwood, James; Skinner, Troy; Richman, Ben

2014-01-01

In order to better understand launch vehicle abort environments, Bangham Engineering Inc. (BEi) built a test assembly that fails sample materials (steel and aluminum plates of various alloys and thicknesses) under quasi-realistic vehicle failure conditions. Samples are exposed to pressures similar to those expected in vehicle failure scenarios and filmed at high speed to increase understanding of complex fracture mechanics. After failure, the fragments of each test sample are collected, catalogued and reconstructed for further study. Post-test analysis shows that aluminum samples consistently produce fewer fragments than steel samples of similar thickness and at similar failure pressures. Video analysis shows that there are several failure 'patterns' that can be observed for all test samples based on configuration. Fragment velocities are also measured from high speed video data. Sample thickness and material are analyzed for trends in failure pressure. Testing is also done with cryogenic and noncryogenic liquid loading on the samples. It is determined that liquid loading and cryogenic temperatures can decrease material fragmentation for sub-flight thicknesses. A method is developed for capture and collection of fragments that is greater than 97 percent effective in recovering sample mass, addressing the generation of tiny fragments. Currently, samples tested do not match actual launch vehicle propellant tank material thicknesses because of size constraints on test assembly, but test findings are used to inform the design and build of another, larger test assembly with the purpose of testing actual vehicle flight materials that include structural components such as iso-grid and friction stir welds.

Intragraft Molecular Pathways Associated with Tolerance Induction in Renal Transplantation.

PubMed

Gallon, Lorenzo; Mathew, James M; Bontha, Sai Vineela; Dumur, Catherine I; Dalal, Pranav; Nadimpalli, Lakshmi; Maluf, Daniel G; Shetty, Aneesha A; Ildstad, Suzanne T; Leventhal, Joseph R; Mas, Valeria R

2018-02-01

The modern immunosuppression regimen has greatly improved short-term allograft outcomes but not long-term allograft survival. Complications associated with immunosuppression, specifically nephrotoxicity and infection risk, significantly affect graft and patient survival. Inducing and understanding pathways underlying clinical tolerance after transplantation are, therefore, necessary. We previously showed full donor chimerism and immunosuppression withdrawal in highly mismatched allograft recipients using a bioengineered stem cell product (FCRx). Here, we evaluated the gene expression and microRNA expression profiles in renal biopsy samples from tolerance-induced FCRx recipients, paired donor organs before implant, and subjects under standard immunosuppression (SIS) without rejection and with acute rejection. Unlike allograft samples showing acute rejection, samples from FCRx recipients did not show upregulation of T cell- and B cell-mediated rejection pathways. Gene expression pathways differed slightly between FCRx samples and the paired preimplantation donor organ samples, but most of the functional gene networks overlapped. Notably, compared with SIS samples, FCRx samples showed upregulation of genes involved in pathways, like B cell receptor signaling. Additionally, prediction analysis showed inhibition of proinflammatory regulators and activation of anti-inflammatory pathways in FCRx samples. Furthermore, integrative analyses (microRNA and gene expression profiling from the same biopsy sample) identified the induction of regulators with demonstrated roles in the downregulation of inflammatory pathways and maintenance of tissue homeostasis in tolerance-induced FCRx samples compared with SIS samples. This pilot study highlights the utility of molecular intragraft evaluation of pathways related to FCRx-induced tolerance and the use of integrative analyses for identifying upstream regulators of the affected downstream molecular pathways. Copyright © 2018 by the American Society of Nephrology.

Denaturing gradient gel electrophoresis profiles of bacteria from the saliva of twenty four different individuals form clusters that showed no relationship to the yeasts present.

PubMed

M Weerasekera, Manjula; H Sissons, Chris; Wong, Lisa; A Anderson, Sally; R Holmes, Ann; D Cannon, Richard

2017-10-01

The aim was to investigate the relationship between groups of bacteria identified by cluster analysis of the DGGE fingerprints and the amounts and diversity of yeast present. Bacterial and yeast populations in saliva samples from 24 adults were analysed using denaturing gradient gel electrophoresis (DGGE) of the bacteria present and by yeast culture. Eubacterial DGGE banding patterns showed considerable variation between individuals. Seventy one different amplicon bands were detected, the band number per saliva sample ranged from 21 to 39 (mean±SD=29.3±4.9). Cluster and principal component analysis of the bacterial DGGE patterns yielded three major clusters containing 20 of the samples. Seventeen of the 24 (71%) saliva samples were yeast positive with concentrations up to 10 3 cfu/mL. Candida albicans was the predominant species in saliva samples although six other yeast species, including Candida dubliniensis, Candida tropicalis, Candida krusei, Candida guilliermondii, Candida rugosa and Saccharomyces cerevisiae, were identified. The presence, concentration, and species of yeast in samples showed no clear relationship to the bacterial clusters. Despite indications of in vitro bacteria-yeast interactions, there was a lack of association between the presence, identity and diversity of yeasts and the bacterial DGGE fingerprint clusters in saliva. This suggests significant ecological individual-specificity of these associations in highly complex in vivo oral biofilm systems under normal oral conditions. Copyright © 2017 Elsevier Ltd. All rights reserved.

Combined Bisulfite Restriction Analysis for brain tissue identification.

PubMed

Samsuwan, Jarunya; Muangsub, Tachapol; Yanatatsaneejit, Pattamawadee; Mutirangura, Apiwat; Kitkumthorn, Nakarin

2018-05-01

According to the tissue-specific methylation database (doi: 10.1016/j.gene.2014.09.060), methylation at CpG locus cg03096975 in EML2 has been preliminarily proven to be specific to brain tissue. In this study, we enlarged sample size and developed a technique for identifying brain tissue in aged samples. Combined Bisulfite Restriction Analysis-for EML2 (COBRA-EML2) technique was established and validated in various organ samples obtained from 108 autopsies. In addition, this technique was also tested for its reliability, minimal DNA concentration detected, and use in aged samples and in samples obtained from specific brain compartments and spinal cord. COBRA-EML2 displayed 100% sensitivity and specificity for distinguishing brain tissue from other tissues, showed high reliability, was capable of detecting minimal DNA concentration (0.015ng/μl), could be used for identifying brain tissue in aged samples. In summary, COBRA-EML2 is a technique to identify brain tissue. This analysis is useful in criminal cases since it can identify the vital organ tissues from small samples acquired from criminal scenes. The results from this analysis can be counted as a medical and forensic marker supporting criminal investigations, and as one of the evidences in court rulings. Copyright © 2018 Elsevier B.V. All rights reserved.

Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens.

PubMed

Wood, Henry M; Belvedere, Ornella; Conway, Caroline; Daly, Catherine; Chalkley, Rebecca; Bickerdike, Melissa; McKinley, Claire; Egan, Phil; Ross, Lisa; Hayward, Bruce; Morgan, Joanne; Davidson, Leslie; MacLennan, Ken; Ong, Thian K; Papagiannopoulos, Kostas; Cook, Ian; Adams, David J; Taylor, Graham R; Rabbitts, Pamela

2010-08-01

The use of next-generation sequencing technologies to produce genomic copy number data has recently been described. Most approaches, however, reply on optimal starting DNA, and are therefore unsuitable for the analysis of formalin-fixed paraffin-embedded (FFPE) samples, which largely precludes the analysis of many tumour series. We have sought to challenge the limits of this technique with regards to quality and quantity of starting material and the depth of sequencing required. We confirm that the technique can be used to interrogate DNA from cell lines, fresh frozen material and FFPE samples to assess copy number variation. We show that as little as 5 ng of DNA is needed to generate a copy number karyogram, and follow this up with data from a series of FFPE biopsies and surgical samples. We have used various levels of sample multiplexing to demonstrate the adjustable resolution of the methodology, depending on the number of samples and available resources. We also demonstrate reproducibility by use of replicate samples and comparison with microarray-based comparative genomic hybridization (aCGH) and digital PCR. This technique can be valuable in both the analysis of routine diagnostic samples and in examining large repositories of fixed archival material.

Gunshot residue (GSR) analysis by single particle inductively coupled plasma mass spectrometry (spICP-MS).

PubMed

Heringer, Rodrigo D; Ranville, James F

2018-05-25

Single particle inductively coupled plasma mass spectrometry (spICP-MS) was investigated as a screening-level technique for the analysis and characterization of inorganic gunshot residue (IGSR) nanoparticles. spICP-MS works with undigested samples whereby nanoparticles (NPs) in a suspension are individually atomized and ionized as they reach the plasma, each resulting in a pulse of analyte ions that can be quantified. The method is rapid, and signals from hundreds of NPs can be collected in 1-2min per sample. The technique is quantitative for NP mass and number concentration when only one element (single element mode) is measured using a quadrupole MS. Likewise, a qualitative elemental fingerprint can be obtained for individual NPs when peak-hopping between two elements (dual element mode). For this proof of concept study, each shooter's hand was sampled with ultrapure water or swab to obtain NPs suspensions. Measurements of antimony, barium, and lead were performed using both analysis modes. With no sample preparation and fully automated sample introduction, it is possible to analyze more than 100 samples in a day. Results show that this technique opens a new perspective for future research on GSR sample identification and characterization and can complement SEM/EDX analysis. Copyright © 2018 Elsevier B.V. All rights reserved.

Efficacy of adrenal venous sampling is increased by point of care cortisol analysis

PubMed Central

Viste, Kristin; Grytaas, Marianne A; Jørstad, Melissa D; Jøssang, Dag E; Høyden, Eivind N; Fotland, Solveig S; Jensen, Dag K; Løvås, Kristian; Thordarson, Hrafnkell; Almås, Bjørg; Mellgren, Gunnar

2013-01-01

Primary aldosteronism (PA) is a common cause of secondary hypertension and is caused by unilateral or bilateral adrenal disease. Treatment options depend on whether the disease is lateralized or not, which is preferably evaluated with selective adrenal venous sampling (AVS). This procedure is technically challenging, and obtaining representative samples from the adrenal veins can prove difficult. Unsuccessful AVS procedures often require reexamination. Analysis of cortisol during the procedure may enhance the success rate. We invited 21 consecutive patients to participate in a study with intra-procedural point of care cortisol analysis. When this assay showed nonrepresentative sampling, new samples were drawn after redirection of the catheter. The study patients were compared using the 21 previous procedures. The intra-procedural cortisol assay increased the success rate from 10/21 patients in the historical cohort to 17/21 patients in the study group. In four of the 17 successful procedures, repeated samples needed to be drawn. Successful sampling at first attempt improved from the first seven to the last seven study patients. Point of care cortisol analysis during AVS improves success rate and reduces the need for reexaminations, in accordance with previous studies. Successful AVS is crucial when deciding which patients with PA will benefit from surgical treatment. PMID:24169597

An analysis of the impact of pre-analytical factors on the urine proteome: Sample processing time, temperature, and proteolysis.

PubMed

Hepburn, Sophie; Cairns, David A; Jackson, David; Craven, Rachel A; Riley, Beverley; Hutchinson, Michelle; Wood, Steven; Smith, Matthew Welberry; Thompson, Douglas; Banks, Rosamonde E

2015-06-01

We have examined the impact of sample processing time delay, temperature, and the addition of protease inhibitors (PIs) on the urinary proteome and peptidome, an important aspect of biomarker studies. Ten urine samples from patients with varying pathologies were each divided and PIs added to one-half, with aliquots of each then processed and frozen immediately, or after a delay of 6 h at 4°C or room temperature (20-22°C), effectively yielding 60 samples in total. Samples were then analyzed by 2D-PAGE, SELDI-TOF-MS, and immunoassay. Interindividual variability in profiles was the dominant feature in all analyses. Minimal changes were observed by 2D-PAGE as a result of delay in processing, temperature, or PIs and no changes were seen in IgG, albumin, β2 -microglobulin, or α1 -microglobulin measured by immunoassay. Analysis of peptides showed clustering of some samples by presence/absence of PIs but the extent was very patient-dependent with most samples showing minimal effects. The extent of processing-induced changes and the benefit of PI addition are patient- and sample-dependent. A consistent processing methodology is essential within a study to avoid any confounding of the results. © 2014 The Authors PROTEOMICS Clinical Applications Published by Wiley-VCH Verlag GmbH & Co. KGaA.

Sample normalization methods in quantitative metabolomics.

PubMed

Wu, Yiman; Li, Liang

2016-01-22

To reveal metabolomic changes caused by a biological event in quantitative metabolomics, it is critical to use an analytical tool that can perform accurate and precise quantification to examine the true concentration differences of individual metabolites found in different samples. A number of steps are involved in metabolomic analysis including pre-analytical work (e.g., sample collection and storage), analytical work (e.g., sample analysis) and data analysis (e.g., feature extraction and quantification). Each one of them can influence the quantitative results significantly and thus should be performed with great care. Among them, the total sample amount or concentration of metabolites can be significantly different from one sample to another. Thus, it is critical to reduce or eliminate the effect of total sample amount variation on quantification of individual metabolites. In this review, we describe the importance of sample normalization in the analytical workflow with a focus on mass spectrometry (MS)-based platforms, discuss a number of methods recently reported in the literature and comment on their applicability in real world metabolomics applications. Sample normalization has been sometimes ignored in metabolomics, partially due to the lack of a convenient means of performing sample normalization. We show that several methods are now available and sample normalization should be performed in quantitative metabolomics where the analyzed samples have significant variations in total sample amounts. Copyright © 2015 Elsevier B.V. All rights reserved.

Buccal swabbing as a noninvasive method to determine bacterial, archaeal, and eukaryotic microbial community structures in the rumen.

PubMed

Kittelmann, Sandra; Kirk, Michelle R; Jonker, Arjan; McCulloch, Alan; Janssen, Peter H

2015-11-01

Analysis of rumen microbial community structure based on small-subunit rRNA marker genes in metagenomic DNA samples provides important insights into the dominant taxa present in the rumen and allows assessment of community differences between individuals or in response to treatments applied to ruminants. However, natural animal-to-animal variation in rumen microbial community composition can limit the power of a study considerably, especially when only subtle differences are expected between treatment groups. Thus, trials with large numbers of animals may be necessary to overcome this variation. Because ruminants pass large amounts of rumen material to their oral cavities when they chew their cud, oral samples may contain good representations of the rumen microbiota and be useful in lieu of rumen samples to study rumen microbial communities. We compared bacterial, archaeal, and eukaryotic community structures in DNAs extracted from buccal swabs to those in DNAs from samples collected directly from the rumen by use of a stomach tube for sheep on four different diets. After bioinformatic depletion of potential oral taxa from libraries of samples collected via buccal swabs, bacterial communities showed significant clustering by diet (R = 0.37; analysis of similarity [ANOSIM]) rather than by sampling method (R = 0.07). Archaeal, ciliate protozoal, and anaerobic fungal communities also showed significant clustering by diet rather than by sampling method, even without adjustment for potentially orally associated microorganisms. These findings indicate that buccal swabs may in future allow quick and noninvasive sampling for analysis of rumen microbial communities in large numbers of ruminants. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Assessment of the impact of landfill on groundwater quality: a case study of the Pirana site in western India.

PubMed

Singh, Umesh Kumar; Kumar, Manish; Chauhan, Rita; Jha, Pawan Kumar; Ramanathan, Al; Subramanian, V

2008-06-01

In present study focus has been given on estimating quality and toxicity of waste with respect to heavy metals and its impact on groundwater quality, using statistical and empirical relationships between different hydrochemical data, so that easy monitoring may be possible which in turn help the sustainable management of landfill site and municipal solid waste. Samples of solid waste, leachate and groundwater were analyzed to evaluate the impact of leachates on groundwater through the comparison of their hydrochemical nature. Results suggest the existence of an empirical relationship between some specific indicator parameters like heavy metals of all three above mentioned sample type. Further, K/Mg ratio also indicates three groundwater samples heavily impacted from leachate contamination. A good number of samples are also showing higher values for NO(3)(-) and Pb than that of World Health Organization (WHO) drinking water regulation. Predominance of Fe and Zn in both groundwater and solid waste samples may be due to metal plating industries in the area. Factor analysis is used as a tool to explain observed relation between numerous variables in term of simpler relation, which may help to deduce the strength of relation. Positive loading of most of the factors for heavy metal clearly shows landfill impact on ground water quality especially along the hydraulic gradient. Cluster analysis, further substantiates the impact of landfill. Two major groups of samples obtained from cluster analysis suggest that one group comprises samples that are severely under the influence of landfill and contaminated leachates along the groundwater flow direction while other assorted with samples without having such influence.

Galaxies driven only by secular evolution?

NASA Astrophysics Data System (ADS)

Verdes-Montenegro, Lourdes

2015-03-01

The AMIGA project (Analysis of the interstellar Medium of Isolated GAlaxies, http://amiga.iaa.es) has identified a significant sample of very isolated (T cc (nearest-neighbor) ~2-3Gyr) galaxies in the local Universe and revealed that they have different properties than galaxies in richer environments. Our analysis of a multiwavelength database includes quantification of degree of isolation, morphologies, as well as FIR and radio line/continuum properties. Properties usually regarded as susceptible to interaction enhancement show lower averages in AMIGA-lower than any galaxy sample yet identified. We find lower MIR/FIR measures (Lisenfeld et al. 2007), low levels of radio continuum emission (Leon et al. 2008), no radioexcess above the radioFIR correlation (0%, Sabater et al.2008), a small number of AGN (22%, Sabater et al. 2012), and lower molecular gas content (Lisenfeld et al. 2011). The late-type spiral majority in our sample show very small bulge/total ratios (largely <0.1) and Sersic indices consistent with an absence of classical bulges (Durbala et al. 2008). They show redder g-r colors and lower color dispersion for AMIGA subtypes (Fernandez-Lorenzo et al. 2012) and show the narrowest (gaussian) distribution of HI profile asymmetries of any sample yet studied. This work has been supported by Grant AYA2011-30491-C02-01 co-financed by MICINN and FEDER funds, and the Junta de Andalucia (Spain) grants P08-FQM-4205 and TIC-114.

The application of a novel optical SPM in biomedicine

NASA Astrophysics Data System (ADS)

Li, Yinli; Chen, Haibo; Wu, Shifa; Song, Linfeng; Zhang, Jian

2005-01-01

As an analysis tool, SPM has been broadly used in biomedicine in recent years, such as AFM and SNOM; they are effective instruments in detecting life nanostructures at atomic level. Atomic force and photon scanning tunneling microscope (AF/PSTM) is one of member of SPM, it can be used to obtain sample" optical and atomic fore images at once scanning, these images include the transmissivity image, reflection index image and topography image. This report mainly introduces the application of AF/PSTM in red blood membrane and the effect of different sample dealt with processes on the experiment result. The materials for preparing red cells membrane samples are anticoagulant blood, isotonic phosphatic buffer solution (PBS) and new two times distilled water. The images of AF/PSTM give real expression to the biology samples" fact despite of different sample dealt with processes, which prove that AF/PSTM suits to biology sample imaging. At the same time, the optical images and the topography image of AF/PSTM of the same sample are complementary with each other; this will make AF/PSTM a facile tool to analysis biologic samples" nanostructure. As another sample, this paper gives the application of AF/PSTM in immunoassay, the result shows that AF/PSTM is suit to analysis biologic sample, and it will become a new tool for biomedicine test.

Genetic analysis of the VP2-encoding gene of canine parvovirus strains from Africa.

PubMed

Dogonyaro, Banenat B; Bosman, Anna-Mari; Sibeko, Kgomotso P; Venter, Estelle H; van Vuuren, Moritz

2013-08-30

Since the emergence of canine parvovirus type-2 (CPV-2) in the early 1970s, it has been evolving into novel genetic and antigenic variants (CPV-2a, 2b and 2c) that are unevenly distributed throughout the world. Genetic characterization of CPV-2 has not been documented in Africa since 1998 apart from the study carried out in Tunisia 2009. A total of 139 field samples were collected from South Africa and Nigeria, detected using PCR and the full length VP2-encoding gene of 27 positive samples were sequenced and genetically analyzed. Nigerian samples (n=6), South Africa (n=19) and vaccine strains (n=2) were compared with existing sequences obtained from GenBank. The results showed the presence of both CPV-2a and 2b in South Africa and only CPV-2a in Nigeria. No CPV-2c strain was detected during this study. Phylogenetic analysis showed a clustering not strictly associated with the geographical origin of the analyzed strains, although most of the South African strains tended to cluster together and the viral strains analyzed in this study were not completely distinct from CPV-2 strains from other parts of the world. Amino acid analysis showed predicted amino acid changes. Copyright © 2013 Elsevier B.V. All rights reserved.

Thermal Analysis of Brazing Seal and Sterilizing Technique to Break Contamination Chain for Mars Sample Return

NASA Technical Reports Server (NTRS)

Bao, Xiaoqi; Badescu, Mircea; Bar-Cohen, Yoseph

2015-01-01

The potential to return Martian samples to Earth for extensive analysis is in great interest of the planetary science community. It is important to make sure the mission would securely contain any microbes that may possibly exist on Mars so that they would not be able to cause any adverse effects on Earth's environment. A brazing sealing and sterilizing technique has been proposed to break the Mars-to-Earth contamination chain. Thermal analysis of the brazing process was conducted for several conceptual designs that apply the technique. Control of the increase of the temperature of the Martian samples is a challenge. The temperature profiles of the Martian samples being sealed in the container were predicted by finite element thermal models. The results show that the sealing and sterilization process can be controlled such that the samples' temperature is maintained below the potentially required level, and that the brazing technique is a feasible approach to break the contamination chain.

Quantitative analysis of fungicide azoxystrobin in agricultural samples with rapid, simple and reliable monoclonal immunoassay.

PubMed

Watanabe, Eiki; Miyake, Shiro

2013-01-15

This work presents analytical performance of a kit-based direct competitive enzyme-linked immunosorbent assay (dc-ELISA) for azoxystrobin detection in agricultural products. The dc-ELISA was sufficiently sensitive for analysis of residue levels close to the maximum residue limits. The dc-ELISA did not show cross-reactivity to other strobilurin analogues. Absorbance decreased with the increase of methanol concentration in sample solution from 2% to 40%, while the standard curve became most linear when the sample solution contained 10% methanol. Agricultural samples were extracted with methanol, and the extracts were diluted with water to 10% methanol adequate. No significant matrix interference was observed. Satisfying recovery was found for all of spiked samples and the results were well agreed with the analysis with liquid chromatography. These results clearly indicate that the kit-based dc-ELISA is suitable for the rapid, simple, quantitative and reliable determination of the fungicide. Copyright © 2012 Elsevier Ltd. All rights reserved.

Evaluation of trace elements in lung samples from coal miners using neutron activation analysis.

PubMed

Saiki, M; Saldiva, P H; Alice, S H

1999-01-01

In this study, instrumental neutron activation analysis was applied to the determination of Sc, La, Ce, Nd, Sm, Eu, Tb, Yb, Lu, Hf, Th, and U in lung samples from miners working in coal mines located in the state of Santa Catarina, Brazil. These results were compared to those from a control group constituted of healthy individuals. The results showed that the elements determined exhibit considerable intersubject variability within a single group of individuals and the mean values of concentrations in miners' lungs were higher than those of normal individuals. Lung samples presented U concentrations varying from 11 to 890 micrograms/kg. Therefore, for some samples, the contribution of the uranium fission products in the analysis of La, Ce, Nd, and Sm was considered by determining the interference correction factors. The accuracy of the results was evaluated by analyzing certified reference materials.

Automation of preparation of nonmetallic samples for analysis by atomic absorption and inductively coupled plasma spectrometry

NASA Technical Reports Server (NTRS)

Wittmann, A.; Willay, G.

1986-01-01

For a rapid preparation of solutions intended for analysis by inductively coupled plasma emission spectrometry or atomic absorption spectrometry, an automatic device called Plasmasol was developed. This apparatus used the property of nonwettability of glassy C to fuse the sample in an appropriate flux. The sample-flux mixture is placed in a composite crucible, then heated at high temperature, swirled until full dissolution is achieved, and then poured into a water-filled beaker. After acid addition, dissolution of the melt, and filling to the mark, the solution is ready for analysis. The analytical results obtained, either for oxide samples or for prereduced iron ores show that the solutions prepared with this device are undistinguished from those obtained by manual dissolutions done by acid digestion or by high temperature fusion. Preparation reproducibility and analytical tests illustrate the performance of Plasmasol.

Analysis of pollen load based on color, physicochemical composition and botanical source.

PubMed

Modro, Anna F H; Silva, Izabel C; Luz, Cynthia F P; Message, Dejair

2009-06-01

Pollen load samples from 10 hives of Apis mellifera (L.) were analyzed based on their physicochemical composition and botanical source, considering color as a parameter for quality control. In seven samples it was possible to establish the occurrence of more than 80% of a single pollen type, characterizing them as unifloral but with protein content variation. One of the samples was exclusively composed of saprophytic fungi (Cladosporium sp.). Comparing the mean results of the fungi loads with those of the nutritional components of pollen load, the former presented higher protein, mineral matter and dry matter and lower organic matter, ethereal extract and total carbohydrate values. The monochromatic samples met the physicochemical specifications regulating pollen load quality. The results showed that homogeneous coloration of the pollen load was not found to be a good indication of unifloral pollen, confirming the importance of physicochemical analysis and melissopalynological analysis for characterization of the quality of commercial pollen load.

Analyzing the Scientific Evolution of Social Work Using Science Mapping

ERIC Educational Resources Information Center

Martínez, Ma Angeles; Cobo, Manuel Jesús; Herrera, Manuel; Herrera-Viedma, Enrique

2015-01-01

Objectives: This article reports the first science mapping analysis of the social work field, which shows its conceptual structure and scientific evolution. Methods: Science Mapping Analysis Software Tool, a bibliometric science mapping tool based on co-word analysis and h-index, is applied using a sample of 18,794 research articles published from…

Whole genome amplification and real-time PCR in forensic casework

PubMed Central

Giardina, Emiliano; Pietrangeli, Ilenia; Martone, Claudia; Zampatti, Stefania; Marsala, Patrizio; Gabriele, Luciano; Ricci, Omero; Solla, Gianluca; Asili, Paola; Arcudi, Giovanni; Spinella, Aldo; Novelli, Giuseppe

2009-01-01

Background WGA (Whole Genome Amplification) in forensic genetics can eliminate the technical limitations arising from low amounts of genomic DNA (gDNA). However, it has not been used to date because any amplification bias generated may complicate the interpretation of results. Our aim in this paper was to assess the applicability of MDA to forensic SNP genotyping by performing a comparative analysis of genomic and amplified DNA samples. A 26-SNPs TaqMan panel specifically designed for low copy number (LCN) and/or severely degraded genomic DNA was typed on 100 genomic as well as amplified DNA samples. Results Aliquots containing 1, 0.1 and 0.01 ng each of 100 DNA samples were typed for a 26-SNPs panel. Similar aliquots of the same DNA samples underwent multiple displacement amplification (MDA) before being typed for the same panel. Genomic DNA samples showed 0% PCR failure rate for all three dilutions, whilst the PCR failure rate of the amplified DNA samples was 0% for the 1 ng and 0.1 ng dilutions and 0.077% for the 0.01 ng dilution. The genotyping results of both the amplified and genomic DNA samples were also compared with reference genotypes of the same samples obtained by direct sequencing. The genomic DNA samples showed genotype concordance rates of 100% for all three dilutions while the concordance rates of the amplified DNA samples were 100% for the 1 ng and 0.1 ng dilutions and 99.923% for the 0.01 ng dilution. Moreover, ten artificially-degraded DNA samples, which gave no results when analyzed by current forensic methods, were also amplified by MDA and genotyped with 100% concordance. Conclusion We investigated the suitability of MDA material for forensic SNP typing. Comparative analysis of amplified and genomic DNA samples showed that a large number of SNPs could be accurately typed starting from just 0.01 ng of template. We found that the MDA genotyping call and accuracy rates were only slightly lower than those for genomic DNA. Indeed, when 10 pg of input DNA was used in MDA, we obtained 99.923% concordance, indicating a genotyping error rate of 1/1299 (7.7 × 10-4). This is quite similar to the genotyping error rate of STRs used in current forensic analysis. Such efficiency and accuracy of SNP typing of amplified DNA suggest that MDA can also generate large amounts of genome-equivalent DNA from a minimal amount of input DNA. These results show for the first time that MDA material is suitable for SNP-based forensic protocols and in general when samples fail to give interpretable STR results. PMID:19366436

Use of multiplex polymerase chain reaction-based assay to conduct epidemiological studies on bovine hemoparasites in Mexico.

PubMed

Figueroa, J V; Alvarez, J A; Ramos, J A; Vega, C A; Buening, G M

1993-01-01

A study was conducted to test the applicability of a Polymerase Chain Reaction (PCR)-based approach for the simultaneous detection of the bovine hemoparasites Babesia bigemina, B. bovis and Anaplasma marginale. Bovine blood samples from cattle ranches of a previously determined enzootic zone in the Yucatan Peninsula of Mexico, were collected from peripheral blood and processed for PCR analysis. Blood samples were subjected to DNA amplification by placing an aliquot in a reaction tube containing oligonucleotide primers specific for DNA of each hemoparasite species. The PCR products were detected by Dot-Blot nucleic acid hybridization utilizing nonradioactive, species-specific, digoxigenin PCR-labeled DNA probes. Four hundred twenty one field samples analyzed by the multiplex PCR-DNA probe assay showed 66.7%, 60.1% and 59.6% prevalence rates for B. bigemina, B. bovis and A. marginale, respectively. The multiplex PCR analysis showed that animals with single, double or triple infection could be detected with the parasite specific DNA probes. The procedure is proposed as a valuable tool for the epidemiological analysis in regions where the hemoparasite species are concurrently infecting cattle.

[Research on Time-frequency Characteristics of Magneto-acoustic Signal of Different Thickness Medium Based on Wave Summing Method].

PubMed

Zhang, Shunqi; Yin, Tao; Ma, Ren; Liu, Zhipeng

2015-08-01

Functional imaging method of biological electrical characteristics based on magneto-acoustic effect gives valuable information of tissue in early tumor diagnosis, therein time and frequency characteristics analysis of magneto-acoustic signal is important in image reconstruction. This paper proposes wave summing method based on Green function solution for acoustic source of magneto-acoustic effect. Simulations and analysis under quasi 1D transmission condition are carried out to time and frequency characteristics of magneto-acoustic signal of models with different thickness. Simulation results of magneto-acoustic signal were verified through experiments. Results of the simulation with different thickness showed that time-frequency characteristics of magneto-acoustic signal reflected thickness of sample. Thin sample, which is less than one wavelength of pulse, and thick sample, which is larger than one wavelength, showed different summed waveform and frequency characteristics, due to difference of summing thickness. Experimental results verified theoretical analysis and simulation results. This research has laid a foundation for acoustic source and conductivity reconstruction to the medium with different thickness in magneto-acoustic imaging.

A more rational, theory-driven approach to analysing the factor structure of the Edinburgh Postnatal Depression Scale.

PubMed

Kozinszky, Zoltan; Töreki, Annamária; Hompoth, Emőke A; Dudas, Robert B; Németh, Gábor

2017-04-01

We endeavoured to analyze the factor structure of the Edinburgh Postnatal Depression Scale (EPDS) during a screening programme in Hungary, using exploratory (EFA) and confirmatory factor analysis (CFA), testing both previously published models and newly developed theory-driven ones, after a critical analysis of the literature. Between April 2011 and January 2015, a sample of 2967 pregnant women (between 12th and 30th weeks of gestation) and 714 women 6 weeks after delivery completed the Hungarian version of the EPDS in South-East Hungary. EFAs suggested unidimensionality in both samples. 33 out of 42 previously published models showed good and 6 acceptable fit with our antepartum data in CFAs, whilst 10 of them showed good and 28 acceptable fit in our postpartum sample. Using multiple fit indices, our theory-driven anhedonia (items 1,2) - anxiety (items 4,5) - low mood (items 8,9) model provided the best fit in the antepartum sample. In the postpartum sample, our theory-driven models were again among the best performing models, including an anhedonia and an anxiety factor together with either a low mood or a suicidal risk factor (items 3,6,10). The EPDS showed moderate within- and between-culture invariability, although this would also need to be re-examined with a theory-driven approach. Copyright © 2017 Elsevier Ireland Ltd. All rights reserved.

