Identifying Dust Sources by Positive Matrix Factorization (PMF)

NASA Astrophysics Data System (ADS)

Engelbrecht, Johann P.

2010-05-01

This presentation is on the source attribution by Positive Matrix Factorization (PMF) of aerosol samples collected in Iraq, a major source of mineral dust in the Middle East. Globally transported mineral dust from North Africa, the Middle East, China, and elsewhere are routinely being sampled at high elevation monitoring sites such as those on the Canary Islands and Hawaii, and many ambient monitoring sites worldwide. Chemical results of these filter samples reflect differences in sources impacting at each site, further complicated by the regional geomorphology and meteorology. Trace elements, isotopes, elemental ratios, and mineralogy are generally being used to pinpoint geological source regions of natural and anthropogenic dusts. A receptor site is seldom impacted by only one source at a time. Dust palls are continually being modified by added dust from soils across which they migrate, also by particle segregation in the dust plume, and precipitation of the coarser particles. The result is that dust is a mixture, with contributions from different sources, each with a different chemical and mineralogical signature. PMF is a non-negative factorization procedure that produces only positive factor scores and loadings, in contrast to classical factor analysis (FA) and Principal Components Analysis (PCA). PMF enables us to resolve factors (chemical signatures) for source types contributing to the ambient chemical data set, and also models the source-type contributions to individual ambient samples. The latter can often be related to specific source regions. PMF was applied separately to two ambient data sets collected in Iraq in 2006, the one on Teflon membrane filters and the other on quartz fiber. Each of the filter types were previously analyzed for different chemical species: Teflon membrane for elements, by XRF and ICP-MS, while quartz fiber filters were analyzed for ions and carbon. [Engelbrecht et al. 2009] A set of 392 Teflon filter samples analyzed for 25

Probabilistic analysis showing that a combination of bacteroides and methanobrevibacter source tracking markers is effective for identifying waters contaminated by human fecal pollution

USGS Publications Warehouse

Johnston, Christopher; Byappanahalli, Muruleedhara N.; Gibson, Jacqueline MacDonald; Ufnar, Jennifer A.; Whitman, Richard L.; Stewart, Jill R.

2013-01-01

Microbial source tracking assays to identify sources of waterborne contamination typically target genetic markers of host-specific microorganisms. However, no bacterial marker has been shown to be 100% host-specific, and cross-reactivity has been noted in studies evaluating known source samples. Using 485 challenge samples from 20 different human and animal fecal sources, this study evaluated microbial source tracking markers including the Bacteroides HF183 16S rRNA, M. smithii nifH, and Enterococcus esp gene targets that have been proposed as potential indicators of human fecal contamination. Bayes' Theorem was used to calculate the conditional probability that these markers or a combination of markers can correctly identify human sources of fecal pollution. All three human-associated markers were detected in 100% of the sewage samples analyzed. Bacteroides HF183 was the most effective marker for determining whether contamination was specifically from a human source, and greater than 98% certainty that contamination was from a human source was shown when both Bacteroides HF183 and M. smithii nifH markers were present. A high degree of certainty was attained even in cases where the prior probability of human fecal contamination was as low as 8.5%. The combination of Bacteroides HF183 and M. smithii nifH source tracking markers can help identify surface waters impacted by human fecal contamination, information useful for prioritizing restoration activities or assessing health risks from exposure to contaminated waters.

Comparison of Microbial and Chemical Source Tracking Markers To Identify Fecal Contamination Sources in the Humber River (Toronto, Ontario, Canada) and Associated Storm Water Outfalls.

PubMed

Staley, Zachery R; Grabuski, Josey; Sverko, Ed; Edge, Thomas A

2016-11-01

Storm water runoff is a major source of pollution, and understanding the components of storm water discharge is essential to remediation efforts and proper assessment of risks to human and ecosystem health. In this study, culturable Escherichia coli and ampicillin-resistant E. coli levels were quantified and microbial source tracking (MST) markers (including markers for general Bacteroidales spp., human, ruminant/cow, gull, and dog) were detected in storm water outfalls and sites along the Humber River in Toronto, Ontario, Canada, and enumerated via endpoint PCR and quantitative PCR (qPCR). Additionally, chemical source tracking (CST) markers specific for human wastewater (caffeine, carbamazepine, codeine, cotinine, acetaminophen, and acesulfame) were quantified. Human and gull fecal sources were detected at all sites, although concentrations of the human fecal marker were higher, particularly in outfalls (mean outfall concentrations of 4.22 log 10 copies, expressed as copy numbers [CN]/100 milliliters for human and 0.46 log 10 CN/100 milliliters for gull). Higher concentrations of caffeine, acetaminophen, acesulfame, E. coli, and the human fecal marker were indicative of greater raw sewage contamination at several sites (maximum concentrations of 34,800 ng/liter, 5,120 ng/liter, 9,720 ng/liter, 5.26 log 10 CFU/100 ml, and 7.65 log 10 CN/100 ml, respectively). These results indicate pervasive sewage contamination at storm water outfalls and throughout the Humber River, with multiple lines of evidence identifying Black Creek and two storm water outfalls with prominent sewage cross-connection problems requiring remediation. Limited data are available on specific sources of pollution in storm water, though our results indicate the value of using both MST and CST methodologies to more reliably assess sewage contamination in impacted watersheds. Storm water runoff is one of the most prominent non-point sources of biological and chemical contaminants which can

Comparison of Microbial and Chemical Source Tracking Markers To Identify Fecal Contamination Sources in the Humber River (Toronto, Ontario, Canada) and Associated Storm Water Outfalls

PubMed Central

Grabuski, Josey; Sverko, Ed; Edge, Thomas A.

2016-01-01

ABSTRACT Storm water runoff is a major source of pollution, and understanding the components of storm water discharge is essential to remediation efforts and proper assessment of risks to human and ecosystem health. In this study, culturable Escherichia coli and ampicillin-resistant E. coli levels were quantified and microbial source tracking (MST) markers (including markers for general Bacteroidales spp., human, ruminant/cow, gull, and dog) were detected in storm water outfalls and sites along the Humber River in Toronto, Ontario, Canada, and enumerated via endpoint PCR and quantitative PCR (qPCR). Additionally, chemical source tracking (CST) markers specific for human wastewater (caffeine, carbamazepine, codeine, cotinine, acetaminophen, and acesulfame) were quantified. Human and gull fecal sources were detected at all sites, although concentrations of the human fecal marker were higher, particularly in outfalls (mean outfall concentrations of 4.22 log10 copies, expressed as copy numbers [CN]/100 milliliters for human and 0.46 log10 CN/100 milliliters for gull). Higher concentrations of caffeine, acetaminophen, acesulfame, E. coli, and the human fecal marker were indicative of greater raw sewage contamination at several sites (maximum concentrations of 34,800 ng/liter, 5,120 ng/liter, 9,720 ng/liter, 5.26 log10 CFU/100 ml, and 7.65 log10 CN/100 ml, respectively). These results indicate pervasive sewage contamination at storm water outfalls and throughout the Humber River, with multiple lines of evidence identifying Black Creek and two storm water outfalls with prominent sewage cross-connection problems requiring remediation. Limited data are available on specific sources of pollution in storm water, though our results indicate the value of using both MST and CST methodologies to more reliably assess sewage contamination in impacted watersheds. IMPORTANCE Storm water runoff is one of the most prominent non-point sources of biological and chemical contaminants

Identifying Emergency Department Patients at Low Risk for a Variceal Source of Upper Gastrointestinal Hemorrhage.

PubMed

Klein, Lauren R; Money, Joel; Maharaj, Kaveesh; Robinson, Aaron; Lai, Tarissa; Driver, Brian E

2017-11-01

Assessing the likelihood of a variceal versus nonvariceal source of upper gastrointestinal bleeding (UGIB) guides therapy, but can be difficult to determine on clinical grounds. The objective of this study was to determine if there are easily ascertainable clinical and laboratory findings that can identify a patient as low risk for a variceal source of hemorrhage. This was a retrospective cohort study of adult ED patients with UGIB between January 2008 and December 2014 who had upper endoscopy performed during hospitalization. Clinical and laboratory data were abstracted from the medical record. The source of the UGIB was defined as variceal or nonvariceal based on endoscopic reports. Binary recursive partitioning was utilized to create a clinical decision rule. The rule was internally validated and test characteristics were calculated with 1,000 bootstrap replications. A total of 719 patients were identified; mean age was 55 years and 61% were male. There were 71 (10%) patients with a variceal UGIB identified on endoscopy. Binary recursive partitioning yielded a two-step decision rule (platelet count > 200 × 10 9 /L and an international normalized ratio [INR] < 1.3), which identified patients who were low risk for a variceal source of hemorrhage. For the bootstrapped samples, the rule performed with 97% sensitivity (95% confidence interval [CI] = 91%-100%) and 49% specificity (95% CI = 44%-53%). Although this derivation study must be externally validated before widespread use, patients presenting to the ED with an acute UGIB with platelet count of >200 × 10 9 /L and an INR of <1.3 may be at very low risk for a variceal source of their upper gastrointestinal hemorrhage. © 2017 by the Society for Academic Emergency Medicine.

Specification of High Activity Gamma-Ray Sources.

ERIC Educational Resources Information Center

International Commission on Radiation Units and Measurements, Washington, DC.

The report is concerned with making recommendations for the specifications of gamma ray sources, which relate to the quantity of radioactive material and the radiation emitted. Primary consideration is given to sources in teletherapy and to a lesser extent those used in industrial radiography and in irradiation units used in industry and research.…

Can we identify source lithology of basalt?

PubMed

Yang, Zong-Feng; Zhou, Jun-Hong

2013-01-01

The nature of source rocks of basaltic magmas plays a fundamental role in understanding the composition, structure and evolution of the solid earth. However, identification of source lithology of basalts remains uncertainty. Using a parameterization of multi-decadal melting experiments on a variety of peridotite and pyroxenite, we show here that a parameter called FC3MS value (FeO/CaO-3*MgO/SiO2, all in wt%) can identify most pyroxenite-derived basalts. The continental oceanic island basalt-like volcanic rocks (MgO>7.5%) (C-OIB) in eastern China and Mongolia are too high in the FC3MS value to be derived from peridotite source. The majority of the C-OIB in phase diagrams are equilibrium with garnet and clinopyroxene, indicating that garnet pyroxenite is the dominant source lithology. Our results demonstrate that many reputed evolved low magnesian C-OIBs in fact represent primary pyroxenite melts, suggesting that many previous geological and petrological interpretations of basalts based on the single peridotite model need to be reconsidered.

Can we identify source lithology of basalt?

PubMed Central

Yang, Zong-Feng; Zhou, Jun-Hong

2013-01-01

The nature of source rocks of basaltic magmas plays a fundamental role in understanding the composition, structure and evolution of the solid earth. However, identification of source lithology of basalts remains uncertainty. Using a parameterization of multi-decadal melting experiments on a variety of peridotite and pyroxenite, we show here that a parameter called FC3MS value (FeO/CaO-3*MgO/SiO2, all in wt%) can identify most pyroxenite-derived basalts. The continental oceanic island basalt-like volcanic rocks (MgO>7.5%) (C-OIB) in eastern China and Mongolia are too high in the FC3MS value to be derived from peridotite source. The majority of the C-OIB in phase diagrams are equilibrium with garnet and clinopyroxene, indicating that garnet pyroxenite is the dominant source lithology. Our results demonstrate that many reputed evolved low magnesian C-OIBs in fact represent primary pyroxenite melts, suggesting that many previous geological and petrological interpretations of basalts based on the single peridotite model need to be reconsidered. PMID:23676779

DYNAMICS OF AQUATIC FECAL CONTAMINATION, FECAL SOURCE IDENTIFICATION, AND CORRELATION OF BACTEROIDALES HOST-SPECIFIC MARKERS DETECTION WITH FECAL PATHOGENS

EPA Science Inventory

Fecal pollution impairs the health and productivity of coastal waters and causes human disease. PCR of host-specific 16S rDNA sequences from anaerobic Bacteroidales bacteria offers a promising method of tracking fecal contamination and identifying its source(s). Before Bacteroida...

Joint source based morphometry identifies linked gray and white matter group differences.

PubMed

Xu, Lai; Pearlson, Godfrey; Calhoun, Vince D

2009-02-01

We present a multivariate approach called joint source based morphometry (jSBM), to identify linked gray and white matter regions which differ between groups. In jSBM, joint independent component analysis (jICA) is used to decompose preprocessed gray and white matter images into joint sources and statistical analysis is used to determine the significant joint sources showing group differences and their relationship to other variables of interest (e.g. age or sex). The identified joint sources are groupings of linked gray and white matter regions with common covariation among subjects. In this study, we first provide a simulation to validate the jSBM approach. To illustrate our method on real data, jSBM is then applied to structural magnetic resonance imaging (sMRI) data obtained from 120 chronic schizophrenia patients and 120 healthy controls to identify group differences. JSBM identified four joint sources as significantly associated with schizophrenia. Linked gray-white matter regions identified in each of the joint sources included: 1) temporal--corpus callosum, 2) occipital/frontal--inferior fronto-occipital fasciculus, 3) frontal/parietal/occipital/temporal--superior longitudinal fasciculus and 4) parietal/frontal--thalamus. Age effects on all four joint sources were significant, but sex effects were significant only for the third joint source. Our findings demonstrate that jSBM can exploit the natural linkage between gray and white matter by incorporating them into a unified framework. This approach is applicable to a wide variety of problems to study linked gray and white matter group differences.

Joint source based morphometry identifies linked gray and white matter group differences

PubMed Central

Xu, Lai; Pearlson, Godfrey; Calhoun, Vince D.

2009-01-01

We present a multivariate approach called joint source based morphometry (jSBM), to identify linked gray and white matter regions which differ between groups. In jSBM, joint independent component analysis (jICA) is used to decompose preprocessed gray and white matter images into joint sources and statistical analysis is used to determine the significant joint sources showing group differences and their relationship to other variables of interest (e.g. age or sex). The identified joint sources are groupings of linked gray and white matter regions with common covariation among subjects. In this study, we first provide a simulation to validate the jSBM approach. To illustrate our method on real data, jSBM is then applied to structural magnetic resonance imaging (sMRI) data obtained from 120 chronic schizophrenia patients and 120 healthy controls to identify group differences. JSBM identified four joint sources as significantly associated with schizophrenia. Linked gray–white matter regions identified in each of the joint sources included: 1) temporal — corpus callosum, 2) occipital/frontal — inferior fronto-occipital fasciculus, 3) frontal/parietal/occipital/temporal —superior longitudinal fasciculus and 4) parietal/frontal — thalamus. Age effects on all four joint sources were significant, but sex effects were significant only for the third joint source. Our findings demonstrate that jSBM can exploit the natural linkage between gray and white matter by incorporating them into a unified framework. This approach is applicable to a wide variety of problems to study linked gray and white matter group differences. PMID:18992825

Combining molecular fingerprints with multidimensional scaling analyses to identify the source of spilled oil from highly similar suspected oils.

PubMed

Zhou, Peiyu; Chen, Changshu; Ye, Jianjun; Shen, Wenjie; Xiong, Xiaofei; Hu, Ping; Fang, Hongda; Huang, Chuguang; Sun, Yongge

2015-04-15

Oil fingerprints have been a powerful tool widely used for determining the source of spilled oil. In most cases, this tool works well. However, it is usually difficult to identify the source if the oil spill accident occurs during offshore petroleum exploration due to the highly similar physiochemical characteristics of suspected oils from the same drilling platform. In this report, a case study from the waters of the South China Sea is presented, and multidimensional scaling analysis (MDS) is introduced to demonstrate how oil fingerprints can be combined with mathematical methods to identify the source of spilled oil from highly similar suspected sources. The results suggest that the MDS calculation based on oil fingerprints and subsequently integrated with specific biomarkers in spilled oils is the most effective method with a great potential for determining the source in terms of highly similar suspected oils. Copyright © 2015 Elsevier Ltd. All rights reserved.

Investigating Salmonella Eko from Various Sources in Nigeria by Whole Genome Sequencing to Identify the Source of Human Infections

PubMed Central

Leekitcharoenphon, Pimlapas; Raufu, Ibrahim; Nielsen, Mette T.; Rosenqvist Lund, Birthe S.; Ameh, James A.; Ambali, Abdul G.; Sørensen, Gitte; Le Hello, Simon; Aarestrup, Frank M.; Hendriksen, Rene S.

2016-01-01

Twenty-six Salmonella enterica serovar Eko isolated from various sources in Nigeria were investigated by whole genome sequencing to identify the source of human infections. Diversity among the isolates was observed and camel and cattle were identified as the primary reservoirs and the most likely source of the human infections. PMID:27228329

Identifying EGRET Sources

NASA Technical Reports Server (NTRS)

Schlegel, E.; Norris, Jay P. (Technical Monitor)

2002-01-01

This project was awarded funding from the CGRO program to support ROSAT and ground-based observations of unidentified sources from data obtained by the EGRET instrument on the Compton Gamma-Ray Observatory. The critical items in the project are the individual ROSAT observations that are used to cover the 99% error circle of the unidentified EGRET source. Each error circle is a degree or larger in diameter. Each ROSAT field is about 30 deg in diameter. Hence, a number (>4) of ROSAT pointings must be obtained for each EGRET source to cover the field. The scheduling of ROSAT observations is carried out to maximize the efficiency of the total schedule. As a result, each pointing is broken into one or more sub-pointings of various exposure times. This project was awarded ROSAT observing time for four unidentified EGRET sources, summarized in the table. The column headings are defined as follows: 'Coverings' = number of observations to cover the error circle; 'SubPtg' = total number of sub-pointings to observe all of the coverings; 'Rec'd' = number of individual sub-pointings received to date; 'CompFlds' = number of individual coverings for which the requested complete exposure has been received. Processing of the data can not occur until a complete exposure has been accumulated for each covering.

Approach to identifying pollutant source and matching flow field

NASA Astrophysics Data System (ADS)

Liping, Pang; Yu, Zhang; Hongquan, Qu; Tao, Hu; Wei, Wang

2013-07-01

Accidental pollution events often threaten people's health and lives, and it is necessary to identify a pollutant source rapidly so that prompt actions can be taken to prevent the spread of pollution. But this identification process is one of the difficulties in the inverse problem areas. This paper carries out some studies on this issue. An approach using single sensor information with noise was developed to identify a sudden continuous emission trace pollutant source in a steady velocity field. This approach first compares the characteristic distance of the measured concentration sequence to the multiple hypothetical measured concentration sequences at the sensor position, which are obtained based on a source-three-parameter multiple hypotheses. Then we realize the source identification by globally searching the optimal values with the objective function of the maximum location probability. Considering the large amount of computation load resulting from this global searching, a local fine-mesh source search method based on priori coarse-mesh location probabilities is further used to improve the efficiency of identification. Studies have shown that the flow field has a very important influence on the source identification. Therefore, we also discuss the impact of non-matching flow fields with estimation deviation on identification. Based on this analysis, a method for matching accurate flow field is presented to improve the accuracy of identification. In order to verify the practical application of the above method, an experimental system simulating a sudden pollution process in a steady flow field was set up and some experiments were conducted when the diffusion coefficient was known. The studies showed that the three parameters (position, emission strength and initial emission time) of the pollutant source in the experiment can be estimated by using the method for matching flow field and source identification.

Identifying sources of emerging organic contaminants in a mixed use watershed using principal components analysis.

PubMed

Karpuzcu, M Ekrem; Fairbairn, David; Arnold, William A; Barber, Brian L; Kaufenberg, Elizabeth; Koskinen, William C; Novak, Paige J; Rice, Pamela J; Swackhamer, Deborah L

2014-01-01

Principal components analysis (PCA) was used to identify sources of emerging organic contaminants in the Zumbro River watershed in Southeastern Minnesota. Two main principal components (PCs) were identified, which together explained more than 50% of the variance in the data. Principal Component 1 (PC1) was attributed to urban wastewater-derived sources, including municipal wastewater and residential septic tank effluents, while Principal Component 2 (PC2) was attributed to agricultural sources. The variances of the concentrations of cotinine, DEET and the prescription drugs carbamazepine, erythromycin and sulfamethoxazole were best explained by PC1, while the variances of the concentrations of the agricultural pesticides atrazine, metolachlor and acetochlor were best explained by PC2. Mixed use compounds carbaryl, iprodione and daidzein did not specifically group with either PC1 or PC2. Furthermore, despite the fact that caffeine and acetaminophen have been historically associated with human use, they could not be attributed to a single dominant land use category (e.g., urban/residential or agricultural). Contributions from septic systems did not clarify the source for these two compounds, suggesting that additional sources, such as runoff from biosolid-amended soils, may exist. Based on these results, PCA may be a useful way to broadly categorize the sources of new and previously uncharacterized emerging contaminants or may help to clarify transport pathways in a given area. Acetaminophen and caffeine were not ideal markers for urban/residential contamination sources in the study area and may need to be reconsidered as such in other areas as well.

77 FR 33642 - Regional Haze: Revisions to Provisions Governing Alternatives to Source-Specific Best Available...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-07

... of the Two-Pronged Test 2. Identification of Affected Class I Areas 3. Control Scenarios Examined 4... two-pronged test to the Transport Rule control scenario and the source-specific BART control scenario... approaches to identify the Class I areas ``affected'' by the Transport Rule as an alternative control program...

Bacterial indicator occurrence and the use of an F+ specific RNA coliphage assay to identify fecal sources in Homosassa Springs, Florida

USGS Publications Warehouse

Griffin, Dale W.; Stokes, Rodger; Rose, J.B.; Paul, J.H.

2000-01-01

A microbiological water quality study of Homosassa Springs State Wildlife Park (HSSWP) and surrounding areas was undertaken. Samples were collected in November of 1997 (seven sites) and again in November of 1998 (nine sites). Fecal bacterial concentrations (total and fecal coliforms, Clostridium perfringens, and enterococci) were measured as relative indicators of fecal contamination. F+-specific coliphage genotyping was performed to determine the source of fecal contamination at the study sites. Bacterial levels were considerably higher at most sites in the 1997 sampling compared to the 1998 sampling, probably because of the greater rainfall that year. In November of 1997, 2 of the 7 sites were in violation of all indicator standards and guidance levels. In November of 1998, 1 of 9 sites was in violation of all indicator standard and guidance levels. The highest concentrations of all fecal indicators were found at a station downstream of the animal holding pens in HSSWP. The lowest levels of indicators were found at the Homosassa Main Spring vent. Levels of fecal indicators downstream of HSSWP (near the point of confluence with the river) were equivalent to those found in the Southeastern Fork and areas upstream of the park influences. F+ specific RNA coliphage analysis indicated that fecal contamination at all sites that tested positive was from animal sources (mammals and birds). These results suggest that animal (indigenous and those in HSSWP) and not human sources influenced microbial water quality in the area of Homosassa River covered by this study.

On Acoustic Source Specification for Rotor-Stator Interaction Noise Prediction

NASA Technical Reports Server (NTRS)

Nark, Douglas M.; Envia, Edmane; Burley, Caesy L.

2010-01-01

This paper describes the use of measured source data to assess the effects of acoustic source specification on rotor-stator interaction noise predictions. Specifically, the acoustic propagation and radiation portions of a recently developed coupled computational approach are used to predict tonal rotor-stator interaction noise from a benchmark configuration. In addition to the use of full measured data, randomization of source mode relative phases is also considered for specification of the acoustic source within the computational approach. Comparisons with sideline noise measurements are performed to investigate the effects of various source descriptions on both inlet and exhaust predictions. The inclusion of additional modal source content is shown to have a much greater influence on the inlet results. Reasonable agreement between predicted and measured levels is achieved for the inlet, as well as the exhaust when shear layer effects are taken into account. For the number of trials considered, phase randomized predictions follow statistical distributions similar to those found in previous statistical source investigations. The shape of the predicted directivity pattern relative to measurements also improved with phase randomization, having predicted levels generally within one standard deviation of the measured levels.

Evaluation of Two Library-Independent Microbial Source Tracking Methods To Identify Sources of Fecal Contamination in French Estuaries▿

PubMed Central

Gourmelon, Michèle; Caprais, Marie Paule; Ségura, Raphaël; Le Mennec, Cécile; Lozach, Solen; Piriou, Jean Yves; Rincé, Alain

2007-01-01

In order to identify the origin of the fecal contamination observed in French estuaries, two library-independent microbial source tracking (MST) methods were selected: (i) Bacteroidales host-specific 16S rRNA gene markers and (ii) F-specific RNA bacteriophage genotyping. The specificity of the Bacteroidales markers was evaluated on human and animal (bovine, pig, sheep, and bird) feces. Two human-specific markers (HF183 and HF134), one ruminant-specific marker (CF193′), and one pig-specific marker (PF163) showed a high level of specificity (>90%). However, the data suggest that the proposed ruminant-specific CF128 marker would be better described as an animal marker, as it was observed in all bovine and sheep feces and 96% of pig feces. F RNA bacteriophages were detected in only 21% of individual fecal samples tested, in 60% of pig slurries, but in all sewage samples. Most detected F RNA bacteriophages were from genotypes II and III in sewage samples and from genotypes I and IV in bovine, pig, and bird feces and from pig slurries. Both MST methods were applied to 28 water samples collected from three watersheds at different times. Classification of water samples as subject to human, animal, or mixed fecal contamination was more frequent when using Bacteroidales markers (82.1% of water samples) than by bacteriophage genotyping (50%). The ability to classify a water sample increased with increasing Escherichia coli or enterococcus concentration. For the samples that could be classified by bacteriophage genotyping, 78% agreed with the classification obtained from Bacteroidales markers. PMID:17557850

Diagnostic Air Quality Model Evaluation of Source-Specific ...

EPA Pesticide Factsheets

Ambient measurements of 78 source-specific tracers of primary and secondary carbonaceous fine particulate matter collected at four midwestern United States locations over a full year (March 2004–February 2005) provided an unprecedented opportunity to diagnostically evaluate the results of a numerical air quality model. Previous analyses of these measurements demonstrated excellent mass closure for the variety of contributing sources. In this study, a carbon-apportionment version of the Community Multiscale Air Quality (CMAQ) model was used to track primary organic and elemental carbon emissions from 15 independent sources such as mobile sources and biomass burning in addition to four precursor-specific classes of secondary organic aerosol (SOA) originating from isoprene, terpenes, aromatics, and sesquiterpenes. Conversion of the source-resolved model output into organic tracer concentrations yielded a total of 2416 data pairs for comparison with observations. While emission source contributions to the total model bias varied by season and measurement location, the largest absolute bias of −0.55 μgC/m3 was attributed to insufficient isoprene SOA in the summertime CMAQ simulation. Biomass combustion was responsible for the second largest summertime model bias (−0.46 μgC/m3 on average). Several instances of compensating errors were also evident; model underpredictions in some sectors were masked by overpredictions in others. The National Exposure Research L

Chagas disease vector blood meal sources identified by protein mass spectrometry

PubMed Central

Keller, Judith I.; Ballif, Bryan A.; St. Clair, Riley M.; Vincent, James J.; Monroy, M. Carlota

2017-01-01

Chagas disease is a complex vector borne parasitic disease involving blood feeding Triatominae (Hemiptera: Reduviidae) insects, also known as kissing bugs, and the vertebrates they feed on. This disease has tremendous impacts on millions of people and is a global health problem. The etiological agent of Chagas disease, Trypanosoma cruzi (Kinetoplastea: Trypanosomatida: Trypanosomatidae), is deposited on the mammalian host in the insect’s feces during a blood meal, and enters the host’s blood stream through mucous membranes or a break in the skin. Identifying the blood meal sources of triatomine vectors is critical in understanding Chagas disease transmission dynamics, can lead to identification of other vertebrates important in the transmission cycle, and aids management decisions. The latter is particularly important as there is little in the way of effective therapeutics for Chagas disease. Several techniques, mostly DNA-based, are available for blood meal identification. However, further methods are needed, particularly when sample conditions lead to low-quality DNA or to assess the risk of human cross-contamination. We demonstrate a proteomics-based approach, using liquid chromatography tandem mass spectrometry (LC-MS/MS) to identify host-specific hemoglobin peptides for blood meal identification in mouse blood control samples and apply LC-MS/MS for the first time to Triatoma dimidiata insect vectors, tracing blood sources to species. In contrast to most proteins, hemoglobin, stabilized by iron, is incredibly stable even being preserved through geologic time. We compared blood stored with and without an anticoagulant and examined field-collected insect specimens stored in suboptimal conditions such as at room temperature for long periods of time. To our knowledge, this is the first study using LC-MS/MS on field-collected arthropod disease vectors to identify blood meal composition, and where blood meal identification was confirmed with more traditional DNA

Bispectral pairwise interacting source analysis for identifying systems of cross-frequency interacting brain sources from electroencephalographic or magnetoencephalographic signals

NASA Astrophysics Data System (ADS)

Chella, Federico; Pizzella, Vittorio; Zappasodi, Filippo; Nolte, Guido; Marzetti, Laura

2016-05-01

Brain cognitive functions arise through the coordinated activity of several brain regions, which actually form complex dynamical systems operating at multiple frequencies. These systems often consist of interacting subsystems, whose characterization is of importance for a complete understanding of the brain interaction processes. To address this issue, we present a technique, namely the bispectral pairwise interacting source analysis (biPISA), for analyzing systems of cross-frequency interacting brain sources when multichannel electroencephalographic (EEG) or magnetoencephalographic (MEG) data are available. Specifically, the biPISA makes it possible to identify one or many subsystems of cross-frequency interacting sources by decomposing the antisymmetric components of the cross-bispectra between EEG or MEG signals, based on the assumption that interactions are pairwise. Thanks to the properties of the antisymmetric components of the cross-bispectra, biPISA is also robust to spurious interactions arising from mixing artifacts, i.e., volume conduction or field spread, which always affect EEG or MEG functional connectivity estimates. This method is an extension of the pairwise interacting source analysis (PISA), which was originally introduced for investigating interactions at the same frequency, to the study of cross-frequency interactions. The effectiveness of this approach is demonstrated in simulations for up to three interacting source pairs and for real MEG recordings of spontaneous brain activity. Simulations show that the performances of biPISA in estimating the phase difference between the interacting sources are affected by the increasing level of noise rather than by the number of the interacting subsystems. The analysis of real MEG data reveals an interaction between two pairs of sources of central mu and beta rhythms, localizing in the proximity of the left and right central sulci.

Using an epiphytic moss to identify previously unknown sources of atmospheric cadmium pollution

Treesearch

Geoffrey H. Donovan; Sarah E. Jovan; Demetrios Gatziolis; Igor Burstyn; Yvonne L. Michael; Michael C. Amacher; Vicente J. Monleon

2016-01-01

Urban networks of air-quality monitors are often too widely spaced to identify sources of air pollutants, especially if they do not disperse far from emission sources. The objectives of this study were to test the use of moss bio-indicators to develop a fine-scale map of atmospherically-derived cadmium and to identify the sources of cadmium in a complex urban setting....

Cause-specific stillbirth and exposure to chemical constituents and sources of fine particulate matter.

PubMed

Ebisu, Keita; Malig, Brian; Hasheminassab, Sina; Sioutas, Constantinos; Basu, Rupa

2018-01-01

The stillbirth rate in the United States is relatively high, but limited evidence is available linking stillbirth with fine particulate matter (PM 2.5 ), its chemical constituents and sources. In this study, we explored associations between cause-specific stillbirth and prenatal exposures to those pollutants with using live birth and stillbirth records from eight California locations during 2002-2009. ICD-10 codes were used to identify cause of stillbirth from stillbirth records. PM 2.5 total mass and chemical constituents were collected from ambient monitors and PM 2.5 sources were quantified using Positive Matrix Factorization. Conditional logistic regression was applied using a nested case-control study design (N = 32,262). We found that different causes of stillbirth were associated with different PM 2.5 sources and/or chemical constituents. For stillbirths due to fetal growth, the odds ratio (OR) per interquartile range increase in gestational age-adjusted exposure to PM 2.5 total mass was 1.23 (95% confidence interval (CI): 1.06, 1.44). Similar associations were found with resuspended soil (OR=1.25, 95% CI: 1.10, 1.42), and secondary ammonium sulfate (OR=1.45, 95% CI: 1.18, 1.78). No associations were found between any pollutants and stillbirths caused by maternal complications. This study highlighted the importance of investigating cause-specific stillbirth and the differential toxicity levels of specific PM 2.5 sources and chemical constituents. Copyright © 2017 Elsevier Inc. All rights reserved.

Full-Sun observations for identifying the source of the slow solar wind

PubMed Central

Brooks, David H.; Ugarte-Urra, Ignacio; Warren, Harry P.

2015-01-01

Fast (>700 km s−1) and slow (~400 km s−1) winds stream from the Sun, permeate the heliosphere and influence the near-Earth environment. While the fast wind is known to emanate primarily from polar coronal holes, the source of the slow wind remains unknown. Here we identify possible sites of origin using a slow solar wind source map of the entire Sun, which we construct from specially designed, full-disk observations from the Hinode satellite, and a magnetic field model. Our map provides a full-Sun observation that combines three key ingredients for identifying the sources: velocity, plasma composition and magnetic topology and shows them as solar wind composition plasma outflowing on open magnetic field lines. The area coverage of the identified sources is large enough that the sum of their mass contributions can explain a significant fraction of the mass loss rate of the solar wind. PMID:25562705

Root Source Analysis/ValuStream[Trade Mark] - A Methodology for Identifying and Managing Risks

NASA Technical Reports Server (NTRS)

Brown, Richard Lee

2008-01-01

Root Source Analysis (RoSA) is a systems engineering methodology that has been developed at NASA over the past five years. It is designed to reduce costs, schedule, and technical risks by systematically examining critical assumptions and the state of the knowledge needed to bring to fruition the products that satisfy mission-driven requirements, as defined for each element of the Work (or Product) Breakdown Structure (WBS or PBS). This methodology is sometimes referred to as the ValuStream method, as inherent in the process is the linking and prioritizing of uncertainties arising from knowledge shortfalls directly to the customer's mission driven requirements. RoSA and ValuStream are synonymous terms. RoSA is not simply an alternate or improved method for identifying risks. It represents a paradigm shift. The emphasis is placed on identifying very specific knowledge shortfalls and assumptions that are the root sources of the risk (the why), rather than on assessing the WBS product(s) themselves (the what). In so doing RoSA looks forward to anticipate, identify, and prioritize knowledge shortfalls and assumptions that are likely to create significant uncertainties/ risks (as compared to Root Cause Analysis, which is most often used to look back to discover what was not known, or was assumed, that caused the failure). Experience indicates that RoSA, with its primary focus on assumptions and the state of the underlying knowledge needed to define, design, build, verify, and operate the products, can identify critical risks that historically have been missed by the usual approaches (i.e., design review process and classical risk identification methods). Further, the methodology answers four critical questions for decision makers and risk managers: 1. What s been included? 2. What's been left out? 3. How has it been validated? 4. Has the real source of the uncertainty/ risk been identified, i.e., is the perceived problem the real problem? Users of the RoSA methodology

Defining the relationship between individuals’ aggregate and maximum source-specific exposures

EPA Science Inventory

The concepts of aggregate and source-specific exposures play an important role in chemical risk management. The concepts of aggregate and source-specific exposures play an important role in chemical risk management. Aggregate exposure to a chemical refers to combined exposures fr...

Identifying sources of nitrogen to Hanalei Bay, Kauai, utilizing the nitrogen isotope signature of macroalgae

USGS Publications Warehouse

Derse, E.; Knee, K.L.; Wankel, Scott D.; Kendall, C.; Berg, C.J.; Paytan, A.

2007-01-01

Sewage effluent, storm runoff, discharge from polluted rivers, and inputs of groundwater have all been suggested as potential sources of land derived nutrients into Hanalei Bay, Kauai. We determined the nitrogen isotopic signatures (??15N) of different nitrate sources to Hanalei Bay along with the isotopic signature recorded by 11 species of macroalgal collected in the Bay. The macroalgae integrate the isotopic signatures of the nitrate sources over time, thus these data along with the nitrate to dissolved inorganic phosphate molar ratios (N:P) of the macroalgae were used to determine the major nitrate source to the bay ecosystem and which of the macro-nutrients is limiting algae growth, respectively. Relatively low ??15N values (average -0.5???) were observed in all algae collected throughout the Bay; implicating fertilizer, rather than domestic sewage, as an important external source of nitrogen to the coastal water around Hanalei. The N:P ratio in the algae compared to the ratio in the Bay waters imply that the Hanalei Bay coastal ecosystem is nitrogen limited and thus, increased nitrogen input may potentially impactthis coastal ecosystem and specifically the coral reefs in the Bay. Identifying the major source of nutrient loading to the Bay is important for risk assessment and potential remediation plans. ?? 2007 American Chemical Society.

Using Multiple-Variable Matching to Identify Cultural Sources of Differential Item Functioning

ERIC Educational Resources Information Center

Wu, Amery D.; Ercikan, Kadriye

2006-01-01

Identifying the sources of differential item functioning (DIF) in international assessments is very challenging, because such sources are often nebulous and intertwined. Even though researchers frequently focus on test translation and content area, few actually go beyond these factors to investigate other cultural sources of DIF. This article…

Inferring Gene Family Histories in Yeast Identifies Lineage Specific Expansions

PubMed Central

Ames, Ryan M.; Money, Daniel; Lovell, Simon C.

2014-01-01

The complement of genes found in the genome is a balance between gene gain and gene loss. Knowledge of the specific genes that are gained and lost over evolutionary time allows an understanding of the evolution of biological functions. Here we use new evolutionary models to infer gene family histories across complete yeast genomes; these models allow us to estimate the relative genome-wide rates of gene birth, death, innovation and extinction (loss of an entire family) for the first time. We show that the rates of gene family evolution vary both between gene families and between species. We are also able to identify those families that have experienced rapid lineage specific expansion/contraction and show that these families are enriched for specific functions. Moreover, we find that families with specific functions are repeatedly expanded in multiple species, suggesting the presence of common adaptations and that these family expansions/contractions are not random. Additionally, we identify potential specialisations, unique to specific species, in the functions of lineage specific expanded families. These results suggest that an important mechanism in the evolution of genome content is the presence of lineage-specific gene family changes. PMID:24921666

Effectiveness of source documents for identifying fatal occupational injuries: a synthesis of studies.

PubMed

Stout, N; Bell, C

1991-06-01

The complete and accurate identification of fatal occupational injuries among the US work force is an important first step in developing work injury prevention efforts. Numerous sources of information, such as death certificates, Workers' Compensation files, Occupational Safety and Health Administration (OSHA) files, medical examiner records, state health and labor department reports, and various combinations of these, have been used to identify cases of work-related fatal injuries. Recent studies have questioned the effectiveness of these sources for identifying such cases. At least 10 studies have used multiple sources to define the universe of fatal work injuries within a state and to determine the capture rates, or proportion of the universe identified, by each source. Results of these studies, which are not all available in published literature, are summarized here in a format that allows researchers to readily compare the ascertainment capabilities of the sources. The overall average capture rates of sources were as follows: death certificates, 81%; medical examiner records, 61%; Workers' Compensation reports, 57%; and OSHA reports 32%. Variations by state and value added through the use of multiple sources are presented and discussed. This meta-analysis of 10 state-based studies summarizes the effectiveness of various source documents for capturing cases of fatal occupational injuries to help researchers make informed decisions when designing occupational injury surveillance systems.

Effectiveness of source documents for identifying fatal occupational injuries: a synthesis of studies.

PubMed Central

Stout, N; Bell, C

1991-01-01

BACKGROUND: The complete and accurate identification of fatal occupational injuries among the US work force is an important first step in developing work injury prevention efforts. Numerous sources of information, such as death certificates, Workers' Compensation files, Occupational Safety and Health Administration (OSHA) files, medical examiner records, state health and labor department reports, and various combinations of these, have been used to identify cases of work-related fatal injuries. Recent studies have questioned the effectiveness of these sources for identifying such cases. METHODS: At least 10 studies have used multiple sources to define the universe of fatal work injuries within a state and to determine the capture rates, or proportion of the universe identified, by each source. Results of these studies, which are not all available in published literature, are summarized here in a format that allows researchers to readily compare the ascertainment capabilities of the sources. RESULTS: The overall average capture rates of sources were as follows: death certificates, 81%; medical examiner records, 61%; Workers' Compensation reports, 57%; and OSHA reports 32%. Variations by state and value added through the use of multiple sources are presented and discussed. CONCLUSIONS: This meta-analysis of 10 state-based studies summarizes the effectiveness of various source documents for capturing cases of fatal occupational injuries to help researchers make informed decisions when designing occupational injury surveillance systems. PMID:1827569

Air quality assessment and the use of specific markers to apportion pollutants to source

NASA Astrophysics Data System (ADS)

Douce, David Stewart

The contributions of specific polluting sources to both indoor and outdoor atmospheric pollution are difficult to determine, as solid and gaseous products from different combustion sources are often similar. Sometimes, however, a marker compound can be identified that is unique to a pollution source (or at least not present in most other local combustion sources) and which will allow assessment of the contribution of that source to total atmospheric pollution.The aim of this study was to identify suitable marker compounds and methods for the apportionment (assessment of percentage contribution) of specific sources to atmospheric pollution. The sources selected were diesel exhaust emissions in outdoor, and environmental tobacco smoke (ETS) in indoor environments. Studies with controlled (laboratory) atmospheres would be followed by field studies using these methods and markers to produce apportionments for these sources to air pollution in selected environments. Initial analysis of such polluting sources was therefore the qualitative analysis of volatile compounds and particulate associated material, both organic and inorganic. Volatile organic compounds were adsorbed onto various resins, while particulate material was sampled onto various filter paper types. Organics were determined by GC-AED and GC-MS, and elements by ICP-MS.1-Nitropyrene was identified as a suitable marker for diesel particulate emissions (<5um). A large volume air sample from Sheffield city centre using 1-nitropyrene as a marker suggested that 63% of atmospheric particulate material (<5um) might be of diesel origin. However the concentration of 1-nitropyrene is low in atmospheric samples, and in the volumes used in routine sampling the amount of 1-nitropyrene was below the limit of detection on the instrument used. In an alternative approach the aliphatic alkane tetracosane (C24) was used as a diesel marker for urban air, with a 1-nitropyrene:tetracosane ratio derived from the average results

Sourcing faecal pollution: a combination of library-dependent and library-independent methods to identify human faecal pollution in non-sewered catchments.

PubMed

Ahmed, W; Stewart, J; Gardner, T; Powell, D; Brooks, P; Sullivan, D; Tindale, N

2007-08-01

Library-dependent (LD) (biochemical fingerprinting of Escherichia coli and enterococci) and library-independent (LI) (PCR detection of human-specific biomarkers) methods were used to detect human faecal pollution in three non-sewered catchments. In all, 550 E. coli isolates and 700 enterococci isolates were biochemically fingerprinted from 18 water samples and compared with metabolic fingerprint libraries of 4508 E. coli and 4833 enterococci isolates. E. coli fingerprints identified human unique biochemical phenotypes (BPTs) in nine out of 18 water samples; similarly, enterococci fingerprints identified human faecal pollution in 10 water samples. Seven samples were tested by PCR for the detection of biomarkers. Human-specific HF134 Bacteroides and enterococci surface protein (esp) biomarkers were detected in five samples. Four samples were also positive for HF183 Bacteroides biomarker. The combination of biomarkers detected human faecal pollution in six out of seven water samples. Of the seven samples analysed for both the indicators/markers, at least one indicator/marker was detected in every sample. Four of the seven PCR-positive samples were also positive for one of the human-specific E. coli or enterococci BPTs. The results indicated human faecal pollution in the studied sub-catchments after storm events. LD and LI methods used in this study complimented each other and provided additional information regarding the polluting sources when one method failed to detect human faecal pollution. Therefore, it is recommended that a combination of methods should be used to identify the source(s) of faecal pollution where possible.

Combinatorial Drug Screening Identifies Ewing Sarcoma-specific Sensitivities.

PubMed

Radic-Sarikas, Branka; Tsafou, Kalliopi P; Emdal, Kristina B; Papamarkou, Theodore; Huber, Kilian V M; Mutz, Cornelia; Toretsky, Jeffrey A; Bennett, Keiryn L; Olsen, Jesper V; Brunak, Søren; Kovar, Heinrich; Superti-Furga, Giulio

2017-01-01

Improvements in survival for Ewing sarcoma pediatric and adolescent patients have been modest over the past 20 years. Combinations of anticancer agents endure as an option to overcome resistance to single treatments caused by compensatory pathways. Moreover, combinations are thought to lessen any associated adverse side effects through reduced dosing, which is particularly important in childhood tumors. Using a parallel phenotypic combinatorial screening approach of cells derived from three pediatric tumor types, we identified Ewing sarcoma-specific interactions of a diverse set of targeted agents including approved drugs. We were able to retrieve highly synergistic drug combinations specific for Ewing sarcoma and identified signaling processes important for Ewing sarcoma cell proliferation determined by EWS-FLI1 We generated a molecular target profile of PKC412, a multikinase inhibitor with strong synergistic propensity in Ewing sarcoma, revealing its targets in critical Ewing sarcoma signaling routes. Using a multilevel experimental approach including quantitative phosphoproteomics, we analyzed the molecular rationale behind the disease-specific synergistic effect of simultaneous application of PKC412 and IGF1R inhibitors. The mechanism of the drug synergy between these inhibitors is different from the sum of the mechanisms of the single agents. The combination effectively inhibited pathway crosstalk and averted feedback loop repression, in EWS-FLI1-dependent manner. Mol Cancer Ther; 16(1); 88-101. ©2016 AACR. ©2016 American Association for Cancer Research.