Quality of omeprazole purchased via the Internet and personally imported into Japan: comparison with products sampled in other Asian countries.

PubMed

Rahman, Mohammad Sofiqur; Yoshida, Naoko; Sugiura, Sakura; Tsuboi, Hirohito; Keila, Tep; Kiet, Heng Bun; Zin, Theingi; Tanimoto, Tsuyoshi; Kimura, Kazuko

2018-03-01

To evaluate the quality of omeprazole personally imported into Japan via the Internet and to compare the quality of these samples with previously collected samples from two other Asian countries. The samples were evaluated by observation, authenticity investigation and pharmacopoeial quality analysis. Quality comparison of some selected samples was carried out by dissolution profiling, Raman spectroscopy and principle component analysis (PCA). Observation of the Internet sites and samples revealed some discrepancies including the delivery of a wrong sample and the selling of omeprazole without a prescription, although it is a prescription medicine. Among the 28 samples analysed, all passed the identification test, 26 (93%) passed the quantity and content uniformity tests and all passed the dissolution test. Dissolution profiling confirmed that all the personally imported omeprazole samples remained intact in the acid medium. On the other hand, six samples from two of the same manufacturers, previously collected during surveys in Cambodia and Myanmar, frequently showed premature omeprazole release in acid. Raman spectroscopy and PCA showed significant variation between omeprazole formulations in personally imported samples and the samples from Cambodia and Myanmar. Our results indicate that the pharmaceutical quality of omeprazole purchased through the Internet was sufficient, as determined by pharmacopeial tests. However, omeprazole formulations distributed in different market segments by the same manufacturers were of diverse quality. Measures are needed to ensure consistent quality of products and to prevent entry of substandard products into the legitimate supply chain. © 2018 The Authors. Tropical Medicine & International Health Published by John Wiley & Sons Ltd.

Characterization of Estrogen and Androgen Activity of Food Contact Materials by Different In Vitro Bioassays (YES, YAS, ERα and AR CALUX) and Chromatographic Analysis (GC-MS, HPLC-MS)

PubMed Central

Osorio, Veronica; Grininger, Angelika; Richter, Alexander; Bergmair, Johannes; Pyerin, Michael; Washüttl, Michael; Tacker, Manfred

2014-01-01

Endocrine active substances (EAS) show structural similarities to natural hormones and are suspected to affect the human endocrine system by inducing hormone dependent effects. Recent studies with in vitro tests suggest that EAS can leach from packaging into food and may therefore pose a risk to human health. Sample migrates from food contact materials were tested for estrogen and androgen agonists and antagonists with different commonly used in vitro tests. Additionally, chemical trace analysis by GC-MS and HPLC-MS was used to identify potential hormone active substances in sample migrates. A GC-MS method to screen migrates for 29 known or potential endocrine active substances was established and validated. Samples were migrated according to EC 10/2011, concentrated by solid phase extraction and tested with estrogen and androgen responsive reporter gene assays based on yeast cells (YES and YAS) or human osteoblast cells (ERα and AR CALUX). A high level of agreement between the different bioassays could be observed by screening for estrogen agonists. Four out of 18 samples tested showed an estrogen activity in a similar range in both, YES and ERα CALUX. Two more samples tested positive in ERα CALUX due to the lower limits of detection in this assay. Androgen agonists could not be detected in any of the tested samples, neither with YAS nor with AR CALUX. When testing for antagonists, significant differences between yeast and human cell-based bioassays were noticed. Using YES and YAS many samples showed a strong antagonistic activity which was not observed using human cell-based CALUX assays. By GC-MS, some known or supposed EAS were identified in sample migrates that showed a biological activity in the in vitro tests. However, no firm conclusions about the sources of the observed hormone activity could be obtained from the chemical results. PMID:25000404

Identification, analysis, and remedial treatment of low guardrail in Virginia.

DOT National Transportation Integrated Search

1981-01-01

Guardrails that are too low may fail to safely redirect errant vehicles; instead, the vehicles may vault the guardrails, resulting in severe accidents. An analysis of data on a small sample of guardrails throughout-Virginia showed that over 80% of th...

Intraoral Laser Welding (ILW): ultrastructural and mechanical analysis

NASA Astrophysics Data System (ADS)

Fornaini, Carlo; Passaretti, Francesca; Villa, Elena; Nammour, Samir

2010-05-01

Nd:YAG, currently used since 1970 in dental laboratories to weld metals on dental prostheses has some limits such great dimensions, high costs and fixed delivery system. Recently it was proposed the possibility to use the Nd:YAG laser device commonly utilised in dental office, to repair broken fixed, removable and orthodontic prostheses and to weld metals directly into the mouth. The aim of this work is to value, through SEM (Scanning Electron Microscope), EDS (Energy Dispersive X-Ray Spectroscopy) and DMA (Dynamic Mechanical Analysis), quality and mechanical strength of the welding process comparing a device normally used in dental lab and a device normally used in dental office for oral surgery. Sixteen CoCrMo metal plates and twenty steel orthodontic wires were divided in four groups: one was welded without metal apposition by laboratory laser, one was welded with metal apposition by laboratory laser, one was welded without metal apposition by office laser and one was welded with metal apposition by office laser. The welding process was analysed by SEM, EDS and DMA to compare the differences between the different samples. By SEM analysis it was seen that the plates welded by office laser without apposition metal showed a greater number of fissurations compared with the other samples. By EDS analysis it was seen a homogeneous composition of the metals in all the samples. The mechanical tests showed a similar elastic behaviour of the samples, with minimal differences between the two devices. No wire broke even under the maximum strength by the Analyser. This study seems to demonstrate that the welding process by office Nd:YAG laser device and the welding process by laboratory Nd:YAG laser device, analysed by SEM, EDS and DMA, showed minimal and not significant differences even if these data will be confirmed by a greater number of samples.

Progressive Sampling Technique for Efficient and Robust Uncertainty and Sensitivity Analysis of Environmental Systems Models: Stability and Convergence

NASA Astrophysics Data System (ADS)

Sheikholeslami, R.; Hosseini, N.; Razavi, S.

2016-12-01

Modern earth and environmental models are usually characterized by a large parameter space and high computational cost. These two features prevent effective implementation of sampling-based analysis such as sensitivity and uncertainty analysis, which require running these computationally expensive models several times to adequately explore the parameter/problem space. Therefore, developing efficient sampling techniques that scale with the size of the problem, computational budget, and users' needs is essential. In this presentation, we propose an efficient sequential sampling strategy, called Progressive Latin Hypercube Sampling (PLHS), which provides an increasingly improved coverage of the parameter space, while satisfying pre-defined requirements. The original Latin hypercube sampling (LHS) approach generates the entire sample set in one stage; on the contrary, PLHS generates a series of smaller sub-sets (also called `slices') while: (1) each sub-set is Latin hypercube and achieves maximum stratification in any one dimensional projection; (2) the progressive addition of sub-sets remains Latin hypercube; and thus (3) the entire sample set is Latin hypercube. Therefore, it has the capability to preserve the intended sampling properties throughout the sampling procedure. PLHS is deemed advantageous over the existing methods, particularly because it nearly avoids over- or under-sampling. Through different case studies, we show that PHLS has multiple advantages over the one-stage sampling approaches, including improved convergence and stability of the analysis results with fewer model runs. In addition, PLHS can help to minimize the total simulation time by only running the simulations necessary to achieve the desired level of quality (e.g., accuracy, and convergence rate).

Uncertainty in monitoring E. coli concentrations in streams and stormwater runoff

NASA Astrophysics Data System (ADS)

Harmel, R. D.; Hathaway, J. M.; Wagner, K. L.; Wolfe, J. E.; Karthikeyan, R.; Francesconi, W.; McCarthy, D. T.

2016-03-01

Microbial contamination of surface waters, a substantial public health concern throughout the world, is typically identified by fecal indicator bacteria such as Escherichia coli. Thus, monitoring E. coli concentrations is critical to evaluate current conditions, determine restoration effectiveness, and inform model development and calibration. An often overlooked component of these monitoring and modeling activities is understanding the inherent random and systematic uncertainty present in measured data. In this research, a review and subsequent analysis was performed to identify, document, and analyze measurement uncertainty of E. coli data collected in stream flow and stormwater runoff as individual discrete samples or throughout a single runoff event. Data on the uncertainty contributed by sample collection, sample preservation/storage, and laboratory analysis in measured E. coli concentrations were compiled and analyzed, and differences in sampling method and data quality scenarios were compared. The analysis showed that: (1) manual integrated sampling produced the lowest random and systematic uncertainty in individual samples, but automated sampling typically produced the lowest uncertainty when sampling throughout runoff events; (2) sample collection procedures often contributed the highest amount of uncertainty, although laboratory analysis introduced substantial random uncertainty and preservation/storage introduced substantial systematic uncertainty under some scenarios; and (3) the uncertainty in measured E. coli concentrations was greater than that of sediment and nutrients, but the difference was not as great as may be assumed. This comprehensive analysis of uncertainty in E. coli concentrations measured in streamflow and runoff should provide valuable insight for designing E. coli monitoring projects, reducing uncertainty in quality assurance efforts, regulatory and policy decision making, and fate and transport modeling.

Nature and time course of acclimation to aluminum in juvenile brook trout (Salvelinus fontinalis): II. Gill histology

USGS Publications Warehouse

Mueller, M.E.; Sanchez, D.A.; Bergman, H.L.; McDonald, D.G.; Rhem, R.G.; Wood, C.M.

1991-01-01

Gill samples from juvenile brook trout (Salvelinus fontinalis) acclimated to low-level aluminum at pH 5.2 showed severe damage by day 4, with necrosis and fusion of secondary lamellae and hyperplasia and hypertrophy of mucous cells. Over the following 20 d, there was a continual process of repair with proliferation and hypertrophy of mucous cells. Qualitative analysis of gill samples plus physiology and mortality data collected in a companion study indicated progressive development (by day 10 onward) of increasing acclimation to Al. Quantitative analysis of gill samples on day 13 showed that mucous cell volume density had tripled and mucous cell area had doubled in Al-exposed fish compared with control fish. A lamellar fusion index showed evidence of fusion in Al-exposed fish by day 4 with recovery to nearly control levels by day 13. Physiological disturbances appear to be directly related to the histological changes observed in the gill epithelium. At the cellular level, changes in either mucous cell production and secretion or changes in mucus chemistry contribute, in part, to acclimation to Al.

First report of Perkinsus beihaiensis in Crassostrea madrasensis from the Indian subcontinent.

PubMed

Sanil, N K; Suja, G; Lijo, J; Vijayan, K K

2012-04-26

Protozoan parasites of the genus Perkinsus are considered important pathogens responsible for mass mortalities in many wild and farmed bivalve populations. The present study was initiated to screen populations of the Indian edible oyster Crassostrea madrasensis, a promising candidate for aquaculture along the Indian coasts, for the presence of Perkinsus spp. The study reports the presence of P. beihaiensis for the first time in C. madrasensis populations from the Indian subcontinent and south Asia. Samples collected from the east and west coasts of India were subjected to Ray's fluid thioglycollate medium (RFTM) culture and histology which indicated the presence of Perkinsus spp. PCR screening of the tissues using specific primers amplified the product specific to the genus Perkinsus. The taxonomic affinities of the parasites were determined by sequencing both internal transcribed spacer (ITS) and actin genes followed by basic local alignment search tool (BLAST) analysis. Analysis based on the ITS sequences showed 98 to 100% identity to Perkinsus spp. (P. beihaiensis and Brazilian Perkinsus sp.). The pairwise genetic distance values and phylogenetic analysis confirmed that 2 of the present samples belonged to the P. beihaiensis clade while the other 4 showed close affinities with the Brazilian Perkinsus sp. clade. The genetic divergence data, close affinity with the Brazilian Perkinsus sp., and co-existence with P. beihaiensis in the same host species in the same habitat show that the remaining 4 samples exhibit some degree of variation from P. beihaiensis. As expected, the sequencing of actin genes did not show any divergence among the samples studied. They probably could be intraspecific variants of P. beihaiensis having a separate lineage in the process of evolution.

Estimation of transit times in a Karst Aquifer system using environmental tracers: Application on the Jeita Aquifer system-Lebanon.

NASA Astrophysics Data System (ADS)

Doummar, Joanna; Hamdan, Ahmad

2016-04-01

Estimating transit times is essential for the assessment of aquifer vulnerability to contaminants. Groundwater in karst aquifer is assumed to be relatively young due to fast preferential pathways; slow flow components are present in water stored in the fissured matrix. Furthermore, transit times are site specific as they depend on recharge rates, temperatures, elevation, and flow media; saturated and unsaturated zones. These differences create significant variation in the groundwater age in karst systems as the water sampled will be a mix of different water that has been transported through different flow pathways (fissured matrix and conduits). Several methods can be applied to estimate water transit time of an aquifer such as artificial tracers, which provide an estimate for fast flow velocities. In this study, groundwater residence times in the Jeita spring aquifer (Lebanon) were estimated using several environmental tracers such as Chlorofluorocarbons (CFCs), Sulfur Hexafluoride (SF6), Helium-Tritium (3H, 3H- 3He). Additional stable isotope and major ion analysis was performed to characterize water types. Groundwater samples were collected from six different wells in the Jeita catchment area (Jurassic Kesrouane aquifer) as well as from the spring and cave itself. The results are reproducible for the Tritium-Helium method, unlike for the CFC/SF6 methods that yielded poor results due to sampling problems. Tritium concentrations in all groundwater samples show nearly the same concentration (~2.73 TU) except for one sample with relatively lower tritium concentration (~2.26 TU). Ages ranging from 0.07 ± 0.07 years to 23.59 ± 0.00 years were obtained. The youngest age is attributed to the spring/ cave while the oldest ages were obtained in wells tapping the fissured matrix. Neon in these samples showed considerable variations and high delta Ne in some samples indicating high excess air. Four (4) samples showed extreme excess air (Delta-Ne is greater than 70 %) and the remaining 3 samples have Delta-Ne in the expected range between (10-35%). Moreover Tritium-Helium analysis has showed some radiogenic Helium (4He) in one sample along with lower tritium concentrations signifying a mixture of new groundwater with old groundwater (older than 50 yrs). Furthermore, this study is complemented with published analysis of a series of 26 artificial tracer experiments performed in the Jeita karst system (Doummar, 2012). Transit times calculated from tracer experiments ranged between 3 and 300 hours (12 days). The shortest ones were recorded in the Jeita subsurface conduit. While injections in sinkholes yielded moderate transit times, fissured matrix and unsaturated zone resulted in relatively long ones. In Lebanon this type of spatial groundwater age dating using environmental tracers was not applied to date, to the exception of grab sample analysis. A second round of sampling for Tritium-Helium, CFCs and SF6 analysis will be undertaken under different flow periods in February 2016 to validate the obtained results. References Geyer, T. 2008: Process-based characterization of flow and transport in karst aquifers at catchment scale. Dissertation, Georg-August-Universität Göttingen, 103 S. Geyer, T., and Doummar, J. 2013. Protection of the Jeita Spring: Bestimmung der mittleren Verweilzeit des Grundwassers im Einzugsgebiet der Jeita Quelle-Libanon. Special report. Protection of the Jeita Spring. Applied Geosciences. Georg August University, Göttingen.

Graft polymerization of guar gum with acryl amide irradiated by microwaves for colonic drug delivery.

PubMed

Shahid, Muhammad; Bukhari, Shazia Anwer; Gul, Yousra; Munir, Hira; Anjum, Fozia; Zuber, Mohammad; Jamil, Tahir; Zia, Khalid Mahmood

2013-11-01

This article is aimed to discuss the modification of guar gum through microwave irradiation by varying the time of irradiation. The characterization of the modified products was carried out using FTIR spectroscopic analysis. The FT-IR spectrum of the pure guar gum (GG) sample showed a broad peak at 3298 cm(-1) while the modified GG sample displayed a peak at 1541 cm(-1) which was absent in the crude sample. The X-ray diffraction (XRD) analysis confirmed the increase in crystallinity due to grafting of the sample with polyacrylamide (GG-g-PAM). Scanning electron microscope (SEM) images revealed that granular form of guar gum was changed into fibrillar structure after grafting. Thermo-gravimetric analysis of the modified samples was also carried out and discussed. The role of guar gum as a matrix for controlled release of drug triamcinolone was evaluated. The GG-acrylamide grafted samples presented a correlation between drug release and time of microwave exposure. The results revealed that such modified product has potential applications in colonic drug delivery system. Copyright © 2013 Elsevier B.V. All rights reserved.

Integrated fluorescence analysis system

DOEpatents

Buican, Tudor N.; Yoshida, Thomas M.

1992-01-01

An integrated fluorescence analysis system enables a component part of a sample to be virtually sorted within a sample volume after a spectrum of the component part has been identified from a fluorescence spectrum of the entire sample in a flow cytometer. Birefringent optics enables the entire spectrum to be resolved into a set of numbers representing the intensity of spectral components of the spectrum. One or more spectral components are selected to program a scanning laser microscope, preferably a confocal microscope, whereby the spectrum from individual pixels or voxels in the sample can be compared. Individual pixels or voxels containing the selected spectral components are identified and an image may be formed to show the morphology of the sample with respect to only those components having the selected spectral components. There is no need for any physical sorting of the sample components to obtain the morphological information.

Capillary sample introduction of polymerase chain reaction (PCR) products separated in ultrathin slab gels.

PubMed

Bullard, K M; Hietpas, P B; Ewing, A G

1998-01-01

Polymerase chain reaction (PCR) amplified short tandem repeat (STR) samples from the HUMVWF locus have been analyzed using a unique sample introduction and separation technique. A single capillary is used to transfer samples onto an ultrathin slab gel (57 microm thin). This ultrathin nondenaturing polyacrylamide gel is used to separate the amplified fragments, and laser-induced fluorescence with ethidium bromide is used for detection. The feasibility of performing STR analysis using this system has been investigated by examining the reproducibility for repeated samples. Reproducibility is examined by comparing the migration of the 14 and 17 HUMVWF alleles on three consecutive separations on the ultrathin slab gel. Using one locus, separations match in migration time with the two alleles 42 s apart for each of the three consecutive separations. This technique shows potential to increase sample throughput in STR analysis techniques although separation resolution still needs to be improved.

PROBING THE DEEP END OF THE MILKY WAY WITH KEPLER : ASTEROSEISMIC ANALYSIS OF 854 FAINT RED GIANTS MISCLASSIFIED AS COOL DWARFS

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mathur, S.; García, R. A.; Beck, P. G.

Asteroseismology has proven to be an excellent tool to determine not only global stellar properties with good precision, but also to infer the stellar structure, dynamics, and evolution for a large sample of Kepler stars. Prior to the launch of the mission, the properties of Kepler targets were inferred from broadband photometry, leading to the Kepler Input Catalog (KIC). The KIC was later revised in the Kepler Star Properties Catalog, based on literature values and an asteroseismic analysis of stars that were unclassified in the KIC. Here, we present an asteroseismic analysis of 45,400 stars that were classified as dwarfsmore » in the Kepler Star Properties Catalog. We found that around 2% of the sample shows acoustic modes in the typical frequency range that put them in the red-giant category rather than the cool dwarf category. We analyze the asteroseismic properties of these stars, derive their surface gravities, masses, and radii, and present updated effective temperatures and distances. We show that the sample is significantly fainter than the previously known oscillating giants in the Kepler field, with the faintest stars reaching down to a Kepler magnitude of Kp ∼ 16. We demonstrate that 404 stars are at distances beyond 5 kpc and that the stars are significantly less massive than for the original Kepler red-giant sample, consistent with a population of distant halo giants. A comparison with a galactic population model shows that up to 40 stars might be genuine halo giants, which would increase the number of known asteroseismic halo stars by a factor of 4. The detections presented here will provide a valuable sample for galactic archeology studies.« less

Microspectroscopic Analysis Of HpD Fluorescence In Bioptic Samples From Human Pre-Malignant And Malignant Lesions Of The Skin

NASA Astrophysics Data System (ADS)

Bottiroli, G.; Dell'Acqua, R.; Jucci, A.; Ricevuti, G.; Sacchi, A. S.

1987-07-01

Microfluorometric analysis was performed on bioptic samples of pre-malignant and malignant cutanous lesions present in the same patients, 48 h after i.v. injection of HpD. Data obtained indicate that actinic keratosis and squamous celle carcinoma show a preferential accumulation if compared to normal skin. The two lesions differ for both intensity and spectral shape of HpD fluorescence. This difference is correlated with a different clinical response to HpD laser phototherapy.

Determination of Phenols and Trimethylamine in Industrial Effluents

NASA Technical Reports Server (NTRS)

Levaggi, D. A.; Feldstein, M.

1971-01-01

For regulatory purposes to control certain odorous compounds the analysis of phenols and trimethylamines in industrial effluents is necessary. The Bay Area Air Pollution Control District laboratory has been determining these gases by gas chromatographic techniques. The procedures for sample collection, preparation for analysis and determination are described in detail. Typical data from various sources showing the effect of proposed regulations is shown. Extensive sampling and usage of these procedures has shown them to be accurate, reliable and suitable to all types of source effluents.

Variance of discharge estimates sampled using acoustic Doppler current profilers from moving boats

USGS Publications Warehouse

Garcia, Carlos M.; Tarrab, Leticia; Oberg, Kevin; Szupiany, Ricardo; Cantero, Mariano I.

2012-01-01

This paper presents a model for quantifying the random errors (i.e., variance) of acoustic Doppler current profiler (ADCP) discharge measurements from moving boats for different sampling times. The model focuses on the random processes in the sampled flow field and has been developed using statistical methods currently available for uncertainty analysis of velocity time series. Analysis of field data collected using ADCP from moving boats from three natural rivers of varying sizes and flow conditions shows that, even though the estimate of the integral time scale of the actual turbulent flow field is larger than the sampling interval, the integral time scale of the sampled flow field is on the order of the sampling interval. Thus, an equation for computing the variance error in discharge measurements associated with different sampling times, assuming uncorrelated flow fields is appropriate. The approach is used to help define optimal sampling strategies by choosing the exposure time required for ADCPs to accurately measure flow discharge.

Coffee aroma: Chemometric comparison of the chemical information provided by three different samplings combined with GC-MS to describe the sensory properties in cup.

PubMed

Bressanello, Davide; Liberto, Erica; Cordero, Chiara; Rubiolo, Patrizia; Pellegrino, Gloria; Ruosi, Manuela R; Bicchi, Carlo

2017-01-01

This study is part of a wider project aiming to correlate the chemical composition of the coffee volatile fraction to its sensory properties with the end-goal of developing an instrumental analysis approach complementary to human sensory profiling. The proposed investigation strategy compares the chemical information concerning coffee aroma and flavor obtained with HS-SPME of the ground coffee and in-solution SBSE/SPME sampling combined with GC-MS to evaluate their compatibility with the cupping evaluation for quality control purposes. Roasted coffee samples with specific sensory properties were analyzed. The chemical results obtained by the three samplings were compared through multivariate analysis, and related to the samples' sensory attributes. Despite the differences between the three sampling approaches, data processing showed that the three methods provide the same kind of chemical information useful for sample discrimination, and that they could be used interchangeably to sample the coffee aroma and flavor. Copyright © 2016 Elsevier Ltd. All rights reserved.

Size and shape stasis in late Pleistocene mammals and birds from Rancho La Brea during the Last Glacial-Interglacial cycle

NASA Astrophysics Data System (ADS)

Prothero, Donald R.; Syverson, Valerie J.; Raymond, Kristina R.; Madan, Meena; Molina, Sarah; Fragomeni, Ashley; DeSantis, Sylvana; Sutyagina, Anastasiya; Gage, Gina L.

2012-11-01

Conventional neo-Darwinian theory views organisms as infinitely sensitive and responsive to their environments, and considers them able to readily change size or shape when they adapt to selective pressures. Yet since 1863 it has been well known that Pleistocene animals and plants do not show much morphological change or speciation in response to the glacial-interglacial climate cycles. We tested this hypothesis with all of the common birds (condors, golden and bald eagles, turkeys, caracaras) and mammals (dire wolves, saber-toothed cats, giant lions, horses, camels, bison, and ground sloths) from Rancho La Brea tar pits in Los Angeles, California, which preserves large samples of many bones from many well-dated pits spanning the 35,000 years of the Last Glacial-Interglacial cycle. Pollen evidence showed the climate changed from chaparral/oaks 35,000 years ago to snowy piñon-juniper forests at the peak glacial 20,000 years ago, then back to the modern chaparral since the glacial-interglacial transition. Based on Bergmann's rule, we would expect peak glacial specimens to have larger body sizes, and based on Allen's rule, peak glacial samples should have shorter and more robust limbs. Yet statistical analysis (ANOVA for parametric samples; Kruskal-Wallis test for non-parametric samples) showed that none of the Pleistocene pit samples is statistically distinct from the rest, indicating complete stasis from 35 ka to 9 ka. The sole exception was the Pit 13 sample of dire wolves (16 ka), which was significantly smaller than the rest, but this did not occur in response to climate change. We also performed a time series analysis of the pit samples. None showed directional change; all were either static or showed a random walk. Thus, the data show that birds and mammals at Rancho La Brea show complete stasis and were unresponsive to the major climate change that occurred at 20 ka, consistent with other studies of Pleistocene animals and plants. Most explanations for such stasis (stabilizing selection, canalization) fail in this setting where climate is changing. One possible explanation is that most large birds and mammals are very broadly adapted and relatively insensitive to changes in their environments, although even the small mammals of the Pleistocene show stasis during climate change, too.

Potency trends of delta9-THC and other cannabinoids in confiscated marijuana from 1980-1997.

PubMed

ElSohly, M A; Ross, S A; Mehmedic, Z; Arafat, R; Yi, B; Banahan, B F

2000-01-01

The analysis of 35,312 cannabis preparations confiscated in the USA over a period of 18 years for delta-9-tetrahydrocannabinol (delta9-THC) and other major cannabinoids is reported. Samples were identified as cannabis, hashish, or hash oil. Cannabis samples were further subdivided into marijuana (loose material, kilobricks and buds), sinsemilla, Thai sticks and ditchweed. The data showed that more than 82% of all confiscated samples were in the marijuana category for every year except 1980 (61%) and 1981 (75%). The potency (concentration of delta9-THC) of marijuana samples rose from less than 1.5% in 1980 to approximately 3.3% in 1983 and 1984, then fluctuated around 3% till 1992. Since 1992, the potency of confiscated marijuana samples has continuously risen, going from 3.1% in 1992 to 4.2% in 1997. The average concentration of delta9-THC in all cannabis samples showed a gradual rise from 3% in 1991 to 4.47% in 1997. Hashish and hash oil, on the other hand, showed no specific potency trends. Other major cannabinoids [cannabidiol (CBD), cannabinol (CBN), and cannabichromene (CBC)] showed no significant change in their concentration over the years.

Doppler Global Velocimeter Development for the Large Wind Tunnels at Ames Research Center

NASA Technical Reports Server (NTRS)

Reinath, Michael S.

1997-01-01

Development of an optical, laser-based flow-field measurement technique for large wind tunnels is described. The technique uses laser sheet illumination and charged coupled device detectors to rapidly measure flow-field velocity distributions over large planar regions of the flow. Sample measurements are presented that illustrate the capability of the technique. An analysis of measurement uncertainty, which focuses on the random component of uncertainty, shows that precision uncertainty is not dependent on the measured velocity magnitude. For a single-image measurement, the analysis predicts a precision uncertainty of +/-5 m/s. When multiple images are averaged, this uncertainty is shown to decrease. For an average of 100 images, for example, the analysis shows that a precision uncertainty of +/-0.5 m/s can be expected. Sample applications show that vectors aligned with an orthogonal coordinate system are difficult to measure directly. An algebraic transformation is presented which converts measured vectors to the desired orthogonal components. Uncertainty propagation is then used to show how the uncertainty propagates from the direct measurements to the orthogonal components. For a typical forward-scatter viewing geometry, the propagation analysis predicts precision uncertainties of +/-4, +/-7, and +/-6 m/s, respectively, for the U, V, and W components at 68% confidence.

Generalized Likelihood Uncertainty Estimation (GLUE) Using Multi-Optimization Algorithm as Sampling Method

NASA Astrophysics Data System (ADS)

Wang, Z.

2015-12-01

For decades, distributed and lumped hydrological models have furthered our understanding of hydrological system. The development of hydrological simulation in large scale and high precision elaborated the spatial descriptions and hydrological behaviors. Meanwhile, the new trend is also followed by the increment of model complexity and number of parameters, which brings new challenges of uncertainty quantification. Generalized Likelihood Uncertainty Estimation (GLUE) has been widely used in uncertainty analysis for hydrological models referring to Monte Carlo method coupled with Bayesian estimation. However, the stochastic sampling method of prior parameters adopted by GLUE appears inefficient, especially in high dimensional parameter space. The heuristic optimization algorithms utilizing iterative evolution show better convergence speed and optimality-searching performance. In light of the features of heuristic optimization algorithms, this study adopted genetic algorithm, differential evolution, shuffled complex evolving algorithm to search the parameter space and obtain the parameter sets of large likelihoods. Based on the multi-algorithm sampling, hydrological model uncertainty analysis is conducted by the typical GLUE framework. To demonstrate the superiority of the new method, two hydrological models of different complexity are examined. The results shows the adaptive method tends to be efficient in sampling and effective in uncertainty analysis, providing an alternative path for uncertainty quantilization.

Laser fluorometric analysis of plants for uranium exploration

USGS Publications Warehouse

Harms, T.F.; Ward, F.N.; Erdman, J.A.

1981-01-01

A preliminary test of biogeochemical exploration for locating uranium occurrences in the Marfa Basin, Texas, was conducted in 1978. Only 6 of 74 plant samples (mostly catclaw mimosa, Mimosa biuncifera) contained uranium in amounts above the detection limit (0.4 ppm in the ash) of the conventional fluorometric method. The samples were then analyzed using a Scintrex UA-3 uranium analyzer* * Use of trade names in this paper is for descriptive purposes only and does not constitute endorsement by the U.S. Geological Survey. - an instrument designed for direct analysis of uranium in water, and which can be conveniently used in a mobile field laboratory. The detection limit for uranium in plant ash (0.05 ppm) by this method is almost an order of magnitude lower than with the fluorometric conventional method. Only 1 of the 74 samples contained uranium below the detection limit of the new method. Accuracy and precision were determined to be satisfactory. Samples of plants growing on mineralized soils and nonmineralized soils show a 15-fold difference in uranium content; whereas the soils themselves (analyzed by delayed neutron activation analysis) show only a 4-fold difference. The method involves acid digestion of ashed tissue, extraction of uranium into ethyl acetate, destruction of the ethyl acetate, dissolution of the residue in 0.005% nitric acid, and measurement. ?? 1981.

Investigation of optical properties and local structure of Gd3+ doped nano-crystalline GeSe2

NASA Astrophysics Data System (ADS)

Hantour, Hanan Hassan

2017-04-01

Pure and Gd-doped nano-crystalline GeSe2 were prepared by the melt-quenching technique. Structure analysis using Rietveld program suggests monoclinic structure for both virgin and doped samples with nano-particle size 41 nm for GeSe2 and 48 nm for Gd-doped sample. A wide optical band gap as estimated from absorbance measurements is 4.1 and 4.8 eV for pure and doped samples in accordance with the confinement effects. Raman spectra show two unresolved components at ˜202 cm-1 with broad line width. Also, well identified low intensity (υ < 145 cm-1) and high intensity (υ > 250 cm-1) bands are detected. For Gd-doped sample, the main band is shifted to lower energies and its full width at half maximum (FWHM) is reduced by ˜50% accompanied by an intensity increase of about ˜17 fold times. The photoluminescence analysis of the pure sample shows a main emission band at ˜604 nm. This band is split into two separated bands with higher intensity. The detected emission bands at wavelength >650 nm are assigned to transmission from 6GJ to the different 6PJ terms.