Using Social Media to Identify Sources of Healthy Food in Urban Neighborhoods.

PubMed

Gomez-Lopez, Iris N; Clarke, Philippa; Hill, Alex B; Romero, Daniel M; Goodspeed, Robert; Berrocal, Veronica J; Vinod Vydiswaran, V G; Veinot, Tiffany C

2017-06-01

An established body of research has used secondary data sources (such as proprietary business databases) to demonstrate the importance of the neighborhood food environment for multiple health outcomes. However, documenting food availability using secondary sources in low-income urban neighborhoods can be particularly challenging since small businesses play a crucial role in food availability. These small businesses are typically underrepresented in national databases, which rely on secondary sources to develop data for marketing purposes. Using social media and other crowdsourced data to account for these smaller businesses holds promise, but the quality of these data remains unknown. This paper compares the quality of full-line grocery store information from Yelp, a crowdsourced content service, to a "ground truth" data set (Detroit Food Map) and a commercially-available dataset (Reference USA) for the greater Detroit area. Results suggest that Yelp is more accurate than Reference USA in identifying healthy food stores in urban areas. Researchers investigating the relationship between the nutrition environment and health may consider Yelp as a reliable and valid source for identifying sources of healthy food in urban environments.

Identifying sediment sources in the sediment TMDL process

USGS Publications Warehouse

Gellis, Allen C.; Fitzpatrick, Faith A.; Schubauer-Berigan, Joseph P.; Landy, R.B.; Gorman Sanisaca, Lillian E.

2015-01-01

Sediment is an important pollutant contributing to aquatic-habitat degradation in many waterways of the United States. This paper discusses the application of sediment budgets in conjunction with sediment fingerprinting as tools to determine the sources of sediment in impaired waterways. These approaches complement monitoring, assessment, and modeling of sediment erosion, transport, and storage in watersheds. Combining the sediment fingerprinting and sediment budget approaches can help determine specific adaptive management plans and techniques applied to targeting hot spots or areas of high erosion.

Method To Identify Specific Inhibiutors Of Imp Dehydrogenase

DOEpatents

Collart, Frank R.; Huberman, Eliezer

2000-11-28

This invention relates to methods to identify specific inhibitors of the purine nucleotide synthesis enzyme, IMP dehydrogenase (IMPDH). IMPDH is an essential enzyme found in all free-living organisms from humans to bacteria and is an important therapeutic target. The invention allows the identification of specific inhibitors of any IMPDH enzyme which can be expressed in a functional form in a recombinant host cell. A variety of eukaryotic or prokaryotic host systems commonly used for the expression of recombinant proteins are suitable for the practice of the invention. The methods are amenable to high throughput systems for the screening of inhibitors generated by combinatorial chemistry or other methods such as antisense molecule production. Utilization of exogenous guanosine as a control component of the methods allows for the identification of inhibitors specific for IMPDH rather than other causes of decreased cell proliferation.

On Identifying the Sound Sources in a Turbulent Flow

NASA Technical Reports Server (NTRS)

Goldstein, M. E.

2008-01-01

A space-time filtering approach is used to divide an unbounded turbulent flow into its radiating and non-radiating components. The result is then used to clarify a number of issues including the possibility of identifying the sources of the sound in such flows. It is also used to investigate the efficacy of some of the more recent computational approaches.

A Nondestructive Method to Identify POP Contamination Sources in Omnivorous Seabirds.

PubMed

Michielsen, Rosanne J; Shamoun-Baranes, Judy; Parsons, John R; Kraak, Michiel H S

2018-03-13

Persistent organic pollutants (POPs) are present in almost all environments due to their high bioaccumulation potential. Especially species that adapted to human activities, like gulls, might be exposed to harmful concentrations of these chemicals. The nature and degree of the exposure to POPs greatly vary between individual gulls, due to their diverse foraging behavior and specialization in certain foraging tactics. Therefore, in order clarify the effect of POP-contaminated areas on gull populations, it is important to identify the sources of POP contamination in individual gulls. Conventional sampling methods applied when studying POP contamination are destructive and ethically undesired. The aim of this literature review was to evaluate the potential of using feathers as a nondestructive method to determine sources of POP contamination in individual gulls. The reviewed data showed that high concentrations of PCBs and PBDEs in feathers together with a large proportion of less bioaccumulative congeners may indicate that the contamination originates from landfills. Low PCB and PBDE concentrations in feathers and a large proportion of more bioaccumulative congeners could indicate that the contamination originates from marine prey. We propose a nondestructive approach to identify the source of contamination in individual gulls based on individual contamination levels and PCB and PBDE congener profiles in feathers. Despite some uncertainties that might be reduced by future research, we conclude that especially when integrated with other methods like GPS tracking and the analysis of stable isotopic signatures, identifying the source of POP contamination based on congener profiles in feathers could become a powerful nondestructive method.

The use of source memory to identify one's own episodic confusion errors.

PubMed

Smith, S M; Tindell, D R; Pierce, B H; Gilliland, T R; Gerkens, D R

2001-03-01

In 4 category cued recall experiments, participants falsely recalled nonlist common members, a semantic confusion error. Errors were more likely if critical nonlist words were presented on an incidental task, causing source memory failures called episodic confusion errors. Participants could better identify the source of falsely recalled words if they had deeply processed the words on the incidental task. For deep but not shallow processing, participants could reliably include or exclude incidentally shown category members in recall. The illusion that critical items actually appeared on categorized lists was diminished but not eradicated when participants identified episodic confusion errors post hoc among their own recalled responses; participants often believed that critical items had been on both the incidental task and the study list. Improved source monitoring can potentially mitigate episodic (but not semantic) confusion errors.

Gulls identified as major source of fecal pollution in coastal waters: a microbial source tracking study.

PubMed

Araújo, Susana; Henriques, Isabel S; Leandro, Sérgio Miguel; Alves, Artur; Pereira, Anabela; Correia, António

2014-02-01

Gulls were reported as sources of fecal pollution in coastal environments and potential vectors of human infections. Microbial source tracking (MST) methods were rarely tested to identify this pollution origin. This study was conducted to ascertain the source of water fecal contamination in the Berlenga Island, Portugal. A total of 169 Escherichia coli isolates from human sewage, 423 isolates from gull feces and 334 water isolates were analyzed by BOX-PCR. An average correct classification of 79.3% was achieved. When an 85% similarity cutoff was applied 24% of water isolates were present in gull feces against 2.7% detected in sewage. Jackknifing resulted in 29.3% of water isolates classified as gull, and 10.8% classified as human. Results indicate that gulls constitute a major source of water contamination in the Berlenga Island. This study validated a methodology to differentiate human and gull fecal pollution sources in a real case of a contaminated beach. © 2013.

Sensitivity and specificity of administrative mortality data for identifying prescription opioid–related deaths

PubMed Central

Gladstone, Emilie; Smolina, Kate; Morgan, Steven G.; Fernandes, Kimberly A.; Martins, Diana; Gomes, Tara

2016-01-01

Background: Comprehensive systems for surveilling prescription opioid–related harms provide clear evidence that deaths from prescription opioids have increased dramatically in the United States. However, these harms are not systematically monitored in Canada. In light of a growing public health crisis, accessible, nationwide data sources to examine prescription opioid–related harms in Canada are needed. We sought to examine the performance of 5 algorithms to identify prescription opioid–related deaths from vital statistics data against data abstracted from the Office of the Chief Coroner of Ontario as a gold standard. Methods: We identified all prescription opioid–related deaths from Ontario coroners’ data that occurred between Jan. 31, 2003, and Dec. 31, 2010. We then used 5 different algorithms to identify prescription opioid–related deaths from vital statistics death data in 2010. We selected the algorithm with the highest sensitivity and a positive predictive value of more than 80% as the optimal algorithm for identifying prescription opioid–related deaths. Results: Four of the 5 algorithms had positive predictive values of more than 80%. The algorithm with the highest sensitivity (75%) in 2010 improved slightly in its predictive performance from 2003 to 2010. Interpretation: In the absence of specific systems for monitoring prescription opioid–related deaths in Canada, readily available national vital statistics data can be used to study prescription opioid–related mortality with considerable accuracy. Despite some limitations, these data may facilitate the implementation of national surveillance and monitoring strategies. PMID:26622006

Sensitivity and specificity of administrative mortality data for identifying prescription opioid-related deaths.

PubMed

Gladstone, Emilie; Smolina, Kate; Morgan, Steven G; Fernandes, Kimberly A; Martins, Diana; Gomes, Tara

2016-03-01

Comprehensive systems for surveilling prescription opioid-related harms provide clear evidence that deaths from prescription opioids have increased dramatically in the United States. However, these harms are not systematically monitored in Canada. In light of a growing public health crisis, accessible, nationwide data sources to examine prescription opioid-related harms in Canada are needed. We sought to examine the performance of 5 algorithms to identify prescription opioid-related deaths from vital statistics data against data abstracted from the Office of the Chief Coroner of Ontario as a gold standard. We identified all prescription opioid-related deaths from Ontario coroners' data that occurred between Jan. 31, 2003, and Dec. 31, 2010. We then used 5 different algorithms to identify prescription opioid-related deaths from vital statistics death data in 2010. We selected the algorithm with the highest sensitivity and a positive predictive value of more than 80% as the optimal algorithm for identifying prescription opioid-related deaths. Four of the 5 algorithms had positive predictive values of more than 80%. The algorithm with the highest sensitivity (75%) in 2010 improved slightly in its predictive performance from 2003 to 2010. In the absence of specific systems for monitoring prescription opioid-related deaths in Canada, readily available national vital statistics data can be used to study prescription opioid-related mortality with considerable accuracy. Despite some limitations, these data may facilitate the implementation of national surveillance and monitoring strategies. © 2016 Canadian Medical Association or its licensors.

Identifying fecal sources in a selected catchment reach using multiple source-tracking tools

USGS Publications Warehouse

Vogel, J.R.; Stoeckel, D.M.; Lamendella, R.; Zelt, R.B.; Santo, Domingo J.W.; Walker, S.R.; Oerther, D.B.

2007-01-01

Given known limitations of current microbial source-tracking (MST) tools, emphasis on small, simple study areas may enhance interpretations of fecal contamination sources in streams. In this study, three MST tools - Escherichia coli repetitive element polymerase chain reaction (rep-PCR), coliphage typing, and Bacteroidales 16S rDNA host-associated markers - were evaluated in a selected reach of Plum Creek in sooth-central Nebraska. Water-quality samples were collected from six sites. One reach was selected for MST evaluation based on observed patterns of E. coli contamination. Despite high E. coli concentrations, coliphages were detected only once among water samples, precluding their use as a MST tool in this setting. Rep-PCR classification of E. coli isolates from both water and sediment samples supported the hypothesis that cattle and wildlife were dominant sources of fecal contamination, with minor contributions by horses and humans. Conversely, neither ruminant nor human sources were detected by Bacteroidales markers in most water samples. In bed sediment, ruminant- and human-associated Bacteroidales markers were detected throughout the interval from 0 to 0.3 m, with detections independent of E. coli concentrations in the sediment. Although results by E. coli-based and Bacteroidales-based MST methods led to similar interpretations, detection of Bacteroidales markers in sediment more commonly than in water indicates that different tools to track fecal contamination (in this case, tools based on Bacteroidales DNA and E. coli isolates) may have varying relevance to the more specific goal of tracking the sources of E. coli in watersheds. This is the first report of simultaneous, toolbox approach application of a library-based and marker-based MST analyses to lowing surface water. ?? ASA, CSSA, SSSA.

Distributed watershed modeling of design storms to identify nonpoint source loading areas

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

Endreny, T.A.; Wood, E.F.

1999-03-01

Watershed areas that generate nonpoint source (NPS) polluted runoff need to be identified prior to the design of basin-wide water quality projects. Current watershed-scale NPS models lack a variable source area (VSA) hydrology routine, and are therefore unable to identify spatially dynamic runoff zones. The TOPLATS model used a watertable-driven VSA hydrology routine to identify runoff zones in a 17.5 km{sup 2} agricultural watershed in central Oklahoma. Runoff areas were identified in a static modeling framework as a function of prestorm watertable depth and also in a dynamic modeling framework by simulating basin response to 2, 10, and 25 yrmore » return period 6 h design storms. Variable source area expansion occurred throughout the duration of each 6 h storm and total runoff area increased with design storm intensity. Basin-average runoff rates of 1 mm h{sup {minus}1} provided little insight into runoff extremes while the spatially distributed analysis identified saturation excess zones with runoff rates equaling effective precipitation. The intersection of agricultural landcover areas with these saturation excess runoff zones targeted the priority potential NPS runoff zones that should be validated with field visits. These intersected areas, labeled as potential NPS runoff zones, were mapped within the watershed to demonstrate spatial analysis options available in TOPLATS for managing complex distributions of watershed runoff. TOPLATS concepts in spatial saturation excess runoff modelling should be incorporated into NPS management models.« less

Amine control for DUV lithography: identifying hidden sources

NASA Astrophysics Data System (ADS)

Kishkovich, Oleg P.; Larson, Carl E.

2000-06-01

The impact of airborne basic molecular contamination (MB) on the performance of chemically amplified (CA) resist systems has been a long standing problem. Low ppb levels of MB may be sufficient for robust 0.25 micrometer lithography with today's advanced CA resist systems combined with adequate chemical air filtration. However, with minimum CD targets heading below 150 nm, the introduction of new resist chemistries for Next Generation Lithography, and the trend towards thinner resists, the impact of MB at low and sub-ppb levels again becomes a critical manufacturing issue. Maximizing process control at aggressive feature sizes requires that the level of MB be maintained below a certain limit, which depends on such parameters as the sensitivity of the CA resist, the type of production tools, product mix, and process characteristics. Three approaches have been identified to reduce the susceptibility of CA resists to MB: effective chemical air filtration, modifications to resist chemistry/processing and cleanroom protocols involving MB monitoring and removal of MB sources from the fab. The final MB concentration depends on the effectiveness of filtration resources and on the total pollution originating from different sources in and out of the cleanroom. There are many well-documented sources of MB. Among these are: ambient air; polluted exhaust from other manufacturing areas re-entering the cleanroom through make-up air handlers; manufacturing process chemicals containing volatile molecular bases; certain cleanroom construction materials, such as paint and ceiling tiles; and volatile, humidifier system boiler additives (corrosion inhibitors), such as morpholine, cyclohexylamine, and dimethylaminoethanol. However, there is also an indeterminate number of other 'hidden' pollution sources, which are neither obvious nor well-documented. None of these sources are new, but they had little impact on earlier semiconductor manufacturing processes because the contamination

Leveraging Diverse Data Sources to Identify and Describe U.S. Health Care Delivery Systems.

PubMed

Cohen, Genna R; Jones, David J; Heeringa, Jessica; Barrett, Kirsten; Furukawa, Michael F; Miller, Dan; Mutti, Anne; Reschovsky, James D; Machta, Rachel; Shortell, Stephen M; Fraze, Taressa; Rich, Eugene

2017-12-15

Health care delivery systems are a growing presence in the U.S., yet research is hindered by the lack of universally agreed-upon criteria to denote formal systems. A clearer understanding of how to leverage real-world data sources to empirically identify systems is a necessary first step to such policy-relevant research. We draw from our experience in the Agency for Healthcare Research and Quality's Comparative Health System Performance (CHSP) initiative to assess available data sources to identify and describe systems, including system members (for example, hospitals and physicians) and relationships among the members (for example, hospital ownership of physician groups). We highlight five national data sources that either explicitly track system membership or detail system relationships: (1) American Hospital Association annual survey of hospitals; (2) Healthcare Relational Services Databases; (3) SK&A Healthcare Databases; (4) Provider Enrollment, Chain, and Ownership System; and (5) Internal Revenue Service 990 forms. Each data source has strengths and limitations for identifying and describing systems due to their varied content, linkages across data sources, and data collection methods. In addition, although no single national data source provides a complete picture of U.S. systems and their members, the CHSP initiative will create an early model of how such data can be combined to compensate for their individual limitations. Identifying systems in a way that can be repeated over time and linked to a host of other data sources will support analysis of how different types of organizations deliver health care and, ultimately, comparison of their performance.

Intra-urban biomonitoring: Source apportionment using tree barks to identify air pollution sources.

PubMed

Moreira, Tiana Carla Lopes; de Oliveira, Regiani Carvalho; Amato, Luís Fernando Lourenço; Kang, Choong-Min; Saldiva, Paulo Hilário Nascimento; Saiki, Mitiko

2016-05-01

It is of great interest to evaluate if there is a relationship between possible sources and trace elements using biomonitoring techniques. In this study, tree bark samples of 171 trees were collected using a biomonitoring technique in the inner city of São Paulo. The trace elements (Al, Ba, Ca, Cl, Cu, Fe, K, Mg, Mn, Na, P, Rb, S, Sr and Zn) were determined by the energy dispersive X-ray fluorescence (EDXRF) spectrometry. The Principal Component Analysis (PCA) was applied to identify the plausible sources associated with tree bark measurements. The greatest source was vehicle-induced non-tailpipe emissions derived mainly from brakes and tires wear-out and road dust resuspension (characterized with Al, Ba, Cu, Fe, Mn and Zn), which was explained by 27.1% of the variance, followed by cement (14.8%), sea salt (11.6%) and biomass burning (10%), and fossil fuel combustion (9.8%). We also verified that the elements related to vehicular emission showed different concentrations at different sites of the same street, which might be helpful for a new street classification according to the emission source. The spatial distribution maps of element concentrations were obtained to evaluate the different levels of pollution in streets and avenues. Results indicated that biomonitoring techniques using tree bark can be applied to evaluate dispersion of air pollution and provide reliable data for the further epidemiological studies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Optical Spectra of Four Objects Identified with Variable Radio Sources

NASA Astrophysics Data System (ADS)

Chavushyan, V.; Mujica, R.; Gorshkov, A. G.; Konnikova, V. K.; Mingaliev, M. G.

2000-06-01

We obtained optical spectra of four objects identified with variable radio sources. Three objects (0029+0554, 0400+0550, 2245+0500) were found to be quasars with redshifts of 1.314, 0.761, and 1.091. One object (2349+0534) has a continuum spectrum characteristic of BL Lac objects. We analyze spectra of the radio sources in the range 0.97-21.7 GHz for the epoch 1997 and in the range 3.9-11.1 GHz for the epoch 1990, as well as the pattern of variability of their flux densities on time scales of 1.5 and 7 years.

A manual to identify sources of fluvial sediment

USGS Publications Warehouse

Gellis, Allen C.; Fitzpatrick, Faith A.; Schubauer-Berigan, Joseph

2016-01-01

Sediment is an important pollutant of concern that can degrade and alter aquatic habitat. A sediment budget is an accounting of the sources, storage, and export of sediment over a defined spatial and temporal scale. This manual focuses on field approaches to estimate a sediment budget. We also highlight the sediment fingerprinting approach to attribute sediment to different watershed sources. Determining the sources and sinks of sediment is important in developing strategies to reduce sediment loads to water bodies impaired by sediment. Therefore, this manual can be used when developing a sediment TMDL requiring identification of sediment sources.The manual takes the user through the seven necessary steps to construct a sediment budget:Decision-making for watershed scale and time period of interestFamiliarization with the watershed by conducting a literature review, compiling background information and maps relevant to study questions, conducting a reconnaissance of the watershedDeveloping partnerships with landowners and jurisdictionsCharacterization of watershed geomorphic settingDevelopment of a sediment budget designData collectionInterpretation and construction of the sediment budgetGenerating products (maps, reports, and presentations) to communicate findings.Sediment budget construction begins with examining the question(s) being asked and whether a sediment budget is necessary to answer these question(s). If undertaking a sediment budget analysis is a viable option, the next step is to define the spatial scale of the watershed and the time scale needed to answer the question(s). Of course, we understand that monetary constraints play a big role in any decision.Early in the sediment budget development process, we suggest getting to know your watershed by conducting a reconnaissance and meeting with local stakeholders. The reconnaissance aids in understanding the geomorphic setting of the watershed and potential sources of sediment. Identifying the potential

Application of classification-tree methods to identify nitrate sources in ground water

USGS Publications Warehouse

Spruill, T.B.; Showers, W.J.; Howe, S.S.

2002-01-01

A study was conducted to determine if nitrate sources in ground water (fertilizer on crops, fertilizer on golf courses, irrigation spray from hog (Sus scrofa) wastes, and leachate from poultry litter and septic systems) could be classified with 80% or greater success. Two statistical classification-tree models were devised from 48 water samples containing nitrate from five source categories. Model I was constructed by evaluating 32 variables and selecting four primary predictor variables (??15N, nitrate to ammonia ratio, sodium to potassium ratio, and zinc) to identify nitrate sources. A ??15N value of nitrate plus potassium 18.2 indicated inorganic or soil organic N. A nitrate to ammonia ratio 575 indicated nitrate from golf courses. A sodium to potassium ratio 3.2 indicated spray or poultry wastes. A value for zinc 2.8 indicated poultry wastes. Model 2 was devised by using all variables except ??15N. This model also included four variables (sodium plus potassium, nitrate to ammonia ratio, calcium to magnesium ratio, and sodium to potassium ratio) to distinguish categories. Both models were able to distinguish all five source categories with better than 80% overall success and with 71 to 100% success in individual categories using the learning samples. Seventeen water samples that were not used in model development were tested using Model 2 for three categories, and all were correctly classified. Classification-tree models show great potential in identifying sources of contamination and variables important in the source-identification process.

Partial and specific source memory for faces associated to other- and self-relevant negative contexts.

PubMed

Bell, Raoul; Giang, Trang; Buchner, Axel

2012-01-01

Previous research has shown a source memory advantage for faces presented in negative contexts. As yet it remains unclear whether participants remember the specific type of context in which the faces were presented or whether they can only remember that the face was associated with negative valence. In the present study, participants saw faces together with descriptions of two different types of negative behaviour and neutral behaviour. In Experiment 1, we examined whether the participants were able to discriminate between two types of other-relevant negative context information (cheating and disgusting behaviour) in a source memory test. In Experiment 2, we assessed source memory for other-relevant negative (threatening) context information (other-aggressive behaviour) and self-relevant negative context information (self-aggressive behaviour). A multinomial source memory model was used to separately assess partial source memory for the negative valence of the behaviour and specific source memory for the particular type of negative context the face was associated with. In Experiment 1, source memory was specific for the particular type of negative context presented (i.e., cheating or disgusting behaviour). Experiment 2 showed that source memory for other-relevant negative information was more specific than source memory for self-relevant information. Thus, emotional source memory may vary in specificity depending on the degree to which the negative emotional context is perceived as threatening.

Contributions to the Nutrient Toolbox: Identifying Drivers, Nutrient Sources, and Attribution of Exceedances

EPA Science Inventory

Nutrients are a leading cause of impairments in the United States, and as a result tools are needed to identify drivers of nutrients and response variables (such as chlorophyll a), nutrient sources, and identify causes of exceedances of water quality thresholds. This presentatio...

Combining Ordinary Kriging with wind directions to identify sources of industrial odors in Portland, Oregon.

PubMed

Eckmann, Ted C; Wright, Samantha G; Simpson, Logan K; Walker, Joe L; Kolmes, Steven A; Houck, James E; Velasquez, Sandra C

2018-01-01

This study combines Ordinary Kriging, odor monitoring, and wind direction data to demonstrate how these elements can be applied to identify the source of an industrial odor. The specific case study used as an example of how to address this issue was the University Park neighborhood of Portland, Oregon (USA) where residents frequently complain about industrial odors, and suspect the main source to be a nearby Daimler Trucks North America LLC manufacturing plant. We collected 19,665 odor observations plus 105,120 wind measurements, using an automated weather station to measure winds in the area at five-minute intervals, logging continuously from December 2014 through November 2015, while we also measured odors at 19 locations, three times per day, using methods from the American Society of the International Association for Testing and Materials. Our results quantify how winds vary with season and time of day when industrial odors were observed versus when they were not observed, while also mapping spatiotemporal patterns in these odors using Ordinary Kriging. Our analyses show that industrial odors were detected most frequently to the northwest of the Daimler plant, mostly when winds blew from the southeast, suggesting Daimler's facility is a likely source for much of this odor.

Combining Ordinary Kriging with wind directions to identify sources of industrial odors in Portland, Oregon

PubMed Central

Kolmes, Steven A.; Houck, James E.; Velasquez, Sandra C.

2018-01-01

This study combines Ordinary Kriging, odor monitoring, and wind direction data to demonstrate how these elements can be applied to identify the source of an industrial odor. The specific case study used as an example of how to address this issue was the University Park neighborhood of Portland, Oregon (USA) where residents frequently complain about industrial odors, and suspect the main source to be a nearby Daimler Trucks North America LLC manufacturing plant. We collected 19,665 odor observations plus 105,120 wind measurements, using an automated weather station to measure winds in the area at five-minute intervals, logging continuously from December 2014 through November 2015, while we also measured odors at 19 locations, three times per day, using methods from the American Society of the International Association for Testing and Materials. Our results quantify how winds vary with season and time of day when industrial odors were observed versus when they were not observed, while also mapping spatiotemporal patterns in these odors using Ordinary Kriging. Our analyses show that industrial odors were detected most frequently to the northwest of the Daimler plant, mostly when winds blew from the southeast, suggesting Daimler’s facility is a likely source for much of this odor. PMID:29385136

Source-specific fine particulate air pollution and systemic inflammation in ischaemic heart disease patients

PubMed Central

Siponen, Taina; Yli-Tuomi, Tarja; Aurela, Minna; Dufva, Hilkka; Hillamo, Risto; Hirvonen, Maija-Riitta; Huttunen, Kati; Pekkanen, Juha; Pennanen, Arto; Salonen, Iiris; Tiittanen, Pekka; Salonen, Raimo O; Lanki, Timo

2015-01-01

Objective To compare short-term effects of fine particles (PM2.5; aerodynamic diameter <2.5 µm) from different sources on the blood levels of markers of systemic inflammation. Methods We followed a panel of 52 ischaemic heart disease patients from 15 November 2005 to 21 April 2006 with clinic visits in every second week in the city of Kotka, Finland, and determined nine inflammatory markers from blood samples. In addition, we monitored outdoor air pollution at a fixed site during the study period and conducted a source apportionment of PM2.5 using the Environmental Protection Agency's model EPA PMF 3.0. We then analysed associations between levels of source-specific PM2.5 and markers of systemic inflammation using linear mixed models. Results We identified five source categories: regional and long-range transport (LRT), traffic, biomass combustion, sea salt, and pulp industry. We found most evidence for the relation of air pollution and inflammation in LRT, traffic and biomass combustion; the most relevant inflammation markers were C-reactive protein, interleukin-12 and myeloperoxidase. Sea salt was not positively associated with any of the inflammatory markers. Conclusions Results suggest that PM2.5 from several sources, such as biomass combustion and traffic, are promoters of systemic inflammation, a risk factor for cardiovascular diseases. PMID:25479755

Identifying protein phosphorylation sites with kinase substrate specificity on human viruses.

PubMed

Bretaña, Neil Arvin; Lu, Cheng-Tsung; Chiang, Chiu-Yun; Su, Min-Gang; Huang, Kai-Yao; Lee, Tzong-Yi; Weng, Shun-Long

2012-01-01

Viruses infect humans and progress inside the body leading to various diseases and complications. The phosphorylation of viral proteins catalyzed by host kinases plays crucial regulatory roles in enhancing replication and inhibition of normal host-cell functions. Due to its biological importance, there is a desire to identify the protein phosphorylation sites on human viruses. However, the use of mass spectrometry-based experiments is proven to be expensive and labor-intensive. Furthermore, previous studies which have identified phosphorylation sites in human viruses do not include the investigation of the responsible kinases. Thus, we are motivated to propose a new method to identify protein phosphorylation sites with its kinase substrate specificity on human viruses. The experimentally verified phosphorylation data were extracted from virPTM--a database containing 301 experimentally verified phosphorylation data on 104 human kinase-phosphorylated virus proteins. In an attempt to investigate kinase substrate specificities in viral protein phosphorylation sites, maximal dependence decomposition (MDD) is employed to cluster a large set of phosphorylation data into subgroups containing significantly conserved motifs. The experimental human phosphorylation sites are collected from Phospho.ELM, grouped according to its kinase annotation, and compared with the virus MDD clusters. This investigation identifies human kinases such as CK2, PKB, CDK, and MAPK as potential kinases for catalyzing virus protein substrates as confirmed by published literature. Profile hidden Markov model is then applied to learn a predictive model for each subgroup. A five-fold cross validation evaluation on the MDD-clustered HMMs yields an average accuracy of 84.93% for Serine, and 78.05% for Threonine. Furthermore, an independent testing data collected from UniProtKB and Phospho.ELM is used to make a comparison of predictive performance on three popular kinase-specific phosphorylation site

Identifying sources of fugitive emissions in industrial facilities using trajectory statistical methods

NASA Astrophysics Data System (ADS)

Brereton, Carol A.; Johnson, Matthew R.

2012-05-01

Fugitive pollutant sources from the oil and gas industry are typically quite difficult to find within industrial plants and refineries, yet they are a significant contributor of global greenhouse gas emissions. A novel approach for locating fugitive emission sources using computationally efficient trajectory statistical methods (TSM) has been investigated in detailed proof-of-concept simulations. Four TSMs were examined in a variety of source emissions scenarios developed using transient CFD simulations on the simplified geometry of an actual gas plant: potential source contribution function (PSCF), concentration weighted trajectory (CWT), residence time weighted concentration (RTWC), and quantitative transport bias analysis (QTBA). Quantitative comparisons were made using a correlation measure based on search area from the source(s). PSCF, CWT and RTWC could all distinguish areas near major sources from the surroundings. QTBA successfully located sources in only some cases, even when provided with a large data set. RTWC, given sufficient domain trajectory coverage, distinguished source areas best, but otherwise could produce false source predictions. Using RTWC in conjunction with CWT could overcome this issue as well as reduce sensitivity to noise in the data. The results demonstrate that TSMs are a promising approach for identifying fugitive emissions sources within complex facility geometries.

Host Specificity and Source of Enterocytozoon bieneusi Genotypes in a Drinking Source Watershed

PubMed Central

Guo, Yaqiong; Alderisio, Kerri A.; Yang, Wenli; Cama, Vitaliano; Xiao, Lihua

2014-01-01

To assess the host specificity of Enterocytozoon bieneusi and to track the sources of E. bieneusi contamination, we genotyped E. bieneusi in wildlife and stormwater from the watershed of New York City's source water, using ribosomal internal transcribed spacer (ITS)-based PCR and sequence analyses. A total of 255 specimens from 23 species of wild mammals and 67 samples from stormwater were analyzed. Seventy-four (29.0%) of the wildlife specimens and 39 (58.2%) of the stormwater samples from streams were PCR positive. Altogether, 20 E. bieneusi genotypes were found, including 8 known genotypes and 12 new ones. Sixteen and five of the genotypes were seen in animals and stormwater from the watershed, respectively, with WL4 being the most common genotype in both animals (35 samples) and stormwater (23 samples). The 20 E. bieneusi genotypes belonged to five genogroups (groups 1, 3, 4, and 7 and an outlier), with only 23/113 (20.4%) E. bieneusi-positive samples belonging to zoonotic genogroup 1 and 3/20 genotypes ever being detected in humans. The two genogroups previously considered host specific, groups 3 and 4, were both detected in multiple groups of mammals. Thus, with the exception of the type IV, Peru11, and D genotypes, which were detected in only 7, 5, and 2 animals, respectively, most E. bieneusi strains in most wildlife samples and all stormwater samples in the watershed had no known public health significance, as these types have not previously been detected in humans. The role of different species of wild mammals in the contribution of E. bieneusi contamination in stormwater was supported by determinations of host-adapted Cryptosporidium species/genotypes in the same water samples. Data from this study indicate that the host specificity of E. bieneusi group 3 is broader than originally thought, and wildlife is the main source of E. bieneusi in stormwater in the watershed. PMID:24141128

METHANE EMISSIONS FROM INDUSTRIAL SOURCES

EPA Science Inventory

The chapter identifies and describes major industrial sources of methane (CH4) emissions. or each source type examined, it identifies CH4 release points and discusses in detail the factors affecting emissions. t also summarizes and discusses available global and country-specific ...

Identifying constituent spectra sources in multispectral images to quantify and locate cervical neoplasia

NASA Astrophysics Data System (ADS)

Baker, Kevin C.; Bambot, Shabbir

2011-02-01

Optical spectroscopy has been shown to be an effective method for detecting neoplasia. Guided Therapeutics has developed LightTouch, a non invasive device that uses a combination of reflectance and fluorescence spectroscopy for identifying early cancer of the human cervix. The combination of the multispectral information from the two spectroscopic modalities has been shown to be an effective method to screen for cervical cancer. There has however been a relative paucity of work in identifying the individual spectral components that contribute to the measured fluorescence and reflectance spectra. This work aims to identify the constituent source spectra and their concentrations. We used non-negative matrix factorization (NNMF) numerical methods to decompose the mixed multispectral data into the constituent spectra and their corresponding concentrations. NNMF is an iterative approach that factorizes the measured data into non-negative factors. The factors are chosen to minimize the root-mean-squared residual error. NNMF has shown promise for feature extraction and identification in the fields of text mining and spectral data analysis. Since both the constituent source spectra and their corresponding concentrations are assumed to be non-negative by nature NNMF is a reasonable approach to deconvolve the measured multispectral data. Supervised learning methods were then used to determine which of the constituent spectra sources best predict the amount of neoplasia. The constituent spectra sources found to best predict neoplasia were then compared with spectra of known biological chromophores.

Identifying risk sources of air contamination by polycyclic aromatic hydrocarbons.

PubMed

Huzlik, Jiri; Bozek, Frantisek; Pawelczyk, Adam; Licbinsky, Roman; Naplavova, Magdalena; Pondelicek, Michael

2017-09-01

This article is directed to determining concentrations of polycyclic aromatic hydrocarbons (PAHs), which are sorbed to solid particles in the air. Pollution sources were identified on the basis of the ratio of benzo[ghi]perylene (BghiPe) to benzo[a]pyrene (BaP). Because various important information is lost by determining the simple ratio of concentrations, least squares linear regression (classic ordinary least squares regression), reduced major axis, orthogonal regression, and Kendall-Theil robust diagnostics were utilized for identification. Statistical evaluation using all aforementioned methods demonstrated different ratios of the monitored PAHs in the intervals examined during warmer and colder periods. Analogous outputs were provided by comparing gradients of the emission factors acquired from the measured concentrations of BghiPe and BaP in motor vehicle exhaust gases. Based on these outputs, it was possible plausibly to state that the influence of burning organic fuels in heating stoves is prevalent in colder periods whereas in warmer periods transport was the exclusive source because other sources of PAH emissions were not found in the examined locations. Copyright © 2017 Elsevier Ltd. All rights reserved.

Hypocretin neuron-specific transcriptome profiling identifies the sleep modulator Kcnh4a.

PubMed

Yelin-Bekerman, Laura; Elbaz, Idan; Diber, Alex; Dahary, Dvir; Gibbs-Bar, Liron; Alon, Shahar; Lerer-Goldshtein, Tali; Appelbaum, Lior

2015-10-01

Sleep has been conserved throughout evolution; however, the molecular and neuronal mechanisms of sleep are largely unknown. The hypothalamic hypocretin/orexin (Hcrt) neurons regulate sleep\\wake states, feeding, stress, and reward. To elucidate the mechanism that enables these various functions and to identify sleep regulators, we combined fluorescence cell sorting and RNA-seq in hcrt:EGFP zebrafish. Dozens of Hcrt-neuron-specific transcripts were identified and comprehensive high-resolution imaging revealed gene-specific localization in all or subsets of Hcrt neurons. Clusters of Hcrt-neuron-specific genes are predicted to be regulated by shared transcription factors. These findings show that Hcrt neurons are heterogeneous and that integrative molecular mechanisms orchestrate their diverse functions. The voltage-gated potassium channel Kcnh4a, which is expressed in all Hcrt neurons, was silenced by the CRISPR-mediated gene inactivation system. The mutant kcnh4a (kcnh4a(-/-)) larvae showed reduced sleep time and consolidation, specifically during the night, suggesting that Kcnh4a regulates sleep.

Evaluation of PCB sources and releases for identifying priorities to reduce PCBs in Washington State (USA).

PubMed

Davies, Holly; Delistraty, Damon

2016-02-01

Polychlorinated biphenyls (PCBs) are ubiquitously distributed in the environment and produce multiple adverse effects in humans and wildlife. As a result, the purpose of our study was to characterize PCB sources in anthropogenic materials and releases to the environment in Washington State (USA) in order to formulate recommendations to reduce PCB exposures. Methods included review of relevant publications (e.g., open literature, industry studies and reports, federal and state government databases), scaling of PCB sources from national or county estimates to state estimates, and communication with industry associations and private and public utilities. Recognizing high associated uncertainty due to incomplete data, we strived to provide central tendency estimates for PCB sources. In terms of mass (high to low), PCB sources include lamp ballasts, caulk, small capacitors, large capacitors, and transformers. For perspective, these sources (200,000-500,000 kg) overwhelm PCBs estimated to reside in the Puget Sound ecosystem (1500 kg). Annual releases of PCBs to the environment (high to low) are attributed to lamp ballasts (400-1500 kg), inadvertent generation by industrial processes (900 kg), caulk (160 kg), small capacitors (3-150 kg), large capacitors (10-80 kg), pigments and dyes (0.02-31 kg), and transformers (<2 kg). Recommendations to characterize the extent of PCB distribution and decrease exposures include assessment of PCBs in buildings (e.g., schools) and replacement of these materials, development of Best Management Practices (BMPs) to contain PCBs, reduction of inadvertent generation of PCBs in consumer products, expansion of environmental monitoring and public education, and research to identify specific PCB congener profiles in human tissues.

SMM-system: A mining tool to identify specific markers in Salmonella enterica.

PubMed

Yu, Shuijing; Liu, Weibing; Shi, Chunlei; Wang, Dapeng; Dan, Xianlong; Li, Xiao; Shi, Xianming

2011-03-01

This report presents SMM-system, a software package that implements various personalized pre- and post-BLASTN tasks for mining specific markers of microbial pathogens. The main functionalities of SMM-system are summarized as follows: (i) converting multi-FASTA file, (ii) cutting interesting genomic sequence, (iii) automatic high-throughput BLASTN searches, and (iv) screening target sequences. The utility of SMM-system was demonstrated by using it to identify 214 Salmonella enterica-specific protein-coding sequences (CDSs). Eighteen primer pairs were designed based on eighteen S. enterica-specific CDSs, respectively. Seven of these primer pairs were validated with PCR assay, which showed 100% inclusivity for the 101 S. enterica genomes and 100% exclusivity of 30 non-S. enterica genomes. Three specific primer pairs were chosen to develop a multiplex PCR assay, which generated specific amplicons with a size of 180bp (SC1286), 238bp (SC1598) and 405bp (SC4361), respectively. This study demonstrates that SMM-system is a high-throughput specific marker generation tool that can be used to identify genus-, species-, serogroup- and even serovar-specific DNA sequences of microbial pathogens, which has a potential to be applied in food industries, diagnostics and taxonomic studies. SMM-system is freely available and can be downloaded from http://foodsafety.sjtu.edu.cn/SMM-system.html. Copyright © 2011 Elsevier B.V. All rights reserved.

The Relative Importance of Specific Self-Efficacy Sources in Pretraining Self-Efficacy Beliefs

ERIC Educational Resources Information Center

Howardson, Garett N.; Behrend, Tara S.

2015-01-01

Self-efficacy is clearly important for learning. Research identifying the most important sources of self-efficacy beliefs, however, has been somewhat limited to date in that different disciplines focus largely on different sources of self-efficacy. Whereas education researchers focus on Bandura's original sources of "enactive mastery,"…

Identification of specific sources of airborne particles emitted from within a complex industrial (steelworks) site

NASA Astrophysics Data System (ADS)

Beddows, D. C. S.; Harrison, Roy M.

2018-06-01

A case study is provided of the development and application of methods to identify and quantify specific sources of emissions from within a large complex industrial site. Methods include directional analysis of concentrations, chemical source tracers and correlations with gaseous emissions. Extensive measurements of PM10, PM2.5, trace gases, particulate elements and single particle mass spectra were made at sites around the Port Talbot steelworks in 2012. By using wind direction data in conjunction with real-time or hourly-average pollutant concentration measurements, it has been possible to locate areas within the steelworks associated with enhanced pollutant emissions. Directional analysis highlights the Slag Handling area of the works as the most substantial source of elevated PM10 concentrations during the measurement period. Chemical analyses of air sampled from relevant wind directions is consistent with the anticipated composition of slags, as are single particle mass spectra. Elevated concentrations of PM10 are related to inverse distance from the Slag Handling area, and concentrations increase with increased wind speed, consistent with a wind-driven resuspension source. There also appears to be a lesser source associated with Sinter Plant emissions affecting PM10 concentrations at the Fire Station monitoring site. The results are compared with a ME2 study using some of the same data, and shown to give a clearer view of the location and characteristics of emission sources, including fugitive dusts.

Medial temporal lobe reinstatement of content-specific details predicts source memory

PubMed Central

Liang, Jackson C.; Preston, Alison R.

2016-01-01

Leading theories propose that when remembering past events, medial temporal lobe (MTL) structures reinstate the neural patterns that were active when those events were initially encoded. Accurate reinstatement is hypothesized to support detailed recollection of memories, including their source. While several studies have linked cortical reinstatement to successful retrieval, indexing reinstatement within the MTL network and its relationship to memory performance has proved challenging. Here, we addressed this gap in knowledge by having participants perform an incidental encoding task, during which they visualized people, places, and objects in response to adjective cues. During a surprise memory test, participants saw studied and novel adjectives and indicated the imagery task they performed for each adjective. A multivariate pattern classifier was trained to discriminate the imagery tasks based on functional magnetic resonance imaging (fMRI) responses from hippocampus and MTL cortex at encoding. The classifier was then tested on MTL patterns during the source memory task. We found that MTL encoding patterns were reinstated during successful source retrieval. Moreover, when participants made source misattributions, errors were predicted by reinstatement of incorrect source content in MTL cortex. We further observed a gradient of content-specific reinstatement along the anterior-posterior axis of hippocampus and MTL cortex. Within anterior hippocampus, we found that reinstatement of person content was related to source memory accuracy, whereas reinstatement of place information across the entire hippocampal axis predicted correct source judgments. Content-specific reinstatement was also graded across MTL cortex, with PRc patterns evincing reactivation of people and more posterior regions, including PHc, showing evidence for reinstatement of places and objects. Collectively, these findings provide key evidence that source recollection relies on reinstatement of past

Medial temporal lobe reinstatement of content-specific details predicts source memory.

PubMed

Liang, Jackson C; Preston, Alison R

2017-06-01

Leading theories propose that when remembering past events, medial temporal lobe (MTL) structures reinstate the neural patterns that were active when those events were initially encoded. Accurate reinstatement is hypothesized to support detailed recollection of memories, including their source. While several studies have linked cortical reinstatement to successful retrieval, indexing reinstatement within the MTL network and its relationship to memory performance has proved challenging. Here, we addressed this gap in knowledge by having participants perform an incidental encoding task, during which they visualized people, places, and objects in response to adjective cues. During a surprise memory test, participants saw studied and novel adjectives and indicated the imagery task they performed for each adjective. A multivariate pattern classifier was trained to discriminate the imagery tasks based on functional magnetic resonance imaging (fMRI) responses from hippocampus and MTL cortex at encoding. The classifier was then tested on MTL patterns during the source memory task. We found that MTL encoding patterns were reinstated during successful source retrieval. Moreover, when participants made source misattributions, errors were predicted by reinstatement of incorrect source content in MTL cortex. We further observed a gradient of content-specific reinstatement along the anterior-posterior axis of hippocampus and MTL cortex. Within anterior hippocampus, we found that reinstatement of person content was related to source memory accuracy, whereas reinstatement of place information across the entire hippocampal axis predicted correct source judgments. Content-specific reinstatement was also graded across MTL cortex, with PRc patterns evincing reactivation of people and more posterior regions, including PHc, showing evidence for reinstatement of places and objects. Collectively, these findings provide key evidence that source recollection relies on reinstatement of past

Identifying equivalent sound sources from aeroacoustic simulations using a numerical phased array

NASA Astrophysics Data System (ADS)

Pignier, Nicolas J.; O'Reilly, Ciarán J.; Boij, Susann

2017-04-01

An application of phased array methods to numerical data is presented, aimed at identifying equivalent flow sound sources from aeroacoustic simulations. Based on phased array data extracted from compressible flow simulations, sound source strengths are computed on a set of points in the source region using phased array techniques assuming monopole propagation. Two phased array techniques are used to compute the source strengths: an approach using a Moore-Penrose pseudo-inverse and a beamforming approach using dual linear programming (dual-LP) deconvolution. The first approach gives a model of correlated sources for the acoustic field generated from the flow expressed in a matrix of cross- and auto-power spectral values, whereas the second approach results in a model of uncorrelated sources expressed in a vector of auto-power spectral values. The accuracy of the equivalent source model is estimated by computing the acoustic spectrum at a far-field observer. The approach is tested first on an analytical case with known point sources. It is then applied to the example of the flow around a submerged air inlet. The far-field spectra obtained from the source models for two different flow conditions are in good agreement with the spectra obtained with a Ffowcs Williams-Hawkings integral, showing the accuracy of the source model from the observer's standpoint. Various configurations for the phased array and for the sources are used. The dual-LP beamforming approach shows better robustness to changes in the number of probes and sources than the pseudo-inverse approach. The good results obtained with this simulation case demonstrate the potential of the phased array approach as a modelling tool for aeroacoustic simulations.