Maps showing mines, quarries, and prospects, with analyses of samples, Gee Creek Wilderness, Polk and Monroe counties, Tennessee

USGS Publications Warehouse

Gazdik, Gertrude C.; Behum, Paul T.

1983-01-01

During the recent U.S. Bureau of Mines field investigation, 21 samples were collected (fig. 2) and were submitted to the Bureau's Reno Metallurgy Research Center, Reno, Nev., for analysis. All samples were tested for 40 elements by semiquantitative spectrographic analyses. Additional testing by atomic absorption, neutron activation, and wet chemical techniques was performed for selected elements on some samples. Two shale samples were submitted to the Bureau of Mines, Tuscaloosa Metallurgy Research Center, Tuscaloosa, Ala., for the evaluation of ceramic properties. 

[Preliminary study on effective components of Tripterygium wilfordii for liver toxicity based on spectrum-effect correlation analysis].

PubMed

Zhao, Xiao-Mei; Pu, Shi-Biao; Zhao, Qing-Guo; Gong, Man; Wang, Jia-Bo; Ma, Zhi-Jie; Xiao, Xiao-He; Zhao, Kui-Jun

2016-08-01

In this paper, the spectrum-effect correlation analysis method was used to explore the main effective components of Tripterygium wilfordii for liver toxicity, and provide reference for promoting the quality control of T. wilfordii. Chinese medicine T.wilfordii was taken as the study object, and LC-Q-TOF-MS was used to characterize the chemical components in T. wilfordii samples from different areas, and their main components were initially identified after referring to the literature. With the normal human hepatocytes (LO2 cell line)as the carrier, acetaminophen as positive medicine, and cell inhibition rate as testing index, the simple correlation analysis and multivariate linear correlation analysis methods were used to screen the main components of T. wilfordii for liver toxicity. As a result, 10 kinds of main components were identified, and the spectrum-effect correlation analysis showed that triptolide may be the toxic component, which was consistent with previous results of traditional literature. Meanwhile it was found that tripterine and demethylzeylasteral may greatly contribute to liver toxicity in multivariate linear correlation analysis. T. wilfordii samples of different varieties or different origins showed large difference in quality, and the T. wilfordii from southwest China showed lower liver toxicity, while those from Hunan and Anhui province showed higher liver toxicity. This study will provide data support for further rational use of T. wilfordii and research on its liver toxicity ingredients. Copyright© by the Chinese Pharmaceutical Association.

Differential expression analysis for RNAseq using Poisson mixed models

PubMed Central

Sun, Shiquan; Hood, Michelle; Scott, Laura; Peng, Qinke; Mukherjee, Sayan; Tung, Jenny

2017-01-01

Abstract Identifying differentially expressed (DE) genes from RNA sequencing (RNAseq) studies is among the most common analyses in genomics. However, RNAseq DE analysis presents several statistical and computational challenges, including over-dispersed read counts and, in some settings, sample non-independence. Previous count-based methods rely on simple hierarchical Poisson models (e.g. negative binomial) to model independent over-dispersion, but do not account for sample non-independence due to relatedness, population structure and/or hidden confounders. Here, we present a Poisson mixed model with two random effects terms that account for both independent over-dispersion and sample non-independence. We also develop a scalable sampling-based inference algorithm using a latent variable representation of the Poisson distribution. With simulations, we show that our method properly controls for type I error and is generally more powerful than other widely used approaches, except in small samples (n <15) with other unfavorable properties (e.g. small effect sizes). We also apply our method to three real datasets that contain related individuals, population stratification or hidden confounders. Our results show that our method increases power in all three data compared to other approaches, though the power gain is smallest in the smallest sample (n = 6). Our method is implemented in MACAU, freely available at www.xzlab.org/software.html. PMID:28369632

Pyrrole Alkaloids with Potential Cancer Chemopreventive Activity Isolated from a Goji Berry-Contaminated Commercial Sample of African Mango

PubMed Central

2015-01-01

Bioassay-guided fractionation of a commercial sample of African mango (Irvingia gabonensis) that was later shown to be contaminated with goji berry (Lycium sp.) led to the isolation of a new pyrrole alkaloid, methyl 2-[2-formyl-5-(hydroxymethyl)-1H-pyrrol-1-yl]propanoate, 1, along with seven known compounds, 2–8. The structures of the isolated compounds were established by analysis of their spectroscopic data. The new compound 1g showed hydroxyl radical-scavenging activity with an ED50 value of 16.7 μM, whereas 4-[formyl-5-(methoxymethyl)-1H-pyrrol-1-yl]butanoic acid (2) was active in both the hydroxyl radical-scavenging (ED50 11.9 μM) and quinone reductase-induction [CD (concentration required to double QR activity) 2.4 μM)] assays used. The isolated compounds were shown to be absent in a taxonomically authenticated African mango sample but present in three separate authentic samples of goji berry (Lycium barbarum) using LC-MS and 1H NMR fingerprinting analysis, including one sample that previously showed inhibitory activity in vivo in a rat esophageal cancer model induced with N-nitrosomethylbenzylamine. Additionally, microscopic features characteristic of goji berry were observed in the commercial African mango sample. PMID:24792835

[Physico-chemical and microbiological evaluation of UHT milk commercialized in three Mercosul countries (Brazil, Argentina and Paraguay)].

PubMed

Domareski, Jackson Luiz; Bandiera, Nataly Simões; Sato, Rafael Tamostu; Aragon-Alegro, Lina Casale; de Santana, Elsa Helena Walter

2010-09-01

With the aim to evaluate the physico-chemical and microbiological quality of UHT milk commercialized in three countries of Mercosul, samples of four different brands were acquired in each city (Foz do Iguaçu-Brazil, Puerto Iguazú-Argentina and Ciudad del Este-Paraguay) and submitted to the following analysis: fat content, titratable acidity, milk ethanol stability (with the following ethanol concentrations: 68, 72, 76 and 80%), total dry extract and no fat dry extract, pH, density and freezing point. Counts of mesophilic and psychrotrophic microorganisms were already done. In the physico-chemical evaluation of UHT milk, a significant number of samples were in disagree with the established patterns for fat content, no fat dry extract, density and freezing point. Except one brand from Brazil, milk samples showed stability to 68% ethanol. pH averages of Brazilian milk were in agree with the patterns and highest values were observed in samples acquired on Paraguay. Observing the microbiological analysis, 37.5%, 62.5% and 12.5% of samples acquired from Brazil, Argentina and Paraguay, respectively, showed counts above the established patterns for mesophilic microorganisms. Counts of psychrotrophic microorganisms were in disagree with the established patterns in 50%, 50% and 100% of samples from Brazil, Argentina and Paraguay, respectively.

Comparative analysis of the antioxidant properties of Icelandic and Hawaiian lichens.

PubMed

Hagiwara, Kehau; Wright, Patrick R; Tabandera, Nicole K; Kelman, Dovi; Backofen, Rolf; Ómarsdóttir, Sesselja; Wright, Anthony D

2016-09-01

Antioxidant activity of symbiotic organisms known as lichens is an intriguing field of research because of its strong contribution to their ability to withstand extremes of physical and biological stress (e.g. desiccation, temperature, UV radiation and microbial infection). We present a comparative study on the antioxidant activities of 76 Icelandic and 41 Hawaiian lichen samples assessed employing the DPPH- and FRAP-based antioxidant assays. Utilizing this unprecedented sample size, we show that while highest individual sample activity is present in the Icelandic dataset, the overall antioxidant activity is higher for lichens found in Hawaii. Furthermore, we report that lichens from the genus Peltigera that have been described as strong antioxidant producers in studies on Chinese, Russian and Turkish lichens also show high antioxidant activities in both Icelandic and Hawaiian lichen samples. Finally, we show that opportunistic sampling of lichens in both Iceland and Hawaii will yield high numbers of lichen species that exclusively include green algae as photobiont. © 2015 Society for Applied Microbiology and John Wiley & Sons Ltd.

Investigation of pyrolysis kinetics of humic acids from low rank Anatolian coal by thermal analysis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tonbul, Y.; Erdogan, S.

2007-07-01

Thermogravimetric analysis (TGA) of humic acid samples from low rank Anatolian (east of Turkey, Bingol) coal were investigated under atmospheric pressure. The samples were subjected for the decomposition of organic matter ambient to 800{sup o} C at four different heating rates (5, 10, 15, and 20 degrees C min{sup -1}). The humic acid samples were started at decomposition between 170 - 206{sup o}C and amount of residues varied 55-60% according to heating rate. Each of samples showed a single step mass loss. TG/DTG data of samples were analyzed to determine activation energy values by Coats and Redfern method and Arrheniusmore » method. Activation energy values are similar obtained from Coats and Redfern method and Arrhenius method and varied from 25 to 29 kJ mol{sup -1}.« less

Sampling, feasibility, and priors in data assimilation

DOE PAGES

Tu, Xuemin; Morzfeld, Matthias; Miller, Robert N.; ...

2016-03-01

Importance sampling algorithms are discussed in detail, with an emphasis on implicit sampling, and applied to data assimilation via particle filters. Implicit sampling makes it possible to use the data to find high-probability samples at relatively low cost, making the assimilation more efficient. A new analysis of the feasibility of data assimilation is presented, showing in detail why feasibility depends on the Frobenius norm of the covariance matrix of the noise and not on the number of variables. A discussion of the convergence of particular particle filters follows. A major open problem in numerical data assimilation is the determination ofmore » appropriate priors, a progress report on recent work on this problem is given. The analysis highlights the need for a careful attention both to the data and to the physics in data assimilation problems.« less

Cultural inter-population differences do not reflect biological distances: an example of interdisciplinary analysis of populations from Eastern Adriatic coast.

PubMed

Bašić, Željana; Fox, Ayano R; Anterić, Ivana; Jerković, Ivan; Polašek, Ozren; Anđelinović, Šimun; Holland, Mitchell M; Primorac, Dragan

2015-06-01

To compare the population group from the Šopot graveyard with population groups from traditional Croatian medieval graveyards by using anthropological, craniometrics, and mitochondrial (mtDNA) analysis and to examine if the cultural differences between population groups reflect biological differences. We determined sex, age at death, pathological, and traumatic changes of skeletal remains from the Šopot graveyard and compared them with a cumulative medieval sample from the same region. We also performed principal component analysis to compare skeletal remains from Šopot with those from Ostrovica and other Central European samples according to 8 cranial measurements. Finally, we compared 46 skeletons from Šopot with medieval (Ostrovica) and contemporary populations using mDNA haplogroup profiling. The remains from Šopot were similar to the cumulative sample in lifestyle and quality of life markers. Principal component analysis showed that they were closely related to Eastern Adriatic coast sites (including Ostrovica and Šopot) in terms of cranial morphology, indicating similar biological makeup. According to mDNA testing, Šopot population showed no significant differences in the haplogroup prevalence from either medieval or contemporary populations. This study shows that the Šopot population does not significantly differ from other medieval populations from this area. Besides similar quality of life markers, these populations also had similar biological markers. Substantial archeological differences can therefore be attributed to apparent cultural influences, which in this case do not reflect biological differences.

Cultural inter-population differences do not reflect biological distances: an example of interdisciplinary analysis of populations from Eastern Adriatic coast

PubMed Central

Bašić, Željana; Fox, Ayano R; Anterić, Ivana; Jerković, Ivan; Polašek, Ozren; Anđelinović, Šimun; Holland, Mitchell M; Primorac, Dragan

2015-01-01

Aim To compare the population group from the Šopot graveyard with population groups from traditional Croatian medieval graveyards by using anthropological, craniometrics, and mitochondrial (mtDNA) analysis and to examine if the cultural differences between population groups reflect biological differences. Methods We determined sex, age at death, pathological, and traumatic changes of skeletal remains from the Šopot graveyard and compared them with a cumulative medieval sample from the same region. We also performed principal component analysis to compare skeletal remains from Šopot with those from Ostrovica and other Central European samples according to 8 cranial measurements. Finally, we compared 46 skeletons from Šopot with medieval (Ostrovica) and contemporary populations using mDNA haplogroup profiling. Results The remains from Šopot were similar to the cumulative sample in lifestyle and quality of life markers. Principal component analysis showed that they were closely related to Eastern Adriatic coast sites (including Ostrovica and Šopot) in terms of cranial morphology, indicating similar biological makeup. According to mDNA testing, Šopot population showed no significant differences in the haplogroup prevalence from either medieval or contemporary populations. Conclusion This study shows that the Šopot population does not significantly differ from other medieval populations from this area. Besides similar quality of life markers, these populations also had similar biological markers. Substantial archeological differences can therefore be attributed to apparent cultural influences, which in this case do not reflect biological differences. PMID:26088847

Experimental testing and constitutive modeling of the mechanical properties of the swine skin tissue.

PubMed

Łagan, Sylwia D; Liber-Kneć, Aneta

2017-01-01

The aim of the study was an estimation of the possibility of using hyperelastic material models to fit experimental data obtained in the tensile test for the swine skin tissue. The uniaxial tensile tests of samples taken from the abdomen and back of a pig was carried out. The mechanical properties of the skin such as the mean Young's modulus, the mean maximum stress and the mean maximum elongation were calculated. The experimental data have been used to identify the parameters in specific strain-energy functions given in seven constitutive models of hyperelastic materials: neo-Hookean, Mooney-Rivlin, Ogden, Yeoh, Martins, Humphrey and Veronda-Westmann. An analysis of errors in fitting of theoretical and experimental data was done. Comparison of load -displacement curves for the back and abdomen regions of skin taken showed a different scope of both the mean maximum loading forces and the mean maximum elongation. Samples which have been prepared from the abdominal area had lower values of the mean maximum load compared to samples from the spine area. The reverse trend was observed during the analysis of the values of elongation. An analysis of the accuracy of model fitting to the experimental data showed that, the least accurate were the model of neo- -Hookean, model of Mooney-Rivlin for the abdominal region and model of Veronda-Westmann for the spine region. An analysis of seven hyperelastic material models showed good correlations between the experimental and the theoretical data for five models.

Electrical relaxation, optical and magnetic studies of nanocrystalline lithium ferrite synthesized by different chemical routes

NASA Astrophysics Data System (ADS)

Cheruku, Rajesh; Govindaraj, G.; Vijayan, Lakshmi

2017-12-01

The nanocrystalline lithium ferrite was synthesized by wet chemical methods such as solution combustion technique, sol-gel, and hydrothermal for a comparative study. Different characterization techniques like x-ray powder diffraction and thermal analysis were employed to confirm the structure and phase. Temperature-dependent Raman analysis was employed to classify the phonon modes associated with precise atomic motions existing in the synthesized materials. Morphology of sample surface was explored by scanning electron microscopy, and elemental analysis was done by energy dispersive spectroscopy analysis. The nanocrystalline nature of the materials was confirmed through transmission electron microscopy. Magnetic properties of these samples were explored through a vibrating sample magnetometer. Ac electrical impedance spectroscopy data were investigated using two Cole-Cole functions, and activation energies were calculated for all materials. Among them, solution combustion prepared lithium ferrite shows the highest conductivity and lowest activation energy.

Headspace Single-Drop Microextraction Gas Chromatography Mass Spectrometry for the Analysis of Volatile Compounds from Herba Asari

PubMed Central

Wang, Guan-Jie; Tian, Li; Fan, Yu-Ming; Qi, Mei-Ling

2013-01-01

A rapid headspace single-drop microextraction gas chromatography mass spectrometry (SDME-GC-MS) for the analysis of the volatile compounds in Herba Asari was developed in this study. The extraction solvent, extraction temperature and time, sample amount, and particle size were optimized. A mixed solvent of n-tridecane and butyl acetate (1 : 1) was finally used for the extraction with sample amount of 0.750 g and 100-mesh particle size at 70°C for 15 min. Under the determined conditions, the pound samples of Herba Asari were directly applied for the analysis. The result showed that SDME-GC–MS method was a simple, effective, and inexpensive way to measure the volatile compounds in Herba Asari and could be used for the analysis of volatile compounds in Chinese medicine. PMID:23607049

Development of methodology for identification the nature of the polyphenolic extracts by FTIR associated with multivariate analysis.

PubMed

Grasel, Fábio dos Santos; Ferrão, Marco Flôres; Wolf, Carlos Rodolfo

2016-01-15

Tannins are polyphenolic compounds of complex structures formed by secondary metabolism in several plants. These polyphenolic compounds have different applications, such as drugs, anti-corrosion agents, flocculants, and tanning agents. This study analyses six different type of polyphenolic extracts by Fourier transform infrared spectroscopy (FTIR) combined with multivariate analysis. Through both principal component analysis (PCA) and hierarchical cluster analysis (HCA), we observed well-defined separation between condensed (quebracho and black wattle) and hydrolysable (valonea, chestnut, myrobalan, and tara) tannins. For hydrolysable tannins, it was also possible to observe the formation of two different subgroups between samples of chestnut and valonea and between samples of tara and myrobalan. Among all samples analysed, the chestnut and valonea showed the greatest similarity, indicating that these extracts contain equivalent chemical compositions and structure and, therefore, similar properties. Copyright © 2015 Elsevier B.V. All rights reserved.

Standardisation of the ion beam facility at Chandigarh cyclotron for simultaneous PIXE and PESA analysis

NASA Astrophysics Data System (ADS)

Verma, Shivcharan; Mohanty, Biraja P.; Singh, Karn P.; Kumar, Ashok

2018-02-01

The proton beam facility at variable energy cyclotron (VEC) Panjab University, Chandigarh, India is being used for Particle Induced X-ray Emission (PIXE) analysis of different environmental, biological and industrial samples. The PIXE method, however, does not provide any information of low Z elements like carbon, nitrogen, oxygen and fluorine. As a result of the increased need for rapid and multi-elemental analysis of biological and environmental samples, the PIXE facility was upgraded and standardized to facilitate simultaneous measurements using PIXE and Proton Elastic Scattering Analysis (PESA). Both PIXE and PESA techniques were calibrated and standardized individually. Finally, the set up was tested by carrying out simultaneous PIXE and PESA measurements using a 2 mm diameter proton beam of 2.7 MeV on few multilayered thin samples. The results obtained show excellent agreement between PIXE and PESA measurements and confirm adequate sensitivity and precision of the experimental set up.

Bioelectrical impedance analysis for bovine milk: Preliminary results

NASA Astrophysics Data System (ADS)

Bertemes-Filho, P.; Valicheski, R.; Pereira, R. M.; Paterno, A. S.

2010-04-01

This work reports the investigation and analysis of bovine milk quality by using biological impedance measurements using electrical impedance spectroscopy (EIS). The samples were distinguished by a first chemical analysis using Fourier transform midinfrared spectroscopy (FTIR) and flow citometry. A set of milk samples (100ml each) obtained from 17 different cows in lactation with and without mastitis were analyzed with the proposed technique using EIS. The samples were adulterated by adding distilled water and hydrogen peroxide in a controlled manner. FTIR spectroscopy and flow cytometry were performed, and impedance measurements were made in a frequency range from 500Hz up to 1MHz with an implemented EIS system. The system's phase shift was compensated by measuring saline solutions. It was possible to show that the results obtained with the Bioelectrical Impedance Analysis (BIA) technique may detect changes in the milk caused by mastitis and the presence of water and hydrogen peroxide in the bovine milk.

PAH Baselines for Amazonic Surficial Sediments: A Case of Study in Guajará Bay and Guamá River (Northern Brazil).

PubMed

Rodrigues, Camila Carneiro Dos Santos; Santos, Ewerton; Ramos, Brunalisa Silva; Damasceno, Flaviana Cardoso; Correa, José Augusto Martins

2018-06-01

The 16 priority PAH were determined in sediment samples from the insular zone of Guajará Bay and Guamá River (Southern Amazon River mouth). Low hydrocarbon levels were observed and naphthalene was the most representative PAH. The low molecular weight PAH represented 51% of the total PAH. Statistical analysis showed that the sampling sites are not significantly different. Source analysis by PAH ratios and principal component analysis revealed that PAH are primary from a few rate of fossil fuel combustion, mainly related to the local small community activity. All samples presented no biological stress or damage potencial according to the sediment quality guidelines. This study discuss baselines for PAH in surface sediments from Amazonic aquatic systems based on source determination by PAH ratios and principal component analysis, sediment quality guidelines and through comparison with previous studies data.

[Social self-positioning as indicator of socioeconomic status].

PubMed

Fernández, E; Alonso, R M; Quer, A; Borrell, C; Benach, J; Alonso, J; Gómez, G

2000-01-01

Self-perceived class results from directly questioning subjects about his or her social class. The aim of this investigation was to analyse self-perceived class in relation to other indicator variables of socioeconomic level. Data from the 1994 Catalan Health Interview Survey, a cross-sectional survey of a representative sample of the non-institutionalised population of Catalonia was used. We conducted a discriminant analysis to compute the degree of right classification when different socioeconomic variables potentially related to self-perceived class were considered. All subjects who directly answered the questionnaire were included (N = 12,245). With the aim of obtaining the discriminant functions in a group of subjects and to validate it in another one, the subjects were divided into two random samples, containing approximately 75% and 25% of subjects (analysis sample, n = 9,248; and validation sample, n = 2,997). The final function for men and women included level of education, social class (based in occupation) and equivalent income. This function correctly classified 40.9% of the subjects in the analysis sample and 39.2% in the validation sample. Two other functions were selected for men and women separately. In men, the function included level of education, professional category, and family income (39.2% of classification in analysis sample and 37.2% in validation sample). In women, the function (level of education, working status, and equivalent income) correctly classified 40.3% of women in analysis sample whereas the percentage was 38.9% in validation sample. The percentages of right classification were higher for the highest and lowest classes. These results show the utility of a simple variable to self-position within the social scale. Self-perceived class is related to education, income, and working determinants.

Developmental toxicity, acute toxicity and mutagenicity testing in freshwater snails Biomphalaria glabrata (Mollusca: Gastropoda) exposed to chromium and water samples.

PubMed

Tallarico, Lenita de Freitas; Borrely, Sueli Ivone; Hamada, Natália; Grazeffe, Vanessa Siqueira; Ohlweiler, Fernanda Pires; Okazaki, Kayo; Granatelli, Amanda Tosatte; Pereira, Ivana Wuo; Pereira, Carlos Alberto de Bragança; Nakano, Eliana

2014-12-01

A protocol combining acute toxicity, developmental toxicity and mutagenicity analysis in freshwater snail Biomphalaria glabrata for application in ecotoxicological studies is described. For acute toxicity testing, LC50 and EC50 values were determined; dominant lethal mutations induction was the endpoint for mutagenicity analysis. Reference toxicant potassium dichromate (K2Cr2O7) was used to characterize B. glabrata sensitivity for toxicity and cyclophosphamide to mutagenicity testing purposes. Compared to other relevant freshwater species, B. glabrata showed high sensitivity: the lowest EC50 value was obtained with embryos at veliger stage (5.76mg/L). To assess the model applicability for environmental studies, influent and effluent water samples from a wastewater treatment plant were evaluated. Gastropod sensitivity was assessed in comparison to the standardized bioassay with Daphnia similis exposed to the same water samples. Sampling sites identified as toxic to daphnids were also detected by snails, showing a qualitatively similar sensitivity suggesting that B. glabrata is a suitable test species for freshwater monitoring. Holding procedures and protocols implemented for toxicity and developmental bioassays showed to be in compliance with international standards for intra-laboratory precision. Thereby, we are proposing this system for application in ecotoxicological studies. Copyright © 2014 Elsevier Inc. All rights reserved.

Toolbox Approaches Using Molecular Markers and 16S rRNA Gene Amplicon Data Sets for Identification of Fecal Pollution in Surface Water.

PubMed

Ahmed, W; Staley, C; Sadowsky, M J; Gyawali, P; Sidhu, J P S; Palmer, A; Beale, D J; Toze, S

2015-10-01

In this study, host-associated molecular markers and bacterial 16S rRNA gene community analysis using high-throughput sequencing were used to identify the sources of fecal pollution in environmental waters in Brisbane, Australia. A total of 92 fecal and composite wastewater samples were collected from different host groups (cat, cattle, dog, horse, human, and kangaroo), and 18 water samples were collected from six sites (BR1 to BR6) along the Brisbane River in Queensland, Australia. Bacterial communities in the fecal, wastewater, and river water samples were sequenced. Water samples were also tested for the presence of bird-associated (GFD), cattle-associated (CowM3), horse-associated, and human-associated (HF183) molecular markers, to provide multiple lines of evidence regarding the possible presence of fecal pollution associated with specific hosts. Among the 18 water samples tested, 83%, 33%, 17%, and 17% were real-time PCR positive for the GFD, HF183, CowM3, and horse markers, respectively. Among the potential sources of fecal pollution in water samples from the river, DNA sequencing tended to show relatively small contributions from wastewater treatment plants (up to 13% of sequence reads). Contributions from other animal sources were rarely detected and were very small (<3% of sequence reads). Source contributions determined via sequence analysis versus detection of molecular markers showed variable agreement. A lack of relationships among fecal indicator bacteria, host-associated molecular markers, and 16S rRNA gene community analysis data was also observed. Nonetheless, we show that bacterial community and host-associated molecular marker analyses can be combined to identify potential sources of fecal pollution in an urban river. This study is a proof of concept, and based on the results, we recommend using bacterial community analysis (where possible) along with PCR detection or quantification of host-associated molecular markers to provide information on the sources of fecal pollution in waterways. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

The Surface Chemical Composition of Lunar Samples and Its Significance for Optical Properties

NASA Technical Reports Server (NTRS)

Gold, T.; Bilson, E.; Baron, R. L.

1976-01-01

The surface iron, titanium, calcium, and silicon concentration in numerous lunar soil and rock samples was determined by Auger electron spectroscopy. All soil samples show a large increase in the iron to oxygen ratio compared with samples of pulverized rock or with results of the bulk chemical analysis. A solar wind simulation experiment using 2 keV energy alpha -particles showed that an ion dose corresponding to approximately 30,000 years of solar wind increased the iron concentration on the surface of the pulverized Apollo 14 rock sample 14310 to the concentration measured in the Apollo 14 soil sample 14163, and the albedo of the pulverized rock decreased from 0.36 to 0.07. The low albedo of the lunar soil is related to the iron + titanium concentration on its surface. A solar wind sputter reduction mechanism is discussed as a possible cause for both the surface chemical and optical properties of the soil.

Dried Blood Spot Analysis Suitable for Therapeutic Drug Monitoring of Voriconazole, Fluconazole, and Posaconazole

PubMed Central

van der Elst, Kim C. M.; Span, Lambert F. R.; van Hateren, Kai; Vermeulen, Karin M.; van der Werf, Tjip S.; Greijdanus, Ben; Kosterink, Jos G. W.; Uges, Donald R. A.

2013-01-01

Invasive aspergillosis and candidemia are important causes of morbidity and mortality in immunocompromised and critically ill patients. The triazoles voriconazole, fluconazole, and posaconazole are widely used for the treatment and prophylaxis of these fungal infections. Due to the variability of the pharmacokinetics of the triazoles among and within individual patients, therapeutic drug monitoring is important for optimizing the efficacy and safety of antifungal treatment. A dried blood spot (DBS) analysis was developed and was clinically validated for voriconazole, fluconazole, and posaconazole in 28 patients. Furthermore, a questionnaire was administered to evaluate the patients' opinions of the sampling method. The DBS analytical method showed linearity over the concentration range measured for all triazoles. Results for accuracy and precision were within accepted ranges; samples were stable at room temperature for at least 12 days; and different hematocrit values and blood spot volumes had no significant influence. The ratio of the drug concentration in DBS samples to that in plasma was 1.0 for voriconazole and fluconazole and 0.9 for posaconazole. Sixty percent of the patients preferred DBS analysis as a sampling method; 15% preferred venous blood sampling; and 25% had no preferred method. There was significantly less perception of pain with the DBS sampling method (P = 0.021). In conclusion, DBS analysis is a reliable alternative to venous blood sampling and can be used for therapeutic drug monitoring of voriconazole, fluconazole, and posaconazole. Patients were satisfied with DBS sampling and had less pain than with venous sampling. Most patients preferred DBS sampling to venous blood sampling. PMID:23896473

Probing dissolved organic matter in the critical zone: a comparison between in situ sampling and aqueous soil extracts

NASA Astrophysics Data System (ADS)

Perdrial, J. N.; Perdrial, N.; Harpold, A. A.; Peterson, A. M.; Vasquez, A.; Chorover, J.

2011-12-01

Analyzing dissolved organic matter (DOM) of soil solution constitutes an integral activity in critical zone science as important insights to nutrient and carbon cycling and mineral weathering processes can be gained. Soil solution can be obtained by a variety of approaches such as by in situ zero-tension and tension samplers or by performing soil extracts in the lab. It is generally preferred to obtain soil solution in situ with the least amount of disturbance. However, in water limited environments, such as in southwestern US, in situ sampling is only possible during few hydrologic events and soil extracts are often employed. In order to evaluate the performance of different sampling approaches for OM analysis, results from aqueous soil extracts were compared with in situ samples obtained from suction cups and passive capillary wick samplers (PCAP's). Soil from an OA-horizon of mixed conifer forest Jemez River Basin Critical Zone Observatory (JRB-CZO) in NM was sampled twice and in situ samples from co-located suction cups and PCAPs were collected 7 times during the 2011 snowmelt period. Dissolved organic carbon and nitrogen concentrations (DOC and DN) as well as OM quality (FTIR, fluorescence spectroscopy and PARAFAC) were analyzed. The aqueous soil extracts (solid:solution = 1:5 mass basis) showed highest DOC and lowest DN concentrations whereas samples collected in-situ had lower DOC and higher DN concentrations. PARAFAC analysis using a four component model showed a dominance of fluorescence in region I and II (protein-like fluorescence) for samples collected in situ indicating the presence of more bio-molecules (proteins). In contrast, the dominant PARAFAC component of the soil extract was found in region 3 (fulvic acid-like fluorescence). FTIR analysis showed high intensity band at 1600 cm-1 in the case of the aqueous soil extract that correspond to asymmetric stretching of carboxyl groups. These preliminary results indicate that aqueous soil extracts likely lead to the underestimation of the amount of biomolecules and the overestimation of fulvic acid contents of soil solutions.

The classification of almonds (Prunus dulcis) by country and variety using UHPLC-HRMS-based untargeted metabolomics.

PubMed

Gil Solsona, R; Boix, C; Ibáñez, M; Sancho, J V

2018-03-01

The aim of this study was to use an untargeted UHPLC-HRMS-based metabolomics approach allowing discrimination between almonds based on their origin and variety. Samples were homogenised, extracted with ACN:H 2 O (80:20) containing 0.1% HCOOH and injected in a UHPLC-QTOF instrument in both positive and negative ionisation modes. Principal component analysis (PCA) was performed to ensure the absence of outliers. Partial least squares - discriminant analysis (PLS-DA) was employed to create and validate the models for country (with five different compounds) and variety (with 20 features), showing more than 95% accuracy. Additional samples were injected and the model was evaluated with blind samples, with more than 95% of samples being correctly classified using both models. MS/MS experiments were carried out to tentatively elucidate the highlighted marker compounds (pyranosides, peptides or amino acids, among others). This study has shown the potential of high-resolution mass spectrometry to perform and validate classification models, also providing information concerning the identification of the unexpected biomarkers which showed the highest discriminant power.

Permethylated-β-Cyclodextrin Capped CdTe Quantum Dot and its Sensitive Fluorescence Analysis of Malachite Green.