Microbial source tracking using host specific FAME profiles of fecal coliforms.

PubMed

Duran, Metin; Haznedaroğlu, Berat Z; Zitomer, Daniel H

2006-01-01

The objective of this study was to investigate the host-specific differences in fatty acid methyl ester (FAME) profiles of fecal coliforms (FC). A known-source library was constructed with 314 FC isolates cultured from 6 possible sources of fecal pollution; 99 isolates from sewage; 29 from bovine; 29 from poultry; 50 from swine; 46 from waterfowl; and 61 from deer. It was found that the hydroxy FAMEs 12:0 2 OH, 12:03 OH, and 14:02 OH were exclusively associated with isolates of human origin. On the other hand, 3 saturated FAMEs, 10:0, 15:0, and 18:0 were found only in isolates from non-human sources, 15:0 being associated with livestock samples only. In addition to the presence of these signature FAMEs, the mean relative masses of 16:1 omega7c and 16:1 ISO/14:03 OH were significantly different between the isolates of human and non-human origins. A linear discriminant function differentiated FC isolates of human origin from those of livestock and wildlife origin at 99% accuracy. These results strongly suggest that the FAME profiles of FC show statistically significant host specificity and may have the potential to be used as a phenotypic microbial source tracking tool.

What Is Nonconsensual Sex? Young Women Identify Sources of Coerced Sex.

PubMed

French, Bryana H; Neville, Helen A

2016-04-12

Extending the American Psychological Association (APA) report on the Sexualization of Girls, this study investigated how young women identified sources of coerced sex. Findings from three focus groups with 25 Black and White adolescent women uncovered a perceived overarching force that "pushed" them to have sex before they felt ready. Participants identified four domains of coerced sex: (a) Sociocultural Context, (b) Internalized Sexual Scripts, (c) Partner Manipulation of Sexual Scripts, and (d) Developmental Status. Coerced sex was a complex system consisting of cultural, peer, and internal messages that create pressures to engage in sexual activities. Future implications for research and practice are presented. © The Author(s) 2016.

Preliminary use of compound-specific stable isotope (CSSI) technique to identify and apportion sediment origin in a small Austrian catchment

NASA Astrophysics Data System (ADS)

Mabit, Lionel; Gibbs, Max; Chen, Xu; Meusburger, Katrin; Toloza, Arsenio; Resch, Christian; Klik, Andreas; Eder, Alexander; Strauss, Peter; Alewell, Christine

2015-04-01

The overall impacts of climate change on agriculture are expected to be negative, threatening global food security. In the agricultural areas of the European Union, water erosion risk is expected to increase by about 80% by the year 2050. Reducing soil erosion and sedimentation-related environmental problems represent a key requirement for mitigating the impact of climate change. A new forensic stable isotope technique, using the compound specific stable isotope (CSSI) signatures of inherent soil organic biomarkers, can discriminate and apportion the source soil contribution from different land uses. Plant communities label the soil where they grow by exuding organic biomarkers. Although all plants produce the same biomarkers, the stable isotopic signature of those biomarkers is different for each plant species. For agri-environmental investigation, the CSSI technique is based on the measurement of carbon-13 (13-C) natural abundance signatures of specific organic compounds such as natural fatty acids (FAs) in the soil. By linking fingerprints of land use to the sediment in deposition zones, this approach has been shown to be a useful technique for determining the source of eroded soil and thereby identifying areas prone to soil degradation. The authors have tested this innovative stable isotopic approach in a small Austrian agricultural catchment located 60 km north of Vienna. A previous fallout radionuclide (i.e. 137-Cs) based investigation established a sedimentation rate of 4 mm/yr in the lowest part of the study site. To gain knowledge about the origin of these sediments, the CSSI technique was then tested using representative samples from the different land-uses of the catchment as source material. Values of 13-C signatures of specific FAs (i.e. C22:0 = Behenic Acid ; C24:0 = Lignoceric Acid) and the bulk 13-C of the sediment mixture and potential landscape sources were analyzed with the mixing models IsoSource and CSSIAR v1.00. Using both mixing models

Panoramic Electrophysiological Mapping but not Electrogram Morphology Identifies Stable Sources for Human Atrial Fibrillation

PubMed Central

Narayan, Sanjiv M.; Shivkumar, Kalyanam; Krummen, David E.; Miller, John M.; Rappel, Wouter-Jan

2013-01-01

Background The foundation for successful arrhythmia ablation is the mapping of electric propagation to identify underlying mechanisms. In atrial fibrillation (AF), however, mapping is difficult so that ablation has often targeted electrogram features, with mixed results. We hypothesized that wide field-of-view (panoramic) mapping of both atria would identify causal mechanisms for AF and allow interpretation of local electrogram features, including complex fractionated atrial electrograms (CFAE). Methods and Results Contact mapping was performed using biatrial multipolar catheters in 36 AF subjects (29 persistent). Stable AF rotors (spiral waves) or focal sources were seen in 35 of 36 cases and targeted for ablation (focal impulse and rotor modulation) before pulmonary vein isolation. In 31 of 36 subjects (86.1%), AF acutely terminated (n=20; 16 to sinus rhythm) or organized (n=11; 19±8% slowing) with 2.5 minutes focal impulse and rotor modulation (interquartile range, 1.0–3.1) at one source, defined as the primary source. Subjects exhibited 2.1±1.0 concurrent AF sources of which the primary, by phase mapping, precessed in limited areas (persistent 2.5±1.7 versus paroxysmal 1.7±0.5 cm2; P=0.30). Notably, source regions showed mixed electrogram amplitudes and CFAE grades that did not differ from surrounding atrium (P=NS). AF sources were not consistently surrounded by CFAE (P=0.67). Conclusions Stable rotors and focal sources for human AF were revealed by contact panoramic mapping (focal impulse and rotor modulation mapping), but not by electrogram footprints. AF sources precessed within areas of ≈2 cm2, with diverse voltage characteristics poorly correlated with CFAE. Most CFAE sites lie remote from AF sources and are not suitable targets for catheter ablation of AF. PMID:23392583

Evaluation of Bayesian approaches to identify DDT source contributions to soils in Southeast China.

PubMed

Zeng, Faming; Yang, Dan; Xing, Xinli; Qi, Shihua

2017-06-01

Dicofol application may be an important source to elevate the dichlorodiphenyltrichloroethane (DDT) residues to soils in Fujian, Southeast China, after the technical DDT was banned, which left DDT residues from the historical application. The DDT residues varied geographically, corresponding to the varied potential sources of DDT. In this study, a novel approach based on the Bayesian method (BM) was developed to identify the source contributions of DDT to soils, composed with both historical DDT and dicofol. The Naive Bayesian classifier was used basing on the subset of the samples, which were determined by chemical analysis independent of the Bayesian approach. The results show that BM (95%) was higher than that using the ratio of o, p'-/p, p'-DDT (84%) to identify DDT source contributions. High detection rate (97%) of dicofol (p, p'-OH-DDT) was observed in the subset, showing dicofol application influenced the DDX levels in soils in Fujian. However, the contribution from historical technical DDT source was greater than that from dicofol in Fujian, indicating historical technical DDT was still an important pollution source to soils. In addition, both the DDX (DDT isomers and derivatives) level and dicofol contribution in non-agricultural soils were higher than other agricultural land uses, especially in hilly regions, the potential cause may be the atmospheric transport of dicofol type DDT, after spraying during daytime, or regional difference on production and application. Copyright © 2017 Elsevier Ltd. All rights reserved.

Application of DNA markers to identify the individual-specific hosts of tsetse feeding on cattle.

PubMed

Torr, S J; Wilson, P J; Schofield, S; Mangwiro, T N; Akber, S; White, B N

2001-03-01

Primer sets for five different ungulate loci were used to obtain individual microsatellite DNA profiles for 29 Mashona cattle from a herd in Zimbabwe. There were 3-13 alleles for each locus and, using the entire suite of five loci, each animal within the herd, including closely related individuals, could be unequivocally distinguished. Wild-caught Glossina pallidipes Austen (Diptera: Glossinidae) were fed on specific cattle and the bloodmeal was profiled 0.5-72 h after feeding. The individual specific sources of the bloodmeals, including mixe meals produced by allowing tsetse to feed on two different cattle, were reliabl identified up to 24 h after feeding. The technique was used in field studies of hos selection by G. pallidipes and G. morsitans morsitans Westwood (Diptera Glossinidae) attracted to pairs of cattle. When the pair comprised an adult and a calf, 100% of meals were from the adult. For some pairs of adult cattle, tsetse were biased significantly towards feeding on one animal, whereas for other pairs there was no such bias. In general, feeding was greater on the animal known to have lower rate of host defensive behaviour. Results suggest that relatively slight differences in the inherent defensive behaviour of cattle produce large difference in host-specific feeding rates when the hosts are adjacent. For flies attracted to pair of cattle, < 2% contained blood from both hosts. The DNA profiling technique will be useful in studying the epidemiology of vector-borne diseases of livestock.

IDENTIFYING SOURCES OF HUMAN EXPOSURE

EPA Science Inventory

Air pollution from ambient sources continues to adversely impact human health in the United States. A fundamental goal for EPA is to implement air quality standards and regulations that reduce health risks associated with exposures to criteria pollutants and air toxics. However...

Reduction of PM emissions from specific sources reflected on key components concentrations of ambient PM10

NASA Astrophysics Data System (ADS)

Minguillon, M. C.; Querol, X.; Monfort, E.; Alastuey, A.; Escrig, A.; Celades, I.; Miro, J. V.

2009-04-01

The relationship between specific particulate emission control and ambient levels of some PM10 components (Zn, As, Pb, Cs, Tl) was evaluated. To this end, the industrial area of Castellón (Eastern Spain) was selected, where around 40% of the EU glazed ceramic tiles and a high proportion of EU ceramic frits (middle product for the manufacture of ceramic glaze) are produced. The PM10 emissions from the ceramic processes were calculated over the period 2000 to 2007 taking into account the degree of implementation of corrective measures throughout the study period. Abatement systems (mainly bag filters) were implemented in the majority of the fusion kilns for frit manufacture in the area as a result of the application of the Directive 1996/61/CE, leading to a marked decrease in PM10 emissions. On the other hand, ambient PM10 sampling was carried out from April 2002 to July 2008 at three urban sites and one suburban site of the area and a complete chemical analysis was made for about 35 % of the collected samples, by means of different techniques (ICP-AES, ICP-MS, Ion Chromatography, selective electrode and elemental analyser). The series of chemical composition of PM10 allowed us to apply a source contribution model (Principal Component Analysis), followed by a multilinear regression analysis, so that PM10 sources were identified and their contribution to bulk ambient PM10 was quantified on a daily basis, as well as the contribution to bulk ambient concentrations of the identified key components (Zn, As, Pb, Cs, Tl). The contribution of the sources identified as the manufacture and use of ceramic glaze components, including the manufacture of ceramic frits, accounted for more than 65, 75, 58, 53, and 53% of ambient Zn, As, Pb, Cs and Tl levels, respectively (with the exception of Tl contribution at one of the sites). The important emission reductions of these sources during the study period had an impact on ambient key components levels, such that there was a high

Identifying (subsurface) anthropogenic heat sources that influence temperature in the drinking water distribution system

NASA Astrophysics Data System (ADS)

Agudelo-Vera, Claudia M.; Blokker, Mirjam; de Kater, Henk; Lafort, Rob

2017-09-01

The water temperature in the drinking water distribution system and at customers' taps approaches the surrounding soil temperature at a depth of 1 m. Water temperature is an important determinant of water quality. In the Netherlands drinking water is distributed without additional residual disinfectant and the temperature of drinking water at customers' taps is not allowed to exceed 25 °C. In recent decades, the urban (sub)surface has been getting more occupied by various types of infrastructures, and some of these can be heat sources. Only recently have the anthropogenic sources and their influence on the underground been studied on coarse spatial scales. Little is known about the urban shallow underground heat profile on small spatial scales, of the order of 10 m × 10 m. Routine water quality samples at the tap in urban areas have shown up locations - so-called hotspots - in the city, with relatively high soil temperatures - up to 7 °C warmer - compared to the soil temperatures in the surrounding rural areas. Yet the sources and the locations of these hotspots have not been identified. It is expected that with climate change during a warm summer the soil temperature in the hotspots can be above 25 °C. The objective of this paper is to find a method to identify heat sources and urban characteristics that locally influence the soil temperature. The proposed method combines mapping of urban anthropogenic heat sources, retrospective modelling of the soil temperature, analysis of water temperature measurements at the tap, and extensive soil temperature measurements. This approach provided insight into the typical range of the variation of the urban soil temperature, and it is a first step to identifying areas with potential underground heat stress towards thermal underground management in cities.

Identifying Source Water and Flow Paths in a Semi-Arid Watershed

NASA Astrophysics Data System (ADS)

Gulvin, C. J.; Miller, S. N.

2016-12-01

Processes controlling water delivery to perennial streams in the semi-arid mountain west are poorly understood, yet necessary to characterize water distribution across the landscape and better protect and manage diminishing water resources. Stream water chemistry profiling and hydrograph separation using stable isotopes can help identify source waters. Weekly stream water samples tested for stable water isotope fractionations, and major cations and anions at seven sites collocated with continuously recording stream depth gauges within a small watershed in southeastern Wyoming is a necessary first-step to identifying seasonally changing source water and flow paths. Sample results will help establish appropriate end members for a mixing analysis, as well as, characterize flow path heterogeneity, transit time distributions, and landscape selectively features. Hourly stream sampling during late-summer thunderstorms and rapid spring melt will help demonstrate if and how stream discharge change is affected by the two different events. Soil water and water extracted from tree xylem will help resolve how water is partitioned in the first 10m of the subsurface. In the face of land use change and a growing demand for water in the area, understanding how the water in small mountain streams is sustained is crucial for the future of agriculture, municipal water supplies, and countless ecosystem services.

Tracing crop-specific sediment sources in agricultural catchments

NASA Astrophysics Data System (ADS)

Blake, William H.; Ficken, Katherine J.; Taylor, Philip; Russell, Mark A.; Walling, Desmond E.

2012-02-01

A Compound Specific Stable Isotope (CSSI) sediment tracing approach is evaluated for the first time in an agricultural catchment setting against established geochemical fingerprinting techniques. The work demonstrates that novel CSSI techniques have the potential to provide important support for soil resource management policies and inform sediment risk assessment for the protection of aquatic habitats and water resources. Analysis of soil material from a range of crop covers in a mixed land-use agricultural catchment shows that the carbon CSSI signatures of particle-reactive fatty acids label surface agricultural soil with distinct crop-specific signatures, thus permitting sediment eroded from each land-cover to be tracked downstream. High resolution sediment sampling during a storm event and analysis for CSSI and conventional geochemical fingerprints elucidated temporal patterns of sediment mobilisation under different crop regimes and the specific contribution that each crop type makes to downstream sediment load. Pasture sources (65% of the catchment area) dominated the sediment load but areal yield (0.13 ± 0.02 t ha - 1 ) was considerably less than that for winter wheat (0.44 ± 0.15 t ha - 1 ). While temporal patterns in crop response matched runoff and erosion response predictions based on plot-scale rainfall simulation experiments, comparison of biomarker and geochemical fingerprinting data indicated that the latter overestimated cultivated land inputs to catchment sediment yield due to inability to discriminate temporary pasture (in rotation) from cultivated land. This discrepancy, however, presents an opportunity since combination of the two datasets revealed the extremely localised nature of erosion from permanent pasture fields in this system (estimated at up to 0.5 t ha - 1 ). The novel use of CSSI and geochemical tracers in tandem provided unique insights into sediment source dynamics that could not have been derived from each method alone. Research

Identifying the origin of waterbird carcasses in Lake Michigan using a neural network source tracking model

USGS Publications Warehouse

Kenow, Kevin P.; Ge, Zhongfu; Fara, Luke J.; Houdek, Steven C.; Lubinski, Brian R.

2016-01-01

Avian botulism type E is responsible for extensive waterbird mortality on the Great Lakes, yet the actual site of toxin exposure remains unclear. Beached carcasses are often used to describe the spatial aspects of botulism mortality outbreaks, but lack specificity of offshore toxin source locations. We detail methodology for developing a neural network model used for predicting waterbird carcass motions in response to wind, wave, and current forcing, in lieu of a complex analytical relationship. This empirically trained model uses current velocity, wind velocity, significant wave height, and wave peak period in Lake Michigan simulated by the Great Lakes Coastal Forecasting System. A detailed procedure is further developed to use the model for back-tracing waterbird carcasses found on beaches in various parts of Lake Michigan, which was validated using drift data for radiomarked common loon (Gavia immer) carcasses deployed at a variety of locations in northern Lake Michigan during September and October of 2013. The back-tracing model was further used on 22 non-radiomarked common loon carcasses found along the shoreline of northern Lake Michigan in October and November of 2012. The model-estimated origins of those cases pointed to some common source locations offshore that coincide with concentrations of common loons observed during aerial surveys. The neural network source tracking model provides a promising approach for identifying locations of botulinum neurotoxin type E intoxication and, in turn, contributes to developing an understanding of the dynamics of toxin production and possible trophic transfer pathways.

Potential use of ionic species for identifying source land-uses of stormwater runoff.

PubMed

Lee, Dong Hoon; Kim, Jin Hwi; Mendoza, Joseph A; Lee, Chang-Hee; Kang, Joo-Hyon

2017-02-01

Identifying critical land-uses or source areas is important to prioritize resources for cost-effective stormwater management. This study investigated the use of information on ionic composition as a fingerprint to identify the source land-use of stormwater runoff. We used 12 ionic species in stormwater runoff monitored for a total of 20 storm events at five sites with different land-use compositions during the 2012-2014 wet seasons. A stepwise forward discriminant function analysis (DFA) with the jack-knifed cross validation approach was used to select ionic species that better discriminate the land-use of its source. Of the 12 ionic species, 9 species (K + , Mg 2+ , Na + , NH 4 + , Br - , Cl - , F - , NO 2 - , and SO 4 2- ) were selected for better performance of the DFA. The DFA successfully differentiated stormwater samples from urban, rural, and construction sites using concentrations of the ionic species (70%, 95%, and 91% of correct classification, respectively). Over 80% of the new data cases were correctly classified by the trained DFA model. When applied to data cases from a mixed land-use catchment and downstream, the DFA model showed the greater impact of urban areas and rural areas respectively in the earlier and later parts of a storm event.

Identifying Rhodamine Dye Plume Sources in Near-Shore Oceanic Environments by Integration of Chemical and Visual Sensors

PubMed Central

Tian, Yu; Kang, Xiaodong; Li, Yunyi; Li, Wei; Zhang, Aiqun; Yu, Jiangchen; Li, Yiping

2013-01-01

This article presents a strategy for identifying the source location of a chemical plume in near-shore oceanic environments where the plume is developed under the influence of turbulence, tides and waves. This strategy includes two modules: source declaration (or identification) and source verification embedded in a subsumption architecture. Algorithms for source identification are derived from the moth-inspired plume tracing strategies based on a chemical sensor. The in-water test missions, conducted in November 2002 at San Clemente Island (California, USA) in June 2003 in Duck (North Carolina, USA) and in October 2010 at Dalian Bay (China), successfully identified the source locations after autonomous underwater vehicles tracked the rhodamine dye plumes with a significant meander over 100 meters. The objective of the verification module is to verify the declared plume source using a visual sensor. Because images taken in near shore oceanic environments are very vague and colors in the images are not well-defined, we adopt a fuzzy color extractor to segment the color components and recognize the chemical plume and its source by measuring color similarity. The source verification module is tested by images taken during the CPT missions. PMID:23507823

40 CFR 148.18 - Waste specific prohibitions-newly listed and identified wastes.

Code of Federal Regulations, 2010 CFR

2010-07-01

... 40 Protection of Environment 22 2010-07-01 2010-07-01 false Waste specific prohibitions-newly listed and identified wastes. 148.18 Section 148.18 Protection of Environment ENVIRONMENTAL PROTECTION AGENCY (CONTINUED) WATER PROGRAMS (CONTINUED) HAZARDOUS WASTE INJECTION RESTRICTIONS Prohibitions on...

Differential Effects of Source-Specific Particulate Matter on Emergency Hospitalizations for Ischemic Heart Disease in Hong Kong

PubMed Central

Pun, Vivian Chit; Yu, Ignatius Tak-sun; Ho, Kin-fai; Qiu, Hong; Sun, Zhiwei

2014-01-01

Background: Ischemic heart disease (IHD) is a major public health concern. Although many epidemiologic studies have reported evidence of adverse effects of particulate matter (PM) mass on IHD, significant knowledge gaps remain regarding the potential impacts of different PM sources. Much the same as PM size, PM sources may influence toxicological characteristics. Objectives: We identified contributing sources to PM10 mass and estimated the acute effects of PM10 sources on daily emergency IHD hospitalizations in Hong Kong. Methods: We analyzed the concentration data of 19 PM10 chemical components measured between 2001 and 2007 by positive matrix factorization to apportion PM10 mass, and used generalized additive models to estimate associations of interquartile range (IQR) increases in PM10 exposures with IHD hospitalization for different lag periods (up to 5 days), adjusted for potential confounders. Results: We identified 8 PM10 sources: vehicle exhaust, soil/road dust, regional combustion, residual oil, fresh sea salt, aged sea salt, secondary nitrate, and secondary sulfate. Vehicle exhaust, secondary nitrate, and secondary sulfate contributed more than half of the PM10 mass. Although associations with IQR increases in 2-day moving averages (lag01) were statistically significant for most sources based on single-source models, only PM10 from vehicle exhaust [1.87% (95% CI: 0.66, 3.10); IQR = 4.9 μg/m3], secondary nitrate [2.28% (95% CI: 1.15, 3.42); IQR = 8.6 μg/m3], and aged sea salt [1.19% (95% CI: 0.04, 2.36); IQR = 5.9 μg/m3] were significantly associated with IHD hospitalizations in the multisource model. Analysis using chemical components provided similar findings. Conclusion: Emergency IHD hospitalization was significantly linked with PM10 from vehicle exhaust, nitrate-rich secondary PM, and sea salt–related PM. Findings may help prioritize toxicological research and guide future monitoring and emission-control polices. Citation: Pun VC, Yu IT, Ho KF

Air pollution source identification

NASA Technical Reports Server (NTRS)

Fordyce, J. S.

1975-01-01

Techniques for air pollution source identification are reviewed, and some results obtained with them are evaluated. Described techniques include remote sensing from satellites and aircraft, on-site monitoring, and the use of injected tracers and pollutants themselves as tracers. The use of a large number of trace elements in ambient airborne particulate matter as a practical means of identifying sources is discussed in detail. Sampling and analysis techniques are described, and it is shown that elemental constituents can be related to specific source types such as those found in the earth's crust and those associated with specific industries. Source identification sytems are noted which utilize charged particle X-ray fluorescence analysis of original field data.

Fatty acid methyl ester analysis to identify sources of soil in surface water.

PubMed

Banowetz, Gary M; Whittaker, Gerald W; Dierksen, Karen P; Azevedo, Mark D; Kennedy, Ann C; Griffith, Stephen M; Steiner, Jeffrey J

2006-01-01

Efforts to improve land-use practices to prevent contamination of surface waters with soil are limited by an inability to identify the primary sources of soil present in these waters. We evaluated the utility of fatty acid methyl ester (FAME) profiles of dry reference soils for multivariate statistical classification of soils collected from surface waters adjacent to agricultural production fields and a wooded riparian zone. Trials that compared approaches to concentrate soil from surface water showed that aluminum sulfate precipitation provided comparable yields to that obtained by vacuum filtration and was more suitable for handling large numbers of samples. Fatty acid methyl ester profiles were developed from reference soils collected from contrasting land uses in different seasons to determine whether specific fatty acids would consistently serve as variables in multivariate statistical analyses to permit reliable classification of soils. We used a Bayesian method and an independent iterative process to select appropriate fatty acids and found that variable selection was strongly impacted by the season during which soil was collected. The apparent seasonal variation in the occurrence of marker fatty acids in FAME profiles from reference soils prevented preparation of a standardized set of variables. Nevertheless, accurate classification of soil in surface water was achieved utilizing fatty acid variables identified in seasonally matched reference soils. Correlation analysis of entire chromatograms and subsequent discriminant analyses utilizing a restricted number of fatty acid variables showed that FAME profiles of soils exposed to the aquatic environment still had utility for classification at least 1 wk after submersion.

Toward identifying specification requirements for digital bone-anchored prosthesis design incorporating substructure fabrication: a pilot study.

PubMed

Eggbeer, Dominic; Bibb, Richard; Evans, Peter

2006-01-01

This paper is the first in a series that aims to identify the specification requirements for advanced digital technologies that may be used to design and fabricate complex, soft tissue facial prostheses. Following a review of previously reported techniques, appropriate and currently available technologies were selected and applied in a pilot study. This study uses a range of optical surface scanning, computerized tomography, computer-aided design, and rapid prototyping technologies to capture, design, and fabricate a bone-anchored auricular prosthesis, including the retentive components. The techniques are assessed in terms of their effectiveness, and the results are used to identify future research and specification requirements to direct developments. The case study identifies that while digital technologies may be used to design implant-retained facial prostheses, many limitations need to be addressed to make the techniques clinically viable. It also identifies the need to develop a more robust specification that covers areas such as resolution, accuracy, materials, and design, against which potential technologies may be assessed. There is a need to develop a specification against which potential technologies may be assessed for their suitability in soft tissue facial prosthetics. The specification will be developed using further experimental research studies.

On the use of coprostanol to identify source of nitrate pollution in groundwater

NASA Astrophysics Data System (ADS)

Nakagawa, Kei; Amano, Hiroki; Takao, Yuji; Hosono, Takahiro; Berndtsson, Ronny

2017-07-01

Investigation of contaminant sources is indispensable for developing effective countermeasures against nitrate (NO3-) pollution in groundwater. Known major nitrogen (N) sources are chemical fertilizers, livestock waste, and domestic wastewater. In general, scatter diagrams of δ18O and δ15N from NO3- can be used to identify these pollution sources. However, this method can be difficult to use for chemical fertilizers and livestock waste sources due to the overlap of δ18O and δ15N ranges. In this study, we propose to use coprostanol as an indicator for the source of pollution. Coprostanol can be used as a fecal contamination indicator because it is a major fecal sterol formed by the conversion of cholesterol by intestinal bacteria in the gut of higher animals. The proposed method was applied to investigate NO3- pollution sources for groundwater in Shimabara, Nagasaki, Japan. Groundwater samples were collected at 33 locations from March 2013 to November 2015. These data were used to quantify relationships between NO3-N, δ15N-NO3-, δ18O-NO3-, and coprostanol. The results show that coprostanol has a potential for source identification of nitrate pollution. For lower coprostanol concentrations (<30 ng L-1) in the nitrate-polluted group, fertilizer is likely to be the predominant source of NO3-. However, higher concentration coprostanol samples in the nitrate-polluted group can be related to pollution from livestock waste. Thus, when conventional diagrams of isotopic ratios cannot distinguish pollution sources, coprostanol may be a useful tool.

PD-1 identifies the patient-specific CD8+ tumor-reactive repertoire infiltrating human tumors

PubMed Central

Gros, Alena; Robbins, Paul F.; Yao, Xin; Li, Yong F.; Turcotte, Simon; Tran, Eric; Wunderlich, John R.; Mixon, Arnold; Farid, Shawn; Dudley, Mark E.; Hanada, Ken-ichi; Almeida, Jorge R.; Darko, Sam; Douek, Daniel C.; Yang, James C.; Rosenberg, Steven A.

2014-01-01

Adoptive transfer of tumor-infiltrating lymphocytes (TILs) can mediate regression of metastatic melanoma; however, TILs are a heterogeneous population, and there are no effective markers to specifically identify and select the repertoire of tumor-reactive and mutation-specific CD8+ lymphocytes. The lack of biomarkers limits the ability to study these cells and develop strategies to enhance clinical efficacy and extend this therapy to other malignancies. Here, we evaluated unique phenotypic traits of CD8+ TILs and TCR β chain (TCRβ) clonotypic frequency in melanoma tumors to identify patient-specific repertoires of tumor-reactive CD8+ lymphocytes. In all 6 tumors studied, expression of the inhibitory receptors programmed cell death 1 (PD-1; also known as CD279), lymphocyte-activation gene 3 (LAG-3; also known as CD223), and T cell immunoglobulin and mucin domain 3 (TIM-3) on CD8+ TILs identified the autologous tumor-reactive repertoire, including mutated neoantigen-specific CD8+ lymphocytes, whereas only a fraction of the tumor-reactive population expressed the costimulatory receptor 4-1BB (also known as CD137). TCRβ deep sequencing revealed oligoclonal expansion of specific TCRβ clonotypes in CD8+PD-1+ compared with CD8+PD-1– TIL populations. Furthermore, the most highly expanded TCRβ clonotypes in the CD8+ and the CD8+PD-1+ populations recognized the autologous tumor and included clonotypes targeting mutated antigens. Thus, in addition to the well-documented negative regulatory role of PD-1 in T cells, our findings demonstrate that PD-1 expression on CD8+ TILs also accurately identifies the repertoire of clonally expanded tumor-reactive cells and reveal a dual importance of PD-1 expression in the tumor microenvironment. PMID:24667641

Identifying content for the glaucoma-specific item bank to measure quality-of-life parameters.

PubMed

Khadka, Jyoti; McAlinden, Colm; Craig, Jamie E; Fenwick, Eva K; Lamoureux, Ecosse L; Pesudovs, Konrad

2015-01-01

Patient-reported outcomes (PROs) have become essential clinical trial end points. However, a comprehensive, multidimensional, patient-relevant, and precise glaucoma-specific PRO instrument is not available. Therefore, the purpose of this study was to identify content for a new, glaucoma-specific, quality-of-life (QOL) item bank. Content identification was undertaken in 5 phases: (1) identification of extant items in glaucoma-specific instruments and the qualitative literature; (2) focus groups and interviews with glaucoma patients; (3) item classification and selection; (4) expert review and revision of items; and (5) cognitive interviews with patients. A total of 737 unique items (extant items from PRO instruments, 247; qualitative articles, 14 items; focus groups and semistructured interviews, 476 items) were identified. These items were classified into 10 QOL domains. Four criteria (item redundancy, item inconsistent with domain definition, item content too narrow to have wider applicability, and item clarity) were used to remove and refine the items. After the cognitive interviews, the final minimally representative item set had a total of 342 unique items belonging to 10 domains: activity limitation (88), mobility (20), visual symptoms (19), ocular surface symptoms (22), general symptoms (15), convenience (39), health concerns (45), emotional well-being (49), social issues (23), and economic issues (22). The systematic content identification process identified 10 QOL domains, which were important to patients with glaucoma. The majority of the items were identified from the patient-specific focus groups and semistructured interviews suggesting that the existing PRO instruments do not adequately address QOL issues relevant to individuals with glaucoma.

From voice to voices: identifying a plurality of Muslim sources in the news media.

PubMed

Munnik, Michael B

2017-03-01

This article identifies a qualitative change in the diversity of actors who represent Muslims in British news media. Hitherto, the literature discussing Muslims and the media has tended to characterize media organizations as institutions which portray Muslims in an essentialized, monolithic way. In contrast, I propose in this article that the process of representation is more complex, including greater agency and engaging a wider diversity of Muslims than the prevailing literature suggests. Sociological studies distinguish between official and unofficial sources who help determine the representations that journalists employ in their texts, and I apply this to Muslim communities in Glasgow. Using qualitative methods drawn from media production analysis, including participant-observation and ethnographic interviews, I identify a shift from a 'gatekeeper' model of representing the community to that of a plurality of sources, which reveals and insists on the diversity of Muslim communities and voices. I will show why a wider range of actors emerged to speak publicly, what differentiates them and how they position themselves as representatives of Muslims. This focus on producers and on source strategies brings fresh insights into a field dominated by content analysis and a 'media-centric' approach.

From voice to voices: identifying a plurality of Muslim sources in the news media

PubMed Central

Munnik, Michael B

2017-01-01

This article identifies a qualitative change in the diversity of actors who represent Muslims in British news media. Hitherto, the literature discussing Muslims and the media has tended to characterize media organizations as institutions which portray Muslims in an essentialized, monolithic way. In contrast, I propose in this article that the process of representation is more complex, including greater agency and engaging a wider diversity of Muslims than the prevailing literature suggests. Sociological studies distinguish between official and unofficial sources who help determine the representations that journalists employ in their texts, and I apply this to Muslim communities in Glasgow. Using qualitative methods drawn from media production analysis, including participant-observation and ethnographic interviews, I identify a shift from a ‘gatekeeper’ model of representing the community to that of a plurality of sources, which reveals and insists on the diversity of Muslim communities and voices. I will show why a wider range of actors emerged to speak publicly, what differentiates them and how they position themselves as representatives of Muslims. This focus on producers and on source strategies brings fresh insights into a field dominated by content analysis and a ‘media-centric’ approach. PMID:29708127

Identifying the Source of Gem Diamonds: Requirements for a Certification System

NASA Astrophysics Data System (ADS)

Shigley, J. E.

2002-05-01

Recent civil conflicts in several countries, in which profits from the sales of gem diamonds have supported the rival factions, have forced the jewelry industry to confront the need to certify the geographic sources of gem diamonds. The goals of this program are to prohibit the sale of so-called "conflict diamonds", and to prevent the loss of consumer confidence. Efforts to identify unique characteristics of gem diamonds have been hampered so far by the absence of chemical or physical features that are diagnostic of particular sources, and the lack of a representative collection of diamonds from major producing areas that would be required for a rigorous scientific study. The jewelry industry has therefore adopted plans to track gem diamonds from the mine through the manufacturing process to the consumer. Practical requirements for implementation of such a certification system will be summarized. Any proposed solutions for determining the sources of gem diamonds by some analytical technique, or for following diamonds from the mine, must take into account the annual production of several tens of millions of carats of rough diamonds, which are transformed during manufacturing into several hundreds of millions of polished gemstones (with an average weight of only about 0.03 carat, or 0.006 gram).

Diagnostic air quality model evaluation of source-specific primary and secondary fine particulate carbon.

PubMed

Napelenok, Sergey L; Simon, Heather; Bhave, Prakash V; Pye, Havala O T; Pouliot, George A; Sheesley, Rebecca J; Schauer, James J

2014-01-01

Ambient measurements of 78 source-specific tracers of primary and secondary carbonaceous fine particulate matter collected at four midwestern United States locations over a full year (March 2004-February 2005) provided an unprecedented opportunity to diagnostically evaluate the results of a numerical air quality model. Previous analyses of these measurements demonstrated excellent mass closure for the variety of contributing sources. In this study, a carbon-apportionment version of the Community Multiscale Air Quality (CMAQ) model was used to track primary organic and elemental carbon emissions from 15 independent sources such as mobile sources and biomass burning in addition to four precursor-specific classes of secondary organic aerosol (SOA) originating from isoprene, terpenes, aromatics, and sesquiterpenes. Conversion of the source-resolved model output into organic tracer concentrations yielded a total of 2416 data pairs for comparison with observations. While emission source contributions to the total model bias varied by season and measurement location, the largest absolute bias of -0.55 μgC/m(3) was attributed to insufficient isoprene SOA in the summertime CMAQ simulation. Biomass combustion was responsible for the second largest summertime model bias (-0.46 μgC/m(3) on average). Several instances of compensating errors were also evident; model underpredictions in some sectors were masked by overpredictions in others.

10 CFR 70.39 - Specific licenses for the manufacture or initial transfer of calibration or reference sources.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 2 2010-01-01 2010-01-01 false Specific licenses for the manufacture or initial transfer... manufacture or initial transfer of calibration or reference sources. (a) An application for a specific license to manufacture or initially transfer calibration or reference sources containing plutonium, for...

Identifying States along the Hematopoietic Stem Cell Differentiation Hierarchy with Single Cell Specificity via Raman Spectroscopy.

PubMed

Ilin, Yelena; Choi, Ji Sun; Harley, Brendan A C; Kraft, Mary L

2015-11-17

A major challenge for expanding specific types of hematopoietic cells ex vivo for the treatment of blood cell pathologies is identifying the combinations of cellular and matrix cues that direct hematopoietic stem cells (HSC) to self-renew or differentiate into cell populations ex vivo. Microscale screening platforms enable minimizing the number of rare HSCs required to screen the effects of numerous cues on HSC fate decisions. These platforms create a strong demand for label-free methods that accurately identify the fate decisions of individual hematopoietic cells at specific locations on the platform. We demonstrate the capacity to identify discrete cells along the HSC differentiation hierarchy via multivariate analysis of Raman spectra. Notably, cell state identification is accurate for individual cells and independent of the biophysical properties of the functionalized polyacrylamide gels upon which these cells are cultured. We report partial least-squares discriminant analysis (PLS-DA) models of single cell Raman spectra enable identifying four dissimilar hematopoietic cell populations across the HSC lineage specification. Successful discrimination was obtained for a population enriched for long-term repopulating HSCs (LT-HSCs) versus their more differentiated progeny, including closely related short-term repopulating HSCs (ST-HSCs) and fully differentiated lymphoid (B cells) and myeloid (granulocytes) cells. The lineage-specific differentiation states of cells from these four subpopulations were accurately identified independent of the stiffness of the underlying biomaterial substrate, indicating subtle spectral variations that discriminated these populations were not masked by features from the culture substrate. This approach enables identifying the lineage-specific differentiation stages of hematopoietic cells on biomaterial substrates of differing composition and may facilitate correlating hematopoietic cell fate decisions with the extrinsic cues that

Mining the Immune Cell Proteome to Identify Ovarian Cancer-Specific Biomarkers

DTIC Science & Technology

2012-03-01

data and are in the process of identifying gene signatures that can be used as biomarkers for the identification of ovarian cancer-specific biomarkers...groups. The groups showed significant difference in age as well as gestational age, which is expected when considering the disease process . Isolation of...MUC4 in intracellular signaling.32 Oligosaccharides attached to the extracellular domains of mucins have also been shown to interact with different

Comparative Transcriptional Profiling of the Axolotl Limb Identifies a Tripartite Regeneration-Specific Gene Program

PubMed Central

Knapp, Dunja; Schulz, Herbert; Rascon, Cynthia Alexander; Volkmer, Michael; Scholz, Juliane; Nacu, Eugen; Le, Mu; Novozhilov, Sergey; Tazaki, Akira; Protze, Stephanie; Jacob, Tina; Hubner, Norbert; Habermann, Bianca; Tanaka, Elly M.

2013-01-01

Understanding how the limb blastema is established after the initial wound healing response is an important aspect of regeneration research. Here we performed parallel expression profile time courses of healing lateral wounds versus amputated limbs in axolotl. This comparison between wound healing and regeneration allowed us to identify amputation-specific genes. By clustering the expression profiles of these samples, we could detect three distinguishable phases of gene expression – early wound healing followed by a transition-phase leading to establishment of the limb development program, which correspond to the three phases of limb regeneration that had been defined by morphological criteria. By focusing on the transition-phase, we identified 93 strictly amputation-associated genes many of which are implicated in oxidative-stress response, chromatin modification, epithelial development or limb development. We further classified the genes based on whether they were or were not significantly expressed in the developing limb bud. The specific localization of 53 selected candidates within the blastema was investigated by in situ hybridization. In summary, we identified a set of genes that are expressed specifically during regeneration and are therefore, likely candidates for the regulation of blastema formation. PMID:23658691

Hydrograph Separations can Identify Contaminant-Specific Pathways for Conservation Targeting in a Tile-Drained Watershed

USDA-ARS?s Scientific Manuscript database

Water quality issues continue to vex agriculture. Understanding contaminant-specific pathways could help clarify effective water quality management strategies in watersheds. Hypothesis: If conducted at nested scales, hydrograph separation techniques can identify contaminant-specific pathways that co...

Evaluation of Two PCR-Based Swine-Specific Fecal Source Tracking Assays (Poster)

EPA Science Inventory

Several PCR-based methods have been proposed to identify swine fecal pollution in environmental waters. However, the specificity and distribution of these targets have not been adequately assessed. Consequently, the utility of these assays in identifying swine fecal contamination...

[Research advances in identifying nitrate pollution sources of water environment by using nitrogen and oxygen stable isotopes].

PubMed

Mao, Wei; Liang, Zhi-wei; Li, Wei; Zhu, Yao; Yanng, Mu-yi; Jia, Chao-jie

2013-04-01

Water body' s nitrate pollution has become a common and severe environmental problem. In order to ensure human health and water environment benign evolution, it is of great importance to effectively identify the nitrate pollution sources of water body. Because of the discrepant composition of nitrogen and oxygen stable isotopes in different sources of nitrate in water body, nitrogen and oxygen stable isotopes can be used to identify the nitrate pollution sources of water environment. This paper introduced the fractionation factors of nitrogen and oxygen stable isotopes in the main processes of nitrogen cycling and the composition of these stable isotopes in main nitrate sources, compared the advantages and disadvantages of five pre-treatment methods for analyzing the nitrogen and oxygen isotopes in nitrate, and summarized the research advances in this aspect into three stages, i. e. , using nitrogen stable isotope alone, using nitrogen and oxygen stable isotopes simultaneously, and combining with mathematical models. The future research directions regarding the nitrate pollution sources identification of water environment were also discussed.

Identifying Methane Sources with an Airborne Pulsed IPDA Lidar System Operating near 1.65 µm

NASA Astrophysics Data System (ADS)

Yerasi, A.; Bartholomew, J.; Tandy, W., Jr.; Emery, W. J.

2016-12-01

Methane is a powerful greenhouse gas that is predicted to play an important role in future global climate trends. It would therefore be beneficial to locate areas that produce methane in significant amounts so that these trends can be better understood. In this investigation, some initial performance test results of a lidar system called the Advanced Leak Detector Lidar - Natural Gas (ALDL-NG) are discussed. The feasibility of applying its fundamental principle of operation to methane source identification is also explored. The ALDL-NG was originally created by the Ball Aerospace & Technologies Corp. to reveal leaks emanating from pipelines that transport natural gas, which is primarily composed of methane. It operates in a pulsed integrated path differential absorption (IPDA) configuration and it is carried by a piloted, single-engine aircraft. In order to detect the presence of natural gas leaks, the laser wavelengths of its online and offline channels operate in the 1.65 µm region. The functionality of the ALDL-NG was tested during a recent field campaign in Colorado. It was determined that the ambient concentration of methane in the troposphere ( 1.8 ppm) could indeed be retrieved from ALDL-NG data with a lower-than-expected uncertainty ( 0.2 ppm). Furthermore, when the ALDL-NG scanned over areas that were presumed to be methane sources (feedlots, landfills, etc.), significantly higher concentrations of methane were retrieved. These results are intriguing because the ALDL-NG was not specifically designed to observe anything beyond natural gas pipelines. Nevertheless, they strongly indicate that utilizing an airborne pulsed IPDA lidar system operating near 1.65 µm may very well be a viable technique for identifying methane sources. Perhaps future lidar systems could build upon the heritage of the ALDL-NG and measure methane concentration with even better precision for a variety of scientific applications.

Quantifying sources of bias in National Healthcare Safety Network laboratory-identified Clostridium difficile infection rates.

PubMed

Haley, Valerie B; DiRienzo, A Gregory; Lutterloh, Emily C; Stricof, Rachel L

2014-01-01

To assess the effect of multiple sources of bias on state- and hospital-specific National Healthcare Safety Network (NHSN) laboratory-identified Clostridium difficile infection (CDI) rates. Sensitivity analysis. A total of 124 New York hospitals in 2010. New York NHSN CDI events from audited hospitals were matched to New York hospital discharge billing records to obtain additional information on patient age, length of stay, and previous hospital discharges. "Corrected" hospital-onset (HO) CDI rates were calculated after (1) correcting inaccurate case reporting found during audits, (2) incorporating knowledge of laboratory results from outside hospitals, (3) excluding days when patients were not at risk from the denominator of the rates, and (4) adjusting for patient age. Data sets were simulated with each of these sources of bias reintroduced individually and combined. The simulated rates were compared with the corrected rates. Performance (ie, better, worse, or average compared with the state average) was categorized, and misclassification compared with the corrected data set was measured. Counting days patients were not at risk in the denominator reduced the state HO rate by 45% and resulted in 8% misclassification. Age adjustment and reporting errors also shifted rates (7% and 6% misclassification, respectively). Changing the NHSN protocol to require reporting of age-stratified patient-days and adjusting for patient-days at risk would improve comparability of rates across hospitals. Further research is needed to validate the risk-adjustment model before these data should be used as hospital performance measures.

An audit of the global carbon budget: identifying and reducing sources of uncertainty

NASA Astrophysics Data System (ADS)

Ballantyne, A. P.; Tans, P. P.; Marland, G.; Stocker, B. D.

2012-12-01

Uncertainties in our carbon accounting practices may limit our ability to objectively verify emission reductions on regional scales. Furthermore uncertainties in the global C budget must be reduced to benchmark Earth System Models that incorporate carbon-climate interactions. Here we present an audit of the global C budget where we try to identify sources of uncertainty for major terms in the global C budget. The atmospheric growth rate of CO2 has increased significantly over the last 50 years, while the uncertainty in calculating the global atmospheric growth rate has been reduced from 0.4 ppm/yr to 0.2 ppm/yr (95% confidence). Although we have greatly reduced global CO2 growth rate uncertainties, there remain regions, such as the Southern Hemisphere, Tropics and Arctic, where changes in regional sources/sinks will remain difficult to detect without additional observations. Increases in fossil fuel (FF) emissions are the primary factor driving the increase in global CO2 growth rate; however, our confidence in FF emission estimates has actually gone down. Based on a comparison of multiple estimates, FF emissions have increased from 2.45 ± 0.12 PgC/yr in 1959 to 9.40 ± 0.66 PgC/yr in 2010. Major sources of increasing FF emission uncertainty are increased emissions from emerging economies, such as China and India, as well as subtle differences in accounting practices. Lastly, we evaluate emission estimates from Land Use Change (LUC). Although relative errors in emission estimates from LUC are quite high (2 sigma ~ 50%), LUC emissions have remained fairly constant in recent decades. We evaluate the three commonly used approaches to estimating LUC emissions- Bookkeeping, Satellite Imagery, and Model Simulations- to identify their main sources of error and their ability to detect net emissions from LUC.; Uncertainties in Fossil Fuel Emissions over the last 50 years.

40 CFR 148.18 - Waste specific prohibitions-newly listed and identified wastes.

Code of Federal Regulations, 2012 CFR

2012-07-01

.... (e) On July 8, 1996, the wastes specified in 40 CFR 261.32 as EPA Hazardous waste numbers K156-K161... 40 Protection of Environment 24 2012-07-01 2012-07-01 false Waste specific prohibitions-newly listed and identified wastes. 148.18 Section 148.18 Protection of Environment ENVIRONMENTAL PROTECTION...

40 CFR 148.18 - Waste specific prohibitions-newly listed and identified wastes.

Code of Federal Regulations, 2011 CFR

2011-07-01

.... (e) On July 8, 1996, the wastes specified in 40 CFR 261.32 as EPA Hazardous waste numbers K156-K161... 40 Protection of Environment 23 2011-07-01 2011-07-01 false Waste specific prohibitions-newly listed and identified wastes. 148.18 Section 148.18 Protection of Environment ENVIRONMENTAL PROTECTION...

40 CFR 148.18 - Waste specific prohibitions-newly listed and identified wastes.

Code of Federal Regulations, 2013 CFR

2013-07-01

.... (e) On July 8, 1996, the wastes specified in 40 CFR 261.32 as EPA Hazardous waste numbers K156-K161... 40 Protection of Environment 24 2013-07-01 2013-07-01 false Waste specific prohibitions-newly listed and identified wastes. 148.18 Section 148.18 Protection of Environment ENVIRONMENTAL PROTECTION...

40 CFR 148.18 - Waste specific prohibitions-newly listed and identified wastes.

Code of Federal Regulations, 2014 CFR

2014-07-01

.... (e) On July 8, 1996, the wastes specified in 40 CFR 261.32 as EPA Hazardous waste numbers K156-K161... 40 Protection of Environment 23 2014-07-01 2014-07-01 false Waste specific prohibitions-newly listed and identified wastes. 148.18 Section 148.18 Protection of Environment ENVIRONMENTAL PROTECTION...

Associations between Source-Specific Fine Particulate Matter and Emergency Department Visits for Respiratory Disease in Four U.S. Cities

PubMed Central

Krall, Jenna R.; Mulholland, James A.; Russell, Armistead G.; Balachandran, Sivaraman; Winquist, Andrea; Tolbert, Paige E.; Waller, Lance A.; Sarnat, Stefanie Ebelt

2016-01-01

Background: Short-term exposure to ambient fine particulate matter (PM2.5) concentrations has been associated with increased mortality and morbidity. Determining which sources of PM2.5 are most toxic can help guide targeted reduction of PM2.5. However, conducting multicity epidemiologic studies of sources is difficult because source-specific PM2.5 is not directly measured, and source chemical compositions can vary between cities. Objectives: We determined how the chemical composition of primary ambient PM2.5 sources varies across cities. We estimated associations between source-specific PM2.5 and respiratory disease emergency department (ED) visits and examined between-city heterogeneity in estimated associations. Methods: We used source apportionment to estimate daily concentrations of primary source-specific PM2.5 for four U.S. cities. For sources with similar chemical compositions between cities, we applied Poisson time-series regression models to estimate associations between source-specific PM2.5 and respiratory disease ED visits. Results: We found that PM2.5 from biomass burning, diesel vehicle, gasoline vehicle, and dust sources was similar in chemical composition between cities, but PM2.5 from coal combustion and metal sources varied across cities. We found some evidence of positive associations of respiratory disease ED visits with biomass burning PM2.5; associations with diesel and gasoline PM2.5 were frequently imprecise or consistent with the null. We found little evidence of associations with dust PM2.5. Conclusions: We introduced an approach for comparing the chemical compositions of PM2.5 sources across cities and conducted one of the first multicity studies of source-specific PM2.5 and ED visits. Across four U.S. cities, among the primary PM2.5 sources assessed, biomass burning PM2.5 was most strongly associated with respiratory health. Citation: Krall JR, Mulholland JA, Russell AG, Balachandran S, Winquist A, Tolbert PE, Waller LA, Sarnat SE. 2017

Associations between Source-Specific Fine Particulate Matter and Emergency Department Visits for Respiratory Disease in Four U.S. Cities.

PubMed

Krall, Jenna R; Mulholland, James A; Russell, Armistead G; Balachandran, Sivaraman; Winquist, Andrea; Tolbert, Paige E; Waller, Lance A; Sarnat, Stefanie Ebelt

2017-01-01

Short-term exposure to ambient fine particulate matter (PM2.5) concentrations has been associated with increased mortality and morbidity. Determining which sources of PM2.5 are most toxic can help guide targeted reduction of PM2.5. However, conducting multicity epidemiologic studies of sources is difficult because source-specific PM2.5 is not directly measured, and source chemical compositions can vary between cities. We determined how the chemical composition of primary ambient PM2.5 sources varies across cities. We estimated associations between source-specific PM2.5 and respiratory disease emergency department (ED) visits and examined between-city heterogeneity in estimated associations. We used source apportionment to estimate daily concentrations of primary source-specific PM2.5 for four U.S. cities. For sources with similar chemical compositions between cities, we applied Poisson time-series regression models to estimate associations between source-specific PM2.5 and respiratory disease ED visits. We found that PM2.5 from biomass burning, diesel vehicle, gasoline vehicle, and dust sources was similar in chemical composition between cities, but PM2.5 from coal combustion and metal sources varied across cities. We found some evidence of positive associations of respiratory disease ED visits with biomass burning PM2.5; associations with diesel and gasoline PM2.5 were frequently imprecise or consistent with the null. We found little evidence of associations with dust PM2.5. We introduced an approach for comparing the chemical compositions of PM2.5 sources across cities and conducted one of the first multicity studies of source-specific PM2.5 and ED visits. Across four U.S. cities, among the primary PM2.5 sources assessed, biomass burning PM2.5 was most strongly associated with respiratory health. Citation: Krall JR, Mulholland JA, Russell AG, Balachandran S, Winquist A, Tolbert PE, Waller LA, Sarnat SE. 2017. Associations between source-specific fine particulate

Travel-time source-specific station correction improves location accuracy

NASA Astrophysics Data System (ADS)

Giuntini, Alessandra; Materni, Valerio; Chiappini, Stefano; Carluccio, Roberto; Console, Rodolfo; Chiappini, Massimo

2013-04-01

Accurate earthquake locations are crucial for investigating seismogenic processes, as well as for applications like verifying compliance to the Comprehensive Test Ban Treaty (CTBT). Earthquake location accuracy is related to the degree of knowledge about the 3-D structure of seismic wave velocity in the Earth. It is well known that modeling errors of calculated travel times may have the effect of shifting the computed epicenters far from the real locations by a distance even larger than the size of the statistical error ellipses, regardless of the accuracy in picking seismic phase arrivals. The consequences of large mislocations of seismic events in the context of the CTBT verification is particularly critical in order to trigger a possible On Site Inspection (OSI). In fact, the Treaty establishes that an OSI area cannot be larger than 1000 km2, and its larger linear dimension cannot be larger than 50 km. Moreover, depth accuracy is crucial for the application of the depth event screening criterion. In the present study, we develop a method of source-specific travel times corrections based on a set of well located events recorded by dense national seismic networks in seismically active regions. The applications concern seismic sequences recorded in Japan, Iran and Italy. We show that mislocations of the order of 10-20 km affecting the epicenters, as well as larger mislocations in hypocentral depths, calculated from a global seismic network and using the standard IASPEI91 travel times can be effectively removed by applying source-specific station corrections.

Evaluation of Two PCR-based Swine-specific Fecal Source Tracking Assays (Abstract)

EPA Science Inventory

Several PCR-based methods have been proposed to identify swine fecal pollution in environmental waters. However, the utility of these assays in identifying swine fecal contamination on a broad geographic scale is largely unknown. In this study, we evaluated the specificity, distr...

40 CFR 268.38 - Waste specific prohibitions-newly identified organic toxicity characteristic wastes and newly...

Code of Federal Regulations, 2010 CFR

2010-07-01

... identified organic toxicity characteristic wastes and newly listed coke by-product and chlorotoluene... specific prohibitions—newly identified organic toxicity characteristic wastes and newly listed coke by-product and chlorotoluene production wastes. (a) Effective December 19, 1994, the wastes specified in 40...

Comparing the effectiveness of using generic and specific search terms in electronic databases to identify health outcomes for a systematic review: a prospective comparative study of literature search methods

PubMed Central

MacLean, Alice; Sweeting, Helen; Hunt, Kate

2012-01-01

Objective To compare the effectiveness of systematic review literature searches that use either generic or specific terms for health outcomes. Design Prospective comparative study of two electronic literature search strategies. The ‘generic’ search included general terms for health such as ‘adolescent health’, ‘health status’, ‘morbidity’, etc. The ‘specific’ search focused on terms for a range of specific illnesses, such as ‘headache’, ‘epilepsy’, ‘diabetes mellitus’, etc. Data sources The authors searched Medline, Embase, the Cumulative Index to Nursing and Allied Health Literature, PsycINFO and the Education Resources Information Center for studies published in English between 1992 and April 2010. Main outcome measures Number and proportion of studies included in the systematic review that were identified from each search. Results The two searches tended to identify different studies. Of 41 studies included in the final review, only three (7%) were identified by both search strategies, 21 (51%) were identified by the generic search only and 17 (41%) were identified by the specific search only. 5 of the 41 studies were also identified through manual searching methods. Studies identified by the two ELS differed in terms of reported health outcomes, while each ELS uniquely identified some of the review's higher quality studies. Conclusions Electronic literature searches (ELS) are a vital stage in conducting systematic reviews and therefore have an important role in attempts to inform and improve policy and practice with the best available evidence. While the use of both generic and specific health terms is conventional for many reviewers and information scientists, there are also reviews that rely solely on either generic or specific terms. Based on the findings, reliance on only the generic or specific approach could increase the risk of systematic reviews missing important evidence and, consequently, misinforming decision makers

Antenatal depressive symptoms associated with specific life events and sources of social support among Italian women.

PubMed

Agostini, Francesca; Neri, Erica; Salvatori, Paola; Dellabartola, Sara; Bozicevic, Laura; Monti, Fiorella

2015-05-01

This study aimed to identify different kinds of stressful life events and social support associated with antenatal depressive symptoms in a sample of pregnant Italian women. We conducted the study at a primary health-care centre in an urban area (northeast Italy). Mainly recruited at antenatal classes, 404 eligible pregnant women completed a socio-demographic questionnaire that included questions about the present pregnancy, the Edinburgh Depression Scale (EDS) to estimate the prevalence of depressive symptoms, the Multidimensional Scale of Perceived Social Support and List of Threatening Experiences Questionnaire to investigate the quality and nature of social support and recent negative life events. Of the 404 women, 60 (14.9 %) scored 13 or higher on the EDS. This group reported significantly lower social support from various sources-family, friends, and significant others; only in primiparous women were depressive symptoms significantly related to lower support from friends. Women with EDS scores equal or higher than 13 also reported a higher occurrence of recent stressful life events-specifically, death or a serious problem with a close friend or relative, unemployment, financial problems, and moving or housing difficulties. Regression analyses showed that women with high levels of social support or with a positive experience of pregnancy were less likely to experience antenatal depressive symptoms. Our results underscore the associations among antenatal depression, specific life stressors, and low social support from various sources. Clinical attention to these psychosocial correlates is recommended toward detecting vulnerability to antenatal depressive symptoms.

Air pollution source identification

NASA Technical Reports Server (NTRS)

Fordyce, J. S.

1975-01-01

The techniques available for source identification are reviewed: remote sensing, injected tracers, and pollutants themselves as tracers. The use of the large number of trace elements in the ambient airborne particulate matter as a practical means of identifying sources is discussed. Trace constituents are determined by sensitive, inexpensive, nondestructive, multielement analytical methods such as instrumental neutron activation and charged particle X-ray fluorescence. The application to a large data set of pairwise correlation, the more advanced pattern recognition-cluster analysis approach with and without training sets, enrichment factors, and pollutant concentration rose displays for each element is described. It is shown that elemental constituents are related to specific source types: earth crustal, automotive, metallurgical, and more specific industries. A field-ready source identification system based on time and wind direction resolved sampling is described.

Application of positive matrix factorization to identify potential sources of PAHs in soil of Dalian, China.

PubMed

Wang, Degao; Tian, Fulin; Yang, Meng; Liu, Chenlin; Li, Yi-Fan

2009-05-01

Soil derived sources of polycyclic aromatic hydrocarbons (PAHs) in the region of Dalian, China were investigated using positive matrix factorization (PMF). Three factors were separated based on PMF for the statistical investigation of the datasets both in summer and winter. These factors were dominated by the pattern of single sources or groups of similar sources, showing seasonal and regional variations. The main sources of PAHs in Dalian soil in summer were the emissions from coal combustion average (46%), diesel engine (30%), and gasoline engine (24%). In winter, the main sources were the emissions from coal-fired boiler (72%), traffic average (20%), and gasoline engine (8%). These factors with strong seasonality indicated that coal combustion in winter and traffic exhaust in summer dominated the sources of PAHs in soil. These results suggested that PMF model was a proper approach to identify the sources of PAHs in soil.

Signatures from Tissue-specific MPSS Libraries Identify Transcripts Preferentially Expressed in the Mouse Inner Ear

PubMed Central

Peters, Linda M.; Belyantseva, Inna A.; Lagziel, Ayala; Battey, James F.; Friedman, Thomas B.; Morell, Robert J.

2007-01-01

Specialization in cell function and morphology is influenced by the differential expression of mRNAs, many of which are expressed at low abundance and restricted to certain cell types. Detecting such transcripts in cDNA libraries may require sequencing millions of clones. Massively parallel signature sequencing (MPSS) is well-suited for identifying transcripts that are expressed in discrete cell types and in low abundance. We have made MPSS libraries from microdissections of three inner ear tissues. By comparing these MPSS libraries to those of 87 other tissues included in the Mouse Reference Transcriptome (MRT) online resource, we have identified genes that are highly enriched in, or specific to, the inner ear. We show by RT-PCR and in situ hybridization that signatures unique to the inner ear libraries identify transcripts with highly specific cell-type localizations. These transcripts serve to illustrate the utility of a resource that is available to the research community. Utilization of these resources will increase the number of known transcription units and expand our knowledge of the tissue-specific regulation of the transcriptome. PMID:17049805

High-Throughput Screening to Identify Regulators of Meiosis-Specific Gene Expression in Saccharomyces cerevisiae.

PubMed

Kassir, Yona

2017-01-01

Meiosis and gamete formation are processes that are essential for sexual reproduction in all eukaryotic organisms. Multiple intracellular and extracellular signals feed into pathways that converge on transcription factors that induce the expression of meiosis-specific genes. Once triggered the meiosis-specific gene expression program proceeds in a cascade that drives progress through the events of meiosis and gamete formation. Meiosis-specific gene expression is tightly controlled by a balance of positive and negative regulatory factors that respond to a plethora of signaling pathways. The budding yeast Saccharomyces cerevisiae has proven to be an outstanding model for the dissection of gametogenesis owing to the sophisticated genetic manipulations that can be performed with the cells. It is possible to use a variety selection and screening methods to identify genes and their functions. High-throughput screening technology has been developed to allow an array of all viable yeast gene deletion mutants to be screened for phenotypes and for regulators of gene expression. This chapter describes a protocol that has been used to screen a library of homozygous diploid yeast deletion strains to identify regulators of the meiosis-specific IME1 gene.

The use of chemical and molecular microbial indicators for faecal source identification.

PubMed

Gilpin, B; James, T; Nourozi, F; Saunders, D; Scholes, P; Savill, M

2003-01-01

Identifying the source of faecal pollution is important to enable appropriate management of faecal pollution of water. We are developing and evaluating a combination of these microbial and chemical indicators better able to identify the source of faecal pollution. These assays make use of a combination of direct PCR, culturing, and colony hybridisation to identify source specific species of Bifidobacterium, Rhodococcus and Bacteroides. In conjunction with assays for (a) fluorescent whitening agents and (b) faecal sterols and stanols, these indicators were able to identify human derived faecal pollution in river water containing inputs from septic tanks, municipal oxidation ponds, farmed animals and feral animals. Differentiating amongst the animal sources was more difficult and will require development of molecular assays for organisms specific to each animal group.

A computational approach to identify cellular heterogeneity and tissue-specific gene regulatory networks.

PubMed

Jambusaria, Ankit; Klomp, Jeff; Hong, Zhigang; Rafii, Shahin; Dai, Yang; Malik, Asrar B; Rehman, Jalees

2018-06-07

The heterogeneity of cells across tissue types represents a major challenge for studying biological mechanisms as well as for therapeutic targeting of distinct tissues. Computational prediction of tissue-specific gene regulatory networks may provide important insights into the mechanisms underlying the cellular heterogeneity of cells in distinct organs and tissues. Using three pathway analysis techniques, gene set enrichment analysis (GSEA), parametric analysis of gene set enrichment (PGSEA), alongside our novel model (HeteroPath), which assesses heterogeneously upregulated and downregulated genes within the context of pathways, we generated distinct tissue-specific gene regulatory networks. We analyzed gene expression data derived from freshly isolated heart, brain, and lung endothelial cells and populations of neurons in the hippocampus, cingulate cortex, and amygdala. In both datasets, we found that HeteroPath segregated the distinct cellular populations by identifying regulatory pathways that were not identified by GSEA or PGSEA. Using simulated datasets, HeteroPath demonstrated robustness that was comparable to what was seen using existing gene set enrichment methods. Furthermore, we generated tissue-specific gene regulatory networks involved in vascular heterogeneity and neuronal heterogeneity by performing motif enrichment of the heterogeneous genes identified by HeteroPath and linking the enriched motifs to regulatory transcription factors in the ENCODE database. HeteroPath assesses contextual bidirectional gene expression within pathways and thus allows for transcriptomic assessment of cellular heterogeneity. Unraveling tissue-specific heterogeneity of gene expression can lead to a better understanding of the molecular underpinnings of tissue-specific phenotypes.

SPARQL-enabled identifier conversion with Identifiers.org

PubMed Central

Wimalaratne, Sarala M.; Bolleman, Jerven; Juty, Nick; Katayama, Toshiaki; Dumontier, Michel; Redaschi, Nicole; Le Novère, Nicolas; Hermjakob, Henning; Laibe, Camille

2015-01-01

Motivation: On the semantic web, in life sciences in particular, data is often distributed via multiple resources. Each of these sources is likely to use their own International Resource Identifier for conceptually the same resource or database record. The lack of correspondence between identifiers introduces a barrier when executing federated SPARQL queries across life science data. Results: We introduce a novel SPARQL-based service to enable on-the-fly integration of life science data. This service uses the identifier patterns defined in the Identifiers.org Registry to generate a plurality of identifier variants, which can then be used to match source identifiers with target identifiers. We demonstrate the utility of this identifier integration approach by answering queries across major producers of life science Linked Data. Availability and implementation: The SPARQL-based identifier conversion service is available without restriction at http://identifiers.org/services/sparql. Contact: sarala@ebi.ac.uk PMID:25638809

SPARQL-enabled identifier conversion with Identifiers.org.

PubMed

Wimalaratne, Sarala M; Bolleman, Jerven; Juty, Nick; Katayama, Toshiaki; Dumontier, Michel; Redaschi, Nicole; Le Novère, Nicolas; Hermjakob, Henning; Laibe, Camille

2015-06-01

On the semantic web, in life sciences in particular, data is often distributed via multiple resources. Each of these sources is likely to use their own International Resource Identifier for conceptually the same resource or database record. The lack of correspondence between identifiers introduces a barrier when executing federated SPARQL queries across life science data. We introduce a novel SPARQL-based service to enable on-the-fly integration of life science data. This service uses the identifier patterns defined in the Identifiers.org Registry to generate a plurality of identifier variants, which can then be used to match source identifiers with target identifiers. We demonstrate the utility of this identifier integration approach by answering queries across major producers of life science Linked Data. The SPARQL-based identifier conversion service is available without restriction at http://identifiers.org/services/sparql. © The Author 2015. Published by Oxford University Press.

Mining Top K Spread Sources for a Specific Topic and a Given Node.

PubMed

Liu, Weiwei; Deng, Zhi-Hong; Cao, Longbing; Xu, Xiaoran; Liu, He; Gong, Xiuwen

2015-11-01

In social networks, nodes (or users) interested in specific topics are often influenced by others. The influence is usually associated with a set of nodes rather than a single one. An interesting but challenging task for any given topic and node is to find the set of nodes that represents the source or trigger for the topic and thus identify those nodes that have the greatest influence on the given node as the topic spreads. We find that it is an NP-hard problem. This paper proposes an effective framework to deal with this problem. First, the topic propagation is represented as the Bayesian network. We then construct the propagation model by a variant of the voter model. The probability transition matrix (PTM) algorithm is presented to conduct the probability inference with the complexity O(θ(3)log2θ), while θ is the number nodes in the given graph. To evaluate the PTM algorithm, we conduct extensive experiments on real datasets. The experimental results show that the PTM algorithm is both effective and efficient.

Empirical Methods for Identifying Specific Peptide-protein Interactions for Smart Reagent Development

DTIC Science & Technology

2012-09-01

orientated immobilization of proteins,” Biotechnology Progress, 22(2), 401-405 ( 2006 ). [26] J. M. Kogot, D. A. Sarkes , I. Val-Addo et al...Empirical Methods for Identifying Specific Peptide-protein Interactions for Smart Reagent Development by Joshua M. Kogot, Deborah A. Sarkes ...Peptide-protein Interactions for Smart Reagent Development Joshua M. Kogot, Deborah A. Sarkes , Dimitra N. Stratis-Cullum, and Paul M

PM2.5-induced changes in cardiac function of hypertensive rats depend on wind direction and specific sources in Steubenville, Ohio.

PubMed

Kamal, Ali S; Rohr, Annette C; Mukherjee, Bhramar; Morishita, Masako; Keeler, Gerald J; Harkema, Jack R; Wagner, James G

2011-06-01

Increases in particulate matter less than 2.5 µm (PM(2.5)) in ambient air is linked to acute cardiovascular morbidity and mortality. Specific components and potential emission sources of PM(2.5) responsible for adverse health effects of cardiovascular function are unclear. Spontaneously hypertensive rats were implemented with radiotelemeters to record ECG responses during inhalation exposure to concentrated ambient particles (CAPs) for 13 consecutive days in Steubenville, OH. Changes in heart rate (HR) and its variability (HRV) were compared to PM(2.5) trace elements in 30-min time frames to capture acute physiological responses with real-time fluctuations in PM(2.5) composition. Using positive matrix factorization, six major source factors were identified: (i) coal/secondary, (ii) mobile sources, (iii) metal coating/processing, (iv) iron/steel manufacturing, (v) lead and (vi) incineration. Exposure-related changes in HR and HRV were dependant on winds predominately from either the northeast (NE) or southwest (SW). During SW winds, the metal processing factor was associated with increased HR, whereas factors of incineration, lead and iron/steel with NE winds were associated with decreased HR. Decreased SDNN was dominated during NE winds by the incinerator factor, and with SW winds by the metal factor. Metals and mobile source factors also had minor impacts on decreased SDNN with NE winds. Individual elemental components loaded onto these factors generally showed significant associations, although there were some discrepancies. Acute cardiovascular changes in response to ambient PM(2.5) exposure can be attributed to specific PM constituents and sources linked with incineration, metal processing, and iron/steel production.

Identifying non-point sources of endocrine active compounds and their biological impacts in freshwater lakes

USGS Publications Warehouse

Baker, Beth H.; Martinovic-Weigelt, Dalma; Ferrey, Mark L.; Barber, Larry B.; Writer, Jeffrey H.; Rosenberry, Donald O.; Kiesling, Richard L.; Lundy, James R.; Schoenfuss, Heiko L.

2014-01-01

Contaminants of emerging concern, particularly endocrine active compounds (EACs), have been identified as a threat to aquatic wildlife. However, little is known about the impact of EACs on lakes through groundwater from onsite wastewater treatment systems (OWTS). This study aims to identify specific contributions of OWTS to Sullivan Lake, Minnesota, USA. Lake hydrology, water chemistry, caged bluegill sunfish (Lepomis macrochirus), and larval fathead minnow (Pimephales promelas) exposures were used to assess whether EACs entered the lake through OWTS inflow and the resultant biological impact on fish. Study areas included two OWTS-influenced near-shore sites with native bluegill spawning habitats and two in-lake control sites without nearby EAC sources. Caged bluegill sunfish were analyzed for plasma vitellogenin concentrations, organosomatic indices, and histological pathologies. Surface and porewater was collected from each site and analyzed for EACs. Porewater was also collected for laboratory exposure of larval fathead minnow, before analysis of predator escape performance and gene expression profiles. Chemical analysis showed EACs present at low concentrations at each study site, whereas discrete variations were reported between sites and between summer and fall samplings. Body condition index and liver vacuolization of sunfish were found to differ among study sites as did gene expression in exposed larval fathead minnows. Interestingly, biological exposure data and water chemistry did not match. Therefore, although results highlight the potential impacts of seepage from OWTS, further investigation of mixture effects and life history factor as well as chemical fate is warranted.

Guiding health promotion efforts with urban Inuit: a community-specific perspective on health information sources and dissemination strategies.

PubMed

McShane, Kelly E; Smylie, Janet K; Hastings, Paul D; Martin, Carmel M

2006-01-01

To develop a community-specific perspective of health information sources and dissemination strategies of urban Inuit to better guide health promotion efforts. Through a collaborative partnership with the Tungasuvvingat Inuit Family Resource Centre, a series of key informant interviews and focus groups were conducted to gather information on specific sources of health information, strategies of health information dissemination, and overall themes in health information processes. Distinct patterns of health information sources and dissemination strategies emerged from the data. Major themes included: the importance of visual learning, community Elders, and cultural interpreters; community cohesion; and the Inuit and non-Inuit distinction. The core sources of health information are family members and sources from within the Inuit community. The principal dissemination strategy for health information was direct communication, either through one-on-one interactions or in groups. This community-specific perspective of health information sources and dissemination strategies shows substantial differences from current mainstream models of health promotion and knowledge translation. Health promotion efforts need to acknowledge the distinct health information processes of this community, and should strive to integrate existing health information sources and strategies of dissemination with those of the community.

Identifying tagging SNPs for African specific genetic variation from the African Diaspora Genome

PubMed Central

Johnston, Henry Richard; Hu, Yi-Juan; Gao, Jingjing; O’Connor, Timothy D.; Abecasis, Gonçalo R.; Wojcik, Genevieve L; Gignoux, Christopher R.; Gourraud, Pierre-Antoine; Lizee, Antoine; Hansen, Mark; Genuario, Rob; Bullis, Dave; Lawley, Cindy; Kenny, Eimear E.; Bustamante, Carlos; Beaty, Terri H.; Mathias, Rasika A.; Barnes, Kathleen C.; Qin, Zhaohui S.; Preethi Boorgula, Meher; Campbell, Monica; Chavan, Sameer; Ford, Jean G.; Foster, Cassandra; Gao, Li; Hansel, Nadia N.; Horowitz, Edward; Huang, Lili; Ortiz, Romina; Potee, Joseph; Rafaels, Nicholas; Ruczinski, Ingo; Scott, Alan F.; Taub, Margaret A.; Vergara, Candelaria; Levin, Albert M.; Padhukasahasram, Badri; Williams, L. Keoki; Dunston, Georgia M.; Faruque, Mezbah U.; Gietzen, Kimberly; Deshpande, Aniket; Grus, Wendy E.; Locke, Devin P.; Foreman, Marilyn G.; Avila, Pedro C.; Grammer, Leslie; Kim, Kwang-Youn A.; Kumar, Rajesh; Schleimer, Robert; De La Vega, Francisco M.; Shringarpure, Suyash S.; Musharoff, Shaila; Burchard, Esteban G.; Eng, Celeste; Hernandez, Ryan D.; Pino-Yanes, Maria; Torgerson, Dara G.; Szpiech, Zachary A.; Torres, Raul; Nicolae, Dan L.; Ober, Carole; Olopade, Christopher O; Olopade, Olufunmilayo; Oluwole, Oluwafemi; Arinola, Ganiyu; Song, Wei; Correa, Adolfo; Musani, Solomon; Wilson, James G.; Lange, Leslie A.; Akey, Joshua; Bamshad, Michael; Chong, Jessica; Fu, Wenqing; Nickerson, Deborah; Reiner, Alexander; Hartert, Tina; Ware, Lorraine B.; Bleecker, Eugene; Meyers, Deborah; Ortega, Victor E.; Maul, Pissamai; Maul, Trevor; Watson, Harold; Ilma Araujo, Maria; Riccio Oliveira, Ricardo; Caraballo, Luis; Marrugo, Javier; Martinez, Beatriz; Meza, Catherine; Ayestas, Gerardo; Francisco Herrera-Paz, Edwin; Landaverde-Torres, Pamela; Erazo, Said Omar Leiva; Martinez, Rosella; Mayorga, Alvaro; Mayorga, Luis F.; Mejia-Mejia, Delmy-Aracely; Ramos, Hector; Saenz, Allan; Varela, Gloria; Marina Vasquez, Olga; Ferguson, Trevor; Knight-Madden, Jennifer; Samms-Vaughan, Maureen; Wilks, Rainford J.; Adegnika, Akim; Ateba-Ngoa, Ulysse; Yazdanbakhsh, Maria

2017-01-01

A primary goal of The Consortium on Asthma among African-ancestry Populations in the Americas (CAAPA) is to develop an ‘African Diaspora Power Chip’ (ADPC), a genotyping array consisting of tagging SNPs, useful in comprehensively identifying African specific genetic variation. This array is designed based on the novel variation identified in 642 CAAPA samples of African ancestry with high coverage whole genome sequence data (~30× depth). This novel variation extends the pattern of variation catalogued in the 1000 Genomes and Exome Sequencing Projects to a spectrum of populations representing the wide range of West African genomic diversity. These individuals from CAAPA also comprise a large swath of the African Diaspora population and incorporate historical genetic diversity covering nearly the entire Atlantic coast of the Americas. Here we show the results of designing and producing such a microchip array. This novel array covers African specific variation far better than other commercially available arrays, and will enable better GWAS analyses for researchers with individuals of African descent in their study populations. A recent study cataloging variation in continental African populations suggests this type of African-specific genotyping array is both necessary and valuable for facilitating large-scale GWAS in populations of African ancestry. PMID:28429804

Identifying elements of the plumbing system beneath Kilauea Volcano, Hawaii, from the source locations of very-long-period signals

USGS Publications Warehouse

Almendros, J.; Chouet, B.; Dawson, P.; Bond, T.

2002-01-01

We analyzed 16 seismic events recorded by the Hawaiian broad-band seismic network at Kilauca Volcano during the period September 9-26, 1999. Two distinct types of event are identified based on their spectral content, very-long-period (VLP) waveform, amplitude decay pattern and particle motion. We locate the VLP signals with a method based on analyses of semblance and particle motion. Different source regions are identified for the two event types. One source region is located at depths of ~1 km beneath the northeast edge of the Halemaumau pit crater. A second region is located at depths of ~8 km below the northwest quadrant of Kilauea caldera. Our study represents the first time that such deep sources have been identified in VLP data at Kilauea. This discovery opens the possibility of obtaining a detailed image of the location and geometry of the magma plumbing system beneath this volcano based on source locations and moment tensor inversions of VLP signals recorded by a permanent, large-aperture broad-band network.

Comparative genome analysis identifies novel nucleic acid diagnostic targets for use in the specific detection of Haemophilus influenzae.

PubMed

Coughlan, Helena; Reddington, Kate; Tuite, Nina; Boo, Teck Wee; Cormican, Martin; Barrett, Louise; Smith, Terry J; Clancy, Eoin; Barry, Thomas

2015-10-01

Haemophilus influenzae is recognised as an important human pathogen associated with invasive infections, including bloodstream infection and meningitis. Currently used molecular-based diagnostic assays lack specificity in correctly detecting and identifying H. influenzae. As such, there is a need to develop novel diagnostic assays for the specific identification of H. influenzae. Whole genome comparative analysis was performed to identify putative diagnostic targets, which are unique in nucleotide sequence to H. influenzae. From this analysis, we identified 2H. influenzae putative diagnostic targets, phoB and pstA, for use in real-time PCR diagnostic assays. Real-time PCR diagnostic assays using these targets were designed and optimised to specifically detect and identify all 55H. influenzae strains tested. These novel rapid assays can be applied to the specific detection and identification of H. influenzae for use in epidemiological studies and could also enable improved monitoring of invasive disease caused by these bacteria. Copyright © 2015 Elsevier Inc. All rights reserved.

Interrogator system for identifying electrical circuits

DOEpatents

Jatko, W.B.; McNeilly, D.R.

1988-04-12

A system for interrogating electrical leads to correctly ascertain the identity of equipment attached to remote ends of the leads is disclosed. The system includes a source of a carrier signal generated in a controller/receiver to be sent over the leads and an identifier unit at the equipment. The identifier is activated by command of the carrier and uses a portion of the carrier to produce a supply voltage. Each identifier is uniquely programmed for a specific piece of equipment, and causes the impedance of the circuit to be modified whereby the carrier signal is modulated according to that program. The modulation can be amplitude, frequency or phase modulation. A demodulator in the controller/receiver analyzes the modulated carrier signal, and if a verified signal is recognized displays and/or records the information. This information can be utilized in a computer system to prepare a wiring diagram of the electrical equipment attached to specific leads. Specific circuit values are given for amplitude modulation, and the system is particularly described for use with thermocouples. 6 figs.

Interrogator system for identifying electrical circuits

DOEpatents

Jatko, William B.; McNeilly, David R.

1988-01-01

A system for interrogating electrical leads to correctly ascertain the identity of equipment attached to remote ends of the leads. The system includes a source of a carrier signal generated in a controller/receiver to be sent over the leads and an identifier unit at the equipment. The identifier is activated by command of the carrier and uses a portion of the carrier to produce a supply voltage. Each identifier is uniquely programmed for a specific piece of equipment, and causes the impedance of the circuit to be modified whereby the carrier signal is modulated according to that program. The modulation can be amplitude, frequency or phase modulation. A demodulator in the controller/receiver analyzes the modulated carrier signal, and if a verified signal is recognized displays and/or records the information. This information can be utilized in a computer system to prepare a wiring diagram of the electrical equipment attached to specific leads. Specific circuit values are given for amplitude modulation, and the system is particularly described for use with thermocouples.

Identifying fine sediment sources to alleviate flood risk caused by fine sediments through catchment connectivity analysis

NASA Astrophysics Data System (ADS)

Twohig, Sarah; Pattison, Ian; Sander, Graham

2017-04-01

Fine sediment poses a significant threat to UK river systems in terms of vegetation, aquatic habitats and morphology. Deposition of fine sediment onto the river bed reduces channel capacity resulting in decreased volume to contain high flow events. Once the in channel problem has been identified managers are under pressure to sustainably mitigate flood risk. With climate change and land use adaptations increasing future pressures on river catchments it is important to consider the connectivity of fine sediment throughout the river catchment and its influence on channel capacity, particularly in systems experiencing long term aggradation. Fine sediment erosion is a continuing concern in the River Eye, Leicestershire. The predominately rural catchment has a history of flooding within the town of Melton Mowbray. Fine sediment from agricultural fields has been identified as a major contributor of sediment delivery into the channel. Current mitigation measures are not sustainable or successful in preventing the continuum of sediment throughout the catchment. Identifying the potential sources and connections of fine sediment would provide insight into targeted catchment management. 'Sensitive Catchment Integrated Modelling Analysis Platforms' (SCIMAP) is a tool often used by UK catchment managers to identify potential sources and routes of sediment within a catchment. SCIMAP is a risk based model that combines hydrological (rainfall) and geomorphic controls (slope, land cover) to identify the risk of fine sediment being transported from source into the channel. A desktop version of SCIMAP was run for the River Eye at a catchment scale using 5m terrain, rainfall and land cover data. A series of SCIMAP model runs were conducted changing individual parameters to determine the sensitivity of the model. Climate Change prediction data for the catchment was used to identify potential areas of future connectivity and erosion risk for catchment managers. The results have been

NOVEL STATISTICAL APPROACH TO EVALUATE SPATIAL DISTRIBUTION OF PM FROM SPECIFIC SOURCE CATEGORIES

EPA Science Inventory

This task addresses aspects of NRC recommendations 10A and 10B. Positive matrix factorization (PMF) is a new statistical techniques for determining the daily contribution to PM mass of specific source categories (auto exhaust, smelters, suspended soil, secondary sulfate, etc.). I...

Specialty-specific multi-source feedback: assuring validity, informing training.

PubMed

Davies, Helena; Archer, Julian; Bateman, Adrian; Dewar, Sandra; Crossley, Jim; Grant, Janet; Southgate, Lesley

2008-10-01

The white paper 'Trust, Assurance and Safety: the Regulation of Health Professionals in the 21st Century' proposes a single, generic multi-source feedback (MSF) instrument in the UK. Multi-source feedback was proposed as part of the assessment programme for Year 1 specialty training in histopathology. An existing instrument was modified following blueprinting against the histopathology curriculum to establish content validity. Trainees were also assessed using an objective structured practical examination (OSPE). Factor analysis and correlation between trainees' OSPE performance and the MSF were used to explore validity. All 92 trainees participated and the assessor response rate was 93%. Reliability was acceptable with eight assessors (95% confidence interval 0.38). Factor analysis revealed two factors: 'generic' and 'histopathology'. Pearson correlation of MSF scores with OSPE performances was 0.48 (P = 0.001) and the histopathology factor correlated more highly (histopathology r = 0.54, generic r = 0.42; t = - 2.76, d.f. = 89, P < 0.01). Trainees scored least highly in relation to ability to use histopathology to solve clinical problems (mean = 4.39) and provision of good reports (mean = 4.39). Three of six doctors whose means were < 4.0 received free text comments about report writing. There were 83 forms with aggregate scores of < 4. Of these, 19.2% included comments about report writing. Specialty-specific MSF is feasible and achieves satisfactory reliability. The higher correlation of the 'histopathology' factor with the OSPE supports validity. This paper highlights the importance of validating an MSF instrument within the specialty-specific context as, in addition to assuring content validity, the PATH-SPRAT (Histopathology-Sheffield Peer Review Assessment Tool) also demonstrates the potential to inform training as part of a quality improvement model.

Identifying calcium sources at an acid deposition-impacted spruce forest: a strontium isotope, alkaline earth element multi-tracer approach

Treesearch

Thomas D. Bullen; Scott W. Bailey

2005-01-01

Depletion of calcium from forest soils has important implications for forest productivity and health. Ca is available to fine feeder roots from a number of soil organic and mineral sources. but identifying the primary source or changes of sources in response to environmental change is problematic. We used strontium isotope and alkaline earth element concentration...

40 CFR 268.38 - Waste specific prohibitions-newly identified organic toxicity characteristic wastes and newly...

Code of Federal Regulations, 2014 CFR

2014-07-01

... identified organic toxicity characteristic wastes and newly listed coke by-product and chlorotoluene... specific prohibitions—newly identified organic toxicity characteristic wastes and newly listed coke by... numbers F037, F038, K107-K112, K117, K118, K123-K126, K131, K132, K136, U328, U353, U359, and soil and...

40 CFR 268.38 - Waste specific prohibitions-newly identified organic toxicity characteristic wastes and newly...

Code of Federal Regulations, 2013 CFR

2013-07-01

... identified organic toxicity characteristic wastes and newly listed coke by-product and chlorotoluene... specific prohibitions—newly identified organic toxicity characteristic wastes and newly listed coke by... numbers F037, F038, K107-K112, K117, K118, K123-K126, K131, K132, K136, U328, U353, U359, and soil and...

40 CFR 268.38 - Waste specific prohibitions-newly identified organic toxicity characteristic wastes and newly...

Code of Federal Regulations, 2012 CFR

2012-07-01

... identified organic toxicity characteristic wastes and newly listed coke by-product and chlorotoluene... specific prohibitions—newly identified organic toxicity characteristic wastes and newly listed coke by... numbers F037, F038, K107-K112, K117, K118, K123-K126, K131, K132, K136, U328, U353, U359, and soil and...

40 CFR 268.38 - Waste specific prohibitions-newly identified organic toxicity characteristic wastes and newly...

Code of Federal Regulations, 2011 CFR

2011-07-01

... identified organic toxicity characteristic wastes and newly listed coke by-product and chlorotoluene... specific prohibitions—newly identified organic toxicity characteristic wastes and newly listed coke by... numbers F037, F038, K107-K112, K117, K118, K123-K126, K131, K132, K136, U328, U353, U359, and soil and...

25 CFR 115.702 - What specific sources of money will be accepted for deposit into a trust account?

Code of Federal Regulations, 2010 CFR

2010-04-01

... 25 Indians 1 2010-04-01 2010-04-01 false What specific sources of money will be accepted for deposit into a trust account? 115.702 Section 115.702 Indians BUREAU OF INDIAN AFFAIRS, DEPARTMENT OF THE INTERIOR FINANCIAL ACTIVITIES TRUST FUNDS FOR TRIBES AND INDIVIDUAL INDIANS Trust Fund Accounts: General Information § 115.702 What specific sources...

Identifying potential sources of Sudan I contamination in Capsicum fruits over its growth period.

PubMed

Wu, Naiying; Gao, Wei; Zhou, Li; Lian, Yunhe; Li, Fengfei; Han, Wenjie

2015-04-15

Sudan dyes in spices are often assumed to arise from cross-contamination or malicious addition. Here, experiments were carried out to identify the potential source of Sudan I-IV in Capsicum fruits through investigation of their contents in native Capsicum tissues, soils and associated agronomic materials. Sudan II-IV was not detected in any of the tested samples. Sudan I was found in almost all samples except for the mulching film. Sudan I concentrations decreased from stems to leaves and then to fruits or roots. Sudan I levels in soils were significantly elevated by vegetation treatment. These results exclude the possibility of soil as the main source for Sudan I contamination in Capsicum fruits. Further study found out pesticide and fertilizer constitutes the major source of Sudan I contamination. This work represents a preliminary step for a detailed Sudan I assessment to support Capsicum management and protection in the studied region. Copyright © 2014 Elsevier Ltd. All rights reserved.

Specific factors influencing information system/information and communication technology sourcing strategies in healthcare facilities.

PubMed

Potančok, Martin; Voříšek, Jiří

2016-09-01

Healthcare facilities use a number of information system/information and communication technologies. Each healthcare facility faces a need to choose sourcing strategies most suitable to ensure provision of information system/information and communication technology services, processes and resources. Currently, it is possible to observe an expansion of sourcing possibilities in healthcare informatics, which creates new requirements for sourcing strategies. Thus, the aim of this article is to identify factors influencing information system/information and communication technology sourcing strategies in healthcare facilities. The identification was based on qualitative research, namely, a case study. This study provides a set of internal and external factors with their impact levels. The findings also show that not enough attention is paid to these factors during decision-making. © The Author(s) 2015.

Using an epiphytic moss to identify previously unknown sources of atmospheric cadmium pollution.