PubMed

Cao, Yujuan; Wei, Jiongling; Wu, Wei; Wang, Song; Hu, Xiaogang; Yu, Ying

2015-09-01

In the present work, the CdTe quantum dots were covalently conjugated with permethylated-β-cyclodextrin (OMe-β-CD) using 1-ethyl-3-(3-dimethylaminopropyl) carbodiimide hydrochloride as cross-linking reagent. The obtained functional quantum dots (OMe-β-CD/QDs) showed highly luminescent, water solubility and photostability as well as good inclusion ability to malachite green. A sensitive fluorescence method was developed for the analysis of malachite green in different samples. The good linearity was 2.0 × 10(-7)-1.0 × 10(-5) mol/L and the limit of detect was 1.7 × 10(-8) mol/L. The recoveries for three environmental water samples were 92.0-108.2 % with relative standard deviation (RSD) of 0.24-1.87 %, while the recovery for the fish sample was 94.3 % with RSD of 1.04 %. The results showed that the present method was sensitive and convenient to determine malachite green in complex samples. Graphical Abstract The analytical mechanism of OMe-β-CD/QDs and its linear response to MG.

Bacterial community analysis of Tatsoi cultivated by hydroponics.

PubMed

Koo, Ok K; Kim, Hun; Kim, Hyun J; Baker, Christopher A; Ricke, Steven C

2016-07-02

Tatsoi (Brassica narinosa) is a popular Asian salad green that is mostly consumed as a source of fresh produce. The purpose of this study was to assess the microbial diversity of Tatsoi cultivated in a hydroponic system and of its ecosystem. Tatsoi leaves, nutrient solution, and perlite/earth samples from a trickle feed system (TFS) and an ebb-and-flow system (EFS) were collected and their microbial communities were analyzed by pyrosequencing analysis. The results showed that most bacteria in the leaves from the TFS contained genus Sporosarcina (99.6%), while Rhizobium (60.4%) was dominant in the leaves from the EFS. Genus Paucibacter (18.21%) and Pelomonas (12.37%) were the most abundant microbiota in the nutrient solution samples of the TFS. In the EFS, the nutrient solution samples contained mostly genus Rhodococcus and Acinetobacter. Potential microbial transfer between the leaves and the ecosystem was observed in the EFS, while samples in the TFS were found to share only one species between the leaves, nutrient solution, and earth. Together, these results show that the bacterial populations in Tatsoi and in its ecosystem are highly diverse based on the cultivation system.

ALK rearrangement in a large series of consecutive non-small cell lung cancers: comparison between a new immunohistochemical approach and fluorescence in situ hybridization for the screening of patients eligible for crizotinib treatment.

PubMed

Alì, Greta; Proietti, Agnese; Pelliccioni, Serena; Niccoli, Cristina; Lupi, Cristiana; Sensi, Elisa; Giannini, Riccardo; Borrelli, Nicla; Menghi, Maura; Chella, Antonio; Ribechini, Alessandro; Cappuzzo, Federico; Melfi, Franca; Lucchi, Marco; Mussi, Alfredo; Fontanini, Gabriella

2014-11-01

Echinoderm microtubule associated proteinlike 4-anaplastic lymphoma receptor tyrosine kinase (EML4-ALK) translocation has been described in a subset of patients with non-small cell lung cancer (NSCLC) and has been shown to have oncogenic activity. Fluorescence in situ hybridization (FISH) is used to detect ALK-positive NSCLC, but it is expensive, time-consuming, and difficult for routine application. To evaluate the potential role of immunohistochemistry (IHC) as a screening tool to identify candidate cases for FISH analysis and for ALK inhibitor therapy in NSCLC. We performed FISH and IHC for ALK and mutational analysis for epidermal growth factor receptor (EGFR) and KRAS in 523 NSCLC specimens. We conducted IHC analysis with the monoclonal antibody D5F3 (Ventana Medical Systems, Tucson, Arizona) and a highly sensitive detection system. We also performed a MassARRAY-based analysis (Sequenom, San Diego, California) in a small subset of 11 samples to detect EML4-ALK rearrangement. Of the 523 NSCLC specimens, 20 (3.8%) were positive for ALK rearrangement by FISH analysis. EGFR and KRAS mutations were identified in 70 (13.4%) and 124 (23.7%) of the 523 tumor samples, respectively. ALK rearrangement and EGFR and KRAS mutations were mutually exclusive. Of 523 tumor samples analyzed, 18 (3.4%) were ALK(+) by IHC, 18 samples (3.4%) had concordant IHC and FISH results, and 2 ALK(+) cases (0.3%) by FISH failed to show ALK protein expression. In the 2 discrepant cases, we did not detect any mass peaks for the EML4-ALK variants by MassARRAY. Our results show that IHC may be a useful technique for selecting NSCLC cases to undergo ALK FISH analysis.

Gene identification for risk of relapse in stage I lung adenocarcinoma patients: a combined methodology of gene expression profiling and computational gene network analysis.

PubMed

Ludovini, Vienna; Bianconi, Fortunato; Siggillino, Annamaria; Piobbico, Danilo; Vannucci, Jacopo; Metro, Giulio; Chiari, Rita; Bellezza, Guido; Puma, Francesco; Della Fazia, Maria Agnese; Servillo, Giuseppe; Crinò, Lucio

2016-05-24

Risk assessment and treatment choice remains a challenge in early non-small-cell lung cancer (NSCLC). The aim of this study was to identify novel genes involved in the risk of early relapse (ER) compared to no relapse (NR) in resected lung adenocarcinoma (AD) patients using a combination of high throughput technology and computational analysis. We identified 18 patients (n.13 NR and n.5 ER) with stage I AD. Frozen samples of patients in ER, NR and corresponding normal lung (NL) were subjected to Microarray technology and quantitative-PCR (Q-PCR). A gene network computational analysis was performed to select predictive genes. An independent set of 79 ADs stage I samples was used to validate selected genes by Q-PCR.From microarray analysis we selected 50 genes, using the fold change ratio of ER versus NR. They were validated both in pool and individually in patient samples (ER and NR) by Q-PCR. Fourteen increased and 25 decreased genes showed a concordance between two methods. They were used to perform a computational gene network analysis that identified 4 increased (HOXA10, CLCA2, AKR1B10, FABP3) and 6 decreased (SCGB1A1, PGC, TFF1, PSCA, SPRR1B and PRSS1) genes. Moreover, in an independent dataset of ADs samples, we showed that both high FABP3 expression and low SCGB1A1 expression was associated with a worse disease-free survival (DFS).Our results indicate that it is possible to define, through gene expression and computational analysis, a characteristic gene profiling of patients with an increased risk of relapse that may become a tool for patient selection for adjuvant therapy.

The use of droplet digital PCR in liquid biopsies: A highly sensitive technique for MYD88 p.(L265P) detection in cerebrospinal fluid.

PubMed

Hiemcke-Jiwa, Laura S; Minnema, Monique C; Radersma-van Loon, Joyce H; Jiwa, N Mehdi; de Boer, Mirthe; Leguit, Roos J; de Weger, Roel A; Huibers, Manon M H

2018-04-01

The gold standard for diagnosis of central nervous system lymphomas still regards a stereotactic brain biopsy, with the risk of major complications for the patient. As tumor cells can be detected in cerebrospinal fluid (CSF), CSF analysis can be used as an alternative. In this respect, mutation analysis in CSF can be of added value to other diagnostic parameters such a cytomorphology and clonality analysis. A well-known example of targeted mutation analysis entails MYD88 p.(L265P) detection, which is present in the majority of Bing Neel syndrome and primary central nervous system lymphoma (PCNSL) patients. Unfortunately, tumor yield in CSF can be very low. Therefore, use of the highly sensitive droplet digital PCR (ddPCR) might be a suitable analysis strategy for targeted mutation detection. We analyzed 26 formalin fixed paraffin embedded (FFPE) samples (8 positive and 18 negative for MYD88 p.(L265P) mutation) by ddPCR, of which the results were compared with next generation sequencing (NGS). Subsequently, 32 CSF samples were analyzed by ddPCR. ddPCR and NGS results on FFPE material showed 100% concordance. Among the 32 CSF samples, 9 belonged to patients with lymphoplasmacytic lymphoma (LPL) and clinical suspicion of Bing Neel syndrome, and 3 belonged to patients with PCNSL. Nine of these samples tested positive for MYD88 p.(L265P) (8 LPL and 1 PCNSL). This study shows that sensitive MYD88 mutation analysis by ddPCR in CSF is highly reliable and can be applied even when DNA input is low. Therefore, ddPCR is of added value to current diagnostic parameters, especially when the available amount of DNA is limited. Copyright © 2017 John Wiley & Sons, Ltd.

Genetic characterization of measles virus in the Philippines, 2008-2011.

PubMed

Centeno, Rex; Fuji, Naoko; Okamoto, Michiko; Dapat, Clyde; Saito, Mariko; Tandoc, Amado; Lupisan, Socorro; Oshitani, Hitoshi

2015-06-03

Large outbreaks of measles occurred in the Philippines in 2010 and 2011. Genetic analysis was performed to identify the genotype of measles virus (MeV) that was responsible for the large outbreaks. A total of 114 representative MeVs that were detected in the Philippines from 2008 to 2011 were analyzed by sequencing the C-terminal region of nucleocapsid (N) gene and partial hemagglutinin (H) gene and by inferring the phylogenetic trees. Genetic analysis showed that genotype D9 was the predominant circulating strain during the 4-year study period. Genotype D9 was detected in 23 samples (92%) by N gene sequencing and 93 samples (94%) by H gene analysis. Sporadic cases of genotype G3 MeV were identified in 2 samples (8%) by N gene sequencing and 6 samples (6%) by H gene analysis. Genotype G3 MeV was detected mainly in Panay Island in 2009 and 2010. Molecular clock analysis of N gene showed that the recent genotype D9 viruses that caused the big outbreaks in 2010 and 2011 diverged from a common ancestor in 2005 in one of the neighboring Southeast Asian countries, where D9 was endemic. These big outbreaks of measles resulted in a spillover and were associated with genotype D9 MeV importation to Japan and the USA. Genotype D9 MeV became endemic and caused two big outbreaks in the Philippines in 2010 and 2011. Genotype G3 MeV was detected sporadically with limited geographic distribution. This study highlights the importance of genetic analysis not only in helping with the assessment of measles elimination program in the country but also in elucidating the transmission dynamics of measles virus.

Routine conventional karyotyping of lymphoma staging bone marrow samples does not contribute clinically relevant information.

PubMed

Nardi, Valentina; Pulluqi, Olja; Abramson, Jeremy S; Dal Cin, Paola; Hasserjian, Robert P

2015-06-01

Bone marrow (BM) evaluation is an important part of lymphoma staging, which guides patient management. Although positive staging marrow is defined as morphologically identifiable disease, such samples often also include flow cytometric analysis and conventional karyotyping. Cytogenetic analysis is a labor-intensive and costly procedure and its utility in this setting is uncertain. We retrospectively reviewed pathological reports of 526 staging marrow specimens in which conventional karyotyping had been performed. All samples originated from a single institution from patients with previously untreated Hodgkin and non-Hodgkin lymphomas presenting in an extramedullary site. Cytogenetic analysis revealed clonal abnormalities in only eight marrow samples (1.5%), all of which were positive for lymphoma by morphologic evaluation. Flow cytometry showed a small clonal lymphoid population in three of the 443 morphologically negative marrow samples (0.7%). Conventional karyotyping is rarely positive in lymphoma staging marrow samples and, in our cohort, the BM karyotype did not contribute clinically relevant information in the vast majority of cases. Our findings suggest that karyotyping should not be performed routinely on BM samples taken to stage previously diagnosed extramedullary lymphomas unless there is pathological evidence of BM involvement by lymphoma. © 2015 Wiley Periodicals, Inc.

E-nose based rapid prediction of early mouldy grain using probabilistic neural networks

PubMed Central

Ying, Xiaoguo; Liu, Wei; Hui, Guohua; Fu, Jun

2015-01-01

In this paper, early mouldy grain rapid prediction method using probabilistic neural network (PNN) and electronic nose (e-nose) was studied. E-nose responses to rice, red bean, and oat samples with different qualities were measured and recorded. E-nose data was analyzed using principal component analysis (PCA), back propagation (BP) network, and PNN, respectively. Results indicated that PCA and BP network could not clearly discriminate grain samples with different mouldy status and showed poor predicting accuracy. PNN showed satisfying discriminating abilities to grain samples with an accuracy of 93.75%. E-nose combined with PNN is effective for early mouldy grain prediction. PMID:25714125

Analysing neutron scattering data using McStas virtual experiments

NASA Astrophysics Data System (ADS)

Udby, L.; Willendrup, P. K.; Knudsen, E.; Niedermayer, Ch.; Filges, U.; Christensen, N. B.; Farhi, E.; Wells, B. O.; Lefmann, K.

2011-04-01

With the intention of developing a new data analysis method using virtual experiments we have built a detailed virtual model of the cold triple-axis spectrometer RITA-II at PSI, Switzerland, using the McStas neutron ray-tracing package. The parameters characterising the virtual instrument were carefully tuned against real experiments. In the present paper we show that virtual experiments reproduce experimentally observed linewidths within 1-3% for a variety of samples. Furthermore we show that the detailed knowledge of the instrumental resolution found from virtual experiments, including sample mosaicity, can be used for quantitative estimates of linewidth broadening resulting from, e.g., finite domain sizes in single-crystal samples.

Mars rover 1988 concepts

NASA Technical Reports Server (NTRS)

Pivirotto, Donna Shirley; Penn, Thomas J.; Dias, William C.

1989-01-01

Results of FY88 studies of a sample-collecting Mars rover are presented. A variety of rover concepts are discussed which include different technical approaches to rover functions. The performance of rovers with different levels of automation is described and compared to the science requirement for 20 to 40 km to be traversed on the Martian surface and for 100 rock and soil samples to be collected. The analysis shows that a considerable amount of automation in roving and sampling is required to meet this requirement. Additional performance evaluation shows that advanced RTG's producing 500 W and 350 WHr of battery storage are needed to supply the rover.

Developing optimum sample size and multistage sampling plans for Lobesia botrana (Lepidoptera: Tortricidae) larval infestation and injury in northern Greece.

PubMed

Ifoulis, A A; Savopoulou-Soultani, M

2006-10-01

The purpose of this research was to quantify the spatial pattern and develop a sampling program for larvae of Lobesia botrana Denis and Schiffermüller (Lepidoptera: Tortricidae), an important vineyard pest in northern Greece. Taylor's power law and Iwao's patchiness regression were used to model the relationship between the mean and the variance of larval counts. Analysis of covariance was carried out, separately for infestation and injury, with combined second and third generation data, for vine and half-vine sample units. Common regression coefficients were estimated to permit use of the sampling plan over a wide range of conditions. Optimum sample sizes for infestation and injury, at three levels of precision, were developed. An investigation of a multistage sampling plan with a nested analysis of variance showed that if the goal of sampling is focusing on larval infestation, three grape clusters should be sampled in a half-vine; if the goal of sampling is focusing on injury, then two grape clusters per half-vine are recommended.

[A novel approach to NIR spectral quantitative analysis: semi-supervised least-squares support vector regression machine].

PubMed

Li, Lin; Xu, Shuo; An, Xin; Zhang, Lu-Da

2011-10-01

In near infrared spectral quantitative analysis, the precision of measured samples' chemical values is the theoretical limit of those of quantitative analysis with mathematical models. However, the number of samples that can obtain accurately their chemical values is few. Many models exclude the amount of samples without chemical values, and consider only these samples with chemical values when modeling sample compositions' contents. To address this problem, a semi-supervised LS-SVR (S2 LS-SVR) model is proposed on the basis of LS-SVR, which can utilize samples without chemical values as well as those with chemical values. Similar to the LS-SVR, to train this model is equivalent to solving a linear system. Finally, the samples of flue-cured tobacco were taken as experimental material, and corresponding quantitative analysis models were constructed for four sample compositions' content(total sugar, reducing sugar, total nitrogen and nicotine) with PLS regression, LS-SVR and S2 LS-SVR. For the S2 LS-SVR model, the average relative errors between actual values and predicted ones for the four sample compositions' contents are 6.62%, 7.56%, 6.11% and 8.20%, respectively, and the correlation coefficients are 0.974 1, 0.973 3, 0.923 0 and 0.948 6, respectively. Experimental results show the S2 LS-SVR model outperforms the other two, which verifies the feasibility and efficiency of the S2 LS-SVR model.

Structural and Mössbauer analysis of pure and Ce-Dy doped cobalt ferrite nanoparticles

NASA Astrophysics Data System (ADS)

Hashim, Mohd.; Meena, Sher Singh; Kumar, Shalendra; Ahmed, Ateeq; Bhatt, Pramod

2018-05-01

Ce and Dy doped Cobalt ferrites with the chemical composition CoCexDyxFe2-2xO4 (x = 0.00 and 0.04) were synthesized via the chemical route using citrate-gel auto-combustion method. The structural analysis has been carried out with the help of x-ray diffraction (XRD). Formation of spinel cubic structure of the ferrites was confirmed by XRD analysis. Mössbauer spectra were recorded for both samples at room temperature. Presence of the well resolved sextet spectra corresponding to A and B sub-lattice clearly shows that both the samples have ferrimagnetic ordering at room temperature. Isomer shift observed from fitting of the Mössbauer spectra infers that Fe3+ ions are in high valence state. The decrease in the hyperfine field due to the doping of Ce and Dy clearly showed that magnetic interactions diluted due to the doping of Ce and Dy ions.

Relationships between diatoms and tidal environments in Oregon and Washington, USA

USGS Publications Warehouse

Sawai, Yuki; Horton, Benjamin P.; Kemp, Andrew C.; Hawkes, Andrea D.; Nagumo, Tamostsu; Nelson, Alan R.

2016-01-01

A new regional dataset comprising 425 intertidal diatom taxa from 175 samples from 11 ecologically diverse Oregon and Washington estuaries illustrates the importance of compiling a large modern dataset from a range of sites. Cluster analyses and detrended correspondence analysis of the diatom assemblages identify distinct vertical zones within supratidal, intertidal and subtidal environments at six of the 11 study sites, but the abundance of some of the most common species varies widely among and within sites. Canonical correspondence analysis of the regional dataset shows relationships between diatom species and tidal exposure, salinity and substratum (grain size and organic content). Correspondence analyses of local datasets show higher values of explained variation than the analysis of the combined regional dataset. Our results emphasize that studies of the autecology of diatom species require many samples from a range of modern environments to adequately characterize species–environment relationships.

Detection and molecular characterization of tomato yellow leaf curl virus naturally infecting Lycopersicon esculentum in Egypt.

PubMed

Rabie, M; Ratti, C; Abdel Aleem, E; Fattouh, F

Tomato yellow leaf curl virus (TYLCV) infections of tomato crops in Egypt were widely spread in 2014. Infected symptomatic tomato plants from different governorates were sampled. TYLCV strains Israel and Mild (TYLCV-IL, TYLCV-Mild) were identified by multiplex and real-time PCR. In addition, nucleotide sequence analysis of the V1 and V2 protein genes, revealed ten TYLCV Egyptian isolates (TYLCV from TY1 to 10). Phylogenetic analysis showed their high degree of relatedness with TYLCV-IL Jordan isolate (98%). Here we have showed the complete nucleotide sequence of the TYLCV Egyptian isolate TY10, sampled from El Beheira. A high degree of similarity to other previously reported Egyptian isolates and isolates from Jordan and Japan reflect the importance of phylogenetic analysis in monitoring virus genetic diversity and possibilities for divergence of more virulent strains or genotypes.

Canine Lat1: molecular structure, distribution and its expression in cancer samples.

PubMed

Ochiai, Hideharu; Morishita, Taiki; Onda, Ken; Sugiyama, Hiroki; Maruo, Takuya

2012-07-01

A full-length cDNA sequence of canine L-type amino acid transporter 1 (Lat1) was determined from a canine brain. The sequence was 1828 bp long and was predicted to encode 485 amino acid polypeptides. The deduced amino acid sequence of canine Lat1 showed 93.2% and 91.1% similarities to those of humans and rats, respectively. Northern blot analysis detected Lat1 expression in the cerebellum at 4 kb, and Western blot analysis showed a single band at 40 kDa. RT-PCR analysis revealed a distinct expression of Lat1 in the pancreas and testis in addition to the cerebrum and cerebellum. Notably, Lat1 expression was observed in the tissues of thyroid cancer, melanoma and hemangiopericytoma. Although the cancer samples examined were not enough, Lat1 may serve as a useful biomarker of cancer cells in veterinary clinic.

Preparation and characteristics of epoxy/clay/B4C nanocomposite at high concentration of boron carbide for neutron shielding application

NASA Astrophysics Data System (ADS)

Kiani, Mohammad Amin; Ahmadi, Seyed Javad; Outokesh, Mohammad; Adeli, Ruhollah; Mohammadi, Aghil

2017-12-01

In this research, the characteristics of the prepared samples in epoxy matrix by means of X-ray diffraction (XRD), energy dispersive X-ray spectroscopy (EDS), as well as scanning electron microscope (SEM) are evaluated. Meanwhile, the obtained mechanical properties of the specimen are investigated. Thermogravimetric analysis (TGA) is also employed to evaluate the thermal degradation of manufactured nanocomposites. The thermal neutron absorption properties of nanocomposites containing 3 wt% of montmorillonite nanoclay (closite30B) have been studied experimentally, using an Am-Be point source. Mechanical tests reveal that the higher B4C concentrations, the more tensile strengths, but lower Young's modulus in all samples under consideration. TGA analysis also shows that thermal stability of the nanocomposite, increases in presence of B4C. Finally, neutron absorption analysis shows that increasing the B4C concentration leads to a nonlinearly build-up of neutron absorption cross section.

Novel and successful free comments method for sensory characterization of chocolate ice cream: A comparative study between pivot profile and comment analysis.

PubMed

Fonseca, Fernando G A; Esmerino, Erick A; Filho, Elson R Tavares; Ferraz, Juliana P; da Cruz, Adriano G; Bolini, Helena M A

2016-05-01

Rapid sensory profiling methods have gained space in the sensory evaluation field. Techniques using direct analysis of the terms generated by consumers are considered easy to perform, without specific training requirements, thus improving knowledge about consumer perceptions on various products. This study aimed to determine the sensory profile of different commercial samples of chocolate ice cream, labeled as conventional and light or diet, using the "comment analysis" and "pivot profile" methods, based on consumers' perceptions. In the comment analysis task, consumers responded to 2 separate open questions describing the sensory attributes they liked or disliked in each sample. In the pivot profile method, samples were served in pairs (consisting of a coded sample and pivot), and consumers indicated the higher and lower intensity attributes in the target sample compared with the pivot. We observed that both methods were able to characterize the different chocolate ice cream samples using consumer perception, with high correlation results and configurational similarity (regression vector coefficient=0.917) between them. However, it is worth emphasizing that comment analysis is performed intuitively by consumers, whereas the pivot profile method showed high analytical and discriminative power even using consumers, proving to be a promising technique for routine application when classical descriptive methods cannot be used. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

The classification of secondary colorectal liver cancer in human biopsy samples using angular dispersive x-ray diffraction and multivariate analysis

NASA Astrophysics Data System (ADS)

Theodorakou, Chrysoula; Farquharson, Michael J.

2009-08-01

The motivation behind this study is to assess whether angular dispersive x-ray diffraction (ADXRD) data, processed using multivariate analysis techniques, can be used for classifying secondary colorectal liver cancer tissue and normal surrounding liver tissue in human liver biopsy samples. The ADXRD profiles from a total of 60 samples of normal liver tissue and colorectal liver metastases were measured using a synchrotron radiation source. The data were analysed for 56 samples using nonlinear peak-fitting software. Four peaks were fitted to all of the ADXRD profiles, and the amplitude, area, amplitude and area ratios for three of the four peaks were calculated and used for the statistical and multivariate analysis. The statistical analysis showed that there are significant differences between all the peak-fitting parameters and ratios between the normal and the diseased tissue groups. The technique of soft independent modelling of class analogy (SIMCA) was used to classify normal liver tissue and colorectal liver metastases resulting in 67% of the normal tissue samples and 60% of the secondary colorectal liver tissue samples being classified correctly. This study has shown that the ADXRD data of normal and secondary colorectal liver cancer are statistically different and x-ray diffraction data analysed using multivariate analysis have the potential to be used as a method of tissue classification.

Comparative analysis of Trichuris muris surface using conventional, low vacuum, environmental and field emission scanning electron microscopy.

PubMed

Lopes Torres, Eduardo José; de Souza, Wanderley; Miranda, Kildare

2013-09-23

The whipworm of the genus Trichuris Roederer, 1791, is a nematode of worldwide distribution and comprises species that parasitize humans and other mammals. Infections caused by Trichuris spp. in mammals can lead to various intestinal diseases of human and veterinary interest. The morphology of Trichuris spp. and other helminths has been mostly studied using conventional scanning electron microscopy of chemically fixed, dried and metal-coated specimens, although this kind of preparation has been shown to introduce a variety of artifacts such as sample shrinking, loss of secreted products and/or hiding of small structures due to sample coating. Low vacuum (LVSEM) and environmental scanning electron microscopy (ESEM) have been applied to a variety of insulator samples, also used in the visualization of hydrated and/or live specimens in their native state. In the present work, we used LVSEM and ESEM to analyze the surface of T. muris and analyze its interaction with the host tissue using freshly fixed or unfixed hydrated samples. Analysis of hydrated samples showed a set of new features on the surface of the parasite and the host tissue, including the presence of the secretory products of the bacillary glands on the surface of the parasite, and the presence of mucous material and eggs on the intestinal surface. Field emission scanning electron microscopy (FESEM) was also applied to reveal the detailed structure of the glandular chambers in fixed, dried and metal coated samples. Taken together, the results show that analysis of hydrated samples may provide new insights in the structural organization of the surface of helminth parasites and its interaction with the infected tissue, suggesting that the application of alternative SEM techniques may open new perspectives for analysis in taxonomy, morphology and host-parasite interaction fields. Copyright © 2013 Elsevier B.V. All rights reserved.

ALK-FISH borderline cases in non-small cell lung cancer: Implications for diagnostics and clinical decision making.

PubMed

von Laffert, Maximilian; Stenzinger, Albrecht; Hummel, Michael; Weichert, Wilko; Lenze, Dido; Warth, Arne; Penzel, Roland; Herbst, Hermann; Kellner, Udo; Jurmeister, Philipp; Schirmacher, Peter; Dietel, Manfred; Klauschen, Frederick

2015-12-01

Fluorescence in-situ hybridization (FISH) for the detection of ALK-rearrangements in non-small cell lung cancer (NSCLC) is based on at first sight clear cut-off criteria (≥15% of tumor cells) for split signals (SS) and single red signals (SRS). However, NSCLC with SS-counts around the cut-off may cause interpretation problems. Tissue microarrays containing 753 surgically resected NSCLCs were independently tested for ALK-alterations by FISH and immunohistochemistry (IHC). Our analysis focused on samples with SS/SRS in the range between 10% and 20% (ALK-FISH borderline group). To better understand the role of these samples in routine diagnostics, we performed statistical analyses to systematically estimate the probability of ALK-FISH-misclassification (false negative or positive) for different numbers of evaluated tumor cell nuclei (30, 50, 100, and 200). 94.3% (710/753) of the cases were classified as unequivocally (<10% or ≥20%) ALK-FISH-negative (93%; 700/753) or positive (1.3%; 10/753) and showed concordant IHC results. 5.7% (43/753) of the samples showed SS/SRS between 10% and 20% of the tumor cells. Out of these, 7% (3/43; ALK-FISH: 14%, 18% and 20%) were positive by ALK-IHC, while 93% (40/43) had no detectable expression of the ALK-protein. Statistical analysis showed that ALK-FISH misclassifications occur frequently for samples with rearrangements between 10% and 20% if ALK-characterization is based on a sharp cut-off point (15%). If results in this interval are defined as equivocal (borderline), statistical sampling-related ALK-FISH misclassifications will occur in less than 1% of the cases if 100 tumor cells are evaluated. While ALK status can be determined robustly for the majority of NSCLC by FISH our analysis showed that ∼6% of the cases belong to a borderline group for which ALK-FISH evaluation has only limited reliability due to statistical sampling effects. These cases should be considered equivocal and therapy decisions should include additional tests and clinical considerations. Copyright © 2015 Elsevier Ireland Ltd. All rights reserved.

Evaluation of the LIA-ANA-Profile-17S for the detection of autoantibodies to nuclear antigens.

PubMed

Yi, Ahram; Lee, Chang-Hoon; Moon, Hee-Won; Kim, Hanah; Hur, Mina; Yun, Yeo-Min

2018-05-01

The diagnostic tests for autoimmune disease include screening for autoantibodies for nuclear antigens (ANA) and antibodies against extractable nuclear antigens (ENA). Using the line immunoassay (LIA) method, various kinds of ENA antibodies can be detected simultaneously. We evaluated the performance of the newly launched LIA-ANA-Profile-17S (Shenzhen YHLO Biotech, Shenzhen, China) as compared to a conventional LIA kit. Residual samples were collected from 200 patients who had been tested for ANA using indirect immunofluorescence. The LIA-ANA-Profile-17S was compared to the EuroLine ANA (Euroimmun, Oberlausitz, Germany) for the analysis of 17 different autoantibodies. The concordance rate and agreement between assays were determined. Samples showing discrepancies between the LIA-ANA-Profile-17S and EuroLine tests were further examined through additional analysis. The overall agreement was moderate (kappa = 0.759, 95% CI = 0.712-0.805). Agreement between assays ranged from weak to almost perfect, except for those tests targeting nucleosomes, histones, and PM-Scl. Of the 57 disparate results between LIA-ANA-Profile-17S and EuroLine, 38 (66.7%) samples tested positive under an additional assay, showing variable patterns between types of autoantibodies. The positive rate of each autoantibody between LIA-ANA-Profile-17S and EuroLine did not differ significantly, except for anti-nucleosome and anti-histone assays in samples from patients diagnosed with systemic lupus erythematosus (P = 0.004 and 0.001, respectively). Compared to those from the conventional EuroLine assay, the LIA-ANA-Profile-17S results showed variable agreement in samples showing different prevalence of each autoantibody. The most frequently detected antibodies showed almost perfect agreement. The LIA-ANA-Profile-17S could play a role in the diagnosis of systemic autoimmune disease in ANA-positive samples. Copyright © 2018 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Improving power and robustness for detecting genetic association with extreme-value sampling design.

PubMed

Chen, Hua Yun; Li, Mingyao

2011-12-01

Extreme-value sampling design that samples subjects with extremely large or small quantitative trait values is commonly used in genetic association studies. Samples in such designs are often treated as "cases" and "controls" and analyzed using logistic regression. Such a case-control analysis ignores the potential dose-response relationship between the quantitative trait and the underlying trait locus and thus may lead to loss of power in detecting genetic association. An alternative approach to analyzing such data is to model the dose-response relationship by a linear regression model. However, parameter estimation from this model can be biased, which may lead to inflated type I errors. We propose a robust and efficient approach that takes into consideration of both the biased sampling design and the potential dose-response relationship. Extensive simulations demonstrate that the proposed method is more powerful than the traditional logistic regression analysis and is more robust than the linear regression analysis. We applied our method to the analysis of a candidate gene association study on high-density lipoprotein cholesterol (HDL-C) which includes study subjects with extremely high or low HDL-C levels. Using our method, we identified several SNPs showing a stronger evidence of association with HDL-C than the traditional case-control logistic regression analysis. Our results suggest that it is important to appropriately model the quantitative traits and to adjust for the biased sampling when dose-response relationship exists in extreme-value sampling designs. © 2011 Wiley Periodicals, Inc.

An Array-Based Analysis of MicroRNA Expression Comparing Matched Frozen and Formalin-Fixed Paraffin-Embedded Human Tissue Samples

PubMed Central

Zhang, Xiao; Chen, Jiamin; Radcliffe, Tom; LeBrun, Dave P.; Tron, Victor A.; Feilotter, Harriet

2008-01-01

MicroRNAs (miRNAs) are small, noncoding RNAs that suppress gene expression at the posttranscriptional level via an antisense RNA-RNA interaction. miRNAs used for array-based profiling are generally purified from either snap-frozen or fresh samples. Because tissues found in most pathology departments are available only in formalin-fixed and paraffin-embedded (FFPE) states, we sought to evaluate miRNA derived from FFPE samples for microarray analysis. In this study, miRNAs extracted from matched snap-frozen and FFPE samples were profiled using the Agilent miRNA array platform (Agilent, Santa Clara, CA). Each miRNA sample was hybridized to arrays containing probes interrogating 470 human miRNAs. Seven cases were compared in either duplicate or triplicate. Intrachip and interchip analyses demonstrated that the processes of miRNA extraction, labeling, and hybridization from both frozen and FFPE samples are highly reproducible and add little variation to the results; technical replicates showed high correlations with one another (Kendall tau, 0.722 to 0.853; Spearman rank correlation coefficient, 0.891 to 0.954). Our results showed consistent high correlations between matched frozen and FFPE samples (Kendall tau, 0.669 to 0.815; Spearman rank correlation coefficient, 0.847 to 0.948), supporting the use of FFPE-derived miRNAs for array-based, gene expression profiling. PMID:18832457

An analysis of the impact of pre‐analytical factors on the urine proteome: Sample processing time, temperature, and proteolysis

PubMed Central

Hepburn, Sophie; Cairns, David A.; Jackson, David; Craven, Rachel A.; Riley, Beverley; Hutchinson, Michelle; Wood, Steven; Smith, Matthew Welberry; Thompson, Douglas

2015-01-01

Purpose We have examined the impact of sample processing time delay, temperature, and the addition of protease inhibitors (PIs) on the urinary proteome and peptidome, an important aspect of biomarker studies. Experimental design Ten urine samples from patients with varying pathologies were each divided and PIs added to one‐half, with aliquots of each then processed and frozen immediately, or after a delay of 6 h at 4°C or room temperature (20–22°C), effectively yielding 60 samples in total. Samples were then analyzed by 2D‐PAGE, SELDI‐TOF‐MS, and immunoassay. Results Interindividual variability in profiles was the dominant feature in all analyses. Minimal changes were observed by 2D‐PAGE as a result of delay in processing, temperature, or PIs and no changes were seen in IgG, albumin, β2‐microglobulin, or α1‐microglobulin measured by immunoassay. Analysis of peptides showed clustering of some samples by presence/absence of PIs but the extent was very patient‐dependent with most samples showing minimal effects. Conclusions and clinical relevance The extent of processing‐induced changes and the benefit of PI addition are patient‐ and sample‐dependent. A consistent processing methodology is essential within a study to avoid any confounding of the results. PMID:25400092

Sample Preparation Techniques for Grain Boundary Characterization of Annealed TRISO-Coated Particles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dunzik-Gougar, M. L.; van Rooyen, I. J.; Hill, C. M.

Crystallographic information about chemical vapor deposition layers of silicon carbide (SiC) is essential to understanding layer performance, especially when the layers are in non planar geometries, such as spherical. We performed electron Back Scatter Diffraction (EBSD) analysis of spherical SiC layers using a different approach to sample focus ion beam milling technique to avoid the negative impacts of traditional sample polishing and to address the need of very small samples of irradiated materials for analysis. Mechanical and chemical grinding and polishing of sample surfaces can introduce lattice strains and result in unequal removal of SiC and surrounding layers of differentmore » material due to the hardness differences of these materials. The nature of layer interfaces is thought to play a key role in performance of the SiC; therefore, analysis of representative samples at these interfacial areas is crucial. In work reported here, a focused ion beam (FIB) was employed in a novel manner to prepare a more representative sample for EBSD analysis from TRISO layers free of effects introduced by mechanical and chemical preparation methods. In addition, the difficulty of handling neutron irradiated microscopic samples such as those analyzed in this work has been simplified with pre tilted mounting stages. Our study showed that although the average grain size of samples may be similar, the grain boundary characteristics may differ significantly. It was also found that low angle grain boundaries, comprises 25% in the FIB-prepared sample vs only 1-2% in the polished sample measured in the same particle. From this study it was determined that results of FIB prepared sample will provide more repeatable results, as the role of sample preparation is eliminated.« less

Sample Preparation Techniques for Grain Boundary Characterization of Annealed TRISO-Coated Particles

DOE PAGES

Dunzik-Gougar, M. L.; van Rooyen, I. J.; Hill, C. M.; ...

2016-08-25

Crystallographic information about chemical vapor deposition layers of silicon carbide (SiC) is essential to understanding layer performance, especially when the layers are in non planar geometries, such as spherical. We performed electron Back Scatter Diffraction (EBSD) analysis of spherical SiC layers using a different approach to sample focus ion beam milling technique to avoid the negative impacts of traditional sample polishing and to address the need of very small samples of irradiated materials for analysis. Mechanical and chemical grinding and polishing of sample surfaces can introduce lattice strains and result in unequal removal of SiC and surrounding layers of differentmore » material due to the hardness differences of these materials. The nature of layer interfaces is thought to play a key role in performance of the SiC; therefore, analysis of representative samples at these interfacial areas is crucial. In work reported here, a focused ion beam (FIB) was employed in a novel manner to prepare a more representative sample for EBSD analysis from TRISO layers free of effects introduced by mechanical and chemical preparation methods. In addition, the difficulty of handling neutron irradiated microscopic samples such as those analyzed in this work has been simplified with pre tilted mounting stages. Our study showed that although the average grain size of samples may be similar, the grain boundary characteristics may differ significantly. It was also found that low angle grain boundaries, comprises 25% in the FIB-prepared sample vs only 1-2% in the polished sample measured in the same particle. From this study it was determined that results of FIB prepared sample will provide more repeatable results, as the role of sample preparation is eliminated.« less

Laser-Induced Breakdown Spectroscopy Based Protein Assay for Cereal Samples.

PubMed

Sezer, Banu; Bilge, Gonca; Boyaci, Ismail Hakki

2016-12-14

Protein content is an important quality parameter in terms of price, nutritional value, and labeling of various cereal samples. However, conventional analysis methods, namely, Kjeldahl and Dumas, have major drawbacks such as long analysis time, titration mistakes, and carrier gas dependence with high purity. For this reason, there is an urgent need for rapid, reliable, and environmentally friendly technologies for protein analysis. The present study aims to develop a new method for protein analysis in wheat flour and whole meal by using laser-induced breakdown spectroscopy (LIBS), which is a multielemental, fast, and simple spectroscopic method. Unlike the Kjeldahl and Dumas methods, it has potential to analyze a high number of samples in considerably short time. In the study, nitrogen peaks in LIBS spectra of wheat flour and whole meal samples with different protein contents were correlated with results of the standard Dumas method with the aid of chemometric methods. A calibration graph showed good linearity with the protein content between 7.9 and 20.9% and a 0.992 coefficient of determination (R 2 ). The limit of detection was calculated as 0.26%. The results indicated that LIBS is a promising and reliable method with its high sensitivity for routine protein analysis in wheat flour and whole meal samples.

Analysis of Soluble Proteins in Natural Cordyceps sinensis from Different Producing Areas by Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis and Two-dimensional Electrophoresis

PubMed Central

Li, Chun-Hong; Zuo, Hua-Li; Zhang, Qian; Wang, Feng-Qin; Hu, Yuan-Jia; Qian, Zheng-Ming; Li, Wen-Jia; Xia, Zhi-Ning; Yang, Feng-Qing

2017-01-01

Background: As one of the bioactive components in Cordyceps sinensis (CS), proteins were rarely used as index components to study the correlation between the protein components and producing areas of natural CS. Objective: Protein components of 26 natural CS samples produced in Qinghai, Tibet, and Sichuan provinces were analyzed and compared to investigate the relationship among 26 different producing areas. Materials and Methods: Proteins from 26 different producing areas were extracted by Tris-HCl buffer with Triton X-100, and separated using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and two-dimensional electrophoresis (2-DE). Results: The SDS-PAGE results indicated that the number of protein bands and optical density curves of proteins in 26 CS samples was a bit different. However, the 2-DE results showed that the numbers and abundance of protein spots in protein profiles of 26 samples were obviously different and showed certain association with producing areas. Conclusions: Based on the expression values of matched protein spots, 26 batches of CS samples can be divided into two main categories (Tibet and Qinghai) by hierarchical cluster analysis. SUMMARY The number of protein bands and optical density curves of proteins in 26 Cordyceps sinensis samples were a bit different on the sodium dodecyl sulfate-polyacrylamide gel electrophoresis protein profilesNumbers and abundance of protein spots in protein profiles of 26 samples were obvious different on two-dimensional electrophoresis mapsTwenty-six different producing areas of natural Cordyceps sinensis samples were divided into two main categories (Tibet and Qinghai) by Hierarchical cluster analysis based on the values of matched protein spots. Abbreviations Used: SDS-PAGE: Sodium dodecyl sulfate polyacrylamide gel electrophoresis, 2-DE: Two-dimensional electrophoresis, Cordyceps sinensis: CS, TCMs: Traditional Chinese medicines PMID:28250651

Analysis of Soluble Proteins in Natural Cordyceps sinensis from Different Producing Areas by Sodium Dodecyl Sulfate-Polyacrylamide Gel Electrophoresis and Two-dimensional Electrophoresis.

PubMed

Li, Chun-Hong; Zuo, Hua-Li; Zhang, Qian; Wang, Feng-Qin; Hu, Yuan-Jia; Qian, Zheng-Ming; Li, Wen-Jia; Xia, Zhi-Ning; Yang, Feng-Qing

2017-01-01

As one of the bioactive components in Cordyceps sinensis (CS), proteins were rarely used as index components to study the correlation between the protein components and producing areas of natural CS. Protein components of 26 natural CS samples produced in Qinghai, Tibet, and Sichuan provinces were analyzed and compared to investigate the relationship among 26 different producing areas. Proteins from 26 different producing areas were extracted by Tris-HCl buffer with Triton X-100, and separated using sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) and two-dimensional electrophoresis (2-DE). The SDS-PAGE results indicated that the number of protein bands and optical density curves of proteins in 26 CS samples was a bit different. However, the 2-DE results showed that the numbers and abundance of protein spots in protein profiles of 26 samples were obviously different and showed certain association with producing areas. Based on the expression values of matched protein spots, 26 batches of CS samples can be divided into two main categories (Tibet and Qinghai) by hierarchical cluster analysis. The number of protein bands and optical density curves of proteins in 26 Cordyceps sinensis samples were a bit different on the sodium dodecyl sulfate-polyacrylamide gel electrophoresis protein profilesNumbers and abundance of protein spots in protein profiles of 26 samples were obvious different on two-dimensional electrophoresis mapsTwenty-six different producing areas of natural Cordyceps sinensis samples were divided into two main categories (Tibet and Qinghai) by Hierarchical cluster analysis based on the values of matched protein spots. Abbreviations Used : SDS-PAGE: Sodium dodecyl sulfate polyacrylamide gel electrophoresis, 2-DE: Two-dimensional electrophoresis, Cordyceps sinensis : CS, TCMs: Traditional Chinese medicines.

Woody Species Diversity in Forest Plantations in a Mountainous Region of Beijing, China: Effects of Sampling Scale and Species Selection

PubMed Central

Zhang, Yuxin; Zhang, Shuang; Ma, Keming; Fu, Bojie; Anand, Madhur

2014-01-01

The role of forest plantations in biodiversity conservation has gained more attention in recent years. However, most work on evaluating the diversity of forest plantations focuses only on one spatial scale; thus, we examined the effects of sampling scale on diversity in forest plantations. We designed a hierarchical sampling strategy to collect data on woody species diversity in planted pine (Pinus tabuliformis Carr.), planted larch (Larix principis-rupprechtii Mayr.), and natural secondary deciduous broadleaf forests in a mountainous region of Beijing, China. Additive diversity partition analysis showed that, compared to natural forests, the planted pine forests had a different woody species diversity partitioning pattern at multi-scales (except the Simpson diversity in the regeneration layer), while the larch plantations did not show multi-scale diversity partitioning patterns that were obviously different from those in the natural secondary broadleaf forest. Compare to the natural secondary broadleaf forests, the effects of planted pine forests on woody species diversity are dependent on the sampling scale and layers selected for analysis. Diversity in the planted larch forest, however, was not significantly different from that in the natural forest for all diversity components at all sampling levels. Our work demonstrated that the species selected for afforestation and the sampling scales selected for data analysis alter the conclusions on the levels of diversity supported by plantations. We suggest that a wide range of scales should be considered in the evaluation of the role of forest plantations on biodiversity conservation. PMID:25545860

The negative effect of environmental geological conditions of some geo-archaeological sites of North Coast and Alexandria

NASA Astrophysics Data System (ADS)

Ibrahim, Hani; Kamh, Gamal

2005-12-01

Three geo-archaeological sites at the North Coast and Alexandria, namely, the Alexandria wall (El Shalalat Park site), Abu Soir temple, and Marina excavations, were investigated to determine the negative impact of a salty environmental condition. The monuments suffer from rock decay of different rates. The geo-archaeological sites were built mainly from oolitic limestone blocks (i.e., the Alexandria wall at the El Shalalat Park site and Abu Soir temple) or excavated on them (i.e., Marina excavations). Field inspection and a lab analysis were carried out to understand the weathering mechanism. Salt weathering criteria such as disintegration, pitting, scaling, exfoliation, and honeycomb are observed on the Alexandria wall and upper parts of the Abu Soir temple, while dangerous cracks are detected on the Marina excavation tombs. The petrographic study of the oolitic limestone samples shows that they consist mainly of oolities and drusy sparite as a cement (oolitic grainstone). Some oolities have quartz grains as nuclei. Hydrochemical analysis shows that the total dissolved salts of extracted solutions of the North Coast quarry samples range from 539 to 686 ppm and dramatically increase (i.e., ten times) for extracted solutions from monument samples, ranging from 5395 to 6880 ppm. The dominant cation is sodium while the dominant anion is chlorine. Acid insoluble residue analysis shows that the carbonate content ranges from 89.2% to 96.4% for fresh samples from quarries and from 9.2% to 94.8% for weathered monument samples. The weight loss of the quarry oolitic limestone samples range from 30.7% to 32.7% and its physical and mechanical properties become worse after being subjected to 15 cycles of a durability simulation soundness test (using a sodium sulphate solution). Our main recommendations are to use suitable grouting for binding the cracks, high durability reconstruction rocks, and suitable cleaning methods to remove salts from the monuments.

Got Milk? Breastfeeding and Milk Analysis of a Mother on Chronic Hemodialysis

PubMed Central

Balzer, Michael S.; Gross, Mechthild M.; Lichtinghagen, Ralf; Haller, Hermann; Schmitt, Roland

2015-01-01

Purpose Women on dialysis rarely become pregnant. However, the overall rate of successful pregnancies is increasing in this patient population and breastfeeding becomes an option for mothers on dialysis. In this study we performed a systematic breast milk composition analysis of a mother on chronic hemodialysis (HD). Methods Specimens of breast milk and blood were collected in regular intervals before and after HD from a 39-year old woman starting on day 10 postpartum. Samples were analyzed for electrolytes, retention solutes, nutrients and other laboratory measurements. Breast milk samples from low-risk mothers matched for postpartum age were used as controls. Results Significantly higher levels of creatinine and urea were found in pre-HD breast milk when compared to post-HD. A similar post-dialytic decrease was only found for uric acid but not for any other investigated parameter. Conversely, sodium and chloride were significantly increased in post-HD samples. Compared to controls creatinine and urea were significantly higher in pre-HD samples while the difference remained only significant for post-HD creatinine. Phosphate was significantly lower in pre- and post-HD breast milk when compared to controls, whereas calcium showed no significant differences. In terms of nutrient components glucose levels showed a strong trend for a decrease, whereas protein, triglycerides and cholesterol did not differ. Similarly, no significant differences were found in iron, potassium and magnesium content. Conclusion To the best of our knowledge this is the first report on a breastfeeding mother on chronic dialysis. Although we found differences in creatinine, urea, sodium, chloride and phosphate, our general analysis showed high similarity of our patient’s breast milk to samples from low-risk control mothers. Significant variations in breast milk composition between pre- and post-HD samples suggest that breastfeeding might be preferably performed after dialysis treatment. In summary, our findings indicate that breastfeeding can be considered a viable option for newborns of mothers on dialysis. PMID:26571490

Shooting Lasers

NASA Image and Video Library

2012-11-02

This picture shows a lab demonstration of the measurement chamber inside the Tunable Laser Spectrometer, an instrument that is part of the Sample Analysis at Mars investigation on NASA Curiosity rover.

The effects of crosslinkers on physical, mechanical, and cytotoxic properties of gelatin sponge prepared via in-situ gas foaming method as a tissue engineering scaffold.

PubMed

Poursamar, S Ali; Lehner, Alexander N; Azami, Mahmoud; Ebrahimi-Barough, Somayeh; Samadikuchaksaraei, Ali; Antunes, A P M

2016-06-01

In this study porous gelatin scaffolds were prepared using in-situ gas foaming, and four crosslinking agents were used to determine a biocompatible and effective crosslinker that is suitable for such a method. Crosslinkers used in this study included: hexamethylene diisocyanate (HMDI), poly(ethylene glycol) diglycidyl ether (epoxy), glutaraldehyde (GTA), and genipin. The prepared porous structures were analyzed using Fourier Transform Infrared Spectroscopy (FT-IR), thermal and mechanical analysis as well as water absorption analysis. The microstructures of the prepared samples were analyzed using Scanning Electron Microscopy (SEM). The effects of the crosslinking agents were studied on the cytotoxicity of the porous structure indirectly using MTT analysis. The affinity of L929 mouse fibroblast cells for attachment on the scaffold surfaces was investigated by direct cell seeding and DAPI-staining technique. It was shown that while all of the studied crosslinking agents were capable of stabilizing prepared gelatin scaffolds, there are noticeable differences among physical and mechanical properties of samples based on the crosslinker type. Epoxy-crosslinked scaffolds showed a higher capacity for water absorption and more uniform microstructures than the rest of crosslinked samples, whereas genipin and GTA-crosslinked scaffolds demonstrated higher mechanical strength. Cytotoxicity analysis showed the superior biocompatibility of the naturally occurring genipin in comparison with other synthetic crosslinking agents, in particular relative to GTA-crosslinked samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Sample pooling for real-time PCR detection and virulence determination of the footrot pathogen Dichelobacter nodosus.

PubMed

Frosth, Sara; König, Ulrika; Nyman, Ann-Kristin; Aspán, Anna

2017-09-01

Dichelobacter nodosus is the principal cause of ovine footrot and strain virulence is an important factor in disease severity. Therefore, detection and virulence determination of D. nodosus is important for proper diagnosis of the disease. Today this is possible by real-time PCR analysis. Analysis of large numbers of samples is costly and laborious; therefore, pooling of individual samples is common in surveillance programs. However, pooling can reduce the sensitivity of the method. The aim of this study was to develop a pooling method for real-time PCR analysis that would allow sensitive detection and simultaneous virulence determination of D. nodosus. A total of 225 sheep from 17 flocks were sampled using ESwabs within the Swedish Footrot Control Program in 2014. Samples were first analysed individually and then in pools of five by real-time PCR assays targeting the 16S rRNA and aprV2/B2 genes of D. nodosus. Each pool consisted of four negative and one positive D. nodosus samples with varying amounts of the bacterium. In the individual analysis, 61 (27.1%) samples were positive in the 16S rRNA and the aprV2/B2 PCR assays and 164 (72.9%) samples were negative. All samples positive in the aprV2/B2 PCR-assay were of aprB2 variant. The pooled analysis showed that all 41 pools were also positive for D. nodosus 16S rRNA and the aprB2 variant. The diagnostic sensitivity for pooled and individual samples was therefore similar. Our method includes concentration of the bacteria before DNA-extraction. This may account for the maintenance of diagnostic sensitivity. Diagnostic sensitivity in the real-time PCR assays of the pooled samples were comparable to the sensitivity obtained for individually analysed samples. Even sub-clinical infections were able to be detected in the pooled PCR samples which is important for control of the disease. This method may therefore be implemented in footrot control programs where it can replace analysis of individual samples.

Quality-Assurance Data for Routine Water Analyses by the U.S. Geological Survey Laboratory in Troy, New York-July 1997 through June 1999

USGS Publications Warehouse

Lincoln, Tricia A.; Horan-Ross, Debra A.; McHale, Michael R.; Lawrence, Gregory B.

2006-01-01

The laboratory for analysis of low-ionic-strength water at the U.S. Geological Survey (USGS) Water Science Center in Troy, N.Y., analyzes samples collected by USGS projects throughout the Northeast. The laboratory's quality-assurance program is based on internal and interlaboratory quality-assurance samples and quality-control procedures that were developed to ensure proper sample collection, processing, and analysis. The quality-assurance/quality-control data for the time period addressed in this report were stored in the laboratory's SAS data-management system, which provides efficient review, compilation, and plotting of data. This report presents and discusses results of quality-assurance and quality- control samples analyzed from July 1997 through June 1999. Results for the quality-control samples for 18 analytical procedures were evaluated for bias and precision. Control charts indicate that data for eight of the analytical procedures were occasionally biased for either high-concentration and (or) low-concentration samples but were within control limits; these procedures were: acid-neutralizing capacity, total monomeric aluminum, total aluminum, ammonium, calcium, chloride, specific conductance, and sulfate. The data from the potassium and sodium analytical procedures are insufficient for evaluation. Results from the filter-blank and analytical-blank analyses indicate that the procedures for 11 of 13 analytes were within control limits, although the concentrations for blanks were occasionally outside the control limits. Blank analysis results for chloride showed that 22 percent of blanks did not meet data-quality objectives and results for dissolved organic carbon showed that 31 percent of the blanks did not meet data-quality objectives. Sampling and analysis precision are evaluated herein in terms of the coefficient of variation obtained for triplicate samples in the procedures for 14 of the 18 analytes. At least 90 percent of the samples met data-quality objectives for all analytes except total aluminum (70 percent of samples met objectives) and potassium (83 percent of samples met objectives). Results of the USGS interlaboratory Standard Reference Sample (SRS) Project indicated good data quality for most constituents over the time period. The P-sample (low-ionic-strength constituents) analysis had good ratings in two of these studies and a satisfactory rating in the third. The results of the T-sample (trace constituents) analysis indicated high data quality with good ratings in all three studies. The N-sample (nutrient constituents) studies had one each of excellent, good, and satisfactory ratings. Results of Environment Canada's National Water Research Institute (NWRI) program indicated that at least 80 percent of the samples met data-quality objectives for 9 of the 13 analytes; the exceptions were dissolved organic carbon, ammonium, chloride, and specific conductance. Data-quality objectives were not met for dissolved organic carbon in two NWRI studies, but all of the samples were within control limits for the last study. Data-quality objectives were not met in 41 percent of samples analyzed for ammonium, 25 percent of samples analyzed for chloride, and 30 percent of samples analyzed for specific conductance. Results from blind reference-sample analyses indicated that data-quality objectives were met by at least 84 percent of the samples analyzed for calcium, chloride, magnesium, pH, and potassium. Data-quality objectives were met by 73 percent of those analyzed for sulfate. The data-quality objective was not met for sodium. The data are insufficient for evaluation of the specific conductance results.

Intratumoral heterogeneity in colorectal carcinoma: trucut sampling for DNA ploidy analysis.

PubMed

Giovagnoli, M R; Giarnieri, E; Midiri, G; Tesoriere, A; Ferraro, S; Vecchione, A

1999-01-01

Solid tumors, such as colorectal carcinomas, consist of cell subpopulations that differ both genetically and in their clinical behavior. Many authors have examined cell kinetics and DNA content in colorectal tumors in correlation to clinical and pathological variables with different results. The interpretation of those results present some difficulties related to tumor heterogeneity that to date are unsolved. Our study is based on a new method of colon cancer sampling for DNA content determination. The aim of this work was to reduce the risk of incorrect DNA evaluation due to tumor heterogeneity. Our study was based on eleven selected cases of T3 colorectal carcinoma. Fresh surgical specimens from the primary tumor site were taken during surgery. For each case at least four samples were taken using a 23 gauge trucut from the outside of the serosa through the tumor to the lumen of the colon. The specimens were stained according to a modified Feulgen method and DNA content was measured by image analysis. Three parameters were evaluated: DNA index, ploidy and proliferation level (considered as the sum of elements corresponding to the S and G2 phases). One of the eleven (9.1%) tumors showed a diploid pattern; four out of eleven (36.4%) cases showed a tetra/polyploid pattern and six out of eleven (54.5%) cases showed an aneuploid pattern. Three tumors were monoclonal (27.3%), one diploid and two aneuploid. Eight were polyclonal (72.7%). Considering the single specimen, seven out of sixty-eight specimens (10.3%) were inadequate because of scanty material. Twenty-five out of the sixty-one adequate specimens (41%) were monoclonal and thirty-six (59%) were polyclonal. Five tumors (three monoclonal and two polyclonal) showed the same cell clones on all the examined samples. The remaining six tumors showed interregional variability. The six of the eight polyclonal cases (75%) multiple stem lines were evident, analyzing only one sample taken close to colon serosa, while in one case (25%) it was necessary to examine two samples in order to see the polyclonality of the lesion. When samples taken close to mucosa where analyzed, however, one sample was not enough to show tumor polyclonality in five of the eight polyclonal examined cases. Proliferation level varied greatly in different parts of the same carcinoma and did not correlate to the site from which the sample was taken. In the present study, we demonstrated that DNA ploidy differences may exist between the superficial and the deep part of the same neoplasia and that tumor samples show a greater variability in the deeper layers. Using trucut samplings, it was possible to point out the majority of aneuploid cell populations close to the serosa. In conclusion, trucut biopsy permits full thickness sampling of the tumoral mass and allows, from few samples, to evaluate the multiple DNA stemlines present in different parts of a colorectal tumor.

A comparison between DART-MS and DSA-MS in the forensic analysis of writing inks.

PubMed

Drury, Nicholas; Ramotowski, Robert; Moini, Mehdi

2018-05-23

Ambient ionization mass spectrometry is gaining momentum in forensic science laboratories because of its high speed of analysis, minimal sample preparation, and information-rich results. One such application of ambient ionization methodology includes the analysis of writing inks from questioned documents where colorants of interest may not be soluble in common solvents, rendering thin layer chromatography (TLC) and separation-mass spectrometry methods such as LC/MS (-MS) impractical. Ambient ionization mass spectrometry uses a variety of ionization techniques such as penning ionization in Direct Analysis in Real Time (DART), and atmospheric pressure chemical ionization in Direct Sample Analysis (DSA), and electrospray ionization in Desorption Electrospray Ionization (DESI). In this manuscript, two of the commonly used ambient ionization techniques are compared: Perkin Elmer DSA-MS and IonSense DART in conjunction with a JEOL AccuTOF MS. Both technologies were equally successful in analyzing writing inks and produced similar spectra. DSA-MS produced less background signal likely because of its closed source configuration; however, the open source configuration of DART-MS provided more flexibility for sample positioning for optimum sensitivity and thereby allowing smaller piece of paper containing writing ink to be analyzed. Under these conditions, the minimum sample required for DART-MS was 1mm strokes of ink on paper, whereas DSA-MS required a minimum of 3mm. Moreover, both techniques showed comparable repeatability. Evaluation of the analytical figures of merit, including sensitivity, linear dynamic range, and repeatability, for DSA-MS and DART-MS analysis is provided. To the forensic context of the technique, DART-MS was applied to the analysis of United States Secret Service ink samples directly on a sampling mesh, and the results were compared with DSA-MS of the same inks on paper. Unlike analysis using separation mass spectrometry, which requires sample preparation, both DART-MS and DSA-MS successfully analyzed writing inks with minimal sample preparation. Copyright © 2018 Elsevier B.V. All rights reserved.

[GSTP1, APC and RASSF1 gene methylation in prostate cancer samples: comparative analysis of MS-HRM method and Infinium HumanMethylation450 BeadChip beadchiparray diagnostic value].

PubMed

Skorodumova, L O; Babalyan, K A; Sultanov, R; Vasiliev, A O; Govorov, A V; Pushkar, D Y; Prilepskaya, E A; Danilenko, S A; Generozov, E V; Larin, A K; Kostryukova, E S; Sharova, E I

2016-11-01

There is a clear need in molecular markers for prostate cancer (PC) risk stratification. Alteration of DNA methylation is one of processes that occur during ÐÑ progression. Methylation-sensitive PCR with high resolution melting curve analysis (MS-HRM) can be used for gene methylation analysis in routine laboratory practice. This method requires very small amounts of DNA for analysis. Numerous results have been accumulated on DNA methylation in PC samples analyzed by the Infinium HumanMethylation450 BeadChip (HM450). However, the consistency of MS-HRM results with chip hybridization results has not been examined yet. The aim of this study was to assess the consistency of results of GSTP1, APC and RASSF1 gene methylation analysis in ÐÑ biopsy samples obtained by MS-HRM and chip hybridization. The methylation levels of each gene determined by MS-HRM were statistically different in the group of PC tissue samples and the samples without signs of tumor growth. Chip hybridization data analysis confirmed the results obtained with the MS-HRM. Differences in methylation levels between tumor tissue and histologically intact tissue of each sample determined by MS-HRM and chip hybridization, were consistent with each other. Thus, we showed that the assessment of GSTP1, APC and RASSF1 gene methylation analysis using MS-HRM is suitable for the design of laboratory assays that will differentiate the PC tissue from the tissue without signs of tumor growth.

Ionic solution and nanoparticle assisted MALDI-MS as bacterial biosensors for rapid analysis of yogurt.

PubMed

Lee, Chia-Hsun; Gopal, Judy; Wu, Hui-Fen

2012-01-15

Bacterial analysis from food samples is a highly challenging task because food samples contain intensive interferences from proteins and carbohydrates. Three different conditions of yogurt were analyzed: (1) the fresh yogurt immediately after purchasing, (2) the yogurt after expiry date stored in the refrigerator and (3) the yogurt left outside, without refrigeration. The shelf lives of both these yogurt was compared in terms of the decrease in bacterial signals. AB which initially contained 10(9) cells/mL drastically reduced to 10(7) cells/mL. However, Lin (Feng-Yin) yogurt which initially (fresh) had 10(8) cells/mL, even after two weeks beyond the expiry period showed no marked drop in bacterial count. Conventional MALDI-MS analysis showed limited sensitivity for analysis of yogurt bacteria amidst the complex milk proteins present in yogurt. A cost effective ionic solution, CrO(4)(2-) solution was used to enable the successful detection of bacterial signals (40-fold increased in sensitivity) selectively without the interference of the milk proteins. 0.035 mg of Ag nanoparticles (NPs) were also found to improve the detection of bacteria 2-6 times in yogurt samples. The current approach can be further applied as a rapid, sensitive and effective platform for bacterial analysis from food. Copyright © 2011 Elsevier B.V. All rights reserved.

Steroid hormones in environmental matrices: extraction method comparison.

PubMed

Andaluri, Gangadhar; Suri, Rominder P S; Graham, Kendon

2017-11-09

The U.S. Environmental Protection Agency (EPA) has developed methods for the analysis of steroid hormones in water, soil, sediment, and municipal biosolids by HRGC/HRMS (EPA Method 1698). Following the guidelines provided in US-EPA Method 1698, the extraction methods were validated with reagent water and applied to municipal wastewater, surface water, and municipal biosolids using GC/MS/MS for the analysis of nine most commonly detected steroid hormones. This is the first reported comparison of the separatory funnel extraction (SFE), continuous liquid-liquid extraction (CLLE), and Soxhlet extraction methods developed by the U.S. EPA. Furthermore, a solid phase extraction (SPE) method was also developed in-house for the extraction of steroid hormones from aquatic environmental samples. This study provides valuable information regarding the robustness of the different extraction methods. Statistical analysis of the data showed that SPE-based methods provided better recovery efficiencies and lower variability of the steroid hormones followed by SFE. The analytical methods developed in-house for extraction of biosolids showed a wide recovery range; however, the variability was low (≤ 7% RSD). Soxhlet extraction and CLLE are lengthy procedures and have been shown to provide highly variably recovery efficiencies. The results of this study are guidance for better sample preparation strategies in analytical methods for steroid hormone analysis, and SPE adds to the choice in environmental sample analysis.