PubMed

Donovan, Geoffrey H; Jovan, Sarah E; Gatziolis, Demetrios; Burstyn, Igor; Michael, Yvonne L; Amacher, Michael C; Monleon, Vicente J

2016-07-15

Urban networks of air-quality monitors are often too widely spaced to identify sources of air pollutants, especially if they do not disperse far from emission sources. The objectives of this study were to test the use of moss bio-indicators to develop a fine-scale map of atmospherically-derived cadmium and to identify the sources of cadmium in a complex urban setting. We collected 346 samples of the moss Orthotrichum lyellii from deciduous trees in December, 2013 using a modified randomized grid-based sampling strategy across Portland, Oregon. We estimated a spatial linear model of moss cadmium levels and predicted cadmium on a 50m grid across the city. Cadmium levels in moss were positively correlated with proximity to two stained-glass manufacturers, proximity to the Oregon-Washington border, and percent industrial land in a 500m buffer, and negatively correlated with percent residential land in a 500m buffer. The maps showed very high concentrations of cadmium around the two stained-glass manufacturers, neither of which were known to environmental regulators as cadmium emitters. In addition, in response to our findings, the Oregon Department of Environmental Quality placed an instrumental monitor 120m from the larger stained-glass manufacturer in October, 2015. The monthly average atmospheric cadmium concentration was 29.4ng/m(3), which is 49 times higher than Oregon's benchmark of 0.6ng/m(3), and high enough to pose a health risk from even short-term exposure. Both stained-glass manufacturers voluntarily stopped using cadmium after the monitoring results were made public, and the monthly average cadmium levels precipitously dropped to 1.1ng/m(3) for stained-glass manufacturer #1 and 0.67ng/m(3) for stained-glass manufacturer #2. Published by Elsevier B.V.

Efficacy of ACL injury risk screening methods in identifying high-risk landing patterns during a sport-specific task.

PubMed

Fox, A S; Bonacci, J; McLean, S G; Saunders, N

2017-05-01

Screening methods sensitive to movement strategies that increase anterior cruciate ligament (ACL) loads are likely to be effective in identifying athletes at-risk of ACL injury. Current ACL injury risk screening methods are yet to be evaluated for their ability to identify athletes' who exhibit high-risk lower limb mechanics during sport-specific maneuvers associated with ACL injury occurrences. The purpose of this study was to examine the efficacy of two ACL injury risk screening methods in identifying high-risk lower limb mechanics during a sport-specific landing task. Thirty-two female athletes were screened using the Landing Error Scoring System (LESS) and Tuck Jump Assessment. Participants' also completed a sport-specific landing task, during which three-dimensional kinematic and kinetic data were collected. One-dimensional statistical parametric mapping was used to examine the relationships between screening method scores, and the three-dimensional hip and knee joint rotation and moment data from the sport-specific landing. Higher LESS scores were associated with reduced knee flexion from 30 to 57 ms after initial contact (P = 0.003) during the sport-specific landing; however, no additional relationships were found. These findings suggest the LESS and Tuck Jump Assessment may have minimal applicability in identifying athletes' who exhibit high-risk landing postures in the sport-specific task examined. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

A spectroscopic tool for identifying sources of origin for materials of military interest

NASA Astrophysics Data System (ADS)

Miziolek, Andrzej W.; De Lucia, Frank C.

2014-05-01

There is a need to identify the source of origin for many items of military interest, including ammunition and weapons that may be circulated and traded in illicit markets. Both fieldable systems (man-portable or handheld) as well as benchtop systems in field and home base laboratories are desired for screening and attribution purposes. Laser Induced Breakdown Spectroscopy (LIBS) continues to show significant capability as a promising new tool for materials identification, matching, and provenance. With the use of the broadband, high resolution spectrometer systems, the LIBS devices can not only determine the elemental inventory of the sample, but they are also capable of elemental fingerprinting to signify sources of origin of various materials. We present the results of an initial study to differentiate and match spent cartridges from different manufacturers and countries. We have found that using Partial Least Squares Discriminant Analysis (PLS-DA) we are able to achieve on average 93.3% True Positives and 5.3% False Positives. These results add to the large body of publications that have demonstrated that LIBS is a particularly suitable tool for source of origin determinations.

Identifying and characterizing major emission point sources as a basis for geospatial distribution of mercury emissions inventories

NASA Astrophysics Data System (ADS)

Steenhuisen, Frits; Wilson, Simon J.

2015-07-01

Mercury is a global pollutant that poses threats to ecosystem and human health. Due to its global transport, mercury contamination is found in regions of the Earth that are remote from major emissions areas, including the Polar regions. Global anthropogenic emission inventories identify important sectors and industries responsible for emissions at a national level; however, to be useful for air transport modelling, more precise information on the locations of emission is required. This paper describes the methodology applied, and the results of work that was conducted to assign anthropogenic mercury emissions to point sources as part of geospatial mapping of the 2010 global anthropogenic mercury emissions inventory prepared by AMAP/UNEP. Major point-source emission sectors addressed in this work account for about 850 tonnes of the emissions included in the 2010 inventory. This work allocated more than 90% of these emissions to some 4600 identified point source locations, including significantly more point source locations in Africa, Asia, Australia and South America than had been identified during previous work to geospatially-distribute the 2005 global inventory. The results demonstrate the utility and the limitations of using existing, mainly public domain resources to accomplish this work. Assumptions necessary to make use of selected online resources are discussed, as are artefacts that can arise when these assumptions are applied to assign (national-sector) emissions estimates to point sources in various countries and regions. Notwithstanding the limitations of the available information, the value of this procedure over alternative methods commonly used to geo-spatially distribute emissions, such as use of 'proxy' datasets to represent emissions patterns, is illustrated. Improvements in information that would facilitate greater use of these methods in future work to assign emissions to point-sources are discussed. These include improvements to both national

Speedup computation of HD-sEMG signals using a motor unit-specific electrical source model.

PubMed

Carriou, Vincent; Boudaoud, Sofiane; Laforet, Jeremy

2018-01-23

Nowadays, bio-reliable modeling of muscle contraction is becoming more accurate and complex. This increasing complexity induces a significant increase in computation time which prevents the possibility of using this model in certain applications and studies. Accordingly, the aim of this work is to significantly reduce the computation time of high-density surface electromyogram (HD-sEMG) generation. This will be done through a new model of motor unit (MU)-specific electrical source based on the fibers composing the MU. In order to assess the efficiency of this approach, we computed the normalized root mean square error (NRMSE) between several simulations on single generated MU action potential (MUAP) using the usual fiber electrical sources and the MU-specific electrical source. This NRMSE was computed for five different simulation sets wherein hundreds of MUAPs are generated and summed into HD-sEMG signals. The obtained results display less than 2% error on the generated signals compared to the same signals generated with fiber electrical sources. Moreover, the computation time of the HD-sEMG signal generation model is reduced to about 90% compared to the fiber electrical source model. Using this model with MU electrical sources, we can simulate HD-sEMG signals of a physiological muscle (hundreds of MU) in less than an hour on a classical workstation. Graphical Abstract Overview of the simulation of HD-sEMG signals using the fiber scale and the MU scale. Upscaling the electrical source to the MU scale reduces the computation time by 90% inducing only small deviation of the same simulated HD-sEMG signals.

The Experiences of Parents with Adolescents Identified as Having a Specific Learning Disability

ERIC Educational Resources Information Center

Seals, Linda J.

2010-01-01

Of the 6.6 million children in the United States who were deemed in 2008 to have a disability that required special instruction, over 39% were classified as specific learning disabled (SLD). This figure translates into a high number of people who are parenting a child identified as having a SLD. Bronfenbrenner's theory of the ecology of human…

COMPETITIVE METAGENOMIC DNA HYBRIDIZATION IDENTIFIES HOST-SPECIFIC MICROBIAL GENETIC MARKERS IN COW FECAL SAMPLES

EPA Science Inventory

Several PCR methods have recently been developed to identify fecal contamination in surface waters. In all cases, researchers have relied on one gene or one microorganism for selection of host specific markers. Here, we describe the application of a genome fragment enrichment met...

COMPETITIVE METAGENOMIC DNA HYBRIDIZATION IDENTIFIES HOST-SPECIFIC GENETIC MARKERS IN CATTLE FECAL SAMPLES - ABSTRACT

EPA Science Inventory

Several PCR methods have recently been developed to identify fecal contamination in surface waters. In all cases, researchers have relied on one gene or one microorganism for selection of host specific markers. Here, we describe the application of a genome fragment enrichment met...

Application of Think Aloud Protocols for Examining and Confirming Sources of Differential Item Functioning Identified by Expert Reviews

ERIC Educational Resources Information Center

Ercikan, Kadriye; Arim, Rubab; Law, Danielle; Domene, Jose; Gagnon, France; Lacroix, Serge

2010-01-01

This paper demonstrates and discusses the use of think aloud protocols (TAPs) as an approach for examining and confirming sources of differential item functioning (DIF). The TAPs are used to investigate to what extent surface characteristics of the items that are identified by expert reviews as sources of DIF are supported by empirical evidence…

Source and specificity of chemical cues mediating shelter preference of Caribbean spiny lobsters (Panulirus argus).

PubMed

Horner, Amy J; Nickles, Scott P; Weissburg, Marc J; Derby, Charles D

2006-10-01

Caribbean spiny lobsters display a diversity of social behaviors, one of the most prevalent of which is gregarious diurnal sheltering. Previous research has demonstrated that shelter selection is chemically mediated, but the source of release and the identity of the aggregation signal are unknown. In this study, we investigated the source and specificity of the aggregation signal in Caribbean spiny lobsters, Panulirus argus. We developed a relatively rapid test of shelter choice in a 5000-l laboratory flume that simulated flow conditions in the spiny lobster's natural environment, and used it to examine the shelter preference of the animals in response to a variety of odorants. We found that both males and females associated preferentially with shelters emanating conspecific urine of either sex, but not with shelters emanating seawater, food odors, or the scent of a predatory octopus. These results demonstrate specificity in the cues mediating sheltering behavior and show that urine is at least one source of the aggregation signal.

Inverse modelling of fluvial sediment connectivity identifies characteristics and spatial distribution of sediment sources in a large river network.

NASA Astrophysics Data System (ADS)

Schmitt, R. J. P.; Bizzi, S.; Kondolf, G. M.; Rubin, Z.; Castelletti, A.

2016-12-01

Field and laboratory evidence indicates that the spatial distribution of transport in both alluvial and bedrock rivers is an adaptation to sediment supply. Sediment supply, in turn, depends on spatial distribution and properties (e.g., grain sizes and supply rates) of individual sediment sources. Analyzing the distribution of transport capacity in a river network could hence clarify the spatial distribution and properties of sediment sources. Yet, challenges include a) identifying magnitude and spatial distribution of transport capacity for each of multiple grain sizes being simultaneously transported, and b) estimating source grain sizes and supply rates, both at network scales. Herein, we approach the problem of identifying the spatial distribution of sediment sources and the resulting network sediment fluxes in a major, poorly monitored tributary (80,000 km2) of the Mekong. Therefore, we apply the CASCADE modeling framework (Schmitt et al. (2016)). CASCADE calculates transport capacities and sediment fluxes for multiple grainsizes on the network scale based on remotely-sensed morphology and modelled hydrology. CASCADE is run in an inverse Monte Carlo approach for 7500 random initializations of source grain sizes. In all runs, supply of each source is inferred from the minimum downstream transport capacity for the source grain size. Results for each realization are compared to sparse available sedimentary records. Only 1 % of initializations reproduced the sedimentary record. Results for these realizations revealed a spatial pattern in source supply rates, grain sizes, and network sediment fluxes that correlated well with map-derived patterns in lithology and river-morphology. Hence, we propose that observable river hydro-morphology contains information on upstream source properties that can be back-calculated using an inverse modeling approach. Such an approach could be coupled to more detailed models of hillslope processes in future to derive integrated models

Diagnostic Air Quality Model Evaluation of Source-Specific Primary and Secondary Fine Particulate Carbon

EPA Science Inventory

Ambient measurements of 78 source-specific tracers of primary and secondary carbonaceous fine particulate matter collected at four midwestern United States locations over a full year (March 2004–February 2005) provided an unprecedented opportunity to diagnostically evaluate...

A Method for Identifying Pollution Sources of Heavy Metals and PAH for a Risk-Based Management of a Mediterranean Harbour

PubMed Central

Moranda, Arianna

2017-01-01

A procedure for assessing harbour pollution by heavy metals and PAH and the possible sources of contamination is proposed. The procedure is based on a ratio-matching method applied to the results of principal component analysis (PCA), and it allows discrimination between point and nonpoint sources. The approach can be adopted when many sources of pollution can contribute in a very narrow coastal ecosystem, both internal and outside but close to the harbour, and was used to identify the possible point sources of contamination in a Mediterranean Harbour (Port of Vado, Savona, Italy). 235 sediment samples were collected in 81 sampling points during four monitoring campaigns and 28 chemicals were searched for within the collected samples. PCA of total samples allowed the assessment of 8 main possible point sources, while the refining ratio-matching identified 1 sampling point as a possible PAH source, 2 sampling points as Cd point sources, and 3 sampling points as C > 12 point sources. By a map analysis it was possible to assess two internal sources of pollution directly related to terminals activity. The study is the prosecution of a previous work aimed at assessing Savona-Vado Harbour pollution levels and suggested strategies to regulate the harbour activities. PMID:29270328

A Method for Identifying Pollution Sources of Heavy Metals and PAH for a Risk-Based Management of a Mediterranean Harbour.

PubMed

Paladino, Ombretta; Moranda, Arianna; Seyedsalehi, Mahdi

2017-01-01

A procedure for assessing harbour pollution by heavy metals and PAH and the possible sources of contamination is proposed. The procedure is based on a ratio-matching method applied to the results of principal component analysis (PCA), and it allows discrimination between point and nonpoint sources. The approach can be adopted when many sources of pollution can contribute in a very narrow coastal ecosystem, both internal and outside but close to the harbour, and was used to identify the possible point sources of contamination in a Mediterranean Harbour (Port of Vado, Savona, Italy). 235 sediment samples were collected in 81 sampling points during four monitoring campaigns and 28 chemicals were searched for within the collected samples. PCA of total samples allowed the assessment of 8 main possible point sources, while the refining ratio-matching identified 1 sampling point as a possible PAH source, 2 sampling points as Cd point sources, and 3 sampling points as C > 12 point sources. By a map analysis it was possible to assess two internal sources of pollution directly related to terminals activity. The study is the prosecution of a previous work aimed at assessing Savona-Vado Harbour pollution levels and suggested strategies to regulate the harbour activities.

Identifying pollution sources and predicting urban air quality using ensemble learning methods

NASA Astrophysics Data System (ADS)

Singh, Kunwar P.; Gupta, Shikha; Rai, Premanjali

2013-12-01

In this study, principal components analysis (PCA) was performed to identify air pollution sources and tree based ensemble learning models were constructed to predict the urban air quality of Lucknow (India) using the air quality and meteorological databases pertaining to a period of five years. PCA identified vehicular emissions and fuel combustion as major air pollution sources. The air quality indices revealed the air quality unhealthy during the summer and winter. Ensemble models were constructed to discriminate between the seasonal air qualities, factors responsible for discrimination, and to predict the air quality indices. Accordingly, single decision tree (SDT), decision tree forest (DTF), and decision treeboost (DTB) were constructed and their generalization and predictive performance was evaluated in terms of several statistical parameters and compared with conventional machine learning benchmark, support vector machines (SVM). The DT and SVM models discriminated the seasonal air quality rendering misclassification rate (MR) of 8.32% (SDT); 4.12% (DTF); 5.62% (DTB), and 6.18% (SVM), respectively in complete data. The AQI and CAQI regression models yielded a correlation between measured and predicted values and root mean squared error of 0.901, 6.67 and 0.825, 9.45 (SDT); 0.951, 4.85 and 0.922, 6.56 (DTF); 0.959, 4.38 and 0.929, 6.30 (DTB); 0.890, 7.00 and 0.836, 9.16 (SVR) in complete data. The DTF and DTB models outperformed the SVM both in classification and regression which could be attributed to the incorporation of the bagging and boosting algorithms in these models. The proposed ensemble models successfully predicted the urban ambient air quality and can be used as effective tools for its management.

Using artificial sweeteners to identify contamination sources and infiltration zones in a coupled river-aquifer system

NASA Astrophysics Data System (ADS)

Bichler, Andrea; Muellegger, Christian; Hofmann, Thilo

2014-05-01

In shallow or unconfined aquifers the infiltration of contaminated river water might be a major threat to groundwater quality. Thus, the identification of possible contamination sources in coupled surface- and groundwater systems is of paramount importance to ensure water quality. Micropollutants like artificial sweeteners are promising markers for domestic waste water in natural water bodies. Compounds, such as artificial sweeteners, might enter the aquatic environment via discharge of waste water treatment plants, leaky sewer systems or septic tanks and are ubiquitously found in waste water receiving waters. The hereby presented field study aims at the (1) identification of contamination sources and (2) delineation of infiltration zones in a connected river-aquifer system. River bank filtrate in the groundwater body was assessed qualitatively and quantitatively using a combined approach of hydrochemical analysis and artificial sweeteners (acesulfame ACE) as waste water markers. The investigated aquifer lies within a mesoscale alpine head water catchment and is used for drinking water production. It is hypothesized that a large proportion of the groundwater flux originates from bank filtrate of a nearby losing stream. Water sampling campaigns in March and July 2012 confirmed the occurrence of artificial sweeteners at the investigated site. The municipal waste water treatment plant was identified as point-source for ACE in the river network. In the aquifer ACE was present in more than 80% of the monitoring wells. In addition, water samples were classified according to their hydrochemical composition, identifying two predominant types of water in the aquifer: (1) groundwater influenced by bank filtrate and (2) groundwater originating from local recharge. In combination with ACE concentrations a third type of water could be discriminated: (3) groundwater influence by bank filtrate but infiltrated prior to the waste water treatment plant. Moreover, the presence of ACE

Identifying nitrogen sources to thermal tide pools in Kapoho, Hawai'i, U.S.A, using a multi-stable isotope approach.

PubMed

Wiegner, Tracy N; Mokiao-Lee, Ambyr U; Johnson, Erik E

2016-02-15

Nitrogen (N) enrichment often results in coastal eutrophication, even in remote areas like Hawai'i. Therefore, determining N sources to coastal waters is important for their management. This study identified N sources to tide pools in Kapoho, Hawai'i, and determined their relative importance using three stable isotopes (δ(15)N, δ(18)O, δ(11)B). Surface waters and macroalgal tissues were collected along 100-m onshore-offshore transects in areas of high groundwater input for three months at low tide. Water samples from possible N sources were also collected. Mixing model output, along with macroalgal δ(15)N values, indicated that agriculture soil (34%) was the largest anthropogenic N source followed by sewage (27%). These findings suggest that more effective fertilizer application techniques and upgrading sewage treatment systems can minimize N leaching into groundwater. Overall, our multi-stable isotope approach for identifying N sources was successful and may be useful in other coastal waters. Copyright © 2015 Elsevier Ltd. All rights reserved.

CloudNeo: a cloud pipeline for identifying patient-specific tumor neoantigens.

PubMed

Bais, Preeti; Namburi, Sandeep; Gatti, Daniel M; Zhang, Xinyu; Chuang, Jeffrey H

2017-10-01

We present CloudNeo, a cloud-based computational workflow for identifying patient-specific tumor neoantigens from next generation sequencing data. Tumor-specific mutant peptides can be detected by the immune system through their interactions with the human leukocyte antigen complex, and neoantigen presence has recently been shown to correlate with anti T-cell immunity and efficacy of checkpoint inhibitor therapy. However computing capabilities to identify neoantigens from genomic sequencing data are a limiting factor for understanding their role. This challenge has grown as cancer datasets become increasingly abundant, making them cumbersome to store and analyze on local servers. Our cloud-based pipeline provides scalable computation capabilities for neoantigen identification while eliminating the need to invest in local infrastructure for data transfer, storage or compute. The pipeline is a Common Workflow Language (CWL) implementation of human leukocyte antigen (HLA) typing using Polysolver or HLAminer combined with custom scripts for mutant peptide identification and NetMHCpan for neoantigen prediction. We have demonstrated the efficacy of these pipelines on Amazon cloud instances through the Seven Bridges Genomics implementation of the NCI Cancer Genomics Cloud, which provides graphical interfaces for running and editing, infrastructure for workflow sharing and version tracking, and access to TCGA data. The CWL implementation is at: https://github.com/TheJacksonLaboratory/CloudNeo. For users who have obtained licenses for all internal software, integrated versions in CWL and on the Seven Bridges Cancer Genomics Cloud platform (https://cgc.sbgenomics.com/, recommended version) can be obtained by contacting the authors. jeff.chuang@jax.org. Supplementary data are available at Bioinformatics online. © The Author(s) 2017. Published by Oxford University Press.

Candidates source regions of martian meteorites as identified by OMEGA/MEx

NASA Astrophysics Data System (ADS)

Ody, A.; Poulet, F.; Quantin, C.; Bibring, J.-P.; Bishop, J. L.; Dyar, M. D.

2015-09-01

The objective of this study is to identify and map spectral analogues of some key martian meteorites (basaltic shergottites Los Angeles, Shergotty, QUE 94201, lherzolitic shergottite ALH A77005, Nakhla, Chassigny and the orthopyroxenite ALH 84001) in order to localize terrain candidates for their source regions. We develop a best fit procedure to reproduce the near-infrared (NIR) spectral properties of the martian surface as seen by the hyperspectral imaging spectrometer OMEGA/MEx from the NIR spectra of the martian meteorites. The fitting process is tested and validated, and Root Mean Square (RMS) global maps for each meteorite are obtained. It is found that basaltic shergottites have NIR spectral properties the most representative of the martian surface with the best spectral analogues found in early Hesperian volcanic provinces. Sites with spectral properties similar to those of ALH A77005 are scarce. They are mainly localized in olivine-bearing regions such as Nili Fossae and small Noachian/early Hesperian terrains. The only plausible source region candidate for Chassigny is the Nili Patera caldera dated to 1.6 Ga. Widespread spectral analogues for the ALH 84001 meteorite are found northeast of Syrtis Major and northwest of the Hellas basin. While this distribution is in agreement with the low-calcium-pyroxene-rich composition and old age (4.1 Ga) of this meteorite, the modal mineralogy of these candidates is not consistent with that of this meteorite. No convincing spectral analogue is found for the Amazonian-aged Nakhla meteorite suggesting that its olivine/high-calcium-pyroxene-rich composition could be representative of the Amazonian terrains buried under dust. Finally, some young rayed craters are proposed as possible candidates for source craters of the studied martian meteorites.

Sensitivity of WRF-chem predictions to dust source function specification in West Asia

NASA Astrophysics Data System (ADS)

Nabavi, Seyed Omid; Haimberger, Leopold; Samimi, Cyrus

2017-02-01

Dust storms tend to form in sparsely populated areas covered by only few observations. Dust source maps, known as source functions, are used in dust models to allocate a certain potential of dust release to each place. Recent research showed that the well known Ginoux source function (GSF), currently used in Weather Research and Forecasting Model coupled with Chemistry (WRF-chem), exhibits large errors over some regions in West Asia, particularly near the IRAQ/Syrian border. This study aims to improve the specification of this critical part of dust forecasts. A new source function based on multi-year analysis of satellite observations, called West Asia source function (WASF), is therefore proposed to raise the quality of WRF-chem predictions in the region. WASF has been implemented in three dust schemes of WRF-chem. Remotely sensed and ground-based observations have been used to verify the horizontal and vertical extent and location of simulated dust clouds. Results indicate that WRF-chem performance is significantly improved in many areas after the implementation of WASF. The modified runs (long term simulations over the summers 2008-2012, using nudging) have yielded an average increase of Spearman correlation between observed and forecast aerosol optical thickness by 12-16 percent points compared to control runs with standard source functions. They even outperform MACC and DREAM dust simulations over many dust source regions. However, the quality of the forecasts decreased with distance from sources, probably due to deficiencies in the transport and deposition characteristics of the forecast model in these areas.

[Groundwater organic pollution source identification technology system research and application].

PubMed

Wang, Xiao-Hong; Wei, Jia-Hua; Cheng, Zhi-Neng; Liu, Pei-Bin; Ji, Yi-Qun; Zhang, Gan

2013-02-01

Groundwater organic pollutions are found in large amount of locations, and the pollutions are widely spread once onset; which is hard to identify and control. The key process to control and govern groundwater pollution is how to control the sources of pollution and reduce the danger to groundwater. This paper introduced typical contaminated sites as an example; then carried out the source identification studies and established groundwater organic pollution source identification system, finally applied the system to the identification of typical contaminated sites. First, grasp the basis of the contaminated sites of geological and hydrogeological conditions; determine the contaminated sites characteristics of pollutants as carbon tetrachloride, from the large numbers of groundwater analysis and test data; then find the solute transport model of contaminated sites and compound-specific isotope techniques. At last, through groundwater solute transport model and compound-specific isotope technology, determine the distribution of the typical site of organic sources of pollution and pollution status; invest identified potential sources of pollution and sample the soil to analysis. It turns out that the results of two identified historical pollution sources and pollutant concentration distribution are reliable. The results provided the basis for treatment of groundwater pollution.

IDENTIFYING COMPOUNDS USING SOURCE CID ON AN ORTHOGONAL ACCELERATION TIME-OF-FLIGHT MASS SPECTROMETER

EPA Science Inventory

Exact mass libraries of ESI and APCI mass spectra are not commercially available In-house libraries are dependent on CID parameters and are instrument specific. The ability to identify compounds without reliance on mass spectral libraries is therefore more crucial for liquid sam...

Historical sources of black carbon identified by PAHs and δ13C in Sanjiang Plain of Northeastern China

NASA Astrophysics Data System (ADS)

Gao, Chuanyu; Liu, Hanxiang; Cong, Jinxin; Han, Dongxue; Zhao, Winston; Lin, Qianxin; Wang, Guoping

2018-05-01

Black carbon (BC), the byproduct of incomplete combustion of fossil fuels and biomass can be stored in soil for a long time and potentially archive changes in natural and human activities. Increasing amounts of BC has been produced from human activities during the past 150 years and has influenced global climate change and carbon cycle. Identifying historical BC sources is important in knowing how historical human activities influenced BC and BC transportation processes in the atmosphere. In this study, PAH components and δ13C-BC in peatland in the Sanjiang Plain were used for identifying and verifying regional BC sources during the last 150 years. Results showed that environment-unfriendly industry developed at the end of the 1950s produced a great amount of BC and contributed the most BC in this period. In other periods, however, BC in the Sanjiang Plain was mainly produced from incomplete biomass burning before the 1990s; particularly, slash-and-burn of pastures and forests during regional reclamation periods between the 1960s and 1980s produced a huge amount of biomass burning BC, which then deposited into the surrounding ecosystems. With the regional reclamation decreasing and environment-friendly industry developing, the proportion of BC emitted and deposited from transportation sources increased and transportation source became an important BC source in the Sanjiang Plain after the 1990s.

Identify source location and release time for pollutants undergoing super-diffusion and decay: Parameter analysis and model evaluation

NASA Astrophysics Data System (ADS)

Zhang, Yong; Sun, HongGuang; Lu, Bingqing; Garrard, Rhiannon; Neupauer, Roseanna M.

2017-09-01

Backward models have been applied for four decades by hydrologists to identify the source of pollutants undergoing Fickian diffusion, while analytical tools are not available for source identification of super-diffusive pollutants undergoing decay. This technical note evaluates analytical solutions for the source location and release time of a decaying contaminant undergoing super-diffusion using backward probability density functions (PDFs), where the forward model is the space fractional advection-dispersion equation with decay. Revisit of the well-known MADE-2 tracer test using parameter analysis shows that the peak backward location PDF can predict the tritium source location, while the peak backward travel time PDF underestimates the tracer release time due to the early arrival of tracer particles at the detection well in the maximally skewed, super-diffusive transport. In addition, the first-order decay adds additional skewness toward earlier arrival times in backward travel time PDFs, resulting in a younger release time, although this impact is minimized at the MADE-2 site due to tritium's half-life being relatively longer than the monitoring period. The main conclusion is that, while non-trivial backward techniques are required to identify pollutant source location, the pollutant release time can and should be directly estimated given the speed of the peak resident concentration for super-diffusive pollutants with or without decay.

Dynamic mobility applications open source application development portal : Task 4 : system requirements specifications : final report.

DOT National Transportation Integrated Search

2016-10-12

This document describes the System Requirements Specifications (SyRS) of the Dynamic Mobility Applications (DMA) Open Source Application Development Portal (OSADP) system in details according to IEEE-Std. 1233-1998. The requirement statements discuss...

Use of stable sulfur isotopes to identify sources of sulfate in Rocky Mountain snowpacks

USGS Publications Warehouse

Mast, M.A.; Turk, J.T.; Ingersoll, G.P.; Clow, D.W.; Kester, C.L.

2001-01-01

Stable sulfur isotope ratios and major ions in bulk snowpack samples were monitored at a network of 52 high-elevation sites along and near the Continental Divide from 1993 to 1999. This information was collected to better define atmospheric deposition to remote areas of the Rocky Mountains and to help identify the major source regions of sulfate in winter deposition. Average annual ??34S values at individual sites ranged from + 4.0 to + 8.2??? and standard deviations ranged from 0.4 to 1.6???. The chemical composition of all samples was extremely dilute and slightly acidic; average sulfate concentrations ranged from 2.4 to 12.2 ??eql-1 and pH ranged from 4.82 to 5.70. The range of ??34S values measured in this study indicated that snowpack sulfur in the Rocky Mountains is primarily derived from anthropogenic sources. A nearly linear relation between ??34S and latitude was observed for sites in New Mexico, Colorado, and southern Wyoming, which indicates that snowpack sulfate in the southern part of the network was derived from two isotopically distinct source regions. Because the major point sources of SO2 in the region are coal-fired powerplants, this pattern may reflect variations in the isotopic composition of coals burned by the plants. The geographic pattern in ??34S for sites farther to the north in Wyoming and Montana was much less distinct, perhaps rflecting the paucity of major point sources of SO2 in the northern part of the network.

BISQUE: locus- and variant-specific conversion of genomic, transcriptomic and proteomic database identifiers.

PubMed

Meyer, Michael J; Geske, Philip; Yu, Haiyuan

2016-05-15

Biological sequence databases are integral to efforts to characterize and understand biological molecules and share biological data. However, when analyzing these data, scientists are often left holding disparate biological currency-molecular identifiers from different databases. For downstream applications that require converting the identifiers themselves, there are many resources available, but analyzing associated loci and variants can be cumbersome if data is not given in a form amenable to particular analyses. Here we present BISQUE, a web server and customizable command-line tool for converting molecular identifiers and their contained loci and variants between different database conventions. BISQUE uses a graph traversal algorithm to generalize the conversion process for residues in the human genome, genes, transcripts and proteins, allowing for conversion across classes of molecules and in all directions through an intuitive web interface and a URL-based web service. BISQUE is freely available via the web using any major web browser (http://bisque.yulab.org/). Source code is available in a public GitHub repository (https://github.com/hyulab/BISQUE). haiyuan.yu@cornell.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Using high-frequency sensors to identify hydroclimatological controls on storm-event variability in catchment nutrient fluxes and source zone activation

NASA Astrophysics Data System (ADS)

Blaen, Phillip; Khamis, Kieran; Lloyd, Charlotte; Krause, Stefan

2017-04-01

At the river catchment scale, storm events can drive highly variable behaviour in nutrient and water fluxes, yet short-term dynamics are frequently missed by low resolution sampling regimes. In addition, nutrient source contributions can vary significantly within and between storm events. Our inability to identify and characterise time dynamic source zone contributions severely hampers the adequate design of land use management practices in order to control nutrient exports from agricultural landscapes. Here, we utilise an 8-month high-frequency (hourly) time series of streamflow, nitrate concentration (NO3) and fluorescent dissolved organic matter concentration (FDOM) derived from optical in-situ sensors located in a headwater agricultural catchment. We characterised variability in flow and nutrient dynamics across 29 storm events. Storm events represented 31% of the time series and contributed disproportionately to nutrient loads (43% of NO3 and 36% of CDOM) relative to their duration. Principal components analysis of potential hydroclimatological controls on nutrient fluxes demonstrated that a small number of components, representing >90% of variance in the dataset, were highly significant model predictors of inter-event variability in catchment nutrient export. Hysteresis analysis of nutrient concentration-discharge relationships suggested spatially discrete source zones existed for NO3 and FDOM, and that activation of these zones varied on an event-specific basis. Our results highlight the benefits of high-frequency in-situ monitoring for characterising complex short-term nutrient dynamics and unravelling connections between hydroclimatological variability and river nutrient export and source zone activation under extreme flow conditions. These new process-based insights are fundamental to underpinning the development of targeted management measures to reduce nutrient loading of surface waters.

Domain-specific impairment of source memory following a right posterior medial temporal lobe lesion.

PubMed

Peters, Jan; Koch, Benno; Schwarz, Michael; Daum, Irene

2007-01-01

This single case analysis of memory performance in a patient with an ischemic lesion affecting posterior but not anterior right medial temporal lobe (MTL) indicates that source memory can be disrupted in a domain-specific manner. The patient showed normal recognition memory for gray-scale photos of objects (visual condition) and spoken words (auditory condition). While memory for visual source (texture/color of the background against which pictures appeared) was within the normal range, auditory source memory (male/female speaker voice) was at chance level, a performance pattern significantly different from the control group. This dissociation is consistent with recent fMRI evidence of anterior/posterior MTL dissociations depending upon the nature of source information (visual texture/color vs. auditory speaker voice). The findings are in good agreement with the view of dissociable memory processing by the perirhinal cortex (anterior MTL) and parahippocampal cortex (posterior MTL), depending upon the neocortical input that these regions receive. (c) 2007 Wiley-Liss, Inc.

What's New in the Site Characterization Tool Box: Molecular Biological Tools to Identify Microorganisms that Degrade Contaminants and Contaminant-Specific Isotope Analysis to Identify Sources and Document Degradation

EPA Science Inventory

In the past, it was necessary to conduct intensive sampling and monitoring of concentrations of contaminants in ground water to trace plumes back to their true source. Now it is possible to determine the ratio of stable isotopes of carbon, hydrogen or chlorine in the contaminan...

Compendium of Immune Signatures Identifies Conserved and Species-Specific Biology in Response to Inflammation.

PubMed

Godec, Jernej; Tan, Yan; Liberzon, Arthur; Tamayo, Pablo; Bhattacharya, Sanchita; Butte, Atul J; Mesirov, Jill P; Haining, W Nicholas

2016-01-19

Gene-expression profiling has become a mainstay in immunology, but subtle changes in gene networks related to biological processes are hard to discern when comparing various datasets. For instance, conservation of the transcriptional response to sepsis in mouse models and human disease remains controversial. To improve transcriptional analysis in immunology, we created ImmuneSigDB: a manually annotated compendium of ∼5,000 gene-sets from diverse cell states, experimental manipulations, and genetic perturbations in immunology. Analysis using ImmuneSigDB identified signatures induced in activated myeloid cells and differentiating lymphocytes that were highly conserved between humans and mice. Sepsis triggered conserved patterns of gene expression in humans and mouse models. However, we also identified species-specific biological processes in the sepsis transcriptional response: although both species upregulated phagocytosis-related genes, a mitosis signature was specific to humans. ImmuneSigDB enables granular analysis of transcriptomic data to improve biological understanding of immune processes of the human and mouse immune systems. Copyright © 2016 Elsevier Inc. All rights reserved.

A microscopy-based screen employing multiplex genome sequencing identifies cargo-specific requirements for dynein velocity

PubMed Central

Tan, Kaeling; Roberts, Anthony J.; Chonofsky, Mark; Egan, Martin J.; Reck-Peterson, Samara L.

2014-01-01

The timely delivery of membranous organelles and macromolecules to specific locations within the majority of eukaryotic cells depends on microtubule-based transport. Here we describe a screening method to identify mutations that have a critical effect on intracellular transport and its regulation using mutagenesis, multicolor-fluorescence microscopy, and multiplex genome sequencing. This screen exploits the filamentous fungus Aspergillus nidulans, which has many of the advantages of yeast molecular genetics but uses long-range microtubule-based transport in a manner more similar to metazoan cells. Using this method, we identified seven mutants that represent novel alleles of components of the intracellular transport machinery: specifically, kinesin-1, cytoplasmic dynein, and the dynein regulators Lis1 and dynactin. The two dynein mutations identified in our screen map to dynein's AAA+ catalytic core. Single-molecule studies reveal that both mutations reduce dynein's velocity in vitro. In vivo these mutants severely impair the distribution and velocity of endosomes, a known dynein cargo. In contrast, another dynein cargo, the nucleus, is positioned normally in these mutants. These results reveal that different dynein functions have distinct stringencies for motor performance. PMID:24403603

Identifying sources of heterogeneity in capture probabilities: An example using the Great Tit Parus major

USGS Publications Warehouse

Senar, J.C.; Conroy, M.J.; Carrascal, L.M.; Domenech, J.; Mozetich, I.; Uribe, F.

1999-01-01

Heterogeneous capture probabilities are a common problem in many capture-recapture studies. Several methods of detecting the presence of such heterogeneity are currently available, and stratification of data has been suggested as the standard method to avoid its effects. However, few studies have tried to identify sources of heterogeneity, or whether there are interactions among sources. The aim of this paper is to suggest an analytical procedure to identify sources of capture heterogeneity. We use data on the sex and age of Great Tits captured in baited funnel traps, at two localities differing in average temperature. We additionally use 'recapture' data obtained by videotaping at feeder (with no associated trap), where the tits ringed with different colours were recorded. This allowed us to test whether individuals in different classes (age, sex and condition) are not trapped because of trap shyness or because o a reduced use of the bait. We used logistic regression analysis of the capture probabilities to test for the effects of age, sex, condition, location and 'recapture method. The results showed a higher recapture probability in the colder locality. Yearling birds (either males or females) had the highest recapture prob abilities, followed by adult males, while adult females had the lowest recapture probabilities. There was no effect of the method of 'recapture' (trap or video tape), which suggests that adult females are less often captured in traps no because of trap-shyness but because of less dependence on supplementary food. The potential use of this methodological approach in other studies is discussed.

Drought Tolerance in Pinus halepensis Seed Sources As Identified by Distinctive Physiological and Molecular Markers

PubMed Central

Taïbi, Khaled; del Campo, Antonio D.; Vilagrosa, Alberto; Bellés, José M.; López-Gresa, María Pilar; Pla, Davinia; Calvete, Juan J.; López-Nicolás, José M.; Mulet, José M.

2017-01-01

Drought is one of the main constraints determining forest species growth, survival and productivity, and therefore one of the main limitations for reforestation or afforestation. The aim of this study is to characterize the drought response at the physiological and molecular level of different Pinus halepensis (common name Aleppo pine) seed sources, previously characterized in field trials as drought-sensitive or drought-tolerant. This approach aims to identify different traits capable of predicting the ability of formerly uncharacterized seedlings to cope with drought stress. Gas-exchange, water potential, photosynthetic pigments, soluble sugars, free amino acids, glutathione and proteomic analyses were carried out on control and drought-stressed seedlings in greenhouse conditions. Gas-exchange determinations were also assessed in field-planted seedlings in order to validate the greenhouse experimental conditions. Drought-tolerant seed sources presented higher values of photosynthetic rates, water use efficiency, photosynthetic pigments and soluble carbohydrates concentrations. We observed the same pattern of variation of photosynthesis rate and maximal efficiency of PSII in field. Interestingly drought-tolerant seed sources exhibited increased levels of glutathione, methionine and cysteine. The proteomic profile of drought tolerant seedlings identified two heat shock proteins and an enzyme related to methionine biosynthesis that were not present in drought sensitive seedlings, pointing to the synthesis of sulfur amino acids as a limiting factor for drought tolerance in Pinus halepensis. Our results established physiological and molecular traits useful as distinctive markers to predict drought tolerance in Pinus halepensis provenances that could be reliably used in reforestation programs in drought prone areas. PMID:28791030

Drought Tolerance in Pinus halepensis Seed Sources As Identified by Distinctive Physiological and Molecular Markers.

PubMed

Taïbi, Khaled; Del Campo, Antonio D; Vilagrosa, Alberto; Bellés, José M; López-Gresa, María Pilar; Pla, Davinia; Calvete, Juan J; López-Nicolás, José M; Mulet, José M

2017-01-01

Drought is one of the main constraints determining forest species growth, survival and productivity, and therefore one of the main limitations for reforestation or afforestation. The aim of this study is to characterize the drought response at the physiological and molecular level of different Pinus halepensis (common name Aleppo pine) seed sources, previously characterized in field trials as drought-sensitive or drought-tolerant. This approach aims to identify different traits capable of predicting the ability of formerly uncharacterized seedlings to cope with drought stress. Gas-exchange, water potential, photosynthetic pigments, soluble sugars, free amino acids, glutathione and proteomic analyses were carried out on control and drought-stressed seedlings in greenhouse conditions. Gas-exchange determinations were also assessed in field-planted seedlings in order to validate the greenhouse experimental conditions. Drought-tolerant seed sources presented higher values of photosynthetic rates, water use efficiency, photosynthetic pigments and soluble carbohydrates concentrations. We observed the same pattern of variation of photosynthesis rate and maximal efficiency of PSII in field. Interestingly drought-tolerant seed sources exhibited increased levels of glutathione, methionine and cysteine. The proteomic profile of drought tolerant seedlings identified two heat shock proteins and an enzyme related to methionine biosynthesis that were not present in drought sensitive seedlings, pointing to the synthesis of sulfur amino acids as a limiting factor for drought tolerance in Pinus halepensis . Our results established physiological and molecular traits useful as distinctive markers to predict drought tolerance in Pinus halepensis provenances that could be reliably used in reforestation programs in drought prone areas.

Specific ultra-violet absorbance as an indicator measurement of merucry sources in an Adirondack River basin

USGS Publications Warehouse

Burns, Douglas A.; Aiken, George R.; Bradley, Paul M.; Journey, Celeste A.; Schelker, Jakob

2013-01-01

The Adirondack region of New York has been identified as a hot spot where high methylmercury concentrations are found in surface waters and biota, yet mercury (Hg) concentrations vary widely in this region. We collected stream and groundwater samples for Hg and organic carbon analyses across the upper Hudson River, a 493 km2 basin in the central Adirondacks to evaluate and model the sources of variation in filtered total Hg (FTHg) concentrations. Variability in FTHg concentrations during the growing seasons (May-Oct) of 2007-2009 in Fishing Brook, a 66-km2 sub-basin, was better explained by specific ultra-violet absorbance at 254 nm (SUVA254), a measure of organic carbon aromaticity, than by dissolved organic carbon (DOC) concentrations, a commonly used Hg indicator. SUVA254 was a stronger predictor of FTHg concentrations during the growing season than during the dormant season. Multiple linear regression models that included SUVA254 values and DOC concentrations could explain 75 % of the variation in FTHg concentrations on an annual basis and 84 % during the growing season. A multiple linear regression landscape modeling approach applied to 27 synoptic sites across the upper Hudson basin found that higher SUVA254 values are associated with gentler slopes, and greater riparian area, and lower SUVA254 values are associated with an increasing influence of open water. We hypothesize that the strong Hg?SUVA254 relation in this basin reflects distinct patterns of FTHg and SUVA254 that are characteristic of source areas that control the mobilization of Hg to surface waters, and that the seasonal influence of these source areas varies in this heterogeneous basin landscape.

Source apportionment of elevated wintertime PAHs by compound-specific radiocarbon analysis

NASA Astrophysics Data System (ADS)

Sheesley, R. J.; Kruså, M.; Krecl, P.; Johansson, C.; Gustafsson, Ã.-.

2009-05-01

Natural abundance radiocarbon analysis facilitates distinct source apportionment between contemporary biomass/biofuel (14C "alive") versus fossil fuel (14C "dead") combustion. Here, the first compound-specific radiocarbon analysis (CSRA) of atmospheric polycyclic aromatic hydrocarbons (PAHs) was demonstrated for a set of samples collected in Lycksele, Sweden a small town with frequent episodes of severe atmospheric pollution in the winter. Renewed interest in using residential wood combustion (RWC) means that this type of seasonal pollution is of increasing concern in many areas. Five individual/paired PAH isolates from three pooled fortnight-long filter collections were analyzed by CSRA: phenanthrene, fluoranthene, pyrene, benzo[b+k]fluoranthene and indeno[cd]pyrene plus benzo[ghi]perylene; phenanthrene was the only compound also analyzed in the gas phase. The measured Δ14C for PAHs spanned from -138.3‰ to 58.0‰. A simple isotopic mass balance model was applied to estimate the fraction biomass (fbiomass) contribution, which was constrained to 71-87% for the individual PAHs. Indeno[cd]pyrene plus benzo[ghi]perylene had an fbiomass of 71%, while fluoranthene and phenanthrene (gas phase) had the highest biomass contribution at 87%. The total organic carbon (TOC, defined as carbon remaining after removal of inorganic carbon) fbiomass was estimated to be 77%, which falls within the range for PAHs. This CSRA data of atmospheric PAHs established that RWC is the dominating source of atmospheric PAHs to this region of the boreal zone with some variations among RWC contributions to specific PAHs.