Solid sorbent air sampling and analytical procedure for methyl-, dimethyl-, ethyl-, and diethylamine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Elskamp, C.J.; Schultz, G.R.

1986-01-01

A sampling and analytical procedure for methyl-, dimethyl-, ethyl-, and diethylamine was developed in order to avoid problems typically encountered in the sampling and analysis of low molecular weight aliphatic amines. Samples are collected with adsorbent tubes containing Amberlite XAD-7 resin coated with the derivatizing reagent, NBD chloride (7-chloro-4-nitrobenzo-2-oxa-1,3-diazole). Analysis is performed by high performance liquid chromatography with the use of a fluorescence and/or UV/visible detector. All four amines can be monitored simultaneously, and neither collection nor storage is affected by humidity. Samples are stable at room temperature for at least two weeks. The methodology has been tested for eachmore » of the four amines at sample loadings equivalent to air concentration ranges of 0.5 to 30 ppm for a sample volume of 10 liters. The method shows promise for determining other airborne primary and secondary low molecular weight aliphatic amines.« less

A Procedure for Analyzing Classroom Dialogue.

ERIC Educational Resources Information Center

Clarke, John A.

Classroom dialogue is an important influence on students' learning, making the structure and content of dialogue important research variables. An analysis of two sample classroom dialogues using the Thematic and Structural Analysis (TSA) Technique shows a positive correlation between the quality of dialogue structure and the level of student…

An epidemiological survey of Theileria infections in small ruminants in central China.

PubMed

Li, Youquan; Zhang, Xiao; Liu, Zhijie; Chen, Ze; Yang, Jifei; He, Haining; Guan, Guiquan; Liu, Aihong; Ren, Qiaoyun; Niu, Qingli; Liu, Junlong; Luo, Jianxun; Yin, Hong

2014-02-24

Here, we conducted an epidemiological study in five regions in central China to assess the impact of theileriosis on small ruminants. PCR analysis and microscopic evaluations of blood smears to detect ovine and caprine theileriosis was conducted, in which 256 blood samples and 250 ticks were collected from sheep and goats, and tested for Theileria uilenbergi, T. luwenshuni, and T. ovis. The 18S rRNA gene sequences were deduced from positive samples and used for phylogenetic analysis. The results showed that T. luwenshuni was found most frequently in the five investigated regions and the prevalence of T. luwenshuni was found to be very high by PCR analysis. In contrast, T. uilenbergi and T. ovis infections were not detected in these regions. Phylogenetic tree analysis showed that all of the newly isolated Theileria spp. was in the same clade as T. luwenshuni. Haemaphysalis longicornis, which can transmit T. luwenshuni, was also detected in the sampled sheep and goats in these regions. Our results provide important data to increase the understanding of the epidemiology of ovine and caprine theileriosis, and will aid in the implementation of measures to control theileriosis transmission to small ruminants in central China. Copyright © 2013. Published by Elsevier B.V.

Overlap of Spoilage-Associated Microbiota between Meat and the Meat Processing Environment in Small-Scale and Large-Scale Retail Distributions.

PubMed

Stellato, Giuseppina; La Storia, Antonietta; De Filippis, Francesca; Borriello, Giorgia; Villani, Francesco; Ercolini, Danilo

2016-07-01

Microbial contamination in food processing plants can play a fundamental role in food quality and safety. The aims of this study were to learn more about the possible influence of the meat processing environment on initial fresh meat contamination and to investigate the differences between small-scale retail distribution (SD) and large-scale retail distribution (LD) facilities. Samples were collected from butcheries (n = 20), including LD (n = 10) and SD (n = 10) facilities, over two sampling campaigns. Samples included fresh beef and pork cuts and swab samples from the knife, the chopping board, and the butcher's hand. The microbiota of both meat samples and environmental swabs were very complex, including more than 800 operational taxonomic units (OTUs) collapsed at the species level. The 16S rRNA sequencing analysis showed that core microbiota were shared by 80% of the samples and included Pseudomonas spp., Streptococcus spp., Brochothrix spp., Psychrobacter spp., and Acinetobacter spp. Hierarchical clustering of the samples based on the microbiota showed a certain separation between meat and environmental samples, with higher levels of Proteobacteria in meat. In particular, levels of Pseudomonas and several Enterobacteriaceae members were significantly higher in meat samples, while Brochothrix, Staphylococcus, lactic acid bacteria, and Psychrobacter prevailed in environmental swab samples. Consistent clustering was also observed when metabolic activities were considered by predictive metagenomic analysis of the samples. An increase in carbohydrate metabolism was predicted for the environmental swabs and was consistently linked to Firmicutes, while increases in pathways related to amino acid and lipid metabolism were predicted for the meat samples and were positively correlated with Proteobacteria Our results highlighted the importance of the processing environment in contributing to the initial microbial levels of meat and clearly showed that the type of retail facility (LD or SD) did not apparently affect the contamination. The study provides an in-depth description of the microbiota of meat and meat processing environments. It highlights the importance of the environment as a contamination source of spoilage bacteria, and it shows that the size of the retail facility does not affect the level and type of contamination. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Isolation and molecular identification of Vibrio spp. by sequencing of 16S rDNA from seafood, meat and meat products in Libya.

PubMed

Azwai, S M; Alfallani, E A; Abolghait, S K; Garbaj, A M; Naas, H T; Moawad, A A; Gammoudi, F T; Rayes, H M; Barbieri, I; Eldaghayes, I M

2016-01-01

The genus Vibrio includes several food-borne pathogens that cause a spectrum of clinical conditions including septicemia, cholera and milder forms of gastroenteritis. Several Vibrio spp. are commonly associated with food-borne transmission including Vibrio cholerae, Vibrio parahemolyticus, and Vibrio vulnificus. Microbiological analysis for enumeration and isolation of Vibrio spp. were carried out for a total of 93 samples of seafood, meat and meat products from different geographic localities in Libya (Tripoli, Regdalin, Janzour and Tobruk). Vibrio spp. were detected by conventional cultural and molecular method using PCR and sequencing of 16S rDNA. Out of the 93 cultured samples only 48 (51.6%) yielded colonies on Thiosulfate Citrate Bile Salt agar (TCBS) with culture characteristics of Vibrio spp. More than half (n=27) of processed seafood samples (n=46) yielded colonies on TCBS, while only 44.6 % of samples of meat and meat products showed colonies on TCBS. Among cultured seafood samples, the highest bacterial count was recorded in clam with a count of 3.8 ×10(4) CFU\\g. Chicken burger samples showed the highest bacterial count with 6.5 ×10(4) CFU\\g. Molecular analysis of the isolates obtained in this study, showed that 11 samples out of 48 (22.9%) were Vibrio spp. Vibrio parahemolyticus was isolated from camel meat for the first time. This study is an initial step to provide a baseline for future molecular research targeting Vibrio spp. foodborne illnesses. This data will be used to provide information on the magnitude of such pathogens in Libyan seafood, meat and meat products.

Isolation and molecular identification of Vibrio spp. by sequencing of 16S rDNA from seafood, meat and meat products in Libya

PubMed Central

Azwai, S.M.; Alfallani, E.A.; Abolghait, S.K.; Garbaj, A.M.; Naas, H.T.; Moawad, A.A.; Gammoudi, F.T.; Rayes, H.M.; Barbieri, I.; Eldaghayes, I.M.

2016-01-01

The genus Vibrio includes several food-borne pathogens that cause a spectrum of clinical conditions including septicemia, cholera and milder forms of gastroenteritis. Several Vibrio spp. are commonly associated with food-borne transmission including Vibrio cholerae, Vibrio parahemolyticus, and Vibrio vulnificus. Microbiological analysis for enumeration and isolation of Vibrio spp. were carried out for a total of 93 samples of seafood, meat and meat products from different geographic localities in Libya (Tripoli, Regdalin, Janzour and Tobruk). Vibrio spp. were detected by conventional cultural and molecular method using PCR and sequencing of 16S rDNA. Out of the 93 cultured samples only 48 (51.6%) yielded colonies on Thiosulfate Citrate Bile Salt agar (TCBS) with culture characteristics of Vibrio spp. More than half (n=27) of processed seafood samples (n=46) yielded colonies on TCBS, while only 44.6 % of samples of meat and meat products showed colonies on TCBS. Among cultured seafood samples, the highest bacterial count was recorded in clam with a count of 3.8 ×104 CFU\\g. Chicken burger samples showed the highest bacterial count with 6.5 ×104 CFU\\g. Molecular analysis of the isolates obtained in this study, showed that 11 samples out of 48 (22.9%) were Vibrio spp. Vibrio parahemolyticus was isolated from camel meat for the first time. This study is an initial step to provide a baseline for future molecular research targeting Vibrio spp. foodborne illnesses. This data will be used to provide information on the magnitude of such pathogens in Libyan seafood, meat and meat products. PMID:27004169

A comparative study of mid-infrared diffuse reflection (DR) and attenuated total reflection (ATR) spectroscopy for the detection of fungal infection on RWA2-corn.

PubMed

Kos, Gregor; Krska, Rudolf; Lohninger, Hans; Griffiths, Peter R

2004-01-01

An investigation into the rapid detection of mycotoxin-producing fungi on corn by two mid-infrared spectroscopic techniques was undertaken. Corn samples from a single genotype (RWA2, blanks, and contaminated with Fusarium graminearum) were ground, sieved and, after appropriate sample preparation, subjected to mid-infrared spectroscopy using two different accessories (diffuse reflection and attenuated total reflection). The measured spectra were evaluated with principal component analysis (PCA) and the blank and contaminated samples were classified by cluster analysis. Reference data for fungal metabolites were obtained with conventional methods. After extraction and clean-up, each sample was analyzed for the toxin deoxynivalenol (DON) by gas chromatography with electron capture detection (GC-ECD) and ergosterol (a parameter for the total fungal biomass) by high-performance liquid chromatography with diode array detection (HPLC-DAD). The concentration ranges for contaminated samples were 880-3600 microg/kg for ergosterol and 300-2600 microg/kg for DON. Classification efficiency was 100% for ATR spectra. DR spectra did not show as obvious a clustering of contaminated and blank samples. Results and trends were also observed in single spectra plots. Quantification using a PLS1 regression algorithm showed good correlation with DON reference data, but a rather high standard error of prediction (SEP) with 600 microg/kg (DR) and 490 microg/kg (ATR), respectively, for ergosterol. Comparing measurement procedures and results showed advantages for the ATR technique, mainly owing to its ease of use and the easier interpretation of results that were better with respect to classification and quantification.

Development and Commissioning of an External Beam Facility in the Union College Ion Beam Analysis Laboratory

NASA Astrophysics Data System (ADS)

Yoskowitz, Joshua; Clark, Morgan; Labrake, Scott; Vineyard, Michael

2015-10-01

We have developed an external beam facility for the 1.1-MV tandem Pelletron accelerator in the Union College Ion Beam Analysis Laboratory. The beam is extracted from an aluminum pipe through a 1 / 4 ' ' diameter window with a 7.5- μm thick Kapton foil. This external beam facility allows us to perform ion beam analysis on samples that cannot be put under vacuum, including wet samples and samples too large to fit into the scattering chamber. We have commissioned the new facility by performing proton induced X-ray emission (PIXE) analysis of several samples of environmental interest. These include samples of artificial turf, running tracks, and a human tooth with an amalgam filling. A 1.7-MeV external proton beam was incident on the samples positioned 2 cm from the window. The resulting X-rays were measured using a silicon drift detector and were analyzed using GUPIX software to determine the concentrations of elements in the samples. The results on the human tooth indicate that while significant concentrations of Hg, Ag, and Sn are present in the amalgam filling, only trace amounts of Hg appear to have leached into the tooth. The artificial turf and running tracks show rather large concentrations of a broad range of elements and trace amounts of Pb in the turf infill.

A rapid fluorescence assay for danofloxacin in beef muscle: effect of muscle type on limit of quantitation.

PubMed

Schneider, Marilyn J

2008-08-01

A simple, rapid fluorescence screening assay was applied to the analysis of beef muscle for danofloxacin at the U.S. tolerance level of 200 ng/g. Muscle samples were homogenized in acetic acid-acetonitrile, the resultant mixture centrifuged, and fluorescence of the supernatants was then measured. The significant difference between the fluorescence of control muscle sample extracts and extracts of samples fortified at 200 ng/g allowed for successful discrimination between the samples. Setting a threshold level at the average 200 ng/g fortified sample extract fluorescence -3sigma allowed for identification of potentially violative samples. Successful analysis of a group of blind fortified samples over a range of concentrations was accomplished in this manner, without any false-negative results. The limits of quantitation for danofloxacin, as well as enrofloxacin, using this assay were determined in three types of beef muscle (hanging tenderloin, neck, and eye round steak), as well as in serum. Significant differences in limits of quantitation were found among the three different muscle types examined, with hanging tenderloin muscle providing the lowest value. This work not only shows the potential for use of the fluorescence screening assay as an alternative to currently used microbial or antibody-based assays for the analysis of danofloxacin in beef muscle, but also suggests that assays using beef muscle may vary in performance depending on the specific muscle selected for analysis.

Capillary microextraction: A new method for sampling methamphetamine vapour.

PubMed

Nair, M V; Miskelly, G M

2016-11-01

Clandestine laboratories pose a serious health risk to first responders, investigators, decontamination companies, and the public who may be inadvertently exposed to methamphetamine and other chemicals used in its manufacture. Therefore there is an urgent need for reliable methods to detect and measure methamphetamine at such sites. The most common method for determining methamphetamine contamination at former clandestine laboratory sites is selected surface wipe sampling, followed by analysis with gas chromatography-mass spectrometry (GC-MS). We are investigating the use of sampling for methamphetamine vapour to complement such wipe sampling. In this study, we report the use of capillary microextraction (CME) devices for sampling airborne methamphetamine, and compare their sampling efficiency with a previously reported dynamic SPME method. The CME devices consisted of PDMS-coated glass filter strips inside a glass tube. The devices were used to dynamically sample methamphetamine vapour in the range of 0.42-4.2μgm -3 , generated by a custom-built vapour dosing system, for 1-15min, and methamphetamine was analysed using a GC-MS fitted with a ChromatoProbe thermal desorption unit. The devices showed good reproducibility (RSD<15%), and a curvilinear pre-equilibrium relationship between sampling times and peak area, which can be utilised for calibration. Under identical sampling conditions, the CME devices were approximately 30 times more sensitive than the dynamic SPME method. The CME devices could be stored for up to 3days after sampling prior to analysis. Consecutive sampling of methamphetamine and its isotopic substitute, d-9 methamphetamine showed no competitive displacement. This suggests that CME devices, pre-loaded with an internal standard, could be a feasible method for sampling airborne methamphetamine at former clandestine laboratories. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Differential gene expression detection and sample classification using penalized linear regression models.

PubMed

Wu, Baolin

2006-02-15

Differential gene expression detection and sample classification using microarray data have received much research interest recently. Owing to the large number of genes p and small number of samples n (p > n), microarray data analysis poses big challenges for statistical analysis. An obvious problem owing to the 'large p small n' is over-fitting. Just by chance, we are likely to find some non-differentially expressed genes that can classify the samples very well. The idea of shrinkage is to regularize the model parameters to reduce the effects of noise and produce reliable inferences. Shrinkage has been successfully applied in the microarray data analysis. The SAM statistics proposed by Tusher et al. and the 'nearest shrunken centroid' proposed by Tibshirani et al. are ad hoc shrinkage methods. Both methods are simple, intuitive and prove to be useful in empirical studies. Recently Wu proposed the penalized t/F-statistics with shrinkage by formally using the (1) penalized linear regression models for two-class microarray data, showing good performance. In this paper we systematically discussed the use of penalized regression models for analyzing microarray data. We generalize the two-class penalized t/F-statistics proposed by Wu to multi-class microarray data. We formally derive the ad hoc shrunken centroid used by Tibshirani et al. using the (1) penalized regression models. And we show that the penalized linear regression models provide a rigorous and unified statistical framework for sample classification and differential gene expression detection.

Comparative analysis of Sambucus nigra and Sambucus australis flowers: development and validation of an HPLC method for raw material quantification and preliminary stability study.

PubMed

Scopel, Marina; Mentz, Lílian Auler; Henriques, Amélia Teresinha

2010-07-01

This work was designed to develop a simple, effective, and reliable LC system to identify a chemical marker and compare Sambucus nigra L. and Sambucus australis Cham. et Schltdl. flower extracts (American and European elder). Rutin was the main constituent of both species. The developed method showed a linear response in the range of 10 to 45 microg x mL(-1) for rutin and 1.75 to 3.25 microg x mL(-1) for samples of the Sambucus species. Precision was determined and the relative standard deviations were 1.75 % for HSN and 1.28 % for HSA for intraday precision and 1.28 % and 1.51 % for inter-day precision, respectively, while accuracy was 97.9 % for HSN and 99.41 % for HSA. Quantification and detection limits as well as robustness were determined, presenting adequate results. The LC method showed an adequate performance for the separation of flavonoid glycosides in S. nigra and S. australis extracts, since the presence of interference had been previously evaluated. The analysis of thirty different samples of S. NIGRA and S. australis of different origins did not show significant variability among them. An accelerated stability study revealed a significant decrease in the first 30 days reaching 57 % in 90 days for S. australis samples and a total decrease of 25 % in 90 days for S. nigra samples, considering rutin as the chemical marker. These results will contribute to quality control analysis routines of these raw materials in pharmaceutical production facilities. Georg Thieme Verlag KG Stuttgart.New York.

Stellar population of the superbubble N 206 in the LMC. I. Analysis of the Of-type stars

NASA Astrophysics Data System (ADS)

Ramachandran, Varsha; Hainich, R.; Hamann, W.-R.; Oskinova, L. M.; Shenar, T.; Sander, A. A. C.; Todt, H.; Gallagher, J. S.

2018-01-01

Context. Massive stars severely influence their environment by their strong ionizing radiation and by the momentum and kinetic energy input provided by their stellar winds and supernovae. Quantitative analyses of massive stars are required to understand how their feedback creates and shapes large scale structures of the interstellar medium. The giant H II region N 206 in the Large Magellanic Cloud contains an OB association that powers a superbubble filled with hot X-ray emitting gas, serving as an ideal laboratory in this context. Aims: We aim to estimate stellar and wind parameters of all OB stars in N 206 by means of quantitative spectroscopic analyses. In this first paper, we focus on the nine Of-type stars located in this region. We determine their ionizing flux and wind mechanical energy. The analysis of nitrogen abundances in our sample probes rotational mixing. Methods: We obtained optical spectra with the multi-object spectrograph FLAMES at the ESO-VLT. When possible, the optical spectroscopy was complemented by UV spectra from the HST, IUE, and FUSE archives. Detailed spectral classifications are presented for our sample Of-type stars. For the quantitative spectroscopic analysis we used the Potsdam Wolf-Rayet model atmosphere code. We determined the physical parameters and nitrogen abundances of our sample stars by fitting synthetic spectra to the observations. Results: The stellar and wind parameters of nine Of-type stars, which are largely derived from spectral analysis are used to construct wind momentum - luminosity relationship. We find that our sample follows a relation close to the theoretical prediction, assuming clumped winds. The most massive star in the N 206 association is an Of supergiant that has a very high mass-loss rate. Two objects in our sample reveal composite spectra, showing that the Of primaries have companions of late O subtype. All stars in our sample have an evolutionary age of less than 4 million yr, with the O2-type star being the youngest. All these stars show a systematic discrepancy between evolutionary and spectroscopic masses. All stars in our sample are nitrogen enriched. Nitrogen enrichment shows a clear correlation with increasing projected rotational velocities. Conclusions: The mechanical energy input from the Of stars alone is comparable to the energy stored in the N 206 superbubble as measured from the observed X-ray and Hα emission.

Optical, electrical and magnetic properties of nanostructured Mn3O4 synthesized through a facile chemical route

NASA Astrophysics Data System (ADS)

Bose, Vipin C.; Biju, V.

2015-02-01

Nanostructured Mn3O4 sample with an average crystallite size of ˜15 nm is synthesized via the reduction of potassium permanganate using hydrazine. The average particle size obtained from the Transmission Electron Microscopy analysis is in good agreement with the average crystallite size estimated from X-ray diffraction analysis. The presence of Mn4+ ions at the octahedral sites is inferred from the results of Raman, UV-visible absorption and X-ray photoelectron spectroscopy analyzes. DC electrical conductivity of the sample in the temperature range 313-423 K, is about five orders of magnitude larger than that reported for single crystalline Mn3O4 sample. The dominant conduction mechanism is identified to be of the polaronic hopping of holes between cations in the octahedral sites. The zero field cooled and field cooled magnetization of the sample is studied in the range 20-300 K. The Curie temperature for the sample is about 45 K, below which the sample is ferrimagnetic. A blocking temperature of 35 K is observed in the field cooled curve. It is observed that the sample shows hysteresis at temperatures below the Curie temperature with no saturation, even at an applied field (20 kOe). The presence of an ordered core and disordered surface of spin arrangements is observed from the magnetization studies. Above the Curie temperature, the sample shows linear dependence of magnetization on applied field with no hysteresis characteristic of paramagnetic phase.

Optimization of whole-transcriptome amplification from low cell density deep-sea microbial samples for metatranscriptomic analysis.

PubMed

Wu, Jieying; Gao, Weimin; Zhang, Weiwen; Meldrum, Deirdre R

2011-01-01

Limitation in sample quality and quantity is one of the big obstacles for applying metatranscriptomic technologies to explore gene expression and functionality of microbial communities in natural environments. In this study, several amplification methods were evaluated for whole-transcriptome amplification of deep-sea microbial samples, which are of low cell density and high impurity. The best amplification method was identified and incorporated into a complete protocol to isolate and amplify deep-sea microbial samples. In the protocol, total RNA was first isolated by a modified method combining Trizol (Invitrogen, CA) and RNeasy (QIAGEN, CA) method, amplified with a WT-Ovation™ Pico RNA Amplification System (NuGEN, CA), and then converted to double-strand DNA from single-strand cDNA with a WT-Ovation™ Exon Module (NuGEN, CA). The products from the whole-transcriptome amplification of deep-sea microbial samples were assessed first through random clone library sequencing. The BLAST search results showed that marine-based sequences are dominant in the libraries, consistent with the ecological source of the samples. The products were then used for next-generation Roche GS FLX Titanium sequencing to obtain metatranscriptome data. Preliminary analysis of the metatranscriptomic data showed good sequencing quality. Although the protocol was designed and demonstrated to be effective for deep-sea microbial samples, it should be applicable to similar samples from other extreme environments in exploring community structure and functionality of microbial communities. Copyright © 2010 Elsevier B.V. All rights reserved.

NS3 protease resistance-associated substitutions in liver tissue and plasma samples from patients infected by hepatitis C virus genotype 1A or 1B.

PubMed

Morsica, Giulia; Andolina, Andrea; Merli, Marco; Messina, Emanuela; Hasson, Hamid; Lazzarin, Adriano; Uberti-Foppa, Caterina; Bagaglio, Sabrina

2017-08-01

The presence of naturally occurring resistance-associated substitutions (RASs) in the HCV-protease domain has been poorly investigated in the liver, the main site of HCV replication. We evaluated the natural resistance of the virus to NS3 protease inhibitors in liver tissue and plasma samples taken from HCV-infected patients. RASs were investigated by means of viral population sequencing in liver tissue samples from 18 HCV-infected patients harbouring genotype 1a or genotype 1b; plasma samples from 12 of these patients were also available for virological investigation. A discordant genotype was found in two of the 12 patients (16.6%) who provided samples from both compartments. Sequence analysis of the NS3 protease domain showed the presence of RASs in four of the 18 liver tissue samples (22.2%), two of which showed cross-resistance to protease inhibitors in clinical use or phase 2-3 trials. The analysis of the 12 paired tissues and plasma samples excluded the presence of RASs in the plasma compartment. The dominance of discordant genotypes in the paired liver and plasma samples of some HCV-infected patients suggests mixed infection possibly leading to the selective advantage of different genotype in the two compartments. The presence of RASs at intra-hepatic level is not uncommon and may lead to the early emergence of cross-resistant strains.

Use of the Keele injector for sample introduction for gas chromatographic analysis of vinclozolin in lettuces.

PubMed

Shim, J H; Lee, Y S; Kim, M R; Lee, C J; Kim, I S

2003-10-10

We examined a Keele injector for sample introduction for gas chromatographic analysis of vinclozolin treated in lettuces. Samples in milligram quantity were introduced into a glass tube in a Keele injector at a gas chromatograph injection port. The glass tube was then crushed to allow the sample to carry onto a capillary column in a normal manner. The standard calibration curve for quantitative detection of vinclozolin was obtained by determining vinclozolin spiked in samples at variable concentrations. The calibration curve showed a linear response to vinclozolin ranging from 0.05 to 1.0 microg/g, giving a slope value of 174.8, the y-intercept value of -2.8146 and the mean r2-value of 0.9994. Limit of quantification for vinclozolin was 0.05 microg/g by this method, comparable to 0.01 microg/g by a normal injector. When samples treated previously with vinclozolin were determined by the Keele injector, vinclozolin was found to be about 30% lower as compared to a normal method, suggesting about 70% recovery of the spiked vinclozolin by the Keele injector. From these results, the Keele injector was suggested to be potential for sample introduction in gas chromatographic analysis of vinclozolin in lettuce samples.

Gene expression profile in cardiovascular disease and preeclampsia: a meta-analysis of the transcriptome based on raw data from human studies deposited in Gene Expression Omnibus.

PubMed

Sitras, V; Fenton, C; Acharya, G

2015-02-01

Cardiovascular disease (CVD) and preeclampsia (PE) share common clinical features. We aimed to identify common transcriptomic signatures involved in CVD and PE in humans. Meta-analysis of individual raw microarray data deposited in GEO, obtained from blood samples of patients with CVD versus controls and placental samples from women with PE versus healthy women with uncomplicated pregnancies. Annotation of cases versus control samples was taken directly from the microarray documentation. Genes that showed a significant differential expression in the majority of experiments were selected for subsequent analysis. Hypergeometric gene list analysis was performed using Bioconductor GOstats package. Bioinformatic analysis was performed in PANTHER. Seven studies in CVD and 5 studies in PE were eligible for meta-analysis. A total of 181 genes were found to be differentially expressed in microarray studies investigating gene expression in blood samples obtained from patients with CVD compared to controls and 925 genes were differentially expressed between preeclamptic and healthy placentas. Among these differentially expressed genes, 22 were common between CVD and PE. Bioinformatic analysis of these genes revealed oxidative stress, p-53 pathway feedback, inflammation mediated by chemokines and cytokines, interleukin signaling, B-cell activation, PDGF signaling, Wnt signaling, integrin signaling and Alzheimer disease pathways to be involved in the pathophysiology of both CVD and PE. Metabolism, development, response to stimulus, immune response and cell communication were the associated biologic processes in both conditions. Gene set enrichment analysis showed the following overlapping pathways between CVD and PE: TGF-β-signaling, apoptosis, graft-versus-host disease, allograft rejection, chemokine signaling, steroid hormone synthesis, type I and II diabetes mellitus, VEGF signaling, pathways in cancer, GNRH signaling, Huntingtons disease and Notch signaling. CVD and PE share same common traits in their gene expression profile indicating common pathways in their pathophysiology. Copyright © 2014 Elsevier Ltd. All rights reserved.

Comparison of Xpert MTB/RIF with line probe assay for detection of rifampin-monoresistant Mycobacterium tuberculosis.

PubMed

Rufai, Syed Beenish; Kumar, Parveen; Singh, Amit; Prajapati, Suneel; Balooni, Veena; Singh, Sarman

2014-06-01

The MTBDRplus line probe assay (LPA) and Xpert MTB/RIF have been endorsed by the World Health Organization for the rapid diagnosis of drug-resistant tuberculosis. However, there is no clarity regarding the superiority of one over the other. In a double-blinded prospective study, we evaluated the efficacy of the Xpert MTB/RIF on samples that were first tested by LPA under the revised national tuberculosis control program of India. A total of 405 sputum samples from suspected drug-resistant tuberculosis patients were included. Of these, 285 smear-positive samples were subjected to LPA. Seventy-two (25.8%) samples showed multidrug resistance, 62 (22.2%) showed rifampin monoresistance, 29 (10.3%) showed isoniazid monoresistance, and 116 (41.5%) were pan-susceptible. Six (2.1%) of the samples gave invalid results. Of the 62 rifampin-monoresistant samples by LPA, 38 (61.4%) showed rifampin resistance, while 21 (33.8%) were found susceptible to rifampin by Xpert MTB/RIF using cartridge version G4. Three (4.8%) samples gave an error. Of the 116 pan-susceptible samples, only 83 were available for Xpert MTB/RIF testing; 4 (5.1%) were rifampin resistant, 74 (94.8%) were susceptible, and 5 (6.0%) showed an error. The 25 discrepant samples were further subjected to MGIT960 drug susceptibility testing. The MGIT960 results showed 100% agreement with LPA results but only 64.4% agreement with Xpert MTB/RIF results. Sequencing analysis of discrepant samples showed 91.3% concordance with LPA but only 8.7% concordance with the Xpert MTB/RIF assay. These findings indicate that by using Xpert MTB/RIF testing we might be underestimating the burden of drug-resistant tuberculosis and indicate that country-specific probes need to be designed to increase the sensitivity of the Xpert MTB/RIF. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Comparison of Xpert MTB/RIF with Line Probe Assay for Detection of Rifampin-Monoresistant Mycobacterium tuberculosis

PubMed Central

Rufai, Syed Beenish; Kumar, Parveen; Singh, Amit; Prajapati, Suneel; Balooni, Veena

2014-01-01

The MTBDRplus line probe assay (LPA) and Xpert MTB/RIF have been endorsed by the World Health Organization for the rapid diagnosis of drug-resistant tuberculosis. However, there is no clarity regarding the superiority of one over the other. In a double-blinded prospective study, we evaluated the efficacy of the Xpert MTB/RIF on samples that were first tested by LPA under the revised national tuberculosis control program of India. A total of 405 sputum samples from suspected drug-resistant tuberculosis patients were included. Of these, 285 smear-positive samples were subjected to LPA. Seventy-two (25.8%) samples showed multidrug resistance, 62 (22.2%) showed rifampin monoresistance, 29 (10.3%) showed isoniazid monoresistance, and 116 (41.5%) were pan-susceptible. Six (2.1%) of the samples gave invalid results. Of the 62 rifampin-monoresistant samples by LPA, 38 (61.4%) showed rifampin resistance, while 21 (33.8%) were found susceptible to rifampin by Xpert MTB/RIF using cartridge version G4. Three (4.8%) samples gave an error. Of the 116 pan-susceptible samples, only 83 were available for Xpert MTB/RIF testing; 4 (5.1%) were rifampin resistant, 74 (94.8%) were susceptible, and 5 (6.0%) showed an error. The 25 discrepant samples were further subjected to MGIT960 drug susceptibility testing. The MGIT960 results showed 100% agreement with LPA results but only 64.4% agreement with Xpert MTB/RIF results. Sequencing analysis of discrepant samples showed 91.3% concordance with LPA but only 8.7% concordance with the Xpert MTB/RIF assay. These findings indicate that by using Xpert MTB/RIF testing we might be underestimating the burden of drug-resistant tuberculosis and indicate that country-specific probes need to be designed to increase the sensitivity of the Xpert MTB/RIF. PMID:24648554

Effect of ambient temperature storage on potable water coliform population estimations.

PubMed Central

Standridge, J H; Delfino, J J

1983-01-01

The effect of the length of time between sampling potable water and performing coliform analyses has been a long-standing controversial issue in environmental microbiology. The issue is of practical importance since reducing the sample-to-analysis time may substantially increase costs for water analysis programs. Randomly selected samples (from those routinely collected throughout the State of Wisconsin) were analyzed for total coliforms after being held at room temperature (20 +/- 2 degrees C) for 24 and 48 h. Differences in results for the two holding times were compared with differences predicted by probability calculations. The study showed that storage of the potable water for up to 48 h had little effect on the public health significance of most samples containing more than two coliforms per 100 ml. PMID:6651296

Rapid quality assessment of Radix Aconiti Preparata using direct analysis in real time mass spectrometry.

PubMed

Zhu, Hongbin; Wang, Chunyan; Qi, Yao; Song, Fengrui; Liu, Zhiqiang; Liu, Shuying

2012-11-08

This study presents a novel and rapid method to identify chemical markers for the quality control of Radix Aconiti Preparata, a world widely used traditional herbal medicine. In the method, the samples with a fast extraction procedure were analyzed using direct analysis in real time mass spectrometry (DART MS) combined with multivariate data analysis. At present, the quality assessment approach of Radix Aconiti Preparata was based on the two processing methods recorded in Chinese Pharmacopoeia for the purpose of reducing the toxicity of Radix Aconiti and ensuring its clinical therapeutic efficacy. In order to ensure the safety and effectivity in clinical use, the processing degree of Radix Aconiti should be well controlled and assessed. In the paper, hierarchical cluster analysis and principal component analysis were performed to evaluate the DART MS data of Radix Aconiti Preparata samples in different processing times. The results showed that the well processed Radix Aconiti Preparata, unqualified processed and the raw Radix Aconiti could be clustered reasonably corresponding to their constituents. The loading plot shows that the main chemical markers having the most influence on the discrimination amongst the qualified and unqualified samples were mainly some monoester diterpenoid aconitines and diester diterpenoid aconitines, i.e. benzoylmesaconine, hypaconitine, mesaconitine, neoline, benzoylhypaconine, benzoylaconine, fuziline, aconitine and 10-OH-mesaconitine. The established DART MS approach in combination with multivariate data analysis provides a very flexible and reliable method for quality assessment of toxic herbal medicine. Copyright © 2012 Elsevier B.V. All rights reserved.

Media-Constructed Anti-Intellectualism: The Portrayal of Experts in Popular US Television Talk Shows.

ERIC Educational Resources Information Center

Holderman, Lisa B.

2003-01-01

Examines the popular portrayal of intellectual expertise through a content analysis of 200 of the 10 top-rated popular US television talk shows. Shows that experts in this sample were typically brought on late in the program, allotted little speaking time, placed among non-experts, frequently interrupted, and sometimes challenged. Indicates that…

Influent of Borax Decahydrate Composition as Additional Flux into Stoneware Bodies

NASA Astrophysics Data System (ADS)

Bakil, Siti Natrah Abd; Hussin, Rosniza; Bakar Aramjat, Abu

2017-08-01

Stoneware is vitrified, has less porosity and requires high sintering temperature. The influent of borax decahydrate composition at sintering temperature 1050°C and 1150°C on the thermal analysis, fracture surface, linear shrinkage, water absorption and modular of rapture (MOR) were investigated. Rectangular sample were produced by uniaxially pressing at 40MPa. The thermal behavior was determined by thermogravimetric and different thermal analysis (TGA-DTA). The Scanning electron microscopy (SEM) was used for fracture surface analysis. The water absorption (%) of the sample were determined using Archimedes’ method. The experimental result showed that content of borax decahydrate have influent the properties of stoneware bodies.

Inventory and mapping of flood inundation using interactive digital image analysis techniques

USGS Publications Warehouse

Rohde, Wayne G.; Nelson, Charles A.; Taranik, J.V.

1979-01-01

LANDSAT digital data and color infra-red photographs were used in a multiphase sampling scheme to estimate the area of agricultural land affected by a flood. The LANDSAT data were classified with a maximum likelihood algorithm. Stratification of the LANDSAT data, prior to classification, greatly reduced misclassification errors. The classification results were used to prepare a map overlay showing the areal extent of flooding. These data also provided statistics required to estimate sample size in a two phase sampling scheme, and provided quick, accurate estimates of areas flooded for the first phase. The measurements made in the second phase, based on ground data and photo-interpretation, were used with two phase sampling statistics to estimate the area of agricultural land affected by flooding These results show that LANDSAT digital data can be used to prepare map overlays showing the extent of flooding on agricultural land and, with two phase sampling procedures, can provide acreage estimates with sampling errors of about 5 percent. This procedure provides a technique for rapidly assessing the areal extent of flood conditions on agricultural land and would provide a basis for designing a sampling framework to estimate the impact of flooding on crop production.

[Heavy metals pollution and analysis of seasonal variation runoff in Xi'an].

PubMed

Yuan, Hong-Lin; Li, Xing-Yu; Wang, Xiao-Chang

2014-11-01

In order to explore heavy metals pollution situation,changes in characteristics, the correlation between each heavy mental and pollution source analysis of Xi'an various regions in different season in one year. This study collected several samples of Xi'an rainfall typical urban trunk roads throughout the year in 2013 and used inductively coupled plasma mass spectrometry (ICP-MS) to determine the level of Fe, Mn, Pb, Zn, Al, Cd of the samples, then, analyzed the seasonal change of heavy mental. Studies have shown that: the heavy metal of Xi'an road runoff pollutes seriously, the concentration of Fe over three times of the national standard and maintain the higher levels throughout the year, meanwhile the concentration with the intensity of human activities increases. The concentration of Mn and Zn in one year show a trends: winter > autumn > summer> spring. Pb concentration increases with the increase in traffic volume, while showing: winter > spring > summer > autumn. Factor analysis shows: Fe and Al was affected by the same sources-natural sources; Zn, Cd affected by anthropogenic sources of large; Mn, Pb affected by the larger traffic sources.

Application of Ion Torrent Sequencing to the Assessment of the Effect of Alkali Ballast Water Treatment on Microbial Community Diversity

PubMed Central

Fujimoto, Masanori; Moyerbrailean, Gregory A.; Noman, Sifat; Gizicki, Jason P.; Ram, Michal L.; Green, Phyllis A.; Ram, Jeffrey L.

2014-01-01

The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12) treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA) prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (p<0.001). UniFrac distance based principal coordinate analysis (PCoA) plots and UPGMA tree analysis revealed that NaOH-treated ballast water microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for <0.5% of the total reads in intake samples but more than 50% of the reads in the treated discharge samples. The only apparent difference in microbial community structure between PMA-processed and non-PMA samples occurred in intake water samples, which exhibited a significantly higher amount of PMA-sensitive cyanobacteria/chloroplast 16S rRNA than their corresponding non-PMA total DNA samples. The community assembly obtained using Ion Torrent sequencing was comparable to that obtained from a subset of samples that were also subjected to 454 pyrosequencing. This study showed the efficacy of alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new Ion Torrent sequencing techniques to microbial community studies. PMID:25222021

Application of ion torrent sequencing to the assessment of the effect of alkali ballast water treatment on microbial community diversity.

PubMed

Fujimoto, Masanori; Moyerbrailean, Gregory A; Noman, Sifat; Gizicki, Jason P; Ram, Michal L; Green, Phyllis A; Ram, Jeffrey L

2014-01-01

The impact of NaOH as a ballast water treatment (BWT) on microbial community diversity was assessed using the 16S rRNA gene based Ion Torrent sequencing with its new 400 base chemistry. Ballast water samples from a Great Lakes ship were collected from the intake and discharge of both control and NaOH (pH 12) treated tanks and were analyzed in duplicates. One set of duplicates was treated with the membrane-impermeable DNA cross-linking reagent propidium mono-azide (PMA) prior to PCR amplification to differentiate between live and dead microorganisms. Ion Torrent sequencing generated nearly 580,000 reads for 31 bar-coded samples and revealed alterations of the microbial community structure in ballast water that had been treated with NaOH. Rarefaction analysis of the Ion Torrent sequencing data showed that BWT using NaOH significantly decreased microbial community diversity relative to control discharge (p<0.001). UniFrac distance based principal coordinate analysis (PCoA) plots and UPGMA tree analysis revealed that NaOH-treated ballast water microbial communities differed from both intake communities and control discharge communities. After NaOH treatment, bacteria from the genus Alishewanella became dominant in the NaOH-treated samples, accounting for <0.5% of the total reads in intake samples but more than 50% of the reads in the treated discharge samples. The only apparent difference in microbial community structure between PMA-processed and non-PMA samples occurred in intake water samples, which exhibited a significantly higher amount of PMA-sensitive cyanobacteria/chloroplast 16S rRNA than their corresponding non-PMA total DNA samples. The community assembly obtained using Ion Torrent sequencing was comparable to that obtained from a subset of samples that were also subjected to 454 pyrosequencing. This study showed the efficacy of alkali ballast water treatment in reducing ballast water microbial diversity and demonstrated the application of new Ion Torrent sequencing techniques to microbial community studies.

Multivariate classification of edible salts: Simultaneous Laser-Induced Breakdown Spectroscopy and Laser-Ablation Inductively Coupled Plasma Mass Spectrometry Analysis

NASA Astrophysics Data System (ADS)

Lee, Yonghoon; Nam, Sang-Ho; Ham, Kyung-Sik; Gonzalez, Jhanis; Oropeza, Dayana; Quarles, Derrick; Yoo, Jonghyun; Russo, Richard E.

2016-04-01

Laser-Induced Breakdown Spectroscopy (LIBS) and Laser-Ablation Inductively Coupled Plasma Mass Spectrometry (LA-ICP-MS), both based on laser ablation sampling, can be employed simultaneously to obtain different chemical fingerprints from a sample. We demonstrated that this analysis approach can provide complementary information for improved classification of edible salts. LIBS could detect several of the minor metallic elements along with Na and Cl, while LA-ICP-MS spectra were used to measure non-metallic and trace heavy metal elements. Principal component analysis using LIBS and LA-ICP-MS spectra showed that their major spectral variations classified the sample salts in different ways. Three classification models were developed by using partial least squares-discriminant analysis based on the LIBS, LA-ICP-MS, and their fused data. From the cross-validation performances and confusion matrices of these models, the minor metallic elements (Mg, Ca, and K) detected by LIBS and the non-metallic (I) and trace heavy metal (Ba, W, and Pb) elements detected by LA-ICP-MS provided complementary chemical information to distinguish particular salt samples.

Laser-induced breakdown spectroscopy for quantitative spectrochemical analysis of geological materials: effects of the matrix and simultaneous determination.

PubMed

Anzano, Jesús M; Villoria, Mark A; Ruíz-Medina, Antonio; Lasheras, Roberto J

2006-08-11

A microscopic laser-induced breakdown spectrometer was used to evaluate the analytical matrix effect commonly observed in the analysis of geological materials. Samples were analyzed in either the powder or pressed pellet forms. Calibration curves of a number of iron and aluminum compounds showed a linear relationship between the elemental concentration and peak intensity. A direct determination of elemental content can thus be made from extrapolation on these calibration curves. To investigate matrix effects, synthetic model samples were prepared from various iron and aluminum compounds spiked with SiO2 and CaCO3. The addition of these matrices had a pronounced analytical effect on those compounds prepared as pressed pellets. However, results indicated the absence of matrix effects when the samples were presented to the laser as loose powders on tape and results were compared to certified values, indicating the reliability of this approach for accurate analysis, provided the sample particle diameters are greater than approximately 100 microm. Finally, the simultaneous analysis of two different elements was demonstrated using powders on tape.

Application of Multivariate Statistical Analysis to Biomarkers in Se-Turkey Crude Oils

NASA Astrophysics Data System (ADS)

Gürgey, K.; Canbolat, S.

2017-11-01

Twenty-four crude oil samples were collected from the 24 oil fields distributed in different districts of SE-Turkey. API and Sulphur content (%), Stable Carbon Isotope, Gas Chromatography (GC), and Gas Chromatography-Mass Spectrometry (GC-MS) data were used to construct a geochemical data matrix. The aim of this study is to examine the genetic grouping or correlations in the crude oil samples, hence the number of source rocks present in the SE-Turkey. To achieve these aims, two of the multivariate statistical analysis techniques (Principle Component Analysis [PCA] and Cluster Analysis were applied to data matrix of 24 samples and 8 source specific biomarker variables/parameters. The results showed that there are 3 genetically different oil groups: Batman-Nusaybin Oils, Adıyaman-Kozluk Oils and Diyarbakir Oils, in addition to a one mixed group. These groupings imply that at least, three different source rocks are present in South-Eastern (SE) Turkey. Grouping of the crude oil samples appears to be consistent with the geographic locations of the oils fields, subsurface stratigraphy as well as geology of the area.

Compositional analysis of genetically modified corn events (NK603, MON88017×MON810 and MON89034×MON88017) compared to conventional corn.

PubMed

Rayan, Ahmed M; Abbott, Louise C

2015-06-01

Compositional analysis of genetically modified (GM) crops continues to be an important part of the overall evaluation in the safety assessment for these materials. The present study was designed to detect the genetic modifications and investigate the compositional analysis of GM corn containing traits of multiple genes (NK603, MON88017×MON810 and MON89034×MON88017) compared with non-GM corn. Values for most biochemical components assessed for the GM corn samples were similar to those of the non-GM control or were within the literature range. Significant increases were observed in protein, fat, fiber and fatty acids of the GM corn samples. The observed increases may be due to the synergistic effect of new traits introduced into corn varieties. Furthermore, SDS-PAGE analysis showed high similarity among the protein fractions of the investigated corn samples. These data indicate that GM corn samples were compositionally equivalent to, and as nutritious as, non-GM corn. Copyright © 2014 Elsevier Ltd. All rights reserved.

Global Sensitivity Analysis of Environmental Models: Convergence, Robustness and Validation

NASA Astrophysics Data System (ADS)

Sarrazin, Fanny; Pianosi, Francesca; Khorashadi Zadeh, Farkhondeh; Van Griensven, Ann; Wagener, Thorsten

2015-04-01

Global Sensitivity Analysis aims to characterize the impact that variations in model input factors (e.g. the parameters) have on the model output (e.g. simulated streamflow). In sampling-based Global Sensitivity Analysis, the sample size has to be chosen carefully in order to obtain reliable sensitivity estimates while spending computational resources efficiently. Furthermore, insensitive parameters are typically identified through the definition of a screening threshold: the theoretical value of their sensitivity index is zero but in a sampling-base framework they regularly take non-zero values. There is little guidance available for these two steps in environmental modelling though. The objective of the present study is to support modellers in making appropriate choices, regarding both sample size and screening threshold, so that a robust sensitivity analysis can be implemented. We performed sensitivity analysis for the parameters of three hydrological models with increasing level of complexity (Hymod, HBV and SWAT), and tested three widely used sensitivity analysis methods (Elementary Effect Test or method of Morris, Regional Sensitivity Analysis, and Variance-Based Sensitivity Analysis). We defined criteria based on a bootstrap approach to assess three different types of convergence: the convergence of the value of the sensitivity indices, of the ranking (the ordering among the parameters) and of the screening (the identification of the insensitive parameters). We investigated the screening threshold through the definition of a validation procedure. The results showed that full convergence of the value of the sensitivity indices is not necessarily needed to rank or to screen the model input factors. Furthermore, typical values of the sample sizes that are reported in the literature can be well below the sample sizes that actually ensure convergence of ranking and screening.

USE OF TOXICITY IDENTIFICATION EVALUATION METHODS TO CHARACTERIZE IDENTIFY, AND CONFIRM HEXAVALENT CHROMIUM TOXICITY IN AN INDUSTRIAL EFFLUENT

EPA Science Inventory

A toxicity identification evaluation (TIE) was conducted on effluent from a major industrial discharger. Initial monitoring showed slight chronic toxicity to Ceriodaphnia dubia; later sample showed substantial toxicity to C. dubia. Chemical analysis detected hexavalent chromium ...

Detection and genetic analysis of human sapoviruses in river water in Japan.

PubMed

Kitajima, Masaaki; Oka, Tomoichiro; Haramoto, Eiji; Katayama, Hiroyuki; Takeda, Naokazu; Katayama, Kazuhiko; Ohgaki, Shinichiro

2010-04-01

We investigated the prevalence of sapoviruses (SaVs) in the Tamagawa River in Japan from April 2003 to March 2004 and performed genetic analysis of the SaV genes identified in river water. A total of 60 river water samples were collected from five sites along the river, and 500 ml was concentrated using the cation-coated filter method. By use of a real-time reverse transcription (RT)-PCR assay, 12 (20%) of the 60 samples were positive for SaV. SaV sequences were obtained from 15 (25%) samples, and a total of 30 SaV strains were identified using six RT-PCR assays followed by cloning and sequence analysis. A newly developed nested RT-PCR assay utilizing a broadly reactive forward primer showed the highest detection efficiency and amplified more diverse SaV genomes in the samples. SaV sequences were frequently detected from November to March, whereas none were obtained in April, July, September, or October. No SaV sequences were detected in the upstream portion of the river, whereas the midstream portion showed high positive rates. Based on phylogenetic analysis, SaV strains identified in the river water samples were classified into nine genotypes, namely, GI/1, GI/2, GI/3, GI/5, GI/untyped, GII/1, GII/2, GII/3, and GV/1. To our knowledge, this is the first study describing seasonal and spatial distributions and genetic diversity of SaVs in river water. A combination of real-time RT-PCR assay and newly developed nested RT-PCR assay is useful for identifying and characterizing SaV strains in a water environment.

Comparison between PGAA and ID-AMS analysis for determining chlorine content in whole rock basalt

NASA Astrophysics Data System (ADS)

di Nicola, L.; Schnabel, C.; Wilcken, K. M.; Gméling, K.

2009-04-01

Accurate determination of chlorine concentrations in terrestrial rocks is of importance for the interpretation of terrestrial in-situ cosmogenic 36Cl. Neutron capture by 35Cl, together with production from Ca and K, is one of the three major production pathways of 36Cl in rocks. Here, we present an inter-comparison of chlorine determinations by two procedures. The first approach is an independent Cl determination by prompt gamma (neutron) activation analysis (PGAA). The second method is isotope dilution based on isotopically-enriched stable chlorine carrier added during chemical sample preparation for accelerator mass spectrometry (ID-AMS). Twenty six (26) whole rock samples have been processed for PGAA and ID-AMS analyses. Elemental analysis by PGAA provides concentrations of major, minor and trace elements including the target elements for 36Cl production (K, Ca, Ti, and Fe), as well as of neutron absorbers and neutron moderators (H, B, Cl, Sm and Gd). The Cl concentrations determined during this study constitute the first inter-comparison for concentrations below 100 μCl/g. Our results show no significant difference in Cl concentrations between methods, and comparable uncertainties. This agreement guarantees that during the procedure we employ for whole rock sample no significant loss of stable chlorine from either the spike or the sample occurs before isotopic equilibration, prior to AgCl precipitation. Furthermore, we show that the elemental analysis by PGAA offers anadvance for the interpretation of 36Cl measurements. It allows simultaneous measurement of major and most trace element concentrations with a precision necessary for calculating the relative contributions to 36Cl production rates of the different mechanisms. Finally, the Cl concentration can be used to optimize the amount of isotopically-enriched spike for AMS-ID sample preparation for 36Cl.

Impact of Nisin-Activated Packaging on Microbiota of Beef Burgers during Storage

PubMed Central

Ferrocino, Ilario; Greppi, Anna; La Storia, Antonietta; Rantsiou, Kalliopi; Ercolini, Danilo

2015-01-01

Beef burgers were stored at 4°C in a vacuum in nisin-activated antimicrobial packaging. Microbial ecology analyses were performed on samples collected between days 0 and 21 of storage to discover the population diversity. Two batches were analyzed using RNA-based denaturing gradient gel electrophoresis (DGGE) and pyrosequencing. The active packaging retarded the growth of the total viable bacteria and lactic acid bacteria. Culture-independent analysis by pyrosequencing of RNA extracted directly from meat showed that Photobacterium phosphoreum, Lactococcus piscium, Lactobacillus sakei, and Leuconostoc carnosum were the major operational taxonomic units (OTUs) shared between control and treated samples. Beta diversity analysis of the 16S rRNA sequence data and RNA-DGGE showed a clear separation between two batches based on the microbiota. Control samples from batch B showed a significant high abundance of some taxa sensitive to nisin, such as Kocuria rhizophila, Staphylococcus xylosus, Leuconostoc carnosum, and Carnobacterium divergens, compared to control samples from batch A. However, only from batch B was it possible to find a significant difference between controls and treated samples during storage due to the active packaging. Predicted metagenomes confirmed differences between the two batches and indicated that the use of nisin-based antimicrobial packaging can determine a reduction in the abundance of specific metabolic pathways related to spoilage. The present study aimed to assess the viable bacterial communities in beef burgers stored in nisin-based antimicrobial packaging, and it highlights the efficacy of this strategy to prolong beef burger shelf life. PMID:26546424

Viscosity of alkaline suspensions of ground black and white pepper samples: An indication or an identification of high dose radiation treatment?

NASA Astrophysics Data System (ADS)

Schreiber, G. A.; Leffke, A.; Mager, M.; Helle, N.; Bögl, K. W.

1994-11-01

Forty-nine pepper samples were taken from retail food stores of different cities in Germany. Most of the black and all white pepper samples showed high viscosity values after jellification in alkaline solution. After irradiation with a γ-ray dose of 6 kGy, viscosity was largely reduced in each case. Some black pepper samples showed a low viscosity level already before irradiation. However, thermoluminescence analysis did not reveal any sign for irradiation treatment prior to examination. Furthermore, the low viscosity level of these samples could not be correlated with a low starch content. It is concluded that the viscosity levels of irradiated white pepper samples clearly reveal high dose irradiation treatment. In case of black peppers it is judged that the method can be used to screen for irradiated samples since it is fast, easy and cheap. However, a positive result should be confirmed by another technique, e.g. thermoluminescence.

Borax as flux on sintering of iron Ancor Steel 1000® under glow discharge

NASA Astrophysics Data System (ADS)

Ariza Suarez, H. G.; Sarmiento Santos, A.; Ortiz Otálora, C. A.

2016-02-01

This work studies the flux effect of borax (di sodium tetraborate decahydrate) on sintering of iron Ancor Steel 1000® in abnormal glow discharge. The incidence of the percentage by weight of borax and the sintering temperature in the process were observed. Samples of powder metallurgical iron were prepared with proportions of 0.50%, 2.0%, 4.0% and 6.0% by weight of borax using the procedures of powder metallurgy. The samples were sintered at 800 and 1100°C for 30min, by glow discharge at low pressure in a reducing atmosphere composed of 20% H2+80% Ar. The samples in compact green-state were analyzed by TGA-DSC to determine the fusion process and mass loss during sintering. The analysis of microhardness and density, shows that at a sintering temperature of 800°C the sample density decreases and the sample microhardness increases with respect to sintered samples without borax. Sintered samples were analysed by DRX showing the absence of precipitates.

Texture and Tempered Condition Combined Effects on Fatigue Behavior in an Al-Cu-Li Alloy

NASA Astrophysics Data System (ADS)

Wang, An; Liu, Zhiyi; Liu, Meng; Wu, Wenting; Bai, Song; Yang, Rongxian

2017-05-01

Texture and tempered condition combined effects on fatigue behavior in an Al-Cu-Li alloy have been investigated using tensile testing, cyclic loading testing, scanning electron microscope (SEM), transmission electron microscopy (TEM) and texture analysis. Results showed that in near-threshold region, T4-tempered samples possessed the lowest fatigue crack propagation (FCP) rate. In Paris regime, T4-tempered sample had similar FCP rate with T6-tempered sample. T83-tempered sample exhibited the greatest FCP rate among the three tempered conditions. 3% pre-stretching in T83-tempered sample resulted in a reducing intensity of Goss texture and facilitated T1 precipitation. SEM results showed that less crack deflection was observed in T83-tempered sample, as compared to other two tempered samples. It was the combined effects of a lower intensity of Goss texture and T1 precipitates retarding the reversible dislocation slipping in the plastic zone ahead the crack tip.

Geochemical characteristics of Heavy metals of river sediment from the main rivers at Texas, USA.

NASA Astrophysics Data System (ADS)

Matsumoto, I.; Hoffman, D.; MacAlister, J.; Ishiga, H.

2008-12-01

Trinity River is one of the biggest rivers which flows through Dallas and Fort Worth two big cities of USA and are highly populated. Trinity river drains into the Gulf of Mexico. Sediment samples collected from various points along the upper and lower streams were subjected to content analysis and elution analysis (using liquate (flow) out test) on the heavy metals like Cd, CN, Pb, Cr, As, Hg, Ni, Zn and Cu from the river sediment for the purpose of environment assessment. A total of 22 sample points were identified from upper stream to lower stream and samples were collected such that almost the whole stream length of Trinity River is covered. Results show that heavy metal content through out the river stream is below the recommended limits posing no immediate environmental threat. However, the experimental results show clear impact of human population in bigger cities on heavy metal concentrations in the river sediments as compared to smaller cities with low human population. It could be seen from the analysis that all the heavy metals show relatively high content and high elution value in Dallas and Fort Worth. As we move away from the big cities, the value of content and elution of sediment decreased by natural dilution effect by the river. And we also present the data of the Colorado and San Antonio rivers.

Effect of liquid immersion of PEDOT: PSS-coated polyester fabric on surface resistance and wettability

NASA Astrophysics Data System (ADS)

Getnet Tadesse, Melkie; Loghin, Carmen; Chen, Yan; Wang, Lichuan; Catalin, Dumitras; Nierstrasz, Vincent

2017-06-01

Coating of textile fabrics with poly (3, 4-ethylenedioxythiophene): poly (styrene sulfonate) (PEDOT:PSS) is one of the methods used for obtaining functional or smart applications. In this work, we prepared PEDOT:PSS polymer with certain additives such as polyethylene glycol, methanol (MeOH), and ethylene glycol on polyester fabric substrates by a simple immersion process. Surface resistance was measured and analyzed with analysis of variance to determine the coating parameters at 95% confidence level. Fourier transform infrared (FTIR) analysis and scanning electron microscopy (SEM) study of the samples were performed. Contact angle and washing fastness measurements were conducted, to observe the wettability and washing fastness of the samples, respectively. Surface resistance values were decreased by a factor of 100, due to conductive enhancers. As the immersion time and temperature condition varies, surface resistance showed no difference, statistically. FTIR analysis supports the idea that the mechanism responsible for the conductivity enhancement is the partial replacement of PSS from PEDOT chain by forming a hydrogen bond with hydroxyl ion (OH) of the conductive enhancers. A SEM images showed that PEDOT:PSS is well distributed to the surface of the fabrics. Contact angle measurements showed morphology change in the samples. The conductivity was reasonably stable after 10 washing cycles. Altogether, an effective simple immersion of coated polyester fabric is presented to achieve functional textiles that offer a broad range of possible applications.

The relationship between childhood conduct disorder and adult antisocial behavior is partially mediated by early-onset alcohol abuse.

PubMed

Khalifa, Najat; Duggan, Conor; Howard, Rick; Lumsden, John

2012-10-01

Early-onset alcohol abuse (EOAA) was previously found to both mediate and moderate the effect of childhood conduct disorder (CD) on adult antisocial behavior (ASB) in an American community sample of young adults (Howard, R., Finn, P. R., Gallagher, J., & Jose, P. (2011). Adolescent-onset alcohol abuse exacerbates the influence of childhood conduct disorder on late adolescent and early adult antisocial behavior. Journal of Forensic Psychiatry and Psychology. Advance online publication. doi:10.1080/14789949.2011.641996). This study tested whether this result would generalize to a British forensic sample comprising 100 male forensic patients with confirmed personality disorder. Results confirmed that those in whom EOAA co-occurred with CD showed the highest level of personality pathology, particularly Cluster B traits and antisocial/borderline comorbidity. Those with co-occurring CD with EOAA, compared with those showing only CD, showed more violence in their criminal history and greater recreational drug use. Regression analysis showed that both EOAA and CD predicted adult ASB when covariates were controlled. Further analysis showed that EOAA significantly mediated but did not moderate the effect of CD on ASB. The failure to demonstrate an exacerbating effect of EOAA on the relationship between CD and ASB likely reflects the high prevalence of CD in this forensic sample. Some implications of these findings are discussed. (PsycINFO Database Record (c) 2012 APA, all rights reserved).

Effect of laser irradiance and wavelength on the analysis of gold- and silver-bearing minerals with laser-induced breakdown spectroscopy

NASA Astrophysics Data System (ADS)

Díaz, Daniel; Molina, Alejandro; Hahn, David

2018-07-01

The influence of laser irradiance and wavelength on the analysis of gold and silver in ore and surrogate samples with laser-induced breakdown spectroscopy (LIBS) was evaluated. Gold-doped mineral samples (surrogates) and ore samples containing naturally-occurring gold and silver were analyzed with LIBS using 1064 and 355 nm laser wavelengths at irradiances from 0.36 × 109 to 19.9 × 109 W/cm2 and 0.97 × 109 to 4.3 × 109 W/cm2, respectively. The LIBS net, background and signal-to-background signals were analyzed. For all irradiances, wavelengths, samples and analytes the calibration curves behaved linearly for concentrations from 1 to 9 μg/g gold (surrogate samples) and 0.7 to 47.0 μg/g silver (ore samples). However, it was not possible to prepare calibration curves for gold-bearing ore samples (at any concentration) nor for gold-doped surrogate samples with gold concentrations below 1 μg/g. Calibration curve parameters for gold-doped surrogate samples were statistically invariant at 1064 and 355 nm. Contrary, the Ag-ore analyte showed higher emission intensity at 1064 nm, but the signal-to-background normalization reduced the effect of laser wavelength of silver calibration plots. The gold-doped calibration curve metrics improved at higher laser irradiance, but that did not translate into lower limits of detection. While coefficients of determination (R2) and limits of detection did not vary significantly with laser wavelength, the LIBS repeatability at 355 nm improved up to a 50% with respect to that at 1064 nm. Plasma diagnostics by the Boltzmann and Stark broadening methods showed that the plasma temperature and electron density did not follow a specific trend as the wavelength changed for the delay and gate times used. This research presents supporting evidence that the LIBS discrete sampling features combined with the discrete and random distribution of gold in minerals hinder gold analysis by LIBS in ore samples; however, the use of higher laser irradiances at 1064 nm increased the probability of sampling and detecting naturally-occurring gold.

Interplay of secondary structures and side-chain contacts in the denatured state of BBA1

NASA Astrophysics Data System (ADS)

Wen, Edward Z.; Luo, Ray

2004-08-01

The denatured state of a miniprotein BBA1 is studied under the native condition with the AMBER/Poisson-Boltzmann energy model and with the self-guided enhanced sampling technique. Forty independent trajectories are collected to sample the highly diversified denatured structures. Our simulation data show that the denatured BBA1 contains high percentage of native helix and native turn, but low percentage of native hairpin. Conditional population analysis indicates that the native helix formation and the native hairpin formation are not cooperative in the denatured state. Side-chain analysis shows that the native hydrophobic contacts are more preferred than the non-native hydrophobic contacts in the denatured BBA1. In contrast, the salt-bridge contacts are more or less nonspecific even if their populations are higher than those of hydrophobic contacts. Analysis of the trajectories shows that the native helix mostly initiates near the N terminus and propagates to the C terminus, and mostly forms from 310-helix/turn to α helix. The same analysis shows that the native turn is important but not necessary in its formation in the denatured BBA1. In addition, the formations of the two strands in the native hairpin are rather asymmetric, demonstrating the likely influence of the protein environment. Energetic analysis shows that the native helix formation is largely driven by electrostatic interactions in denatured BBA1. Further, the native helix formation is associated with the breakup of non-native salt-bridge contacts and the accumulation of native salt-bridge contacts. However, the native hydrophobic contacts only show a small increase upon the native helix formation while the non-native hydrophobic contacts stay essentially the same, different from the evolution of hydrophobic contacts observed in an isolated helix folding.