Identifying dissolved organic carbon sources at a gaged headwater catchment using FDOM sensors

NASA Astrophysics Data System (ADS)

Malzone, J. M.; Shanley, J. B.

2014-12-01

The United States Geological Survey's (USGS) W-9 gage at the headwaters of Sleepers River, Vermont has been monitored for dissolved organic carbon (DOC) concentration for more than 20 years. However, the sources of this DOC during base flow and hydrologic events remain unclear. The major objectives of this research were to identify sources of DOC during storm events and to explain the observed DOC-streamflow counterclockwise hysteresis during hydrologic events. Two main hypotheses to explain hysteresis during hydrologic events were tested: (1) distant headwater wetlands are the major DOC source, which lags behind peak flow due to travel time; and (2) the entire watershed contributes to the DOC at the gage, but the response of DOC lags behind the period when groundwater contributes most to streamflow. Sources of DOC were tracked using fluorescent dissolved organic matter (FDOM) sensors in surface water and groundwater wells. Wells were installed at four depths, 0.3, 0.6, 0.9, and 1.2 m, at four sites: a peaty low-gradient riparian area near the headwaters; a mid-hillslope area on a long hillslope mid-watershed; a near-stream area on a long hillslope mid-watershed; and a low-gradient tributary confluence area just above the gage. During storm events, FDOM and hydraulic head were measured at the nested groundwater wells. Samples for DOC analysis were also taken to determine the relationship between FDOM and DOC. Results suggest that both distant sources and the greater watershed played a role in the transport of DOC to the W-9 gage. Distant peaty sources dominated during large storms and contributed the highest surface water FDOM measurements. The peak FDOM at the gage was therefore best described as a result of transport. However, export from these distant sources terminated rapidly and did not explain continued elevated FDOM at the gage. Groundwater across the watershed exhibited hysteresis analogous to that in the stream itself, with FDOM peaking as head receded

Bacterial community composition associated with freshwater algae: species specificity vs. dependency on environmental conditions and source community.

PubMed

Eigemann, Falk; Hilt, Sabine; Salka, Ivette; Grossart, Hans-Peter

2013-03-01

We studied bacterial associations with the green alga Desmodesmus armatus and the diatom Stephanodiscus minutulus under changing environmental conditions and bacterial source communities, to evaluate whether bacteria-algae associations are species-specific or more generalized and determined by external factors. Axenic and xenic algae were incubated in situ with and without allelopathically active macrophytes, and in the laboratory with sterile and nonsterile lake water and an allelochemical, tannic acid (TA). Bacterial community composition (BCC) of algae-associated bacteria was analyzed by denaturing gradient gel electrophoresis (DGGE), nonmetric multidimensional scaling, cluster analyses, and sequencing of DGGE bands. BCC of xenic algal cultures of both species were not significantly affected by changes in their environment or bacterial source community, except in the case of TA additions. Species-specific interactions therefore appear to overrule the effects of environmental conditions and source communities. The BCC of xenic and axenic D. armatus cultures subjected to in situ bacterial colonization, however, had lower similarities (ca. 55%), indicating that bacterial precolonization is a strong factor for bacteria-algae associations irrespective of environmental conditions and source community. Our findings emphasize the ecological importance of species-specific bacteria-algae associations with important repercussions for other processes, such as the remineralization of nutrients, and organic matter dynamics. © 2012 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

Using ensemble models to identify and apportion heavy metal pollution sources in agricultural soils on a local scale.

PubMed

Wang, Qi; Xie, Zhiyi; Li, Fangbai

2015-11-01

This study aims to identify and apportion multi-source and multi-phase heavy metal pollution from natural and anthropogenic inputs using ensemble models that include stochastic gradient boosting (SGB) and random forest (RF) in agricultural soils on the local scale. The heavy metal pollution sources were quantitatively assessed, and the results illustrated the suitability of the ensemble models for the assessment of multi-source and multi-phase heavy metal pollution in agricultural soils on the local scale. The results of SGB and RF consistently demonstrated that anthropogenic sources contributed the most to the concentrations of Pb and Cd in agricultural soils in the study region and that SGB performed better than RF. Copyright © 2015 Elsevier Ltd. All rights reserved.

Source-specific speciation profiles of PM2.5 for heavy metals and their anthropogenic emissions in China.

PubMed

Liu, Yayong; Xing, Jia; Wang, Shuxiao; Fu, Xiao; Zheng, Haotian

2018-08-01

Heavy metals are concerned for its adverse effect on human health and long term burden on biogeochemical cycling in the ecosystem. In this study, a provincial-level emission inventory of 13 kinds of heavy metals including V, Cr, Mn, Co, Ni, Cu, Zn, As, Cd, Sn, Sb, Ba and Pb from 10 anthropogenic sources was developed for China, based on the 2015 national emission inventory of primary particulate matters and source category-specific speciation profiles collected from 50 previous studies measured in China. Uncertainties associated with the speciation profiles were also evaluated. Our results suggested that total emissions of the 13 types of heavy metals in China are estimated at about 58000 ton for the year 2015. The iron production is the dominant source of heavy metal, contributing 42% of total emissions of heavy metals. The emissions of heavy metals vary significantly at regional scale, with largest amount of emissions concentrated in northern and eastern China. Particular, high emissions of Cr, Co, Ni, As and Sb (contributing 8%-18% of the national emissions) are found in Shandong where has large capacity of industrial production. Uncertainty analysis suggested that the implementation of province-specific source profiles in this study significantly reduced the emission uncertainties from (-89%, 289%) to (-99%, 91%), particularly for coal combustion. However, source profiles for industry sectors such as non-metallic mineral manufacturing are quite limited, resulting in a relative high uncertainty. The high-resolution emission inventories of heavy metals are essential not only for their distribution, deposition and transport studies, but for the design of policies to redress critical atmospheric environmental hazards at local and regional scales. Detailed investigation on source-specific profile in China are still needed to achieve more accurate estimations of heavy metals in the future. Copyright © 2018 Elsevier Ltd. All rights reserved.

Anterior cruciate ligament injury: Identifying information sources and risk factor awareness among the general population.

PubMed

Nagano, Yasuharu; Yako-Suketomo, Hiroko; Natsui, Hiroaki

2018-01-01

Raising awareness on a disorder is important for its prevention and for promoting public health. However, for sports injuries like the anterior cruciate ligament (ACL) injury no studies have investigated the awareness on risk factors for injury and possible preventative measures in the general population. The sources of information among the population are also unclear. The purpose of the present study was to identify these aspects of public awareness about the ACL injury. A questionnaire was randomly distributed among the general population registered with a web based questionnaire supplier, to recruit 900 participants who were aware about the ACL injury. The questionnaire consisted of two parts: Question 1 asked them about their sources of information regarding the ACL injury; Question 2 asked them about the risk factors for ACL injury. Multivariate logistic regression was used to determine the information sources that provide a good understanding of the risk factors. The leading source of information for ACL injury was television (57.0%). However, the results of logistic regression analysis revealed that television was not an effective medium to create awareness about the risk factors, among the general population. Instead "Lecture by a coach", "Classroom session on Health", and "Newspaper" were significantly more effective in creating a good awareness of the risk factors (p < 0.001).

[Study on UPLC specific chromatogram of Lily and its specific peaks compositions analysis by QTOF-MS].

PubMed

Nie, Hui; Yan, Hui; Qian, Da-Wei; Duan, Jin-Ao; Ou, Yang-Zhen; Qian, Ye-Fei; Guan, Han-Liang

2013-07-01

To establish the UPLC specific chromatogram of Lily and analyze the specific peaks compositions by ESI-QTOF-MS. The samples were conducted by ACQUITY UPLC BEH C18 Column (2.1 mm x 100 mm, 1.7 microm) and eluted with acetonitrile and 0.1% formic acid at the flow rate of 0.4 mL/min. The detection wavelength was set at 320 nm and column temperature was 35 degrees C. Negative ion mode was chosen for qualitative analysis. The capillary voltage was set at 3.0 kV. The nebulization gas was set to 600 L/h at 350 degrees C, and the source temperature was 120 degrees C. The specific chromatogram of Lily was obtained. There were 19 common peaks. Twelve phenylpropenoid glycerides compositions were identified. Among them, 6 compositions were identified by comparison with the reference substances and others were identified by MS and MS2 data. UPLC specific chromatogram can be used for the quality evaluation of Lily, giving support to quality control comprehensively.

Specific phenotypic traits of Starmerella bacillaris regarding nitrogen source consumption and central carbon metabolites production during wine fermentation.

PubMed

Englezos, Vasileios; Cocolin, Luca; Rantsiou, Kalliopi; Ortiz-Julien, Anne; Bloem, Audrey; Dequin, Sylvie; Camarasa, Carole

2018-06-01

Over the last past years, the potential of non-Saccharomyces yeasts to improve the sensory quality of wine has been well recognized. In particular, the use of Starmerella bacillaris in mixed fermentations with Saccharomyces cerevisiae was reported as an appropriate way to enhance glycerol formation and reduce ethanol production. However, during sequential fermentation, many factors as the inoculation timing, strain combination and physical and biochemical interactions can affect yeast growth, fermentation process and/or metabolite synthesis. Among them, yeast assimilable nitrogen (YAN) availability, due to its role in the control of growth and fermentation, has been identified as a key parameter. Consequently, a comprehensive understanding of the metabolic specificities and the nitrogen requirements would be valuable to better exploit the potential of Starm. bacillaris during wine fermentation. In this study, marked differences in the consumption of the total and individual nitrogen sources were registered between the two species, while the two Starm. bacillaris strains generally behaved uniformly. Starm. bacillaris strains are differentiated by their preferential uptake of ammonium compared with amino acids that are poorly assimilated or even produced (alanine). Otherwise, the non- Saccharomyces yeast exhibits low activity through the acetaldehyde pathway, which triggers an important redistribution of fluxes through the central carbon metabolic network. In particular, the formation of metabolites deriving from the two glycolytic intermediates glyceraldehyde-3-phosphate and pyruvate is substantially increased during fermentations by Starm. bacillaris This knowledge will be useful to better control the fermentation process in mixed fermentation with Starm. bacillaris and S. cerevisiae IMPORTANCE Mixed fermentations using a controlled inoculation of Starm. bacillaris and S. cerevisiae starter cultures represent a feasible way to modulate wine composition that takes

An HTS-compatible 3D colony formation assay to identify tumor-specific chemotherapeutics.

PubMed

Horman, Shane R; To, Jeremy; Orth, Anthony P

2013-12-01

There has been increasing interest in the development of cellular behavior models that take advantage of three-dimensional (3D) cell culture. To enable assessment of differential perturbagen impacts on cell growth in 2D and 3D, we have miniaturized and adapted for high-throughput screening (HTS) the soft agar colony formation assay, employing a laser-scanning cytometer to image and quantify multiple cell types simultaneously. The assay is HTS compatible, providing high-quality, image-based, replicable data for multiple, co-cultured cell types. As proof of concept, we subjected colorectal carcinoma colonies in 3D soft agar to a mini screen of 1528 natural product compounds. Hit compounds from the primary screen were rescreened in an HTS 3D co-culture matrix containing colon stromal cells and cancer cells. By combining tumor cells and normal, nontransformed colon epithelial cells in one primary screening assay, we were able to obtain differential IC50 data, thereby distinguishing tumor-specific compounds from general cytotoxic compounds. Moreover, we were able to identify compounds that antagonized tumor colony formation in 3D only, highlighting the importance of this assay in identifying agents that interfere with 3D tumor structural growth. This screening platform provides a fast, simple, and robust method for identification of tumor-specific agents in a biologically relevant microenvironment.

Tracking the Sources of Fecal Contaminations: an Interdisciplinary Toolbox

NASA Astrophysics Data System (ADS)

Jeanneau, L.; Jarde, E.; Derrien, M.; Gruau, G.; Solecki, O.; Pourcher, A.; Marti, R.; Wéry, N.; Caprais, M.; Gourmelon, M.; Mieszkin, S.; Jadas-Hécart, A.; Communal, P.

2011-12-01

Fecal contaminations of inland and coastal waters induce risks to human health and economic losses. In order to improve water management, it is necessary to identify the sources of contamination, which implies the development of specific markers. In order to be considered as a valuable host-specific marker, one must (1) be source specific, (2) occur in high concentration in polluting matrices, (3) exhibit extra-intestinal persistence similar to fecal indicator bacteria (FIB) and (4) not grow out of the host. However, up to day no single marker has fulfilled all those criteria. Thus, it has been suggested to use a combination of markers in order to generate more reliable data. This has lead to the development of a Microbial Source Tracking (MST) toolbox including FIB and microbial and chemical specific markers in order to differentiate between human, bovine and porcine fecal contaminations. Those specific markers are, (1) genotypes of F-specific RNA bacteriophages, (2) bacterial markers belonging to the Bacteroidales (human-specific HF183, ruminant-specific Rum-2-Bac and pig-specific Pig-2-Bac markers), to the Bifidobacterium (Bifidobacterium adolescentis) and pig-specific Lactobacillus amylovorus, (3) fecal stanols and (4) caffeine. The development of this MST toolbox was composed of four steps, from the molecular scale to the watershed scale. At the molecular scale, the specificity and the concentration of those markers were studied in cattle and pig manures and in waste water treatment plant (WWTP) effluents and influents. At the microcosm scale, the transfer of bovine and porcine specific markers was investigated by rainfall simulations on agricultural plots amended with cattle or pig manure. Moreover, the relative persistence of FIB and human, porcine and bovine specific markers was investigated in freshwater and seawater microcosms inoculated with a WWTP influent, pig manure and cow manure. Finally, the aforementioned MST toolbox has been validated at the

A forward chemical screen in zebrafish identifies a retinoic acid derivative with receptor specificity.

PubMed

Das, Bhaskar C; McCartin, Kellie; Liu, Ting-Chun; Peterson, Randall T; Evans, Todd

2010-04-02

Retinoids regulate key developmental pathways throughout life, and have potential uses for differentiation therapy. It should be possible to identify novel retinoids by coupling new chemical reactions with screens using the zebrafish embryonic model. We synthesized novel retinoid analogues and derivatives by amide coupling, obtaining 80-92% yields. A small library of these compounds was screened for bioactivity in living zebrafish embryos. We found that several structurally related compounds significantly affect development. Distinct phenotypes are generated depending on time of exposure, and we characterize one compound (BT10) that produces specific cardiovascular defects when added 1 day post fertilization. When compared to retinoic acid (ATRA), BT10 shows similar but not identical changes in the expression pattern of embryonic genes that are known targets of the retinoid pathway. Reporter assays determined that BT10 interacts with all three RAR receptor sub-types, but has no activity for RXR receptors, at all concentrations tested. Our screen has identified a novel retinoid with specificity for retinoid receptors. This lead compound may be useful for manipulating components of retinoid signaling networks, and may be further derivatized for enhanced activity.

Transport of Cryptosporidium, Giardia, Source-specific Indicator Organisms, and Standard Water Quality Constituents During Storm Events

NASA Astrophysics Data System (ADS)

Sturdevant-Rees, P. L.; Bourdeau, D.; Baker, R.; Long, S. C.; Barten, P. K.

2004-05-01

Microbial and water-quality measurements are collected during storm events under a variety of meteorological and land-use conditions in order to 1) identify risk of Cryptosporidium oocysts, Giardia cysts and other constituents, including microbial indicator organisms, entering surface waters from various land uses during periods of surface runoff; 2) optimize storm sampling procedures for these parameters; and 3) optimize strategies for accurate determination of constituent loads. The investigation is focused on four isolated land uses: forested with free ranging wildlife, beaver influenced forested with free ranging wildlife, residential/commercial, and dairy farm grazing/pastureland using an upstream and downstream sampling strategy. Traditional water-quality analyses include pH, temperature, turbidity, conductivity, total suspended solids, total phosphorus, total Kjeldahl-nitrogen, and ammonia nitrogen, Giardia cysts and Cryptosporidium oocysts. Total coliforms and fecal coliforms are measured as industry standard microbial analyses. Sorbitol-fermenting Bifidobacteria, Rhodococcus coprophilus, Clostridium perfringens spores, and Somatic and F-specific coliphages are measured at select sites as potential alternative source-specific indicator organisms. Upon completion of the project, the final database will consist of wet weather transport data for a set of parameters during twenty-four distinct storm-events in addition to monthly baseline data. A subset of the results to date will be presented, with focus placed on demonstrating the impact of beaver on constituent loadings over a variety of hydrologic and meteorological conditions.

On the potential of using peculiarities of the protein intrinsic disorder distribution in mitochondrial cytochrome b to identify the source of animal meats

PubMed Central

Yacoub, Haitham A.; Sadek, Mahmoud A.; Uversky, Vladimir N.

2017-01-01

ABSTRACT This study was conducted to identify the source of animal meat based on the peculiarities of protein intrinsic disorder distribution in mitochondrial cytochrome b (mtCyt-b). The analysis revealed that animal and avian species can be discriminated based on the proportions of the two groups of residues, Leu+Ile, and Ser+Pro+Ala, in the amino acid sequences of their mtCyt-b. Although levels of the overall intrinsic disorder in mtCyt-b is not very high, the peculiarities of disorder distribution within the sequences of mtCyt-b from different species varies in a rather specific way. In fact, positions and intensities of disorder/flexibility “signals” in the corresponding disorder profiles are relatively unique for avian and animal species. Therefore, it is possible to devise a set of simple rules based on the peculiarities of disorder profiles of their mtCyt-b proteins to discriminate among species. This intrinsic disorder-based analysis represents a new technique that could be used to provide a promising solution for identification of the source of meats. PMID:28331777

Functional genomics identifies specific vulnerabilities in PTEN-deficient breast cancer.

PubMed

Tang, Yew Chung; Ho, Szu-Chi; Tan, Elisabeth; Ng, Alvin Wei Tian; McPherson, John R; Goh, Germaine Yen Lin; Teh, Bin Tean; Bard, Frederic; Rozen, Steven G

2018-03-22

-SSL patterns of activity in a large proportion of PTEN-deficient breast cancer cell lines and are potential specific vulnerabilities in PTEN-deficient breast cancer. Furthermore, the NUAK1 PTEN-SSL vulnerability identified by RNA interference techniques can be recapitulated and exploited using the small molecule kinase inhibitor HTH-01-015. Thus, NUAK1 inhibition may be an effective strategy for precision treatment of PTEN-deficient breast tumors.

Genome-wide oxidative bisulfite sequencing identifies sex-specific methylation differences in the human placenta

PubMed Central

Johnson, Michelle D; Dopierala, Justyna

2018-01-01

ABSTRACT DNA methylation is an important regulator of gene function. Fetal sex is associated with the risk of several specific pregnancy complications related to placental function. However, the association between fetal sex and placental DNA methylation remains poorly understood. We carried out whole-genome oxidative bisulfite sequencing in the placentas of two healthy female and two healthy male pregnancies generating an average genome depth of coverage of 25x. Most highly ranked differentially methylated regions (DMRs) were located on the X chromosome but we identified a 225 kb sex-specific DMR in the body of the CUB and Sushi Multiple Domains 1 (CSMD1) gene on chromosome 8. The sex-specific differential methylation pattern observed in this region was validated in additional placentas using in-solution target capture. In a new RNA-seq data set from 64 female and 67 male placentas, CSMD1 mRNA was 1.8-fold higher in male than in female placentas (P value = 8.5 × 10−7, Mann-Whitney test). Exon-level quantification of CSMD1 mRNA from these 131 placentas suggested a likely placenta-specific CSMD1 isoform not detected in the 21 somatic tissues analyzed. We show that the gene body of an autosomal gene, CSMD1, is differentially methylated in a sex- and placental-specific manner, displaying sex-specific differences in placental transcript abundance. PMID:29376485

Using Soluble Reactive Phosphorus and Ammonia to Identify Point Source Discharge from Large Livestock Facilities

NASA Astrophysics Data System (ADS)

Borrello, M. C.; Scribner, M.; Chessin, K.

2013-12-01

A growing body of research draws attention to the negative environmental impacts on surface water from large livestock facilities. These impacts are mostly in the form of excessive nutrient loading resulting in significantly decreased oxygen levels. Over-application of animal waste on fields as well as direct discharge into surface water from facilities themselves has been identified as the main contributor to the development of hypoxic zones in Lake Erie, Chesapeake Bay and the Gulf of Mexico. Some regulators claim enforcement of water quality laws is problematic because of the nature and pervasiveness of non-point source impacts. Any direct discharge by a facility is a violation of permits governed by the Clean Water Act, unless the facility has special dispensation for discharge. Previous research by the principal author and others has shown runoff and underdrain transport are the main mechanisms by which nutrients enter surface water. This study utilized previous work to determine if the effects of non-point source discharge can be distinguished from direct (point-source) discharge using simple nutrient analysis and dissolved oxygen (DO) parameters. Nutrient and DO parameters were measured from three sites: 1. A stream adjacent to a field receiving manure, upstream of a large livestock facility with a history of direct discharge, 2. The same stream downstream of the facility and 3. A stream in an area relatively unimpacted by large-scale agriculture (control site). Results show that calculating a simple Pearson correlation coefficient (r) of soluble reactive phosphorus (SRP) and ammonia over time as well as temperature and DO, distinguishes non-point source from point source discharge into surface water. The r value for SRP and ammonia for the upstream site was 0.01 while the r value for the downstream site was 0.92. The control site had an r value of 0.20. Likewise, r values were calculated on temperature and DO for each site. High negative correlations

77 FR 4735 - Regional Haze: Revisions to Provisions Governing Alternatives to Source-Specific Best Available...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-01-31

... ENVIRONMENTAL PROTECTION AGENCY 40 CFR Parts 51 and 52 [EPA-HQ-OAR-2011-0729; FRL-9624-4] RIN 2060-AR05 Regional Haze: Revisions to Provisions Governing Alternatives to Source-Specific Best Available Retrofit Technology (BART) Determinations, Limited SIP Approvals, and Federal Implementation Plans AGENCY...

Identifying sources of tick blood meals using unidentified tandem mass spectral libraries.

PubMed

Önder, Özlem; Shao, Wenguang; Kemps, Brian D; Lam, Henry; Brisson, Dustin

2013-01-01

Rapid and reliable identification of the vertebrate species on which a disease vector previously parasitized is imperative to study ecological factors that affect pathogen distribution and can aid the development of public health programs. Here we describe a proteome profiling technique designed to identify the source of blood meals of haematophagous arthropods. This method employs direct spectral matching and thus does not require a priori knowledge of any genetic or protein sequence information. Using this technology, we detect remnants of blood in blacklegged ticks (Ixodes scapularis) and correctly determine the vertebrate species from which the blood was derived, even 6 months after the tick had fed. This biological fingerprinting methodology is sensitive, fast, cost-effective and can potentially be adapted for other biological and medical applications when existing genome-based methods are impractical or ineffective.

Identifying the TeV gamma-ray source MGRO J2228+61, FINALLY!

NASA Astrophysics Data System (ADS)

Aliu, Ester

2012-09-01

New VERITAS observations of MGRO J2228+61 allow us to associate its TeV emission with the enigmatic radio supernova remnant SNR G106.3+2.7. This remnant is part of a large complex that includes the Boomerang pulsar and nebula. The reduced field suggests that the TeV emission is not powered by the Boomerang, but instead associated with a much larger remnant. A recent SUZAKU X-ray observation of the smaller gamma-ray error box reveals two possible pulsar candidates. We propose short ACIS exposures to identify these sources to determine if one or both can be responsible for the gamma-ray emission. This will allow us to address the long standing problem on the nature of both MGRO J2228+61 and SNR G106.3+2.7.

Recent advances in cross-cultural measurement in psychiatric epidemiology: utilizing 'what matters most' to identify culture-specific aspects of stigma.

PubMed

Yang, Lawrence Hsin; Thornicroft, Graham; Alvarado, Ruben; Vega, Eduardo; Link, Bruce George

2014-04-01

While stigma measurement across cultures has assumed growing importance in psychiatric epidemiology, it is unknown to what extent concepts arising from culture have been incorporated. We utilize a formulation of culture-as the everyday interactions that 'matter most' to individuals within a cultural group-to identify culturally-specific stigma dynamics relevant to measurement. A systematic literature review from January 1990 to September 2012 was conducted using PsycINFO, Medline and Google Scholar to identify articles studying: (i) mental health stigma-related concepts; (ii) ≥ 1 non-Western European cultural group. From 5292 abstracts, 196 empirical articles were located. The vast majority of studies (77%) utilized adaptations of existing Western-developed stigma measures to new cultural groups. Extremely few studies (2.0%) featured quantitative stigma measures derived within a non-Western European cultural group. A sizeable amount (16.8%) of studies employed qualitative methods to identify culture-specific stigma processes. The 'what matters most' perspective identified cultural ideals of the everyday activities that comprise 'personhood' of 'preserving lineage' among specific Asian groups, 'fighting hard to overcome problems and taking advantage of immigration opportunities' among specific Latino-American groups, and 'establishing trust among religious institutions due to institutional discrimination' among African-American groups. These essential cultural interactions shaped culture-specific stigma manifestations. Mixed method studies (3.6%) corroborated these qualitative results. Quantitatively-derived, culturally-specific stigma measures were lacking. Further, the vast majority of qualitative studies on stigma were conducted without using stigma-specific frameworks. We propose the 'what matters most' approach to address this key issue in future research.

Identifying airborne metal particles sources near an optoelectronic and semiconductor industrial park

NASA Astrophysics Data System (ADS)

Chen, Ho-Wen; Chen, Wei-Yea; Chang, Cheng-Nan; Chuang, Yen-Hsun; Lin, Yu-Hao

2016-06-01

The recently developed Central Taiwan Science Park (CTSP) in central Taiwan is home to an optoelectronic and semiconductor industrial cluster. Therefore, exploring the elemental compositions and size distributions of airborne particles emitted from the CTSP would help to prevent pollution. This study analyzed size-fractionated metal-rich particle samples collected in upwind and downwind areas of CTSP during Jan. and Oct. 2013 by using micro-orifice uniform deposited impactor (MOUDI). Correlation analysis, hierarchical cluster analysis and particle mass-size distribution analysis are performed to identify the source of metal-rich particle near the CTSP. Analyses of elemental compositions and particle size distributions emitted from the CTSP revealed that the CTSP emits some metals (V, As, In Ga, Cd and Cu) in the ultrafine particles (< 1 μm). The statistical analysis combines with the particle mass-size distribution analysis could provide useful source identification information. In airborne particles with the size of 0.32 μm, Ga could be a useful pollution index for optoelectronic and semiconductor emission in the CTSP. Meanwhile, the ratios of As/Ga concentration at the particle size of 0.32 μm demonstrates that humans near the CTSP would be potentially exposed to GaAs ultrafine particles. That is, metals such as Ga and As and other metals that are not regulated in Taiwan are potentially harmful to human health.

Source Credibility in Tobacco Control Messaging

PubMed Central

Schmidt, Allison M.; Ranney, Leah M.; Pepper, Jessica K.; Goldstein, Adam O.

2016-01-01

Objectives Perceived credibility of a message’s source can affect persuasion. This paper reviews how beliefs about the source of tobacco control messages may encourage attitude and behavior change. Methods We conducted a series of searches of the peer-reviewed literature using terms from communication and public health fields. We reviewed research on source credibility, its underlying concepts, and its relation to the persuasiveness of tobacco control messages. Results We recommend an agenda for future research to bridge the gaps between communication literature on source credibility and tobacco control research. Our recommendations are to study the impact of source credibility on persuasion with long-term behavior change outcomes, in different populations and demographic groups, by developing new credibility measures that are topic- and organization-specific, by measuring how credibility operates across media platforms, and by identifying factors that enhance credibility and persuasion. Conclusions This manuscript reviews the state of research on source credibility and identifies gaps that are maximally relevant to tobacco control communication. Knowing first whether a source is perceived as credible, and second, how to enhance perceived credibility, can inform the development of future tobacco control campaigns and regulatory communications. PMID:27525298

JETSPIN: A specific-purpose open-source software for simulations of nanofiber electrospinning

NASA Astrophysics Data System (ADS)

Lauricella, Marco; Pontrelli, Giuseppe; Coluzza, Ivan; Pisignano, Dario; Succi, Sauro

2015-12-01

We present the open-source computer program JETSPIN, specifically designed to simulate the electrospinning process of nanofibers. Its capabilities are shown with proper reference to the underlying model, as well as a description of the relevant input variables and associated test-case simulations. The various interactions included in the electrospinning model implemented in JETSPIN are discussed in detail. The code is designed to exploit different computational architectures, from single to parallel processor workstations. This paper provides an overview of JETSPIN, focusing primarily on its structure, parallel implementations, functionality, performance, and availability.

Incorporating deep learning with convolutional neural networks and position specific scoring matrices for identifying electron transport proteins.

PubMed

Le, Nguyen-Quoc-Khanh; Ho, Quang-Thai; Ou, Yu-Yen

2017-09-05

In several years, deep learning is a modern machine learning technique using in a variety of fields with state-of-the-art performance. Therefore, utilization of deep learning to enhance performance is also an important solution for current bioinformatics field. In this study, we try to use deep learning via convolutional neural networks and position specific scoring matrices to identify electron transport proteins, which is an important molecular function in transmembrane proteins. Our deep learning method can approach a precise model for identifying of electron transport proteins with achieved sensitivity of 80.3%, specificity of 94.4%, and accuracy of 92.3%, with MCC of 0.71 for independent dataset. The proposed technique can serve as a powerful tool for identifying electron transport proteins and can help biologists understand the function of the electron transport proteins. Moreover, this study provides a basis for further research that can enrich a field of applying deep learning in bioinformatics. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Functional Semi-Blind Source Separation Identifies Primary Motor Area Without Active Motor Execution.

PubMed

Porcaro, Camillo; Cottone, Carlo; Cancelli, Andrea; Salustri, Carlo; Tecchio, Franca

2018-04-01

High time resolution techniques are crucial for investigating the brain in action. Here, we propose a method to identify a section of the upper-limb motor area representation (FS_M1) by means of electroencephalographic (EEG) signals recorded during a completely passive condition (FS_M1bySS). We delivered a galvanic stimulation to the median nerve and we applied to EEG the semi-Blind Source Separation (s-BSS) algorithm named Functional Source Separation (FSS). In order to prove that FS_M1bySS is part of FS_M1, we also collected EEG in a motor condition, i.e. during a voluntary movement task (isometric handgrip) and in a rest condition, i.e. at rest with eyes open and closed. In motor condition, we show that the cortico-muscular coherence (CMC) of FS_M1bySS does not differ from FS_ M1 CMC (0.04 for both sources). Moreover, we show that the FS_M1bySS's ongoing whole band activity during Motor and both rest conditions displays high mutual information and time correlation with FS_M1 (above 0.900 and 0.800, respectively) whereas much smaller ones with the primary somatosensory cortex [Formula: see text] (about 0.300 and 0.500, [Formula: see text]). FS_M1bySS as a marker of the upper-limb FS_M1 representation obtainable without the execution of an active motor task is a great achievement of the FSS algorithm, relevant in most experimental, neurological and psychiatric protocols.

A Bottom-Up Proteomic Approach to Identify Substrate Specificity of Outer-Membrane Protease OmpT.

PubMed

Wood, Sarah E; Sinsinbar, Gaurav; Gudlur, Sushanth; Nallani, Madhavan; Huang, Che-Fan; Liedberg, Bo; Mrksich, Milan

2017-12-22

Identifying peptide substrates that are efficiently cleaved by proteases gives insights into substrate recognition and specificity, guides development of inhibitors, and improves assay sensitivity. Peptide arrays and SAMDI mass spectrometry were used to identify a tetrapeptide substrate exhibiting high activity for the bacterial outer-membrane protease (OmpT). Analysis of protease activity for the preferred residues at the cleavage site (P1, P1') and nearest-neighbor positions (P2, P2') and their positional interdependence revealed FRRV as the optimal peptide with the highest OmpT activity. Substituting FRRV into a fragment of LL37, a natural substrate of OmpT, led to a greater than 400-fold improvement in OmpT catalytic efficiency, with a k cat /K m value of 6.1×10 6  L mol -1  s -1 . Wild-type and mutant OmpT displayed significant differences in their substrate specificities, demonstrating that even modest mutants may not be suitable substitutes for the native enzyme. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A Manual to Identify Sources of Fluvial Sediment

EPA Science Inventory

Sedimentation is one of the main causes of stream/river aquatic life use impairments in R3. Currently states lack standard guidance on appropriate tools available to quantify sediment sources and develop sediment budgets in TMDL Development. Methods for distinguishing sediment t...

Microbial source tracking: a tool for identifying sources of microbial contamination in the food chain.

PubMed

Fu, Ling-Lin; Li, Jian-Rong

2014-01-01

The ability to trace fecal indicators and food-borne pathogens to the point of origin has major ramifications for food industry, food regulatory agencies, and public health. Such information would enable food producers and processors to better understand sources of contamination and thereby take corrective actions to prevent transmission. Microbial source tracking (MST), which currently is largely focused on determining sources of fecal contamination in waterways, is also providing the scientific community tools for tracking both fecal bacteria and food-borne pathogens contamination in the food chain. Approaches to MST are commonly classified as library-dependent methods (LDMs) or library-independent methods (LIMs). These tools will have widespread applications, including the use for regulatory compliance, pollution remediation, and risk assessment. These tools will reduce the incidence of illness associated with food and water. Our aim in this review is to highlight the use of molecular MST methods in application to understanding the source and transmission of food-borne pathogens. Moreover, the future directions of MST research are also discussed.

Quantitative sediment source attribution with compound-specific isotope analysis in a C3 plant-dominated catchment (central Switzerland)

NASA Astrophysics Data System (ADS)

Alewell, Christine; Birkholz, Axel; Meusburger, Katrin; Schindler Wildhaber, Yael; Mabit, Lionel

2016-03-01

As sediment loads impact freshwater systems and infrastructure, their origin in complex landscape systems is of crucial importance for sustainable management of agricultural catchments. We differentiated the sediment source contribution to a lowland river in central Switzerland by using compound-specific isotope analysis (CSIA). We found a clear distinction of sediment sources originating from forest and agricultural land use. Our results demonstrate that it is possible to reduce the uncertainty of sediment source attribution in: (i) using compound content (in our case, long-chain fatty acids; FAs) rather than soil organic matter content to transfer δ13C signal of FAs to soil contribution and (ii) restricting the investigation to the long-chain FAs (> C22 : 0) not to introduce errors due to aquatic contributions from algae and microorganisms. Results showed unambiguously that during base flow, agricultural land contributed up to 65 % of the suspended sediments, while forest was the dominant sediment source during high flow. This indicates that connectivity of sediment source areas within the river changes between base and high flow conditions. Uncertainty, which might occur in complex, large-scale studies due to undetected source attribution and/or CSSI signature degradation, is low because of limited data complexity in our study (i.e., two-three sources and two tracers). Our findings are the first published results highlighting (i) significant differences in compound-specific stable isotope (CSSI) signature of sediment sources from land uses dominated by C3 plant cultivation and (ii) the use of these differences to quantify sediment contribution to a small river.

LC-MS/MS Identification of Species-Specific Muscle Peptides in Processed Animal Proteins.

PubMed

Marchis, Daniela; Altomare, Alessandra; Gili, Marilena; Ostorero, Federica; Khadjavi, Amina; Corona, Cristiano; Ru, Giuseppe; Cappelletti, Benedetta; Gianelli, Silvia; Amadeo, Francesca; Rumio, Cristiano; Carini, Marina; Aldini, Giancarlo; Casalone, Cristina

2017-12-06

An innovative analytical strategy has been applied to identify signature peptides able to distinguish among processed animal proteins (PAPs) derived from bovine, pig, fish, and milk products. Proteomics was first used to elucidate the proteome of each source. Starting from the identified proteins and using a funnel based approach, a set of abundant and well characterized peptides with suitable physical-chemical properties (signature peptides) and specific for each source was selected. An on-target LC-ESI-MS/MS method (MRM mode) was set up using standard peptides and was then applied to selectively identify the PAP source and also to distinguish proteins from bovine carcass and milk proteins. We believe that the method described meets the request of the European Commission which has developed a strategy for gradually lifting the "total ban" toward "species to species ban", therefore requiring official methods for species-specific discrimination in feed.

BACTERIA SOURCE TRACKING AND HOST SPECIES SPECIFICITY ANALYSIS

EPA Science Inventory

Point and non-point pollution sources of fecal pollution on a watershed adversely impact the quality of drinking source waters and recreational waters. States are required to develop total maximum daily loads (TMDLs) and devise best management practices (BMPs) to reduce the pollu...

Identifying Greater Sage-Grouse source and sink habitats for conservation planning in an energy development landscape.

PubMed

Kirol, Christopher P; Beck, Jeffrey L; Huzurbazar, Snehalata V; Holloran, Matthew J; Miller, Scott N

2015-06-01

Conserving a declining species that is facing many threats, including overlap of its habitats with energy extraction activities, depends upon identifying and prioritizing the value of the habitats that remain. In addition, habitat quality is often compromised when source habitats are lost or fragmented due to anthropogenic development. Our objective was to build an ecological model to classify and map habitat quality in terms of source or sink dynamics for Greater Sage-Grouse (Centrocercus urophasianus) in the Atlantic Rim Project Area (ARPA), a developing coalbed natural gas field in south-central Wyoming, USA. We used occurrence and survival modeling to evaluate relationships between environmental and anthropogenic variables at multiple spatial scales and for all female summer life stages, including nesting, brood-rearing, and non-brooding females. For each life stage, we created resource selection functions (RSFs). We weighted the RSFs and combined them to form a female summer occurrence map. We modeled survival also as a function of spatial variables for nest, brood, and adult female summer survival. Our survival-models were mapped as survival probability functions individually and then combined with fixed vital rates in a fitness metric model that, when mapped, predicted habitat productivity (productivity map). Our results demonstrate a suite of environmental and anthropogenic variables at multiple scales that were predictive of occurrence and survival. We created a source-sink map by overlaying our female summer occurrence map and productivity map to predict habitats contributing to population surpluses (source habitats) or deficits (sink habitat) and low-occurrence habitats on the landscape. The source-sink map predicted that of the Sage-Grouse habitat within the ARPA, 30% was primary source, 29% was secondary source, 4% was primary sink, 6% was secondary sink, and 31% was low occurrence. Our results provide evidence that energy development and avoidance of

Identifying functional cancer-specific miRNA-mRNA interactions in testicular germ cell tumor.

PubMed

Sedaghat, Nafiseh; Fathy, Mahmood; Modarressi, Mohammad Hossein; Shojaie, Ali

2016-09-07

Testicular cancer is the most common cancer in men aged between 15 and 35 and more than 90% of testicular neoplasms are originated at germ cells. Recent research has shown the impact of microRNAs (miRNAs) in different types of cancer, including testicular germ cell tumor (TGCT). MicroRNAs are small non-coding RNAs which affect the development and progression of cancer cells by binding to mRNAs and regulating their expressions. The identification of functional miRNA-mRNA interactions in cancers, i.e. those that alter the expression of genes in cancer cells, can help delineate post-regulatory mechanisms and may lead to new treatments to control the progression of cancer. A number of sequence-based methods have been developed to predict miRNA-mRNA interactions based on the complementarity of sequences. While necessary, sequence complementarity is, however, not sufficient for presence of functional interactions. Alternative methods have thus been developed to refine the sequence-based interactions using concurrent expression profiles of miRNAs and mRNAs. This study aims to find functional cancer-specific miRNA-mRNA interactions in TGCT. To this end, the sequence-based predicted interactions are first refined using an ensemble learning method, based on two well-known methods of learning miRNA-mRNA interactions, namely, TaLasso and GenMiR++. Additional functional analyses were then used to identify a subset of interactions to be most likely functional and specific to TGCT. The final list of 13 miRNA-mRNA interactions can be potential targets for identifying TGCT-specific interactions and future laboratory experiments to develop new therapies. Copyright © 2016 Elsevier Ltd. All rights reserved.

Into the deep: Evaluation of SourceTracker for assessment of faecal contamination of coastal waters.

PubMed

Henry, Rebekah; Schang, Christelle; Coutts, Scott; Kolotelo, Peter; Prosser, Toby; Crosbie, Nick; Grant, Trish; Cottam, Darren; O'Brien, Peter; Deletic, Ana; McCarthy, David

2016-04-15

Faecal contamination of recreational waters is an increasing global health concern. Tracing the source of the contaminant is a vital step towards mitigation and disease prevention. Total 16S rRNA amplicon data for a specific environment (faeces, water, soil) and computational tools such as the Markov-Chain Monte Carlo based SourceTracker can be applied to microbial source tracking (MST) and attribution studies. The current study applied artificial and in-laboratory derived bacterial communities to define the potential and limitations associated with the use of SourceTracker, prior to its application for faecal source tracking at three recreational beaches near Port Phillip Bay (Victoria, Australia). The results demonstrated that at minimum multiple model runs of the SourceTracker modelling tool (i.e. technical replicates) were required to identify potential false positive predictions. The calculation of relative standard deviations (RSDs) for each attributed source improved overall predictive confidence in the results. In general, default parameter settings provided high sensitivity, specificity, accuracy and precision. Application of SourceTracker to recreational beach samples identified treated effluent as major source of human-derived faecal contamination, present in 69% of samples. Site-specific sources, such as raw sewage, stormwater and bacterial populations associated with the Yarra River estuary were also identified. Rainfall and associated sand resuspension at each location correlated with observed human faecal indicators. The results of the optimised SourceTracker analysis suggests that local sources of contamination have the greatest effect on recreational coastal water quality. Copyright © 2016 Elsevier Ltd. All rights reserved.

Mercury Isotopes as Proxies to Identify Sources and Environmental Impacts of Mercury in Sphalerites

PubMed Central

Yin, Runsheng; Feng, Xinbin; Hurley, James P.; Krabbenhoft, David P.; Lepak, Ryan F.; Hu, Ruizhong; Zhang, Qian; Li, Zhonggen; Bi, Xianwu

2016-01-01

During the past few years, evidence of mass independent fractionation (MIF) for mercury (Hg) isotopes have been reported in the Earth’s surface reservoirs, mainly assumed to be formed during photochemical processes. However, the magnitude of Hg-MIF in interior pools of the crust is largely unknown. Here, we reported significant variation in Hg-MIF signature (Δ199Hg: −0.24 ~ + 0.18‰) in sphalerites collected from 102 zinc (Zn) deposits in China, indicating that Hg-MIF can be recorded into the Earth’s crust during geological recycling of crustal material. Changing magnitudes of Hg-MIF signals were observed in Zn deposits with different formations, evidence that Hg isotopes (especially Hg-MIF) can be a useful tracer to identify sources (syngenetic and epigenetic) of Hg in mineral deposits. The average isotopic composition in studied sphalerites (δ202Hgaverage: −0.58‰; Δ199Hgaverage: +0.03‰) may be used to fingerprint Zn smelting activities, one of the largest global Hg emission sources. PMID:26728705

Identifying children with specific reading disabilities from listening and reading discrepancy scores.

PubMed

Spring, C; French, L

1990-01-01

A method of identifying children with specific reading disabilities by identifying discrepancies between their reading and listening comprehension scores was validated with disabled and nondisabled readers in Grades 4, 5, and 6. The method is based on a modification of the reading comprehension subtest of the Peabody Individual Achievement Test (Dunn & Markwardt, 1970). In this modification, even-numbered sentences are read by subjects, and odd-numbered sentences are read by the test administrator as subjects listen. The features of this test that reduce demands on working memory, thereby making it suitable for the detection of a discrepancy between reading and listening comprehension in readers with disabilities, are discussed. A significant group-by-modality interaction was obtained. Children with reading disabilities scored significantly lower on reading than on listening comprehension, while nondisabled readers scored slightly higher, but not significantly so, on reading than on listening comprehension. The appropriateness of this method as a substitute for the traditional method, which is based on the detection of a discrepancy between intelligence and reading and which has recently been proscribed in certain school districts, is discussed. Issues concerning the listening comprehension skills of disabled readers are also discussed.

Male specific genes from dioecious white campion identified by fluorescent differential display.

PubMed

Scutt, Charles P; Jenkins, Tom; Furuya, Masaki; Gilmartin, Philip M

2002-05-01

Fluorescent differential display (FDD) has been used to screen for cDNAs that are differentially up-regulated in male flowers of the dioecious plant Silene latifolia in which an X/Y chromosome system of sex determination operates. To adapt FDD to the cloning of large numbers of differential cDNAs, a novel method of confirming the differential expression of these has been devised. FDD gels were Southern electro-blotted and probed with mixtures of individual cDNA clones derived from different FDD product ligation reactions. These Southern blots were then stripped and re-probed with further mixtures of individual cloned FDD products to identify the maximum number of recombinant clones carrying the true differential amplification products. Of 135 differential bands identified by FDD, 56 differential amplification products were confirmed; these represent 23 unique differentially expressed genes as determined by virtual Northern analysis and two genes expressed at or below the level of detection by virtual Northern analysis. These two low expressed genes show bands of hybridization on genomic Southern blots that are specific to male plants, indicating that they are derived from, or closely related to, Y chromosome genes.

Spatial and Temporal Dust Source Variability in Northern China Identified Using Advanced Remote Sensing Analysis

NASA Technical Reports Server (NTRS)

Taramelli, A.; Pasqui, M.; Barbour, J.; Kirschbaum, D.; Bottai, L.; Busillo, C.; Calastrini, F.; Guarnieri, F.; Small, C.

2013-01-01

The aim of this research is to provide a detailed characterization of spatial patterns and temporal trends in the regional and local dust source areas within the desert of the Alashan Prefecture (Inner Mongolia, China). This problem was approached through multi-scale remote sensing analysis of vegetation changes. The primary requirements for this regional analysis are high spatial and spectral resolution data, accurate spectral calibration and good temporal resolution with a suitable temporal baseline. Landsat analysis and field validation along with the low spatial resolution classifications from MODIS and AVHRR are combined to provide a reliable characterization of the different potential dust-producing sources. The representation of intra-annual and inter-annual Normalized Difference Vegetation Index (NDVI) trend to assess land cover discrimination for mapping potential dust source using MODIS and AVHRR at larger scale is enhanced by Landsat Spectral Mixing Analysis (SMA). The combined methodology is to determine the extent to which Landsat can distinguish important soils types in order to better understand how soil reflectance behaves at seasonal and inter-annual timescales. As a final result mapping soil surface properties using SMA is representative of responses of different land and soil cover previously identified by NDVI trend. The results could be used in dust emission models even if they are not reflecting aggregate formation, soil stability or particle coatings showing to be critical for accurately represent dust source over different regional and local emitting areas.

Coupling genetics and proteomics to identify aphid proteins associated with vector-specific transmission of polerovirus (luteoviridae).

PubMed

Yang, Xiaolong; Thannhauser, T W; Burrows, Mary; Cox-Foster, Diana; Gildow, Fred E; Gray, Stewart M

2008-01-01

Cereal yellow dwarf virus-RPV (CYDV-RPV) is transmitted specifically by the aphids Rhopalosiphum padi and Schizaphis graminum in a circulative nonpropagative manner. The high level of vector specificity results from the vector aphids having the functional components of the receptor-mediated endocytotic pathways to allow virus to transverse the gut and salivary tissues. Studies of F(2) progeny from crosses of vector and nonvector genotypes of S. graminum showed that virus transmission efficiency is a heritable trait regulated by multiple genes acting in an additive fashion and that gut- and salivary gland-associated factors are not genetically linked. Utilizing two-dimensional difference gel electrophoresis to compare the proteomes of vector and nonvector parental and F(2) genotypes, four aphid proteins (S4, S8, S29, and S405) were specifically associated with the ability of S. graminum to transmit CYDV-RPV. The four proteins were coimmunoprecipitated with purified RPV, indicating that the aphid proteins are capable of binding to virus. Analysis by mass spectrometry identified S4 as a luciferase and S29 as a cyclophilin, both of which have been implicated in macromolecular transport. Proteins S8 and S405 were not identified from available databases. Study of this unique genetic system coupled with proteomic analysis indicated that these four virus-binding aphid proteins were specifically inherited and conserved in different generations of vector genotypes and suggests that they play a major role in regulating polerovirus transmission.

Estimation of contribution ratios of pollutant sources to a specific section based on an enhanced water quality model.

PubMed

Cao, Bibo; Li, Chuan; Liu, Yan; Zhao, Yue; Sha, Jian; Wang, Yuqiu

2015-05-01

Because water quality monitoring sections or sites could reflect the water quality status of rivers, surface water quality management based on water quality monitoring sections or sites would be effective. For the purpose of improving water quality of rivers, quantifying the contribution ratios of pollutant resources to a specific section is necessary. Because physical and chemical processes of nutrient pollutants are complex in water bodies, it is difficult to quantitatively compute the contribution ratios. However, water quality models have proved to be effective tools to estimate surface water quality. In this project, an enhanced QUAL2Kw model with an added module was applied to the Xin'anjiang Watershed, to obtain water quality information along the river and to assess the contribution ratios of each pollutant source to a certain section (the Jiekou state-controlled section). Model validation indicated that the results were reliable. Then, contribution ratios were analyzed through the added module. Results show that among the pollutant sources, the Lianjiang tributary contributes the largest part of total nitrogen (50.43%), total phosphorus (45.60%), ammonia nitrogen (32.90%), nitrate (nitrite + nitrate) nitrogen (47.73%), and organic nitrogen (37.87%). Furthermore, contribution ratios in different reaches varied along the river. Compared with pollutant loads ratios of different sources in the watershed, an analysis of contribution ratios of pollutant sources for each specific section, which takes the localized chemical and physical processes into consideration, was more suitable for local-regional water quality management. In summary, this method of analyzing the contribution ratios of pollutant sources to a specific section based on the QUAL2Kw model was found to support the improvement of the local environment.

COMBUSTION AREA SOURCES: DATA SOURCES

EPA Science Inventory

The report identifies, documents, and evaluates data sources for stationary area source emissions, including solid waste and agricultural burning. Area source emissions of particulate matter, sulfur dioxide, oxides of nitrogen, reactive volatile organic compounds, and carbon mon...

The tissue microarray data exchange specification: A community-based, open source tool for sharing tissue microarray data

PubMed Central

Berman, Jules J; Edgerton, Mary E; Friedman, Bruce A

2003-01-01

Background Tissue Microarrays (TMAs) allow researchers to examine hundreds of small tissue samples on a single glass slide. The information held in a single TMA slide may easily involve Gigabytes of data. To benefit from TMA technology, the scientific community needs an open source TMA data exchange specification that will convey all of the data in a TMA experiment in a format that is understandable to both humans and computers. A data exchange specification for TMAs allows researchers to submit their data to journals and to public data repositories and to share or merge data from different laboratories. In May 2001, the Association of Pathology Informatics (API) hosted the first in a series of four workshops, co-sponsored by the National Cancer Institute, to develop an open, community-supported TMA data exchange specification. Methods A draft tissue microarray data exchange specification was developed through workshop meetings. The first workshop confirmed community support for the effort and urged the creation of an open XML-based specification. This was to evolve in steps with approval for each step coming from the stakeholders in the user community during open workshops. By the fourth workshop, held October, 2002, a set of Common Data Elements (CDEs) was established as well as a basic strategy for organizing TMA data in self-describing XML documents. Results The TMA data exchange specification is a well-formed XML document with four required sections: 1) Header, containing the specification Dublin Core identifiers, 2) Block, describing the paraffin-embedded array of tissues, 3)Slide, describing the glass slides produced from the Block, and 4) Core, containing all data related to the individual tissue samples contained in the array. Eighty CDEs, conforming to the ISO-11179 specification for data elements constitute XML tags used in the TMA data exchange specification. A set of six simple semantic rules describe the complete data exchange specification. Anyone

A NEW HIGH RESOLUTION MASS SPECTROMETRY TECHNIQUE FOR IDENTIFYING PHARMACEUTICALS AND POTENTIAL ENDOCRINE DISRUPTORS IN DRINKING WATER SOURCES

EPA Science Inventory

A New High Resolution Mass Spectrometry Technique for Identifying Pharmaceuticals and Potential Endocrine Disruptors in Drinking Water Sources

Andrew H. Grange and G. Wayne Sovocool U.S.EPA, ORD, NERL, ESD, ECB, P.O. Box 93478, Las Vegas, NV 891933478

Mass spectra...

Identifying Military and Combat-Specific Risk Factors for Child Adjustment: Comparing High and Low Risk Military Families and Civilian Families

DTIC Science & Technology

2016-08-01

Award Number: W81XWH-12-2-0034 TITLE: Identifying Military and Combat-Specific Risk Factors for Child Adjustment: Comparing High and Low Risk...2. REPORT TYPE Final 3. DATES COVERED (From - To) 15May2012 - 31Aug2016 Identifying Military and Combat-Specific Risk Factors for Child Adjustment...deployment and has a child between the age of 3 and 7 and comparison groups of civilain single parent families (N=200) and civilian dual parent

Self-Referencing Enhances Memory Specificity with Age

PubMed Central

Hamami, Ayala; Serbun, Sarah J.; Gutchess, Angela H.

2011-01-01

Self-referencing has been identified as an advantageous mnemonic strategy for young and older adults. However, little research has investigated the ways in which self-referencing may influence older adults’ memory for details, which is typically impaired with age, beyond memory for the item itself. Experiment 1 assessed the effects of self- and other-referencing on memory for visually detailed pictures of objects in thirty-two young and thirty-two older adults. Results indicate that self- and close other-referencing similarly enhance general (item) and specific (detail) recognition for both young and older adults relative to the distant other condition. Experiment 2 extended these findings to source memory, with young and older adults encoding verbal information in self-referent, semantic, and structural conditions. Findings suggest that self-referencing provides an age-equivalent boost in general memory and specific memory for specific source details. We conclude that the mnemonic benefits of referencing the self extend to specific memory for visual and verbal information across the lifespan. PMID:21480719

Identifying Sources of Long-Distance Transported Pollution to the Arctic using δ13C in CH4 and Particle Dispersion Modelling

NASA Astrophysics Data System (ADS)

France, J. L.; Fisher, R. E.; Lowry, D.; Lanoiselle, M.; Cain, M.; Pyle, J. A.; Illingworth, S.; Allen, G.; Gallagher, M. W.; O'Shea, S.; Muller, J.; Bauguitte, S.; Nisbet, E. G.

2013-12-01

A stratified pollution plume of increased CH4 was identified at ~2000ft to ~7000ft altitude between the North coast of Norway and Svalbard on 21st July, 2012. The increased CH4 was identified through continuous CH4 measurements using a fast greenhouse gas analyser on board the NERC FAAM aircraft as part of the MAMM (Methane in the Arctic: Measurements and Modelling) campaign. Measurements of δ13C in CH4 on air samples taken whilst the aircraft was in the pollution plume demonstrate that the plume has a δ13C in CH4 source signature of -70 ‰. (×2.1 ‰). A δ13C source signature of -70 ‰ (×2.1 ‰) is within the expected boundaries of δ13C for wetland emissions in the Arctic (-70 to - 60‰ (Dlugokencky, Nisbet, Fisher, & Lowry, 2011)). The NAME (Numerical Atmospheric-dispersion Modelling Environment) model was run backwards from the measurement locations to identify periods where the measured air mass was in contact with the surface (lowest 300 m of the atmosphere). Combining the results together show that the likely source of the elevated methane measured is from wetlands located in North-West Russia. By sampling stratified air at altitude using the FAAM aircraft as a measurement platform, the joint application of isotopic source identification and NAME modelling allows identification of methane plumes from sources that we would otherwise not be able to sample, due to either remote access and / or political reasons (providing that suitable meteorological conditions exist). The use of this joined up approach will give us an extra tool in adding data to the global inventory of δ13C in CH4 source signatures and will enable better understanding of the sources of above background concentrations of CH4 to the Arctic. References. Dlugokencky, E. J., Nisbet, E. G., Fisher, R., & Lowry, D. (2011). Global atmospheric methane: budget, changes and dangers. Philosophical transactions. Series A, Mathematical, physical, and engineering sciences, 369(1943), 2058-72. doi

The Use of Patient-Specific Induced Pluripotent Stem Cells (iPSCs) to Identify Osteoclast Defects in Rare Genetic Bone Disorders

PubMed Central

Chen, I-Ping

2014-01-01

More than 500 rare genetic bone disorders have been described, but for many of them only limited treatment options are available. Challenges for studying these bone diseases come from a lack of suitable animal models and unavailability of skeletal tissues for studies. Effectors for skeletal abnormalities of bone disorders may be abnormal bone formation directed by osteoblasts or anomalous bone resorption by osteoclasts, or both. Patient-specific induced pluripotent stem cells (iPSCs) can be generated from somatic cells of various tissue sources and in theory can be differentiated into any desired cell type. However, successful differentiation of hiPSCs into functional bone cells is still a challenge. Our group focuses on the use of human iPSCs (hiPSCs) to identify osteoclast defects in craniometaphyseal dysplasia. In this review, we describe the impact of stem cell technology on research for better treatment of such disorders, the generation of hiPSCs from patients with rare genetic bone disorders and current protocols for differentiating hiPSCs into osteoclasts. PMID:25621177

Identifying Sources of Volatile Organic Compounds and Aldehydes in a High Performance Building

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

Ortiz, Anna C.; Russell, Marion; Lee, Wen-Yee

The developers of the Paharpur Business Center (PBC) and Software Technology Incubator Park in New Delhi, India offer an environmentally sustainable building with a strong emphasis on energy conservation, waste minimization and superior indoor air quality (IAQ). To achieve the IAQ goal, the building utilizes a series of air cleaning technologies for treating the air entering the building. These technologies include an initial water wash followed by ultraviolet light treatment and biolfiltration using a greenhouse located on the roof and numerous plants distributed throughout the building. Even with the extensive treatment of makeup air and room air in the PBC,more » a recent study found that the concentrations of common volatile organic compounds and aldehydes appear to rise incrementally as the air passes through the building from the supply to the exhaust. This finding highlights the need to consider the minimization of chemical sources in buildings in combination with the use of advanced air cleaning technologies when seeking to achieve superior IAQ. The goal of this project was to identify potential source materials for indoor chemicals in the PBC. Samples of building materials, including wood paneling (polished and unpolished), drywall, and plastic from a hydroponic drum that was part of the air cleaning system, were collected from the building for testing. All materials were collected from the PBC building and shipped to the Lawrence Berkeley National Laboratory (LBNL) for testing. The materials were pre-conditioned for two different time periods before measuring material and chemical specific emission factors for a range of VOCs and Aldehydes. Of the six materials tested, we found that the highest emitter of formaldehyde was new plywood paneling. Although polish and paint contribute to some VOC emissions, the main influence of the polish was in altering the capacity of the surface to accumulate formaldehyde. Neither the new nor aged polish contributed

Identifying Military and Combat Specific Risk Factors for Child Adjustment: Comparing High and Low Risk Military Families and Civilian Families

DTIC Science & Technology

2016-06-01

Award Number: W81XWH-12-2-0034 TITLE: Identifying Military and Combat-Specific Risk Factors for Child Adjustment: Comparing High and Low Risk...2. REPORT TYPE Annual 3. DATES COVERED (From - To) 15 May - 2013 - 14 May 2014. Identifying Military and Combat-Specific Risk Factors for Child ...parents (N=200) whose spouse/partner is currently in a “low perceived risk” deployment and has a child between the age of 3 and 7 and comparison

Identifying sources and processes controlling the sulphur cycle in the Canyon Creek watershed, Alberta, Canada.

PubMed

Nightingale, Michael; Mayer, Bernhard

2012-01-01

Sources and processes affecting the sulphur cycle in the Canyon Creek watershed in Alberta (Canada) were investigated. The catchment is important for water supply and recreational activities and is also a source of oil and natural gas. Water was collected from 10 locations along an 8 km stretch of Canyon Creek including three so-called sulphur pools, followed by the chemical and isotopic analyses on water and its major dissolved species. The δ(2)H and δ(18)O values of the water plotted near the regional meteoric water line, indicating a meteoric origin of the water and no contribution from deeper formation waters. Calcium, magnesium and bicarbonate were the dominant ions in the upstream portion of the watershed, whereas sulphate was the dominant anion in the water from the three sulphur pools. The isotopic composition of sulphate (δ(34)S and δ(18)O) revealed three major sulphate sources with distinct isotopic compositions throughout the catchment: (1) a combination of sulphate from soils and sulphide oxidation in the bedrock in the upper reaches of Canyon Creek; (2) sulphide oxidation in pyrite-rich shales in the lower reaches of Canyon Creek and (3) dissolution of Devonian anhydrite constituting the major sulphate source for the three sulphur pools in the central portion of the watershed. The presence of H(2)S in the sulphur pools with δ(34)S values ∼30 ‰ lower than those of sulphate further indicated the occurrence of bacterial (dissimilatory) sulphate reduction. This case study reveals that δ(34)S values of surface water systems can vary by more than 20 ‰ over short geographic distances and that isotope analyses are an effective tool to identify sources and processes that govern the sulphur cycle in watersheds.

Medicina ToO of the non-identified gamma-ray source AGL J1412-0522

NASA Astrophysics Data System (ADS)

Egron, Elise; Pilia, Maura; Righini, Simona; Pellizzoni, Alberto; Loru, Sara; Giroletti, Marcello

2017-09-01

Following the AGILE detection of a non-identified gamma-ray source AGL J1412-0522 on 5-7 August 2017 (ATel #10623), we performed radio observations with the 32-m Medicina radio telescope at 8.5 GHz (with 680 MHz bandwidth) on 9 August 2017 from 12:40 to 19:00 UTC and on 10 August 2017 from 14:00 to 17:50 UTC. We carried out squared on-the-fly maps of 45.5'x45.5' centered on the gamma-ray position (ra=14:12:06.0, dec=-05:22:14.9) to take into account the 0.4 deg position error from AGILE results.

Transcriptome Analysis of Mycobacteria-Specific CD4+ T Cells Identified by Activation-Induced Expression of CD154.

PubMed

Kunnath-Velayudhan, Shajo; Goldberg, Michael F; Saini, Neeraj K; Johndrow, Christopher T; Ng, Tony W; Johnson, Alison J; Xu, Jiayong; Chan, John; Jacobs, William R; Porcelli, Steven A

2017-10-01

Analysis of Ag-specific CD4 + T cells in mycobacterial infections at the transcriptome level is informative but technically challenging. Although several methods exist for identifying Ag-specific T cells, including intracellular cytokine staining, cell surface cytokine-capture assays, and staining with peptide:MHC class II multimers, all of these have significant technical constraints that limit their usefulness. Measurement of activation-induced expression of CD154 has been reported to detect live Ag-specific CD4 + T cells, but this approach remains underexplored and, to our knowledge, has not previously been applied in mycobacteria-infected animals. In this article, we show that CD154 expression identifies adoptively transferred or endogenous Ag-specific CD4 + T cells induced by Mycobacterium bovis bacillus Calmette-Guérin vaccination. We confirmed that Ag-specific cytokine production was positively correlated with CD154 expression by CD4 + T cells from bacillus Calmette-Guérin-vaccinated mice and show that high-quality microarrays can be performed from RNA isolated from CD154 + cells purified by cell sorting. Analysis of microarray data demonstrated that the transcriptome of CD4 + CD154 + cells was distinct from that of CD154 - cells and showed major enrichment of transcripts encoding multiple cytokines and pathways of cellular activation. One notable finding was the identification of a previously unrecognized subset of mycobacteria-specific CD4 + T cells that is characterized by the production of IL-3. Our results support the use of CD154 expression as a practical and reliable method to isolate live Ag-specific CD4 + T cells for transcriptomic analysis and potentially for a range of other studies in infected or previously immunized hosts. Copyright © 2017 by The American Association of Immunologists, Inc.

Mineralogical Composition and Potential Dust Source of Playas in the Western U.S. and Australia as Remotely Identified Through Imaging Spectroscopy.

NASA Astrophysics Data System (ADS)

Raming, L. W.; Farrand, W. H.; Bowen, B.

2015-12-01

Playas are significant dust sources and as a result are potentially hazardous to human health. The composition of the dust is a function of the mineralogical content of the playa and associated brines. Playas are found in arid climates globally, however they are challenging to map geologically as they are often hard to access, have subtle variations in mineralogy, and are topographically featureless. This study uses remote sensing in the form of imaging spectroscopy to map the mineralogical composition of five playas from different geologic settings: Railroad Valley Playa, Nevada, USA; Bonneville Salt Flats, Utah, USA; White Sands National Monument, New Mexico, USA; Lake Brown, Western Australia, Australia; and Lake Tyrrell, Victoria, Australia.Multiple spectrometers were used for this study; these include the multispectral sensor ASTER, and the hyperspectral sensors AVIRIS, HICO, and HyMap. All scenes were processed in ENVI and corrected to at surface reflectance using FLAASH, QUAC or Empirical Line methods. Minerals were identified through a standard end-member extraction approach and mapped using multi-range spectral feature fitting and other methods. Additionally, remote data are combined with in-situ field-based spectra and sample-based laboratory spectra.Initial results suggest various and differing mineralogy between playas. The most abundant mineralogy includes clay minerals such as illite and montmorillonite and evaporites such as gypsum. Additionally there has been identification of Fe absorption bands in the visible / near infrared at White Sands National Monument, and Lake Brown and Lake Tyrell, suggesting the presence of iron bearing minerals. Further research will provide a more comprehensive list of minerals identified by absorption features as related to specific sensors. Collectively, these analyses will be used characterize overall patterns in playa surface mineralogy and to evaluate the parameters that influence playa dust source composition.

The influence of plantation and seed-source elevation on wood specific gravity of 29-year-old ponderosa pines

Treesearch

R. M. Echols; M. T. Conkle

1971-01-01

Genetic, environmental, and age effects were found in 29-yr-old ponderosa pine progenies from different elevational sources, when they were grown at 960, 2730, and 5650 ft elevation in the Sierra Nevada of California. Wood specific gravity decreased as elevation of seed parents increased, and all genotypes produced significantly lower specific gravity wood in the high-...

Surveillance methods for identifying, characterizing, and monitoring tobacco products: potential reduced exposure products as an example

PubMed Central

O’Connor, Richard J.; Cummings, K. Michael; Rees, Vaughan W.; Connolly, Gregory N.; Norton, Kaila J.; Sweanor, David; Parascandola, Mark; Hatsukami, Dorothy K.; Shields, Peter G.

2015-01-01

Tobacco products are widely sold and marketed, yet integrated data systems for identifying, tracking, and characterizing products are lacking. Tobacco manufacturers recently have developed potential reduction exposure products (PREPs) with implied or explicit health claims. Currently, a systematic approach for identifying, defining, and evaluating PREPs sold at the local, state or national levels in the US has not been developed. Identifying, characterizing, and monitoring new tobacco products could be greatly enhanced with a responsive surveillance system. This paper critically reviews available surveillance data sources for identifying and tracking tobacco products, including PREPs, evaluating strengths and weaknesses of potential data sources in light of their reliability and validity. Absent regulations mandating disclosure of product-specific information, it is likely that public health officials will need to rely on a variety of imperfect data sources to help identify, characterize, and monitor tobacco products, including PREPs. PMID:19959680

Identifying sources of methane sampled in the Arctic using δ13C in CH4 and Lagrangian particle dispersion modelling.

NASA Astrophysics Data System (ADS)

Cain, Michelle; France, James; Pyle, John; Warwick, Nicola; Fisher, Rebecca; Lowry, Dave; Allen, Grant; O'Shea, Sebastian; Illingworth, Samuel; Jones, Ben; Gallagher, Martin; Welpott, Axel; Muller, Jennifer; Bauguitte, Stephane; George, Charles; Hayman, Garry; Manning, Alistair; Myhre, Catherine Lund; Lanoisellé, Mathias; Nisbet, Euan

2016-04-01

An airmass of enhanced methane was sampled during a research flight at ~600 m to ~2000 m altitude between the North coast of Norway and Svalbard on 21 July 2012. The largest source of methane in the summertime Arctic is wetland emissions. Did this enhancement in methane come from wetland emissions? The airmass was identified through continuous methane measurements using a Los Gatos fast greenhouse gas analyser on board the UK's BAe-146 Atmospheric Research Aircraft (ARA) as part of the MAMM (Methane in the Arctic: Measurements and Modelling) campaign. A Lagrangian particle dispersion model (the UK Met Office's NAME model) was run backwards to identify potential methane source regions. This was combined with a methane emission inventory to create "pseudo observations" to compare with the aircraft observations. This modelling was used to constrain the δ13C CH4 wetland source signature (where δ13C CH4 is the ratio of 13C to 12C in methane), resulting in a most likely signature of -73‰ (±4‰7‰). The NAME back trajectories suggest a methane source region of north-western Russian wetlands, and -73‰ is consistent with in situ measurements of wetland methane at similar latitudes in Scandinavia. This analysis has allowed us to study emissions from remote regions for which we do not have in situ observations, giving us an extra tool in the determination of the isotopic source variation of global methane emissions.

PTESFinder: a computational method to identify post-transcriptional exon shuffling (PTES) events.

PubMed

Izuogu, Osagie G; Alhasan, Abd A; Alafghani, Hani M; Santibanez-Koref, Mauro; Elliott, David J; Elliot, David J; Jackson, Michael S

2016-01-13

Transcripts, which have been subject to Post-transcriptional exon shuffling (PTES), have an exon order inconsistent with the underlying genomic sequence. These have been identified in a wide variety of tissues and cell types from many eukaryotes, and are now known to be mostly circular, cytoplasmic, and non-coding. Although there is no uniformly ascribed function, several have been shown to be involved in gene regulation. Accurate identification of these transcripts can, however, be difficult due to artefacts from a wide variety of sources. Here, we present a computational method, PTESFinder, to identify these transcripts from high throughput RNAseq data. Uniquely, it systematically excludes potential artefacts emanating from pseudogenes, segmental duplications, and template switching, and outputs both PTES and canonical exon junction counts to facilitate comparative analyses. In comparison with four existing methods, PTESFinder achieves highest specificity and comparable sensitivity at a variety of read depths. PTESFinder also identifies between 13 % and 41.6 % more structures, compared to publicly available methods recently used to identify human circular RNAs. With high sensitivity and specificity, user-adjustable filters that target known sources of false positives, and tailored output to facilitate comparison of transcript levels, PTESFinder will facilitate the discovery and analysis of these poorly understood transcripts.

Open-Source Radiation Exposure Extraction Engine (RE3) with Patient-Specific Outlier Detection.

PubMed

Weisenthal, Samuel J; Folio, Les; Kovacs, William; Seff, Ari; Derderian, Vana; Summers, Ronald M; Yao, Jianhua

2016-08-01

We present an open-source, picture archiving and communication system (PACS)-integrated radiation exposure extraction engine (RE3) that provides study-, series-, and slice-specific data for automated monitoring of computed tomography (CT) radiation exposure. RE3 was built using open-source components and seamlessly integrates with the PACS. RE3 calculations of dose length product (DLP) from the Digital imaging and communications in medicine (DICOM) headers showed high agreement (R (2) = 0.99) with the vendor dose pages. For study-specific outlier detection, RE3 constructs robust, automatically updating multivariable regression models to predict DLP in the context of patient gender and age, scan length, water-equivalent diameter (D w), and scanned body volume (SBV). As proof of concept, the model was trained on 811 CT chest, abdomen + pelvis (CAP) exams and 29 outliers were detected. The continuous variables used in the outlier detection model were scan length (R (2)  = 0.45), D w (R (2) = 0.70), SBV (R (2) = 0.80), and age (R (2) = 0.01). The categorical variables were gender (male average 1182.7 ± 26.3 and female 1047.1 ± 26.9 mGy cm) and pediatric status (pediatric average 710.7 ± 73.6 mGy cm and adult 1134.5 ± 19.3 mGy cm).

Quantitative microbial faecal source tracking with sampling guided by hydrological catchment dynamics.

PubMed

Reischer, G H; Haider, J M; Sommer, R; Stadler, H; Keiblinger, K M; Hornek, R; Zerobin, W; Mach, R L; Farnleitner, A H

2008-10-01

The impairment of water quality by faecal pollution is a global public health concern. Microbial source tracking methods help to identify faecal sources but the few recent quantitative microbial source tracking applications disregarded catchment hydrology and pollution dynamics. This quantitative microbial source tracking study, conducted in a large karstic spring catchment potentially influenced by humans and ruminant animals, was based on a tiered sampling approach: a 31-month water quality monitoring (Monitoring) covering seasonal hydrological dynamics and an investigation of flood events (Events) as periods of the strongest pollution. The detection of a ruminant-specific and a human-specific faecal Bacteroidetes marker by quantitative real-time PCR was complemented by standard microbiological and on-line hydrological parameters. Both quantitative microbial source tracking markers were detected in spring water during Monitoring and Events, with preponderance of the ruminant-specific marker. Applying multiparametric analysis of all data allowed linking the ruminant-specific marker to general faecal pollution indicators, especially during Events. Up to 80% of the variation of faecal indicator levels during Events could be explained by ruminant-specific marker levels proving the dominance of ruminant faecal sources in the catchment. Furthermore, soil was ruled out as a source of quantitative microbial source tracking markers. This study demonstrates the applicability of quantitative microbial source tracking methods and highlights the prerequisite of considering hydrological catchment dynamics in source tracking study design.

Machine-learning identifies substance-specific behavioral markers for opiate and stimulant dependence.

PubMed

Ahn, Woo-Young; Vassileva, Jasmin

2016-04-01

Recent animal and human studies reveal distinct cognitive and neurobiological differences between opiate and stimulant addictions; however, our understanding of the common and specific effects of these two classes of drugs remains limited due to the high rates of polysubstance-dependence among drug users. The goal of the current study was to identify multivariate substance-specific markers classifying heroin dependence (HD) and amphetamine dependence (AD), by using machine-learning approaches. Participants included 39 amphetamine mono-dependent, 44 heroin mono-dependent, 58 polysubstance dependent, and 81 non-substance dependent individuals. The majority of substance dependent participants were in protracted abstinence. We used demographic, personality (trait impulsivity, trait psychopathy, aggression, sensation seeking), psychiatric (attention deficit hyperactivity disorder, conduct disorder, antisocial personality disorder, psychopathy, anxiety, depression), and neurocognitive impulsivity measures (Delay Discounting, Go/No-Go, Stop Signal, Immediate Memory, Balloon Analogue Risk, Cambridge Gambling, and Iowa Gambling tasks) as predictors in a machine-learning algorithm. The machine-learning approach revealed substance-specific multivariate profiles that classified HD and AD in new samples with high degree of accuracy. Out of 54 predictors, psychopathy was the only classifier common to both types of addiction. Important dissociations emerged between factors classifying HD and AD, which often showed opposite patterns among individuals with HD and AD. These results suggest that different mechanisms may underlie HD and AD, challenging the unitary account of drug addiction. This line of work may shed light on the development of standardized and cost-efficient clinical diagnostic tests and facilitate the development of individualized prevention and intervention programs for HD and AD. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Machine-learning identifies substance-specific behavioral markers for opiate and stimulant dependence

PubMed Central

Ahn, Woo-Young; Vassileva, Jasmin

2016-01-01

Background Recent animal and human studies reveal distinct cognitive and neurobiological differences between opiate and stimulant addictions; however, our understanding of the common and specific effects of these two classes of drugs remains limited due to the high rates of polysubstance-dependence among drug users. Methods The goal of the current study was to identify multivariate substance-specific markers classifying heroin dependence (HD) and amphetamine dependence (AD), by using machine-learning approaches. Participants included 39 amphetamine mono-dependent, 44 heroin mono-dependent, 58 polysubstance dependent, and 81 non-substance dependent individuals. The majority of substance dependent participants were in protracted abstinence. We used demographic, personality (trait impulsivity, trait psychopathy, aggression, sensation seeking), psychiatric (attention deficit hyperactivity disorder, conduct disorder, antisocial personality disorder, psychopathy, anxiety, depression), and neurocognitive impulsivity measures (Delay Discounting, Go/No-Go, Stop Signal, Immediate Memory, Balloon Analogue Risk, Cambridge Gambling, and Iowa Gambling tasks) as predictors in a machine-learning algorithm. Results The machine-learning approach revealed substance-specific multivariate profiles that classified HD and AD in new samples with high degree of accuracy. Out of 54 predictors, psychopathy was the only classifier common to both types of addiction. Important dissociations emerged between factors classifying HD and AD, which often showed opposite patterns among individuals with HD and AD. Conclusions These results suggest that different mechanisms may underlie HD and AD, challenging the unitary account of drug addiction. This line of work may shed light on the development of standardized and cost-efficient clinical diagnostic tests and facilitate the development of individualized prevention and intervention programs for HD and AD. PMID:26905209

Identifying context-specific competencies required by community Australian Football sports trainers.

PubMed

Donaldson, Alex; Finch, Caroline F

2012-08-01

First-aid is a recommended injury prevention and risk management strategy in community sport; however, little is known about the sport-specific competencies required by first-aid providers. To achieve expert consensus on the competencies required by community Australian Football (community-AF) sports trainers. A three-round online Delphi process. Community-AF. 16 Australian sports first-aid and community-AF experts. Rating of competencies as either 'essential', 'expected', 'ideal' or 'not required'. Results After Round 3, 47 of the 77 (61%) competencies were endorsed as 'essential' or 'expected' for a sports trainer to effectively perform the activities required to the standards expected at a community-AF club by ≥75% of experts. These competencies covered: the role of the sports trainer; the responsibilities of the sports trainer; emergency management; injury and illness assessment and immediate management; taping; and injury prevention and risk management. Four competencies (5%) were endorsed as 'ideal' or 'not required' by ≥85% of experts and were excluded from further consideration. The 26 competencies where consensus was not reached were retained as second-tier, optional competencies. Sports trainers are important members of on-field first-aid teams, providing support to both injured players and other sports medicine professionals. The competencies identified in this study provide the basis of a proposed two-tiered community-AF-specific sports trainer education structure that can be implemented by the peak sports body. This includes six mandatory modules, relating to the 'required' competencies, and a further six optional modules covering competencies on which consensus was not reached.

MONKEY: Identifying conserved transcription-factor binding sitesin multiple alignments using a binding site-specific evolutionarymodel

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

Moses, Alan M.; Chiang, Derek Y.; Pollard, Daniel A.

2004-10-28

We introduce a method (MONKEY) to identify conserved transcription-factor binding sites in multispecies alignments. MONKEY employs probabilistic models of factor specificity and binding site evolution, on which basis we compute the likelihood that putative sites are conserved and assign statistical significance to each hit. Using genomes from the genus Saccharomyces, we illustrate how the significance of real sites increases with evolutionary distance and explore the relationship between conservation and function.

Eliminating Unwanted Far-Field Excitation in Objective-Type TIRF. Part I. Identifying Sources of Nonevanescent Excitation Light

PubMed Central

Brunstein, Maia; Teremetz, Maxime; Hérault, Karine; Tourain, Christophe; Oheim, Martin

2014-01-01

Total internal reflection fluorescence microscopy (TIRFM) achieves subdiffraction axial sectioning by confining fluorophore excitation to a thin layer close to the cell/substrate boundary. However, it is often unknown how thin this light sheet actually is. Particularly in objective-type TIRFM, large deviations from the exponential intensity decay expected for pure evanescence have been reported. Nonevanescent excitation light diminishes the optical sectioning effect, reduces contrast, and renders TIRFM-image quantification uncertain. To identify the sources of this unwanted fluorescence excitation in deeper sample layers, we here combine azimuthal and polar beam scanning (spinning TIRF), atomic force microscopy, and wavefront analysis of beams passing through the objective periphery. Using a variety of intracellular fluorescent labels as well as negative staining experiments to measure cell-induced scattering, we find that azimuthal beam spinning produces TIRFM images that more accurately portray the real fluorophore distribution, but these images are still hampered by far-field excitation. Furthermore, although clearly measureable, cell-induced scattering is not the dominant source of far-field excitation light in objective-type TIRF, at least for most types of weakly scattering cells. It is the microscope illumination optical path that produces a large cell- and beam-angle invariant stray excitation that is insensitive to beam scanning. This instrument-induced glare is produced far from the sample plane, inside the microscope illumination optical path. We identify stray reflections and high-numerical aperture aberrations of the TIRF objective as one important source. This work is accompanied by a companion paper (Pt.2/2). PMID:24606927

Genome-wide meta-analysis identifies novel gender specific loci associated with thyroid antibodies level in Croatians.

PubMed

Matana, Antonela; Popović, Marijana; Boutin, Thibaud; Torlak, Vesela; Brdar, Dubravka; Gunjača, Ivana; Kolčić, Ivana; Boraska Perica, Vesna; Punda, Ante; Polašek, Ozren; Hayward, Caroline; Barbalić, Maja; Zemunik, Tatijana

2018-04-18

Autoimmune thyroid diseases (AITD) are multifactorial endocrine diseases most frequently accompanied by Tg and TPO autoantibodies. Both antibodies have a higher prevalence in females and act under a strong genetic influence. To identify novel variants underlying thyroid antibody levels, we performed GWAS meta-analysis on the plasma levels of TgAb and TPOAb in three Croatian cohorts, as well as gender specific GWAS and a bivariate analysis. No significant association was detected with the level of TgAb and TPOAb in the meta-analysis of GWAS or bivariate results for all individuals. The bivariate analysis in females only revealed a genome-wide significant association for the locus near GRIN3A (rs4457391, P = 7.76 × 10 -9 ). The same locus had borderline association with TPOAb levels in females (rs1935377, P = 8.58 × 10 -8 ). In conclusion, we identified a novel gender specific locus associated with TgAb and TPOAb levels. Our findings provide a novel insight into genetic and gender differences associated with thyroid antibodies. Copyright © 2018 Elsevier Inc. All rights reserved.

GSHSite: Exploiting an Iteratively Statistical Method to Identify S-Glutathionylation Sites with Substrate Specificity

PubMed Central

Chen, Yi-Ju; Lu, Cheng-Tsung; Huang, Kai-Yao; Wu, Hsin-Yi; Chen, Yu-Ju; Lee, Tzong-Yi

2015-01-01

S-glutathionylation, the covalent attachment of a glutathione (GSH) to the sulfur atom of cysteine, is a selective and reversible protein post-translational modification (PTM) that regulates protein activity, localization, and stability. Despite its implication in the regulation of protein functions and cell signaling, the substrate specificity of cysteine S-glutathionylation remains unknown. Based on a total of 1783 experimentally identified S-glutathionylation sites from mouse macrophages, this work presents an informatics investigation on S-glutathionylation sites including structural factors such as the flanking amino acids composition and the accessible surface area (ASA). TwoSampleLogo presents that positively charged amino acids flanking the S-glutathionylated cysteine may influence the formation of S-glutathionylation in closed three-dimensional environment. A statistical method is further applied to iteratively detect the conserved substrate motifs with statistical significance. Support vector machine (SVM) is then applied to generate predictive model considering the substrate motifs. According to five-fold cross-validation, the SVMs trained with substrate motifs could achieve an enhanced sensitivity, specificity, and accuracy, and provides a promising performance in an independent test set. The effectiveness of the proposed method is demonstrated by the correct identification of previously reported S-glutathionylation sites of mouse thioredoxin (TXN) and human protein tyrosine phosphatase 1b (PTP1B). Finally, the constructed models are adopted to implement an effective web-based tool, named GSHSite (http://csb.cse.yzu.edu.tw/GSHSite/), for identifying uncharacterized GSH substrate sites on the protein sequences. PMID:25849935

Use of mass spectrometry fingerprinting to identify urinary metabolites after consumption of specific foods.

PubMed

Lloyd, Amanda J; Favé, Gaëlle; Beckmann, Manfred; Lin, Wanchang; Tailliart, Kathleen; Xie, Long; Mathers, John C; Draper, John

2011-10-01

The lack of robust biological markers of dietary exposure hinders the quantitative understanding of causal relations between diet and health. We aimed to develop an efficient procedure to discover metabolites in urine that may have future potential as biomarkers of acute exposure to foods of high public health importance. Twenty-four participants were provided with a test breakfast in which the cereal component of a standardized breakfast was replaced by 1 of 4 foods of high public health importance; 1.5-, 3-, and 4.5-h postprandial urine samples were collected. Flow infusion electrospray-ionization mass spectrometry followed by supervised multivariate data analysis was used to discover signals resulting from consumption of each test food. Fasted-state urine samples provided a universal comparator for food biomarker lead discovery in postprandial urine. The filtering of data features associated with consumption of the common components of the standardized breakfast improved discrimination models and readily identified metabolites that showed consumption of specific test foods. A combination of trimethylamine-N-oxide and 1-methylhistidine was associated with salmon consumption. Novel ascorbate derivatives were discovered in urine after consumption of either broccoli or raspberries. Sulphonated caffeic acid and sulphonated methyl-epicatechin concentrations increased dramatically after consumption of raspberries. This biomarker lead discovery strategy can identify urinary metabolites associated with acute exposure to individual foods. Future studies are required to validate the specificity and utility of potential biomarkers in an epidemiologic context.

Tracing Scientific Facilities through the Research Literature Using Persistent Identifiers

NASA Astrophysics Data System (ADS)

Mayernik, M. S.; Maull, K. E.

2016-12-01

Tracing persistent identifiers to their source publications is an easy task when authors use them, since it is a simple matter of matching the persistent identifier to the specific text string of the identifier. However, trying to understand if a publication uses the resource behind an identifier when such identifier is not referenced explicitly is a harder task. In this research, we explore the effectiveness of alternative strategies of associating publications with uses of the resource referenced by an identifier when it may not be explicit. This project is explored within the context of the NCAR supercomputer, where we are broadly interesting in the science that can be traced to the usage of the NCAR supercomputing facility, by way of the peer-reviewed research publications that utilize and reference it. In this project we explore several ways of drawing linkages between publications and the NCAR supercomputing resources. Identifying and compiling peer-reviewed publications related to NCAR supercomputer usage are explored via three sources: 1) User-supplied publications gathered through a community survey, 2) publications that were identified via manual searching of the Google scholar search index, and 3) publications associated with National Science Foundation (NSF) grants extracted from a public NSF database. These three sources represent three styles of collecting information about publications that likely imply usage of the NCAR supercomputing facilities. Each source has strengths and weaknesses, thus our discussion will explore how our publication identification and analysis methods vary in terms of accuracy, reliability, and effort. We will also discuss strategies for enabling more efficient tracing of research impacts of supercomputing facilities going forward through the assignment of a persistent web identifier to the NCAR supercomputer. While this solution has potential to greatly enhance our ability to trace the use of the facility through

State of the art molecular markers for fecal pollution source tracking in water.

PubMed

Roslev, Peter; Bukh, Annette S

2011-03-01

Most environmental waters are susceptible to fecal contamination from animal and/or human pollution sources. To attenuate or eliminate such contamination, it is often critical that the pollution sources are rapidly and correctly identified. Fecal pollution source tracking (FST) is a promising research area that aims to identify the origin(s) of fecal pollution in water. This mini-review focuses on the potentials and limitations of library independent molecular markers that are exclusively or strongly associated with fecal pollution from humans and different animals. Fecal-source-associated molecular markers include nucleic acid sequences from prokaryotes and viruses associated with specific biological hosts, but also sequences such as mitochondrial DNA retrieved directly from humans and animals. However, some fecal-source-associated markers may not be absolutely specific for a given source type, and apparent specificity and frequency established in early studies are sometimes compromised by new studies suggesting variation in specificity and abundance on a regional, global and/or temporal scale. It is therefore recommended that FST studies are based on carefully selected arrays of markers, and that identification of human and animal contributions are based on a multi-marker toolkit with several markers for each source category. Furthermore, future FST studies should benefit from increased knowledge regarding sampling strategies and temporal and spatial variability of marker ratios. It will also be important to obtain a better understanding of marker persistence and the quantitative relationship between marker abundance and the relative contribution from individual fecal pollution source types. A combination of enhanced pathogen screening methods, and validated quantitative source tracking techniques could then contribute significantly to future management of environmental water quality including improved microbial risk assessment.

Pre-study feasibility and identifying sensitivity analyses for protocol pre-specification in comparative effectiveness research.

PubMed

Girman, Cynthia J; Faries, Douglas; Ryan, Patrick; Rotelli, Matt; Belger, Mark; Binkowitz, Bruce; O'Neill, Robert

2014-05-01

The use of healthcare databases for comparative effectiveness research (CER) is increasing exponentially despite its challenges. Researchers must understand their data source and whether outcomes, exposures and confounding factors are captured sufficiently to address the research question. They must also assess whether bias and confounding can be adequately minimized. Many study design characteristics may impact on the results; however, minimal if any sensitivity analyses are typically conducted, and those performed are post hoc. We propose pre-study steps for CER feasibility assessment and to identify sensitivity analyses that might be most important to pre-specify to help ensure that CER produces valid interpretable results.

Understanding identifiability as a crucial step in uncertainty assessment

NASA Astrophysics Data System (ADS)

Jakeman, A. J.; Guillaume, J. H. A.; Hill, M. C.; Seo, L.

2016-12-01

The topic of identifiability analysis offers concepts and approaches to identify why unique model parameter values cannot be identified, and can suggest possible responses that either increase uniqueness or help to understand the effect of non-uniqueness on predictions. Identifiability analysis typically involves evaluation of the model equations and the parameter estimation process. Non-identifiability can have a number of undesirable effects. In terms of model parameters these effects include: parameters not being estimated uniquely even with ideal data; wildly different values being returned for different initialisations of a parameter optimisation algorithm; and parameters not being physically meaningful in a model attempting to represent a process. This presentation illustrates some of the drastic consequences of ignoring model identifiability analysis. It argues for a more cogent framework and use of identifiability analysis as a way of understanding model limitations and systematically learning about sources of uncertainty and their importance. The presentation specifically distinguishes between five sources of parameter non-uniqueness (and hence uncertainty) within the modelling process, pragmatically capturing key distinctions within existing identifiability literature. It enumerates many of the various approaches discussed in the literature. Admittedly, improving identifiability is often non-trivial. It requires thorough understanding of the cause of non-identifiability, and the time, knowledge and resources to collect or select new data, modify model structures or objective functions, or improve conditioning. But ignoring these problems is not a viable solution. Even simple approaches such as fixing parameter values or naively using a different model structure may have significant impacts on results which are too often overlooked because identifiability analysis is neglected.