Rock images classification by using deep convolution neural network

NASA Astrophysics Data System (ADS)

Cheng, Guojian; Guo, Wenhui

2017-08-01

Granularity analysis is one of the most essential issues in authenticate under microscope. To improve the efficiency and accuracy of traditional manual work, an convolutional neural network based method is proposed for granularity analysis from thin section image, which chooses and extracts features from image samples while build classifier to recognize granularity of input image samples. 4800 samples from Ordos basin are used for experiments under colour spaces of HSV, YCbCr and RGB respectively. On the test dataset, the correct rate in RGB colour space is 98.5%, and it is believable in HSV and YCbCr colour space. The results show that the convolution neural network can classify the rock images with high reliability.

Magnetic graphene composites as both an adsorbent for sample enrichment and a MALDI-TOF MS matrix for the detection of nitropolycyclic aromatic hydrocarbons in PM2.5.

PubMed

Zhang, Jiangang; Zhang, Li; Li, Ruijin; Hu, Di; Ma, Nengxuan; Shuang, Shaomin; Cai, Zongwei; Dong, Chuan

2015-03-07

A simple and rapid method that uses synthesized magnetic graphene composites as both an adsorbent for enrichment and as a matrix in MALDI-TOF MS analysis was developed for the detection of nitropolycyclic hydrocarbons (nitro-PAHs) in PM2.5 samples. Three nitro-PAHs were detected down to sub pg μL(-1) levels based on calculations from an instrumental signal-to-noise better than 3, which shows the feasibility of using the new materials in MALDI-TOF MS as a potential powerful analytical approach for the analysis of nitro-PAHs in PM2.5 samples.

Marital assortment for genetic similarity.

PubMed

Eckman, Ronael E; Williams, Robert; Nagoshi, Craig

2002-10-01

The present study involved analyses of a Caucasian American sample (n=949) and a Japanese American sample (n=400) for factors supporting Genetic Similarity Theory (GST). The analyses found no evidence for the presence of genetic similarity between spouses in either sample for the blood group analyses of nine loci. All results indicated random mating for blood group genes. The results did not provide consistent substantial support to show that spousal similarity is correlated with the degree of genetic component of a trait for a set of seventeen individual differences variables, with only the Caucasian sample yielding significant correlations for this analysis. A third analysis examining the correlation between presence of spousal genetic similarity and spousal similarity on observable traits was not performed because spousal genetic similarity was not observed in either sample. The overall implication of the study is that GST is not supported as an explanation for spousal similarity in humans.

Genetic variability in environmental isolates of Legionella pneumophila from Comunidad Valenciana (Spain).

PubMed

Coscollá, Mireia; Gosalbes, María José; Catalán, Vicente; González-Candelas, Fernando

2006-06-01

Legionella pneumophila is associated to recurrent outbreaks in several Comunidad Valenciana (Spain) localities, especially in Alcoi, where social and climatic conditions seem to provide an excellent environment for bacterial growth. We have analysed the nucleotide sequences of three loci from 25 environmental isolates from Alcoi and nearby locations sampled over 3 years. The analysis of these isolates has revealed a substantial level of genetic variation, with consistent patterns of variability across loci, and comparable to that found in a large, European-wide sampling of clinical isolates. Among the tree loci studied, fliC showed the highest level of nucleotide diversity. The analysis of isolates sampled in different years revealed a clear differentiation, with samples from 2001 being significantly distinct from those obtained in 2002 and 2003. Furthermore, although linkage disequilibrium measures indicate a clonal nature for population structure in this sample, the presence of some recombination events cannot be ruled out.

Interference by the activated sludge matrix on the analysis of soluble microbial products in wastewater.

PubMed

Potvin, Christopher M; Zhou, Hongde

2011-11-01

The objective of this study was to demonstrate the effects of complex matrix effects caused by chemical materials on the analysis of key soluble microbial products (SMP) including proteins, humics, carbohydrates, and polysaccharides in activated sludge samples. Emphasis was placed on comparison of the commonly used standard curve technique with standard addition (SA), a technique that differs in that the analytical responses are measured for sample solutions spiked with known quantities of analytes. The results showed that using SA provided a great improvement in compensating for SMP recovery and thus improving measurement accuracy by correcting for matrix effects. Analyte recovery was found to be highly dependent on sample dilution, and changed due to extraction techniques, storage conditions and sample composition. Storage of sample extracts by freezing changed SMP concentrations dramatically, as did storage at 4°C for as little as 1d. Copyright © 2011 Elsevier Ltd. All rights reserved.

Sensory profile and acceptability for pitanga (Eugenia uniflora L.) nectar with different sweeteners.

PubMed

Freitas, Mírian Luisa Faria; Dutra, Mariana Borges de Lima; Bolini, Helena Maria André

2016-12-01

The objective of this study was to evaluate the sensory properties and acceptability of pitanga nectar samples prepared with sucrose and different sweeteners (sucralose, aspartame, stevia with 40% rebaudioside A, stevia with 95% rebaudioside A, neotame, and a 2:1 cyclamate/saccharin blend). A total of 13 assessors participated in a quantitative descriptive analysis and evaluated the samples in relation to the descriptor terms. The acceptability test was carried out by 120 fruit juice consumers. The results of the quantitative descriptive analysis of pitanga nectar showed that samples prepared with sucralose, aspartame, and the 2:1 cyclamate/saccharin blend had sensory profiles similar to that of the sample prepared with sucrose. Consumers' most accepted samples were prepared with sucrose, sucralose, aspartame, and neotame. The sweeteners that have the greatest potential to replace sucrose in pitanga nectar are sucralose and aspartame. © The Author(s) 2016.

Characterization of mineral phases of agricultural soil samples of Colombian coffee using Mössbauer spectroscopy and X-ray diffraction

NASA Astrophysics Data System (ADS)

Rodríguez, Humberto Bustos; Lozano, Dagoberto Oyola; Martínez, Yebrayl Antonio Rojas; Pinilla, Marlene Rivera; Alcázar, German Antonio Pérez

2012-03-01

Soil chemical analysis, X-ray diffraction (XRD) and Mössbauer spectrometry (MS) of 57Fe were used to characterize mineral phases of samples taken from the productive layer (horizon A) of agricultural coffee soil from Tolima (Colombia). Chemical analysis shows the chemical and textural parameters of samples from two different regions of Tolima, i.e., Ibagué and Santa Isabel. By XRD phases like illite (I), andesine (A) and quartz (Q) in both samples were identified. The quantity of these phases is different for the two samples. The MS spectra taken at room temperature were adjusted by using five doublets, three of them associated to Fe + 3 type sites and the other two to Fe + 2 type sites. According to their isomer shift and quadrupole splitting the presence of phases like illite (detected by DRX), nontronite and biotite (not detected by XRD) can be postulated.

Analysis of Phyllostachys pubescens bamboo residues for liquefaction: chemical components, infrared spectroscopy, and thermogravimetry

Treesearch

Jinqiu Qi; Chung-Yun Hse; Todd F. Shupe

2013-01-01

Residues of Phyllostachys pubescens bamboo obtained from central Louisiana, USA, were comprehensively investigated for use in liquefaction. The results showed that bamboo branches had the highest Klason lignin and ash content, about 26% and 2.75%, respectively. The epidermis layer sample had relatively higher carbohydrate content, while the wax layer sample had the...

Seroconversions for Coxiella and Rickettsial Pathogens among US Marines Deployed to Afghanistan, 2001-2010.

PubMed

Farris, Christina M; Pho, Nhien; Myers, Todd E; Richards, Allen L

2016-08-01

We assessed serum samples from 1,000 US Marines deployed to Afghanistan during 2001-2010 to find evidence of 4 rickettsial pathogens. Analysis of predeployment and postdeployment samples showed that 3.4% and 0.5% of the Marines seroconverted for the causative agents of Q fever and spotted fever group rickettsiosis, respectively.

A timed solenoid injector for flow analysis.

PubMed

Rothwell, S D; Woolf, A A

1985-05-01

Samples can be reproducibly injected into flow-streams by timed switching of a sample stream with a miniature solenoid valve and timer circuit. The device is simpler to assemble and use than the standard rotary valve and a direct comparison under the same operating conditions shows that the solenoid valve is an adequate replacement for the rotary valve.

Analysis of the Microstructure of Titles in the INSPEC Data-Base

ERIC Educational Resources Information Center

And Others; Lynch, Michael F.

1973-01-01

A high degree of constancy has been found in the microstructure of titles of samples of the INSPEC data base taken over a three-year period. Character and digram frequencies are relatively stable, while variable-length character-strings characterizing samples separated by three years in time show close similarities. (2 references) (Author/SJ)

Impact of cultivation on characterisation of species composition of soil bacterial communities.

PubMed

McCaig, A E.; Grayston, S J.; Prosser, J I.; Glover, L A.

2001-03-01

The species composition of culturable bacteria in Scottish grassland soils was investigated using a combination of Biolog and 16S rDNA analysis for characterisation of isolates. The inclusion of a molecular approach allowed direct comparison of sequences from culturable bacteria with sequences obtained during analysis of DNA extracted directly from the same soil samples. Bacterial strains were isolated on Pseudomonas isolation agar (PIA), a selective medium, and on tryptone soya agar (TSA), a general laboratory medium. In total, 12 and 21 morphologically different bacterial cultures were isolated on PIA and TSA, respectively. Biolog and sequencing placed PIA isolates in the same taxonomic groups, the majority of cultures belonging to the Pseudomonas (sensu stricto) group. However, analysis of 16S rDNA sequences proved more efficient than Biolog for characterising TSA isolates due to limitations of the Microlog database for identifying environmental bacteria. In general, 16S rDNA sequences from TSA isolates showed high similarities to cultured species represented in sequence databases, although TSA-8 showed only 92.5% similarity to the nearest relative, Bacillus insolitus. In general, there was very little overlap between the culturable and uncultured bacterial communities, although two sequences, PIA-2 and TSA-13, showed >99% similarity to soil clones. A cloning step was included prior to sequence analysis of two isolates, TSA-5 and TSA-14, and analysis of several clones confirmed that these cultures comprised at least four and three sequence types, respectively. All isolate clones were most closely related to uncultured bacteria, with clone TSA-5.1 showing 99.8% similarity to a sequence amplified directly from the same soil sample. Interestingly, one clone, TSA-5.4, clustered within a novel group comprising only uncultured sequences. This group, which is associated with the novel, deep-branching Acidobacterium capsulatum lineage, also included clones isolated during direct analysis of the same soil and from a wide range of other sample types studied elsewhere. The study demonstrates the value of fine-scale molecular analysis for identification of laboratory isolates and indicates the culturability of approximately 1% of the total population but under a restricted range of media and cultivation conditions.

The Circumplex Pattern of the Life Styles Inventory: A Reanalysis.

ERIC Educational Resources Information Center

Levin, Joseph

1991-01-01

A reanalysis of the intercorrelation matrix from a principal components analysis of the Life Styles Inventory was conducted using a Canadian sample. Using nonmetric multidimensional scaling, analyses show an almost perfect circumplex pattern. Results illustrate the inadequacy of factor analytic procedures for the analysis and representation of a…

Thirty Years of Vegetation Change in the Coastal Santa Cruz Mountains of Northern California Detected Using Landsat Satellite Image Analysis

NASA Technical Reports Server (NTRS)

Potter, Christopher

2015-01-01

Results from Landsat satellite image times series analysis since 1983 of this study area showed gradual, statistically significant increases in the normalized difference vegetation index (NDVI) in more than 90% of the (predominantly second-growth) evergreen forest locations sampled.

Ultrasonic density measurement cell design and simulation of non-ideal effects.

PubMed

Higuti, Ricardo Tokio; Buiochi, Flávio; Adamowski, Júlio Cezar; de Espinosa, Francisco Montero

2006-07-01

This paper presents a theoretical analysis of a density measurement cell using an unidimensional model composed by acoustic and electroacoustic transmission lines in order to simulate non-ideal effects. The model is implemented using matrix operations, and is used to design the cell considering its geometry, materials used in sensor assembly, range of liquid sample properties and signal analysis techniques. The sensor performance in non-ideal conditions is studied, considering the thicknesses of adhesive and metallization layers, and the effect of residue of liquid sample which can impregnate on the sample chamber surfaces. These layers are taken into account in the model, and their effects are compensated to reduce the error on density measurement. The results show the contribution of residue layer thickness to density error and its behavior when two signal analysis methods are used.

Chemical profiling of guarana seeds (Paullinia cupana) from different geographical origins using UPLC-QTOF-MS combined with chemometrics.

PubMed

da Silva, Givaldo Souza; Canuto, Kirley Marques; Ribeiro, Paulo Riceli Vasconcelos; de Brito, Edy Sousa; Nascimento, Madson Moreira; Zocolo, Guilherme Julião; Coutinho, Janclei Pereira; de Jesus, Raildo Mota

2017-12-01

Paullinia cupana, commonly known as guarana, is an Amazonian fruit whose seeds are used to produce the powdered guarana, which is rich in caffeine and consumed for its stimulating activity. The metabolic profile of guarana from the two largest producing regions was investigated using UPLC-MS combined with multivariate statistical analysis. The principal component analysis (PCA) showed significant differences between samples produced in the states of Bahia and Amazonas. The metabolites responsible for the differentiation were identified by orthogonal partial least squares discriminant analysis (OPLS-DA). Fourteen phenolic compounds were characterized in guarana powder samples, and catechin, epicatechin, B-type procyanidin dimer, A-type procyanidin trimer and A-type procyanidin dimer were the main compounds responsible for the geographical variation of the samples. Copyright © 2017. Published by Elsevier Ltd.

Bacterial communities in soil samples from the Mingyong Glacier of southwestern China.

PubMed

Li, Haoyu; Taj, Muhammad Kamran; Ji, Xiuling; Zhang, Qi; Lin, Liangbing; Zhou, Zhimei; Wei, Yunlin

2017-05-01

The present study was an effort to determine the bacterial diversity of soils in Mingyong Glacier located at the Meili Snow Mountains of southwestern China. Mingyong Glacier has different climatic zones within a very narrow area, and bacterial community diversity in this low temperature area remains largely unknown. In this study, soil samples were collected from four different climatic zones: M11A (dry warm valley), M14 (forest), M15 (grass land), and M16 (glacier zones). Phylogenetic analysis based on 16S rRNA gene V6 hypervariable region showed high bacterial abundance in the glacier. The number of Operational Taxonomic Units ranged from 2.24×10 3 to 5.56×10 3 in soil samples. Statistical analysis of 16S rRNA gene clone libraries results showed that bacterial diversity in zones M11A，M14 and M16 are higher than in zone M15. The bacterial community structures are clearly distinguishable, and phylogenetic analysis showed that the predominant phyla were Proteobacteria, Deinococcus-Thermus, Firmicutes, Actinobacteria, and Nitrospirae in Mingyong Glacier. Seventy-nine different orders from four zones have been isolated. Bacterial diversity and distribution of bacterial communities related to the anthropogenic perturbations in zone (M15) were confirmed by diversity index analysis, and the diversity index of other three zones was satisfactory through this analysis software. The results suggest that bacterial diversity and distribution analyses using bacterial 16S rRNA gene V6 hypervariable region were successful, and bacterial communities in this area not only had the same bacterial phyla compared to other glaciers but also had their own rare species.

Highly Reproducible Label Free Quantitative Proteomic Analysis of RNA Polymerase Complexes*

PubMed Central

Mosley, Amber L.; Sardiu, Mihaela E.; Pattenden, Samantha G.; Workman, Jerry L.; Florens, Laurence; Washburn, Michael P.

2011-01-01

The use of quantitative proteomics methods to study protein complexes has the potential to provide in-depth information on the abundance of different protein components as well as their modification state in various cellular conditions. To interrogate protein complex quantitation using shotgun proteomic methods, we have focused on the analysis of protein complexes using label-free multidimensional protein identification technology and studied the reproducibility of biological replicates. For these studies, we focused on three highly related and essential multi-protein enzymes, RNA polymerase I, II, and III from Saccharomyces cerevisiae. We found that label-free quantitation using spectral counting is highly reproducible at the protein and peptide level when analyzing RNA polymerase I, II, and III. In addition, we show that peptide sampling does not follow a random sampling model, and we show the need for advanced computational models to predict peptide detection probabilities. In order to address these issues, we used the APEX protocol to model the expected peptide detectability based on whole cell lysate acquired using the same multidimensional protein identification technology analysis used for the protein complexes. Neither method was able to predict the peptide sampling levels that we observed using replicate multidimensional protein identification technology analyses. In addition to the analysis of the RNA polymerase complexes, our analysis provides quantitative information about several RNAP associated proteins including the RNAPII elongation factor complexes DSIF and TFIIF. Our data shows that DSIF and TFIIF are the most highly enriched RNAP accessory factors in Rpb3-TAP purifications and demonstrate our ability to measure low level associated protein abundance across biological replicates. In addition, our quantitative data supports a model in which DSIF and TFIIF interact with RNAPII in a dynamic fashion in agreement with previously published reports. PMID:21048197

Detecting and Estimating Contamination of Human DNA Samples in Sequencing and Array-Based Genotype Data

PubMed Central

Jun, Goo; Flickinger, Matthew; Hetrick, Kurt N.; Romm, Jane M.; Doheny, Kimberly F.; Abecasis, Gonçalo R.; Boehnke, Michael; Kang, Hyun Min

2012-01-01

DNA sample contamination is a serious problem in DNA sequencing studies and may result in systematic genotype misclassification and false positive associations. Although methods exist to detect and filter out cross-species contamination, few methods to detect within-species sample contamination are available. In this paper, we describe methods to identify within-species DNA sample contamination based on (1) a combination of sequencing reads and array-based genotype data, (2) sequence reads alone, and (3) array-based genotype data alone. Analysis of sequencing reads allows contamination detection after sequence data is generated but prior to variant calling; analysis of array-based genotype data allows contamination detection prior to generation of costly sequence data. Through a combination of analysis of in silico and experimentally contaminated samples, we show that our methods can reliably detect and estimate levels of contamination as low as 1%. We evaluate the impact of DNA contamination on genotype accuracy and propose effective strategies to screen for and prevent DNA contamination in sequencing studies. PMID:23103226

Recovery and Utilization of Palm Oil Mill Effluent Source as Value-Added Food Products.

PubMed

Teh, Soek Sin; Hock Ong, Augustine Soon; Mah, Siau Hui

2017-01-01

The environmental impacts of palm oil mill effluent (POME) have been a concern due to the water pollution and greenhouse gases emissions. Thus, this study was conducted to recover the value-added products from POME source before being discharged. The samples, before (X) and after (Y) the pre-recovery system in the clarification tank were sampled and analysed and proximate analysis indicated that both samples are energy rich source of food due to high contents of fats and carbohydrates. GCMS analysis showed that the oil extracts contain predominantly palmitic, oleic, linoleic and stearic acids. Regiospecific analysis of oil extracts by quantitative 13 C-NMR spectroscopy demonstrated that both oil extracts contain similar degree of saturation of fatty acids at sn-2 and sn-1,3 positions. The samples are rich in various phytonutrients, pro-vitamin A, vitamin E, squalene and phytosterols, thus contributing to exceptionally high total flavonoid contents and moderate antioxidant activities. Overall, samples X and Y are good alternative food sources, besides reducing the environmental impact of POME.

Evaluation of DNA extraction methods for the analysis of microbial community in biological activated carbon.

PubMed

Zheng, Lu; Gao, Naiyun; Deng, Yang

2012-01-01

It is difficult to isolate DNA from biological activated carbon (BAC) samples used in water treatment plants, owing to the scarcity of microorganisms in BAC samples. The aim of this study was to identify DNA extraction methods suitable for a long-term, comprehensive ecological analysis of BAC microbial communities. To identify a procedure that can produce high molecular weight DNA, maximizes detectable diversity and is relatively free from contaminants, the microwave extraction method, the cetyltrimethylammonium bromide (CTAB) extraction method, a commercial DNA extraction kit, and the ultrasonic extraction method were used for the extraction of DNA from BAC samples. Spectrophotometry, agarose gel electrophoresis and polymerase chain reaction (PCR)-restriction fragment length polymorphisms (RFLP) analysis were conducted to compare the yield and quality of DNA obtained using these methods. The results showed that the CTAB method produce the highest yield and genetic diversity of DNA from BAC samples, but DNA purity was slightly less than that obtained with the DNA extraction-kit method. This study provides a theoretical basis for establishing and selecting DNA extraction methods for BAC samples.

Determination of the botanical origin of honey by front-face synchronous fluorescence spectroscopy.

PubMed

Lenhardt, Lea; Zeković, Ivana; Dramićanin, Tatjana; Dramićanin, Miroslav D; Bro, Rasmus

2014-01-01

Front-face synchronous fluorescence spectroscopy combined with chemometrics is used to classify honey samples according to their botanical origin. Synchronous fluorescence spectra of three monofloral (linden, sunflower, and acacia), polyfloral (meadow mix), and fake (fake acacia and linden) honey types (109 samples) were collected in an excitation range of 240-500 nm for synchronous wavelength intervals of 30-300 nm. Chemometric analysis of the gathered data included principal component analysis and partial least squares discriminant analysis. Mean cross-validated classification errors of 0.2 and 4.8% were found for a model that accounts only for monofloral samples and for a model that includes both the monofloral and polyfloral groups, respectively. The results demonstrate that single synchronous fluorescence spectra of different honeys differ significantly because of their distinct physical and chemical characteristics and provide sufficient data for the clear differentiation among honey groups. The spectra of fake honey samples showed pronounced differences from those of genuine honey, and these samples are easily recognized on the basis of their synchronous fluorescence spectra. The study demonstrated that this method is a valuable and promising technique for honey authentication.

Spectrochemical analysis of powder using 355 nm Nd-YAG laser-induced low-pressure plasma.

PubMed

Lie, Zener S; Pardede, M; Hedwig, R; Suliyanti, M M; Kurniawan, Koo Hendrik; Munadi; Lee, Yong-Inn; Kagawa, Kiichiro; Hattori, Isamu; Tjia, May On

2008-04-01

The applicability of spectrochemical analysis of minute amounts of powder samples was investigated using an ultraviolet Nd-YAG laser (355 nm) and low-pressure ambient air. A large variety of chemical powder samples of different composition were employed in the experiment. These included a mixture of copper(II) sulfate pentahydrate, zinc sulfide, and chromium(III) sulfate n-hydrate powders, baby powder, cosmetic powders, gold films, zinc supplement tablet, and muds and soils from different areas. The powder samples were prepared by pulverizing the original samples to an average size of around 30 microm in order to trap them in the tiny micro holes created on the surface of the quartz subtarget. It was demonstrated that in all cases studied, good quality spectra were obtained with low background, free from undesirable contamination by the subtarget elements and featuring ppm sensitivity. A further measurement revealed a linear calibration curve with zero intercept. These results clearly show the potential application of this technique for practical qualitative and quantitative spectrochemical analysis of powder samples in various fields of study and investigation.

Automated tumor analysis for molecular profiling in lung cancer

PubMed Central

Boyd, Clinton; James, Jacqueline A.; Loughrey, Maurice B.; Hougton, Joseph P.; Boyle, David P.; Kelly, Paul; Maxwell, Perry; McCleary, David; Diamond, James; McArt, Darragh G.; Tunstall, Jonathon; Bankhead, Peter; Salto-Tellez, Manuel

2015-01-01

The discovery and clinical application of molecular biomarkers in solid tumors, increasingly relies on nucleic acid extraction from FFPE tissue sections and subsequent molecular profiling. This in turn requires the pathological review of haematoxylin & eosin (H&E) stained slides, to ensure sample quality, tumor DNA sufficiency by visually estimating the percentage tumor nuclei and tumor annotation for manual macrodissection. In this study on NSCLC, we demonstrate considerable variation in tumor nuclei percentage between pathologists, potentially undermining the precision of NSCLC molecular evaluation and emphasising the need for quantitative tumor evaluation. We subsequently describe the development and validation of a system called TissueMark for automated tumor annotation and percentage tumor nuclei measurement in NSCLC using computerized image analysis. Evaluation of 245 NSCLC slides showed precise automated tumor annotation of cases using Tissuemark, strong concordance with manually drawn boundaries and identical EGFR mutational status, following manual macrodissection from the image analysis generated tumor boundaries. Automated analysis of cell counts for % tumor measurements by Tissuemark showed reduced variability and significant correlation (p < 0.001) with benchmark tumor cell counts. This study demonstrates a robust image analysis technology that can facilitate the automated quantitative analysis of tissue samples for molecular profiling in discovery and diagnostics. PMID:26317646

Effect of phase transformation on optical and dielectric properties of zirconium oxide nanoparticles

NASA Astrophysics Data System (ADS)

Chintaparty, Rajababu; Palagiri, Bhavani; Reddy Nagireddy, Ramamanohar; subbha Reddy Imma Reddy, Venkata

2015-09-01

Zirconium oxide nanoparticle (ZrO2) is synthesized by the hydrothermal method at different calcination temperatures. The structural analysis is carried out by X-ray diffraction and Raman spectra. The sample prepared at 400 °C and 1100 °C showed the cubic and monoclinic phase, respectively, and the sample calcined at 600 °C and 800 °C showed the mixed phase with co-existence of cubic and monoclinic phases. Furthermore, the morphology and particle size of these samples were investigated by scanning electron microscope (SEM) and transmission electron microscope (TEM) analysis. The band gap estimated from UV-Vis spectra of ZrO2 (zirconia) nanocrystalline materials calcined at different temperatures from 400 °C to 1100 °C was in the range of 2.6-4.2 eV. The frequency dependence of dielectric constant and dielectric loss was investigated at room temperature. The low frequency region of dielectric constant is attributed to space charge effects.

Dose Assessment of Los Alamos National Laboratory-Derived Residual Radionuclides in Soils within C Tracts (C-2, C-3, and C-4) for Land Transfer Decisions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gillis, Jessica M.; Whicker, Jeffrey J.

2016-01-26

Three separate Sampling and Analysis Plans (SAPs) were prepared for tracts C-2, C-3, and C-4. The objective of sampling was to confirm, within the stated statistical confidence limits, that the mean levels of potential radioactive residual contamination in soils in the C Tracts are documented, in appropriate units, and are below the 15 mrem/y (150 μSv/y) Screening Action Levels (SALs). Results show that radionuclide concentration upper-bound 95% confidence levels were close to background levels, with the exception of Pu-239 and Cs-137 being slightly elevated above background, and all measurements were below the ALs and meet the real property release criteriamore » for future construction or recreational use. A follow-up ALARA analysis showed that the costs of cleanup of the soil in areas of elevated concentration and confirmatory sampling would far exceed any benefit from dose reduction.« less

Colorimeter and scanning electron microscopy analysis of teeth submitted to internal bleaching.

PubMed

Martin-Biedma, Benjamin; Gonzalez-Gonzalez, Teresa; Lopes, Manuela; Lopes, Luis; Vilar, Rui; Bahillo, José; Varela-Patiño, Purificación

2010-02-01

This in vitro study compared the tooth color and the ultrastructure of internal dental tissues before and after internal bleaching. Sodium perborate was placed in the pulp chamber of endodontically treated molars and sealed with intermediate restorative material. The test samples were stored in a physiologic solution, and the bleaching agent was replaced every 7 days. A control group was used. After 1 month, the colors of the test and control samples were measured with a colorimeter, and the internal surfaces were observed under field emission scanning electron microscopy (FESEM). Statistically significant differences were found between the test and control sample colors. The FESEM ultrastructure analysis of the internal enamel and dentin surfaces did not show any changes after the internal bleaching. The results of the present study show that sodium perborate is effective in bleaching nonvital teeth and does not produce ultrastructural changes in the dental tissues. Copyright 2010 American Association of Endodontists. Published by Elsevier Inc. All rights reserved.

Tuning of thermoelectric properties with changing Se content in Sb2Te3

NASA Astrophysics Data System (ADS)

Das, D.; Malik, K.; Deb, A. K.; Kulbachinskii, V. A.; Kytin, V. G.; Chatterjee, S.; Das, D.; Dhara, S.; Bandyopadhyay, S.; Banerjee, A.

2016-02-01

Polycrystalline Sb2Te3-x Se x (0.0≤ x≤1.0) samples were synthesized by the solid-state reaction method. The structural analysis showed that up to the maximal concentration of Se, the samples possess rhombohedral crystal symmetry (space group R\\bar{3}m ). The increase of Se content increases the resistivity of the samples. The variation of phonon frequencies, observed from the Raman spectroscopic study, depicts an anomalous behaviour around x=0.2 . The sample Sb2Te2.8Se0.2 also shows maximum Seebeck coefficient, carrier concentration and thermoelectric power factor. The nature of the scattering mechanism controlling the thermopower data has been explored. The thermoelectric properties of the synthesized materials have been analyzed theoretically in the frame of the Boltzmann equation approach.

XANES Identification of Plutonium Speciation in RFETS Samples

DOE Office of Scientific and Technical Information (OSTI.GOV)

LoPresti, V.; Conradson, S.D.; Clark, D.L.

2009-06-03

Using primarily X-ray absorption near edge spectroscopy (XANES) with standards run in tandem with samples, probable plutonium speciation was determined for 13 samples from contaminated soil, acid-splash or fire-deposition building interior surfaces, or asphalt pads from the Rocky Flats Environmental Technology Site (RFETS). Save for extreme oxidizing situations, all other samples were found to be of Pu(IV) speciation, supporting the supposition that such contamination is less likely to show mobility off site. EXAFS analysis conducted on two of the 13 samples supported the validity of the XANES features employed as determinants of the plutonium valence.

A Simple and Robust Method for Partially Matched Samples Using the P-Values Pooling Approach

PubMed Central

Kuan, Pei Fen; Huang, Bo

2013-01-01

This paper focuses on statistical analyses in scenarios where some samples from the matched pairs design are missing, resulting in partially matched samples. Motivated by the idea of meta-analysis, we recast the partially matched samples as coming from two experimental designs, and propose a simple yet robust approach based on the weighted Z-test to integrate the p-values computed from these two designs. We show that the proposed approach achieves better operating characteristics in simulations and a case study, compared to existing methods for partially matched samples. PMID:23417968

Microbial Successions and Metabolite Changes during Fermentation of Salted Shrimp (Saeu-Jeot) with Different Salt Concentrations

PubMed Central

Lee, Se Hee; Jung, Ji Young; Jeon, Che Ok

2014-01-01

To investigate the effects of salt concentration on saeu-jeot (salted shrimp) fermentation, four sets of saeu-jeot samples with 20%, 24%, 28%, and 32% salt concentrations were prepared, and the pH, bacterial and archaeal abundances, bacterial communities, and metabolites were monitored during the entire fermentation period. Quantitative PCR showed that Bacteria were much more abundant than Archaea in all saeu-jeot samples, suggesting that bacterial populations play more important roles than archaeal populations even in highly salted samples. Community analysis indicated that Vibrio, Photobacterium, Psychrobacter, Pseudoalteromonas, and Enterovibrio were identified as the initially dominant genera, and the bacterial successions were significantly different depending on the salt concentration. During the early fermentation period, Salinivibrio predominated in the 20% salted samples, whereas Staphylococcus, Halomonas, and Salimicrobium predominated in the 24% salted samples; eventually, Halanaerobium predominated in the 20% and 24% salted samples. The initially dominant genera gradually decreased as the fermentation progressed in the 28% and 32% salted samples, and eventually Salimicrobium became predominant in the 28% salted samples. However, the initially dominant genera still remained until the end of fermentation in the 32% salted samples. Metabolite analysis showed that the amino acid profile and the initial glycerol increase were similar in all saeu-jeot samples regardless of the salt concentration. After 30–80 days of fermentation, the levels of acetate, butyrate, and methylamines in the 20% and 24% salted samples increased with the growth of Halanaerobium, even though the amino acid concentrations steadily increased until approximately 80–107 days of fermentation. This study suggests that a range of 24–28% salt concentration in saeu-jeot fermentation is appropriate for the production of safe and tasty saeu-jeot. PMID:24587230