Coupling Genetics and Proteomics To Identify Aphid Proteins Associated with Vector-Specific Transmission of Polerovirus (Luteoviridae)▿

PubMed Central

Yang, Xiaolong; Thannhauser, T. W.; Burrows, Mary; Cox-Foster, Diana; Gildow, Fred E.; Gray, Stewart M.

2008-01-01

Cereal yellow dwarf virus-RPV (CYDV-RPV) is transmitted specifically by the aphids Rhopalosiphum padi and Schizaphis graminum in a circulative nonpropagative manner. The high level of vector specificity results from the vector aphids having the functional components of the receptor-mediated endocytotic pathways to allow virus to transverse the gut and salivary tissues. Studies of F2 progeny from crosses of vector and nonvector genotypes of S. graminum showed that virus transmission efficiency is a heritable trait regulated by multiple genes acting in an additive fashion and that gut- and salivary gland-associated factors are not genetically linked. Utilizing two-dimensional difference gel electrophoresis to compare the proteomes of vector and nonvector parental and F2 genotypes, four aphid proteins (S4, S8, S29, and S405) were specifically associated with the ability of S. graminum to transmit CYDV-RPV. The four proteins were coimmunoprecipitated with purified RPV, indicating that the aphid proteins are capable of binding to virus. Analysis by mass spectrometry identified S4 as a luciferase and S29 as a cyclophilin, both of which have been implicated in macromolecular transport. Proteins S8 and S405 were not identified from available databases. Study of this unique genetic system coupled with proteomic analysis indicated that these four virus-binding aphid proteins were specifically inherited and conserved in different generations of vector genotypes and suggests that they play a major role in regulating polerovirus transmission. PMID:17959668

Targeting the Sources of Fecal Contamination using Dog-, Human-, and Ruminant- Specific Markers in the Lake Herrick Watershed, Georgia.

NASA Astrophysics Data System (ADS)

Saintil, T.; Radcliffe, D. E.; Rasmussen, T. C.; Habteselassie, M.; Sowah, R.; Kannan, A.

2016-12-01

The Lake Herrick Watershed is about 1.5 km2 and covers portions of the University of Georgia's East campus, the Oconee Forest, residential and commercial landuse. Lake Herrick, a recreational site on the University of Georgia campus, was closed in 2002 due to fecal contamination. Subsequent monitoring confirmed persistent contamination, which led to a permanent closure to swimming, boating, and fishing. While fecal coliform abundance is a standard metric for determining human health risks, Geldreich (1970) showed that fecal abundance does not necessarily correlate with the presence of pathogens. Nor does it identify pollution sources, which are needed to mitigate health risks. Two inflow tributaries and the outlet stream were monitored for discharge, fecal coliform, forms of nitrogen and phosphorus and other water-quality data to quantify lake influent and effluent bacteria loads. Fecal sources were identified using the human HF183 genetic marker (Seurinck et al., 2005), the ruminant BacR marker (Reischer et al., 2006), and the dog mitochondrial DNA (mtDNA) marker (Tambalo et al., 2012). Preliminary results confirm high concentrations of E. coli and Enterococci, above the State's limit of 124 MPN/100 mL, in both baseflows and stormflows. The findings also suggest that the E. coli and Enterococci loads from the inlet tributaries are on average higher compared to the bacteria loads coming out of the outlet stream. The human markers were detectable at all three sites but most of the samples were not quantifiable. The ruminant markers were quantifiable at both inlets but no ruminant markers were found at the outlet. The dog markers were detectable but not quantifiable at both inlets and no dog markers were detected at the outlet. Statistical analyses will be used to establish relationships between the nutrients data, the fecal concentrations, and the gene-specific markers.

Joint-specific DNA methylation and transcriptome signatures in rheumatoid arthritis identify distinct pathogenic processes

PubMed Central

Ai, Rizi; Hammaker, Deepa; Boyle, David L.; Morgan, Rachel; Walsh, Alice M.; Fan, Shicai; Firestein, Gary S.; Wang, Wei

2016-01-01

Stratifying patients on the basis of molecular signatures could facilitate development of therapeutics that target pathways specific to a particular disease or tissue location. Previous studies suggest that pathogenesis of rheumatoid arthritis (RA) is similar in all affected joints. Here we show that distinct DNA methylation and transcriptome signatures not only discriminate RA fibroblast-like synoviocytes (FLS) from osteoarthritis FLS, but also distinguish RA FLS isolated from knees and hips. Using genome-wide methods, we show differences between RA knee and hip FLS in the methylation of genes encoding biological pathways, such as IL-6 signalling via JAK-STAT pathway. Furthermore, differentially expressed genes are identified between knee and hip FLS using RNA-sequencing. Double-evidenced genes that are both differentially methylated and expressed include multiple HOX genes. Joint-specific DNA signatures suggest that RA disease mechanisms might vary from joint to joint, thus potentially explaining some of the diversity of drug responses in RA patients. PMID:27282753

Specification Reformulation During Specification Validation

NASA Technical Reports Server (NTRS)

Benner, Kevin M.

1992-01-01

The goal of the ARIES Simulation Component (ASC) is to uncover behavioral errors by 'running' a specification at the earliest possible points during the specification development process. The problems to be overcome are the obvious ones the specification may be large, incomplete, underconstrained, and/or uncompilable. This paper describes how specification reformulation is used to mitigate these problems. ASC begins by decomposing validation into specific validation questions. Next, the specification is reformulated to abstract out all those features unrelated to the identified validation question thus creating a new specialized specification. ASC relies on a precise statement of the validation question and a careful application of transformations so as to preserve the essential specification semantics in the resulting specialized specification. This technique is a win if the resulting specialized specification is small enough so the user my easily handle any remaining obstacles to execution. This paper will: (1) describe what a validation question is; (2) outline analysis techniques for identifying what concepts are and are not relevant to a validation question; and (3) identify and apply transformations which remove these less relevant concepts while preserving those which are relevant.

A novel assay to identify the trafficking proteins that bind to specific vesicle populations

PubMed Central

Bentley, Marvin; Banker, Gary

2016-01-01

Here we describe a method capable of identifying interactions between candidate trafficking proteins and a defined vesicle population in intact cells. The assay involves the expression of an FKBP12-rapamycin–binding domain (FRB)–tagged candidate vesicle-binding protein that can be inducibly linked to an FKBP-tagged molecular motor. If the FRB-tagged candidate protein binds the labeled vesicles, then linking the FRB and FKBP domains recruits motors to the vesicles and causes a predictable, highly distinctive change in vesicle trafficking. We describe two versions of the assay: a general protocol for use in cells with a typical microtubule-organizing center and a specialized protocol designed to detect protein-vesicle interactions in cultured neurons. We have successfully used this assay to identify kinesins and Rabs that bind to a variety of different vesicle populations. In principle, this assay could be used to investigate interactions between any category of vesicle trafficking proteins and any vesicle population that can be specifically labeled. PMID:26621371

Beta Atomic Contacts: Identifying Critical Specific Contacts in Protein Binding Interfaces

PubMed Central

Liu, Qian; Kwoh, Chee Keong; Hoi, Steven C. H.

2013-01-01

Specific binding between proteins plays a crucial role in molecular functions and biological processes. Protein binding interfaces and their atomic contacts are typically defined by simple criteria, such as distance-based definitions that only use some threshold of spatial distance in previous studies. These definitions neglect the nearby atomic organization of contact atoms, and thus detect predominant contacts which are interrupted by other atoms. It is questionable whether such kinds of interrupted contacts are as important as other contacts in protein binding. To tackle this challenge, we propose a new definition called beta (β) atomic contacts. Our definition, founded on the β-skeletons in computational geometry, requires that there is no other atom in the contact spheres defined by two contact atoms; this sphere is similar to the van der Waals spheres of atoms. The statistical analysis on a large dataset shows that β contacts are only a small fraction of conventional distance-based contacts. To empirically quantify the importance of β contacts, we design βACV, an SVM classifier with β contacts as input, to classify homodimers from crystal packing. We found that our βACV is able to achieve the state-of-the-art classification performance superior to SVM classifiers with distance-based contacts as input. Our βACV also outperforms several existing methods when being evaluated on several datasets in previous works. The promising empirical performance suggests that β contacts can truly identify critical specific contacts in protein binding interfaces. β contacts thus provide a new model for more precise description of atomic organization in protein quaternary structures than distance-based contacts. PMID:23630569

Identifying the source of colours in the Jovian atmosphere

NASA Astrophysics Data System (ADS)

Braude, Ashwin; Irwin, Patrick; Orton, Glenn S.; Fletcher, Leigh

2016-10-01

We wish to identify the source of Jupiter's colours through spectral analysis of images of Jupiter in the visible-to-near-infrared in conjunction with observations made by Juno in the mid-infrared and at super-high frequency. Three sets of observations were made of Jupiter by the MUSE integral-field spectrograph between 2014-2016 in the spectral range 0.48-0.93um, and reduced using a standard pipeline. Some large high-altitude hazes were observed in 2014 in the North Tropical Zone and the North Temperate Belt which appeared to have vanished by 2016. A single spectral image cube from 2014 was selected for analysis, and attempts at retrieving vertical cloud profiles, imaginary refractive indices and single-scattering albedos using the Nemesis radiative transfer model were made in different locations on Jupiter corresponding to the most prominent features close to the Equatorial region. Differences in lower tropospheric cloud altitude and opacity were found between the zones and the belts, and the belt cloud particles were seen to be significantly more blue-absorbing than the zone particles. Attempts were made at retrieving the real refractive index of the cloud particles in the upper tropospheric haze, where the majority of the colour-producing particles, or 'chromophores', are thought to be located, and values of refractive index greater than that of ammonia ice were observed, indicating the presence of a foreign substance. Further ground-based observations from MUSE in the visible and from TEXES in the mid-Infrared combined with localised observations from Juno later this year should shed more light on the origin of the colour-producing substance in the Jovian clouds, as well as of any seasonal changes in colour.

Atmospheric polycyclic aromatic hydrocarbons in the urban environment: Occurrence, toxicity and source apportionment.

PubMed

Mishra, Nitika; Ayoko, Godwin A; Morawska, Lidia

2016-01-01

Polycyclic Aromatic Hydrocarbons (PAHs) represent a major class of toxic pollutants because of their carcinogenic and mutagenic characteristics. People living in urban areas are regularly exposed to PAHs because of abundance of their emission sources. Within this context, this study aimed to: (i) identify and quantify the levels of ambient PAHs in an urban environment; (ii) evaluate their toxicity; and (iii) identify their sources as well as the contribution of specific sources to measured concentrations. Sixteen PAHs were identified and quantified in air samples collected from Brisbane. Principal Component Analysis - Absolute Principal Component Scores (PCA-APCS) was used in order to conduct source apportionment of the measured PAHs. Vehicular emissions, natural gas combustion, petrol emissions and evaporative/unburned fuel were the sources identified; contributing 56%, 21%, 15% and 8% of the total PAHs emissions, respectively, all of which need to be considered for any pollution control measures implemented in urban areas. Copyright © 2015 Elsevier Ltd. All rights reserved.

Data Sources for an Environmental Quality Index: Availability, Quality, and Utility

PubMed Central

Rappazzo, Kristen; Messer, Lynne C.

2011-01-01

Objectives. An environmental quality index (EQI) for all counties in the United States is under development to explore the relationship between environmental insults and human health. The EQI is potentially useful for investigators researching health disparities to account for other concurrent environmental conditions. This article focused on the identification and assessment of data sources used in developing the EQI. Data source strengths, limitations, and utility were addressed. Methods. Five domains were identified that contribute to environmental quality: air, water, land, built, and sociodemographic environments. An inventory of possible data sources was created. Data sources were evaluated for appropriate spatial and temporal coverage and data quality. Results. The overall data inventory identified multiple data sources for each domain. From the inventory (187 sources, 617 records), the air, water, land, built environment, and sociodemographic domains retained 2, 9, 7, 4, and 2 data sources for inclusion in the EQI, respectively. However, differences in data quality, geographic coverage, and data availability existed between the domains. Conclusions. The data sources identified for use in the EQI may be useful to researchers, advocates, and communities to explore specific environmental quality questions. PMID:21836111

Biological characterization of v. Cholerae-specific bacteriophages isolated from water sources in Georgia.

PubMed

Elbakidze, T; Kokashvili, T; Janelidze, N; Porchkhidze, K; Koberidze, T; Tediashvili, M

2015-03-01

Vibrio cholerae, a widely spread bacterium in various marine, fresh, and brackish water environments, can cause a devastating diarrheal disease - cholera and also mild forms of gastroenteritis. Bacterial viruses are natural controllers of bacterial population density in water systems. The goal of this study was to isolate and characterize V. cholerae-specific bacteriophages occurring in the Georgian coastal zone of the Black Sea and inland water reservoirs in the eastern part of Georgia. During 2006-2009, 71 phages lytic to V. cholerae were collected from these aquatic environments. The phage isolation rate was varying from 8% to 15%, depending on the sampling season and site, and the abundance of host bacteria. The majority of phages specific to V. cholerae were collected from freshwater sources. The phage isolation showed seasonal character covering warm period -from April to September. Based on basic characteristics of primary phage isolates (lytic spectrum, virion morphology and DNA restriction profiles) 23 V. cholerae -specific phages were selected for series of consecutive screenings. Comparatively wide spectrum of lytic activity was revealed in case of 14 phages specific to V. cholerae O1, and one phage - VchBS3, active against non-O1 V. cholerae. Three phages active against V. cholerae non-O1 and six V. cholerae O1 -specific phages have been studied in detail for a number of biological features (stability in different solutions, temperature-, pH- and UV- sensitivity, influence of high ionic strength etc.), considered to be additional important characteristics for selection of phages with therapeutic potential.

Characterization of particulate matter sources in an urban environment.

PubMed

Mazzei, F; D'Alessandro, A; Lucarelli, F; Nava, S; Prati, P; Valli, G; Vecchi, R

2008-08-15

Daily time series measurements of elements or compounds are widely used to apportion the contribution of specific sources of particulate matter concentration in the atmosphere. We present results obtained for the urban area of Genoa (Italy) based on several hundred of PM10, PM2.5 and PM1 daily samples collected in sites with different geo-morphological and urbanization characteristics. Elemental concentrations of Na to Pb were obtained through Energy Dispersive X-Ray Fluorescence (ED-XRF), and the contributions of specific sources of particulate matter (PM) concentration were apportioned through Positive Matrix Factorization (PMF). By sampling at different sites we were able to obtain, in each PM fraction, the average and stable values for the tracers of specific sources, in particular traffic (Cu, Zn, Pb) and heavy oil combustion (V, Ni). We could also identify and quote the contamination of anthropogenic PM in "natural" sources (sea, soil dust). Sampling at several sites in the same urban area allowed us to resolve local characteristics as well as to quote average values.

Genome of the Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels

PubMed Central

van Leeuwen, Elisabeth M.; Karssen, Lennart C.; Deelen, Joris; Isaacs, Aaron; Medina-Gomez, Carolina; Mbarek, Hamdi; Kanterakis, Alexandros; Trompet, Stella; Postmus, Iris; Verweij, Niek; van Enckevort, David J.; Huffman, Jennifer E.; White, Charles C.; Feitosa, Mary F.; Bartz, Traci M.; Manichaikul, Ani; Joshi, Peter K.; Peloso, Gina M.; Deelen, Patrick; van Dijk, Freerk; Willemsen, Gonneke; de Geus, Eco J.; Milaneschi, Yuri; Penninx, Brenda W.J.H.; Francioli, Laurent C.; Menelaou, Androniki; Pulit, Sara L.; Rivadeneira, Fernando; Hofman, Albert; Oostra, Ben A.; Franco, Oscar H.; Leach, Irene Mateo; Beekman, Marian; de Craen, Anton J.M.; Uh, Hae-Won; Trochet, Holly; Hocking, Lynne J.; Porteous, David J.; Sattar, Naveed; Packard, Chris J.; Buckley, Brendan M.; Brody, Jennifer A.; Bis, Joshua C.; Rotter, Jerome I.; Mychaleckyj, Josyf C.; Campbell, Harry; Duan, Qing; Lange, Leslie A.; Wilson, James F.; Hayward, Caroline; Polasek, Ozren; Vitart, Veronique; Rudan, Igor; Wright, Alan F.; Rich, Stephen S.; Psaty, Bruce M.; Borecki, Ingrid B.; Kearney, Patricia M.; Stott, David J.; Adrienne Cupples, L.; Neerincx, Pieter B.T.; Elbers, Clara C.; Francesco Palamara, Pier; Pe'er, Itsik; Abdellaoui, Abdel; Kloosterman, Wigard P.; van Oven, Mannis; Vermaat, Martijn; Li, Mingkun; Laros, Jeroen F.J.; Stoneking, Mark; de Knijff, Peter; Kayser, Manfred; Veldink, Jan H.; van den Berg, Leonard H.; Byelas, Heorhiy; den Dunnen, Johan T.; Dijkstra, Martijn; Amin, Najaf; Joeri van der Velde, K.; van Setten, Jessica; Kattenberg, Mathijs; van Schaik, Barbera D.C.; Bot, Jan; Nijman, Isaäc J.; Mei, Hailiang; Koval, Vyacheslav; Ye, Kai; Lameijer, Eric-Wubbo; Moed, Matthijs H.; Hehir-Kwa, Jayne Y.; Handsaker, Robert E.; Sunyaev, Shamil R.; Sohail, Mashaal; Hormozdiari, Fereydoun; Marschall, Tobias; Schönhuth, Alexander; Guryev, Victor; Suchiman, H. Eka D.; Wolffenbuttel, Bruce H.; Platteel, Mathieu; Pitts, Steven J.; Potluri, Shobha; Cox, David R.; Li, Qibin; Li, Yingrui; Du, Yuanping; Chen, Ruoyan; Cao, Hongzhi; Li, Ning; Cao, Sujie; Wang, Jun; Bovenberg, Jasper A.; Jukema, J. Wouter; van der Harst, Pim; Sijbrands, Eric J.; Hottenga, Jouke-Jan; Uitterlinden, Andre G.; Swertz, Morris A.; van Ommen, Gert-Jan B.; de Bakker, Paul I.W.; Eline Slagboom, P.; Boomsma, Dorret I.; Wijmenga, Cisca; van Duijn, Cornelia M.

2015-01-01

Variants associated with blood lipid levels may be population-specific. To identify low-frequency variants associated with this phenotype, population-specific reference panels may be used. Here we impute nine large Dutch biobanks (~35,000 samples) with the population-specific reference panel created by the Genome of the Netherlands Project and perform association testing with blood lipid levels. We report the discovery of five novel associations at four loci (P value <6.61 × 10−4), including a rare missense variant in ABCA6 (rs77542162, p.Cys1359Arg, frequency 0.034), which is predicted to be deleterious. The frequency of this ABCA6 variant is 3.65-fold increased in the Dutch and its effect (βLDL-C=0.135, βTC=0.140) is estimated to be very similar to those observed for single variants in well-known lipid genes, such as LDLR. PMID:25751400

GMRT discovery of PSR J1544+4937: An eclipsing black-widow pulsar identified with a Fermi-LAT source

DOE PAGES

Bhattacharyya, B.; Roy, J.; Ray, P. S.; ...

2013-07-29

Using the Giant Metrewave Radio Telescope, we performed deep observations to search for radio pulsations in the directions of unidentified Fermi-Large Area Telescope γ-ray sources. We report the discovery of an eclipsing black-widow millisecond pulsar, PSR J1544+4937, identified with the uncataloged γ-ray source FERMI J1544.2+4941. This 2.16 ms pulsar is in a 2.9 hr compact circular orbit with a very low mass companion (Mc > 0.017M ⊙). At 322 MHz this pulsar is found to be eclipsing for 13% of its orbit, whereas at 607 MHz the pulsar is detected throughout the low-frequency eclipse phase. Variations in the eclipse ingressmore » phase are observed, indicating a clumpy and variable eclipsing medium. Moreover, additional short-duration absorption events are observed around the eclipse boundaries. Finally, using the radio timing ephemeris we were able to detect γ-ray pulsations from this pulsar, confirming it as the source powering the γ-ray emission.« less

Levels and source apportionment of children's lead exposure: could urinary lead be used to identify the levels and sources of children's lead pollution?

PubMed

Cao, Suzhen; Duan, Xiaoli; Zhao, Xiuge; Wang, Beibei; Ma, Jin; Fan, Delong; Sun, Chengye; He, Bin; Wei, Fusheng; Jiang, Guibin

2015-04-01

As a highly toxic heavy metal, the pollution and exposure risks of lead are of widespread concern for human health. However, the collection of blood samples for use as an indicator of lead pollution is not always feasible in most cohort or longitudinal studies, especially those involving children health. To evaluate the potential use of urinary lead as an indicator of exposure levels and source apportionment, accompanying with environmental media samples, lead concentrations and isotopic measurements (expressed as (207)Pb/(206)Pb, (208)Pb/(206)Pb and (204)Pb/(206)Pb) were investigated and compared between blood and urine from children living in the vicinities of a typical coking plant and lead-acid battery factory. The results showed urinary lead might not be a preferable proxy for estimating blood lead levels. Fortunately, urinary lead isotopic measurements could be used as an alternative for identifying the sources of children's lead exposure, which coincided well with the blood lead isotope ratio analysis. Copyright © 2015 Elsevier Ltd. All rights reserved.

Combining MODIS, MISR, CALIOP, OMI, AERONET, and Models to Identify the Spatial and Temporal Distribution, Characterization, and Magnitude of Missing Urban and Wildfire Emissions Sources throughout Asia.

NASA Astrophysics Data System (ADS)

Cohen, J. B.

2016-12-01

Due to intense and changing levels of emissions as well as highly non-linear chemical processing, the concentrations of aerosols and thus their impacts are not well known. Urban areas consist of the majority of the emissions of these species and their precursors over large periods of time, while wildfires contribute very large spikes, concentrated in space and over a period of weeks to months. Yet due to urban and economic expansion, as well as clouds amd low intensity burning, the spatial and temporal profiles of these species are changing, with both new sources appearing and old sources decreasing. New work incorporates measurements at different spatial andboptical resolutions from MODIS, MISR, and OMI, coupled with new sampling approaches with CALIOP and AERONET to search for, characterize, and spatially and temporally constrain aerosols. An advanced modeling system including aerosol chemistry, physics, optics, and transport, using a multi-modal and both externally mixed and core-shell mixing is used to quantify the magnitudes of these missing sources. Comparisons between the model and additional dozens of ground stations show extreme improvement when these new sources are included. This new approach is shown to identify new source regions of emissions, many of which were previously non-urbanized or were not found to contain any fire hotspots. In addition, the use of new models run under conditions including both missing local sources from regions such as the expanded urban areas in Southeast and East Asia and advanced chemical and aerosol routines, allow for a comprehensive analysis to be performed. The impacts of insitu chemistry, horizontal, and vertical transport of species, both on the Regional and Continental scale are also included. It is shown that for proper identification, especially on intra-annual and inter-annual variations, this approach is a large improvement throughout Asia, ranging from India, to Indonesia, to China and Japan. Results specific

LC-QTOF-MS identification of porcine-specific peptide in heat treated pork identifies candidate markers for meat species determination.

PubMed

Sarah, S A; Faradalila, W N; Salwani, M S; Amin, I; Karsani, S A; Sazili, A Q

2016-05-15

The purpose of this study was to identify porcine-specific peptide markers from thermally processed meat that could differentiate pork from beef, chevon and chicken meat. In the initial stage, markers from tryptic digested protein of chilled, boiled and autoclaved pork were identified using LC-QTOF-MS. An MRM method was then established for verification. A thorough investigation of LC-QTOF-MS data showed that only seven porcine-specific peptides were consistently detected. Among these peptides, two were derived from lactate dehydrogenase, one from creatine kinase, and four from serum albumin protein. However, MRM could only detect four peptides (EVTEFAK, LVVITAGAR, FVIER and TVLGNFAAFVQK) that were consistently present in pork samples. In conclusion, meat species determination through a tandem mass spectrometry platform shows high potential in providing scientifically valid and reliable results even at peptide level. Besides, the specificity and selectivity offered by the proteomics approach also provide a robust platform for Halal authentication. Copyright © 2015 Elsevier Ltd. All rights reserved.

An Investigation to Validate the Grammar and Phonology Screening (GAPS) Test to Identify Children with Specific Language Impairment

PubMed Central

van der Lely, Heather K. J.; Payne, Elisabeth; McClelland, Alastair

2011-01-01

Background The extraordinarily high incidence of grammatical language impairments in developmental disorders suggests that this uniquely human cognitive function is “fragile”. Yet our understanding of the neurobiology of grammatical impairments is limited. Furthermore, there is no “gold-standard” to identify grammatical impairments and routine screening is not undertaken. An accurate screening test to identify grammatical abilities would serve the research, health and education communities, further our understanding of developmental disorders, and identify children who need remediation, many of whom are currently un-diagnosed. A potential realistic screening tool that could be widely administered is the Grammar and Phonology Screening (GAPS) test – a 10 minute test that can be administered by professionals and non-professionals alike. Here we provide a further step in evaluating the validity and accuracy (sensitivity and specificity) of the GAPS test in identifying children who have Specific Language Impairment (SLI). Methods and Findings We tested three groups of children; two groups aged 3;6–6:6, a typically developing (n = 30) group, and a group diagnosed with SLI: (n = 11) (Young (Y)-SLI), and a further group aged 6;9–8;11 with SLI (Older (O)-SLI) (n = 10) who were above the test age norms. We employed a battery of language assessments including the GAPS test to assess the children's language abilities. For Y-SLI children, analyses revealed a sensitivity and specificity at the 5th and 10th percentile of 1.00 and 0.98, respectively, and for O-SLI children at the 10th and 15th percentile .83 and .90, respectively. Conclusions The findings reveal that the GAPS is highly accurate in identifying impaired vs. non-impaired children up to 6;8 years, and has moderate-to-high accuracy up to 9 years. The results indicate that GAPS is a realistic tool for the early identification of grammatical abilities and impairment in young children. A larger

Diverse origins of Arctic and Subarctic methane point source emissions identified with multiply-substituted isotopologues

NASA Astrophysics Data System (ADS)

Douglas, P. M. J.; Stolper, D. A.; Smith, D. A.; Walter Anthony, K. M.; Paull, C. K.; Dallimore, S.; Wik, M.; Crill, P. M.; Winterdahl, M.; Eiler, J. M.; Sessions, A. L.

2016-09-01

Methane is a potent greenhouse gas, and there are concerns that its natural emissions from the Arctic could act as a substantial positive feedback to anthropogenic global warming. Determining the sources of methane emissions and the biogeochemical processes controlling them is important for understanding present and future Arctic contributions to atmospheric methane budgets. Here we apply measurements of multiply-substituted isotopologues, or clumped isotopes, of methane as a new tool to identify the origins of ebullitive fluxes in Alaska, Sweden and the Arctic Ocean. When methane forms in isotopic equilibrium, clumped isotope measurements indicate the formation temperature. In some microbial methane, however, non-equilibrium isotope effects, probably related to the kinetics of methanogenesis, lead to low clumped isotope values. We identify four categories of emissions in the studied samples: thermogenic methane, deep subsurface or marine microbial methane formed in isotopic equilibrium, freshwater microbial methane with non-equilibrium clumped isotope values, and mixtures of deep and shallow methane (i.e., combinations of the first three end members). Mixing between deep and shallow methane sources produces a non-linear variation in clumped isotope values with mixing proportion that provides new constraints for the formation environment of the mixing end-members. Analyses of microbial methane emitted from lakes, as well as a methanol-consuming methanogen pure culture, support the hypothesis that non-equilibrium clumped isotope values are controlled, in part, by kinetic isotope effects induced during enzymatic reactions involved in methanogenesis. Our results indicate that these kinetic isotope effects vary widely in microbial methane produced in Arctic lake sediments, with non-equilibrium Δ18 values spanning a range of more than 5‰.

Determining the depth of certain gravity sources without a priori specification of their structural index

NASA Astrophysics Data System (ADS)

Zhou, Shuai; Huang, Danian

2015-11-01

We have developed a new method for the interpretation of gravity tensor data based on the generalized Tilt-depth method. Cooper (2011, 2012) extended the magnetic Tilt-depth method to gravity data. We take the gradient-ratio method of Cooper (2011, 2012) and modify it so that the source type does not need to be specified a priori. We develop the new method by generalizing the Tilt-depth method for depth estimation for different types of source bodies. The new technique uses only the three vertical tensor components of the full gravity tensor data observed or calculated at different height plane to estimate the depth of the buried bodies without a priori specification of their structural index. For severely noise-corrupted data, our method utilizes different upward continuation height data, which can effectively reduce the influence of noise. Theoretical simulations of the gravity source model with and without noise illustrate the ability of the method to provide source depth information. Additionally, the simulations demonstrate that the new method is simple, computationally fast and accurate. Finally, we apply the method using the gravity data acquired over the Humble Salt Dome in the USA as an example. The results show a good correspondence to the previous drilling and seismic interpretation results.

Identifying and Quantifying Sources of Fall Chinook Salmon Spawning Gravel to the Snake River in Hells Canyon

NASA Astrophysics Data System (ADS)

Welcker, C. W.; Burke, M.

2015-12-01

The Snake River in Hells Canyon supports a growing population of spawning Fall Chinook Salmon (Oncorhynchus tshawytscha) immediately downstream of the Hells Canyon Complex (HCC) of hydroelectric dams for the last 60 years. The long-term survival of this salmon run depends on the input of spawning gravel (25-150 mm) from local tributaries balancing the losses of spawning gravel through attrition and export out of the reach between the HCC and the Salmon River confluence. We are working to quantify the gravel input of these local tributaries at different time-scales and put this into the context of historical supply and transport. Long-term total sediment production rates of these tributaries estimated through various methods have varied by over 2 orders of magnitude, but we have recently completed 10Be work to constrain these estimates. We are measuring the change in storage of Fall Chinook spawning-size gravel through repeat multibeam echosounder surveys of the riverbed. The limited amount of repeat data collected to date has shown complex patterns of change in the riverbed. One possible driver of this complexity is the episodic and spatially variable nature of sediment inputs from these tributaries. We are attempting to quantify the frequency of the debris flows or floods capable of transporting spawning gravel through digitizing historic imagery of the last 60 years to determine the recurrence interval. We are measuring the magnitude of these events by surveying tributary fans pre and post-event to measure the sediment volume and particle size produced by specific events. These floods and debris flows are driven by extreme rainfall or snowmelt events, so we have also reconstructed historical meteorological conditions to identify the triggering conditions for transport, and identify the areas where snowmelt or rainfall is the more likely trigger. We are currently testing whether the unique bedrock geology of Hells Canyon can be used as a tracer to identify the

Measuring the Electronic Properties of DNA-Specific Schottky Diodes Towards Detecting and Identifying Basidiomycetes DNA

PubMed Central

Periasamy, Vengadesh; Rizan, Nastaran; Al-Ta’ii, Hassan Maktuff Jaber; Tan, Yee Shin; Tajuddin, Hairul Annuar; Iwamoto, Mitsumasa

2016-01-01

The discovery of semiconducting behavior of deoxyribonucleic acid (DNA) has resulted in a large number of literatures in the study of DNA electronics. Sequence-specific electronic response provides a platform towards understanding charge transfer mechanism and therefore the electronic properties of DNA. It is possible to utilize these characteristic properties to identify/detect DNA. In this current work, we demonstrate a novel method of DNA-based identification of basidiomycetes using current-voltage (I-V) profiles obtained from DNA-specific Schottky barrier diodes. Electronic properties such as ideality factor, barrier height, shunt resistance, series resistance, turn-on voltage, knee-voltage, breakdown voltage and breakdown current were calculated and used to quantify the identification process as compared to morphological and molecular characterization techniques. The use of these techniques is necessary in order to study biodiversity, but sometimes it can be misleading and unreliable and is not sufficiently useful for the identification of fungi genera. Many of these methods have failed when it comes to identification of closely related species of certain genus like Pleurotus. Our electronics profiles, both in the negative and positive bias regions were however found to be highly characteristic according to the base-pair sequences. We believe that this simple, low-cost and practical method could be useful towards identifying and detecting DNA in biotechnology and pathology. PMID:27435636

Measuring the Electronic Properties of DNA-Specific Schottky Diodes Towards Detecting and Identifying Basidiomycetes DNA

NASA Astrophysics Data System (ADS)

Periasamy, Vengadesh; Rizan, Nastaran; Al-Ta'Ii, Hassan Maktuff Jaber; Tan, Yee Shin; Tajuddin, Hairul Annuar; Iwamoto, Mitsumasa

2016-07-01

The discovery of semiconducting behavior of deoxyribonucleic acid (DNA) has resulted in a large number of literatures in the study of DNA electronics. Sequence-specific electronic response provides a platform towards understanding charge transfer mechanism and therefore the electronic properties of DNA. It is possible to utilize these characteristic properties to identify/detect DNA. In this current work, we demonstrate a novel method of DNA-based identification of basidiomycetes using current-voltage (I-V) profiles obtained from DNA-specific Schottky barrier diodes. Electronic properties such as ideality factor, barrier height, shunt resistance, series resistance, turn-on voltage, knee-voltage, breakdown voltage and breakdown current were calculated and used to quantify the identification process as compared to morphological and molecular characterization techniques. The use of these techniques is necessary in order to study biodiversity, but sometimes it can be misleading and unreliable and is not sufficiently useful for the identification of fungi genera. Many of these methods have failed when it comes to identification of closely related species of certain genus like Pleurotus. Our electronics profiles, both in the negative and positive bias regions were however found to be highly characteristic according to the base-pair sequences. We believe that this simple, low-cost and practical method could be useful towards identifying and detecting DNA in biotechnology and pathology.

PM10 source apportionment in a Swiss Alpine valley impacted by highway traffic.

PubMed

Ducret-Stich, Regina E; Tsai, Ming-Yi; Thimmaiah, Devraj; Künzli, Nino; Hopke, Philip K; Phuleria, Harish C

2013-09-01

Although trans-Alpine highway traffic exhaust is one of the major sources of air pollution along the highway valleys of the Alpine regions, little is known about its contribution to residential exposure and impact on respiratory health. In this paper, source-specific contributions to particulate matter with an aerodynamic diameter < 10 μm (PM10) and their spatio-temporal distribution were determined for later use in a pediatric asthma panel study in an Alpine village. PM10 sources were identified by positive matrix factorization using chemical trace elements, elemental, and organic carbon from daily PM10 filters collected between November 2007 and June 2009 at seven locations within the village. Of the nine sources identified, four were directly road traffic-related: traffic exhaust, road dust, tire and brake wear, and road salt contributing 16 %, 8 %, 1 %, and 2 % to annual PM10 concentrations, respectively. They showed a clear dependence with distance to highway. Additional contributions were identified from secondary particles (27 %), biomass burning (18 %), railway (11 %), and mineral dust including a local construction site (13 %). Comparing these source contributions with known source-specific biomarkers (e.g., levoglucosan, nitro-polycyclic aromatic hydrocarbons) showed high agreement with biomass burning, moderate with secondary particles (in winter), and lowest agreement with traffic exhaust.

Improvements in the Protein Identifier Cross-Reference service.

PubMed

Wein, Samuel P; Côté, Richard G; Dumousseau, Marine; Reisinger, Florian; Hermjakob, Henning; Vizcaíno, Juan A

2012-07-01

The Protein Identifier Cross-Reference (PICR) service is a tool that allows users to map protein identifiers, protein sequences and gene identifiers across over 100 different source databases. PICR takes input through an interactive website as well as Representational State Transfer (REST) and Simple Object Access Protocol (SOAP) services. It returns the results as HTML pages, XLS and CSV files. It has been in production since 2007 and has been recently enhanced to add new functionality and increase the number of databases it covers. Protein subsequences can be Basic Local Alignment Search Tool (BLAST) against the UniProt Knowledgebase (UniProtKB) to provide an entry point to the standard PICR mapping algorithm. In addition, gene identifiers from UniProtKB and Ensembl can now be submitted as input or mapped to as output from PICR. We have also implemented a 'best-guess' mapping algorithm for UniProt. In this article, we describe the usefulness of PICR, how these changes have been implemented, and the corresponding additions to the web services. Finally, we explain that the number of source databases covered by PICR has increased from the initial 73 to the current 102. New resources include several new species-specific Ensembl databases as well as the Ensembl Genome ones. PICR can be accessed at http://www.ebi.ac.uk/Tools/picr/.

Sensitivity and Specificity of Cetuximab-IRDye800CW to Identify Regional Metastatic Disease in Head and Neck Cancer.

PubMed

Rosenthal, Eben L; Moore, Lindsay S; Tipirneni, Kiranya; de Boer, Esther; Stevens, Todd M; Hartman, Yolanda E; Carroll, William R; Zinn, Kurt R; Warram, Jason M

2017-08-15

Purpose: Comprehensive cervical lymphadenectomy can be associated with significant morbidity and poor quality of life. This study evaluated the sensitivity and specificity of cetuximab-IRDye800CW to identify metastatic disease in patients with head and neck cancer. Experimental Design: Consenting patients scheduled for curative resection were enrolled in a clinical trial to evaluate the safety and specificity of cetuximab-IRDye800CW. Patients ( n = 12) received escalating doses of the study drug. Where indicated, cervical lymphadenectomy accompanied primary tumor resection, which occurred 3 to 7 days following intravenous infusion of cetuximab-IRDye800CW. All 471 dissected lymph nodes were imaged with a closed-field, near-infrared imaging device during gross processing of the fresh specimens. Intraoperative imaging of exposed neck levels was performed with an open-field fluorescence imaging device. Blinded assessments of the fluorescence data were compared to histopathology to calculate sensitivity, specificity, negative predictive value (NPV), and positive predictive value (PPV). Results: Of the 35 nodes diagnosed pathologically positive, 34 were correctly identified with fluorescence imaging, yielding a sensitivity of 97.2%. Of the 435 pathologically negative nodes, 401 were correctly assessed using fluorescence imaging, yielding a specificity of 92.7%. The NPV was determined to be 99.7%, and the PPV was 50.7%. When 37 fluorescently false-positive nodes were sectioned deeper (1 mm) into their respective blocks, metastatic cancer was found in 8.1% of the recut nodal specimens, which altered staging in two of those cases. Conclusions: Fluorescence imaging of lymph nodes after systemic cetuximab-IRDye800CW administration demonstrated high sensitivity and was capable of identifying additional positive nodes on deep sectioning. Clin Cancer Res; 23(16); 4744-52. ©2017 AACR . ©2017 American Association for Cancer Research.

Potential Sources of Polarized Light from a Plant Canopy

NASA Technical Reports Server (NTRS)

Vanderbilt, Vern; Daughtry, Craig; Dahlgren, Robert

2016-01-01

Field measurements have demonstrated that sunlight polarized during a first surface reflection by shiny leaves dominates the optical polarization of the light reflected by shiny-leafed plant canopies having approximately spherical leaf angle probability density functions ("Leaf Angle Distributions" - LAD). Yet for other canopies - specifically those without shiny leaves and/or spherical LADs - potential sources of optically polarized light may not always be obvious. Here we identify possible sources of polarized light within those other canopies and speculate on the ecologically important information polarization measurements of those sources might contain.

Isotopic Characterisation of Methane Emissions: use of Keeling-plot Methods to Identify Source Signatures in Boreal Wetlands and Other Settings

NASA Astrophysics Data System (ADS)

Fisher, R. E.; Lowry, D.; France, J.; Lanoiselle, M.; Zazzeri, G.; Nisbet, E. G.

2012-12-01

Different methane sources have different δ13CCH4 and δDCH4 signatures, which potentially provides a powerful constraint on models of methane emission budgets. However source signatures remain poorly known and need to be studied in more detail if isotopic measurements of ambient air are to be used to constrain regional and global emissions. The Keeling plot method (plotting δ13CCH4 or δDCH4 against 1/CH4 concentration in samples of ambient air in the close vicinity of known sources) directly assesses the source signature of the methane that is actually emitted to the air. This contrasts with chamber studies, measuring air within a chamber, where local micro-meteorological and microbiological processes are occurring. Keeling plot methods have been applied to a wide variety of settings in this study. The selection of appropriate background measurements for Keeling plot analysis is also considered. The method has been used on a local scale to identify the source signature of summer emissions from subarctic wetlands in Fennoscandia. Samples are collected from low height (0.3-3m) over the wetlands during 24-hour periods, to collect daily emissions maxima (warm late afternoons), inversion maxima (at the coldest time of the 24hr daylight: usually earliest morning), and ambient minima when mixing occurs (often mid afternoon). Some results are comparable to parallel chamber studies, but in other cases there are small but significant shifts between CH4 in chamber air and CH4 that is dispersing in the above-ground air. On a regional to continental scale the isotopic signature of bulk sources of emissions can be identified using Keeling plots. The methodology is very applicable for use in urban and urban-rural settings. For example, the winter SE monsoon sweeps from inland central Asia over China to Hong Kong. Application of back trajectory analysis and Keeling plot methods implied coal emissions may be a significant Chinese source of methane in January, although in other

Source Identification of Human Biological Materials and Its Prospect in Forensic Science.

PubMed

Zou, K N; Gui, C; Gao, Y; Yang, F; Zhou, H G

2016-06-01

Source identification of human biological materials in crime scene plays an important role in reconstructing the crime process. Searching specific genetic markers to identify the source of different human biological materials is the emphasis and difficulty of the research work of legal medical experts in recent years. This paper reviews the genetic markers which are used for identifying the source of human biological materials and studied widely, such as DNA methylation, mRNA, microRNA, microflora and protein, etc. By comparing the principles and methods of source identification of human biological materials using different kinds of genetic markers, different source of human biological material owns suitable marker types and can be identified by detecting single genetic marker or combined multiple genetic markers. Though there is no uniform standard and method for identifying the source of human biological materials in forensic laboratories at present, the research and development of a series of mature and reliable methods for distinguishing different human biological materials play the role as forensic evidence which will be the future development direction. Copyright© by the Editorial Department of Journal of Forensic Medicine.

Parallel RNAi screens across different cell lines identify generic and cell type-specific regulators of actin organization and cell morphology.

PubMed

Liu, Tao; Sims, David; Baum, Buzz

2009-01-01

In recent years RNAi screening has proven a powerful tool for dissecting gene functions in animal cells in culture. However, to date, most RNAi screens have been performed in a single cell line, and results then extrapolated across cell types and systems. Here, to dissect generic and cell type-specific mechanisms underlying cell morphology, we have performed identical kinome RNAi screens in six different Drosophila cell lines, derived from two distinct tissues of origin. This analysis identified a core set of kinases required for normal cell morphology in all lines tested, together with a number of kinases with cell type-specific functions. Most significantly, the screen identified a role for minibrain (mnb/DYRK1A), a kinase associated with Down's syndrome, in the regulation of actin-based protrusions in CNS-derived cell lines. This cell type-specific requirement was not due to the peculiarities in the morphology of CNS-derived cells and could not be attributed to differences in mnb expression. Instead, it likely reflects differences in gene expression that constitute the cell type-specific functional context in which mnb/DYRK1A acts. Using parallel RNAi screens and gene expression analyses across cell types we have identified generic and cell type-specific regulators of cell morphology, which include mnb/DYRK1A in the regulation of protrusion morphology in CNS-derived cell lines. This analysis reveals the importance of using different cell types to gain a thorough understanding of gene function across the genome and, in the case of kinases, the difficulties of using the differential gene expression to predict function.

Characterization of sources and loadings of fecal pollutants using microbial source tracking assays in urban and rural areas of the Grand River Watershed, Southwestern Ontario.

PubMed

Lee, Dae-Young; Lee, Hung; Trevors, Jack T; Weir, Susan C; Thomas, Janis L; Habash, Marc

2014-04-15

Sources of fecal water pollution were assessed in the Grand River and two of its tributaries (Ontario, Canada) using total and host-specific (human and bovine) Bacteroidales genetic markers in conjunction with reference information, such as land use and weather. In-stream levels of the markers and culturable Escherichia coli were also monitored during multiple rain events to gain information on fecal loadings to catchment from diffuse sources. Elevated human-specific marker levels were accurately identified in river water impacted by a municipal wastewater treatment plant (WWTP) effluent and at a downstream site in the Grand River. In contrast, the bovine-specific marker showed high levels of cattle fecal pollution in two tributaries, both of which are characterized as intensely farmed areas. The bovine-specific Bacteroidales marker increased with rainfall in the agricultural tributaries, indicating enhanced loading of cattle-derived fecal pollutants to river from non-point sources following rain events. However, rain-triggered fecal loading was not substantiated in urban settings, indicating continuous inputs of human-originated fecal pollutants from point sources, such as WWTP effluent. This study demonstrated that the Bacteroidales source tracking assays, in combination with land use information and hydrological data, may provide additional insight into the spatial and temporal distribution of source-specific fecal contamination in streams impacted by varying land uses. Using the approach described in this study may help to characterize impacted water sources and to design targeted land use management plans in other watersheds in the future. Copyright © 2014 Elsevier Ltd. All rights reserved.

TargetLink, a new method for identifying the endogenous target set of a specific microRNA in intact living cells.

PubMed

Xu, Yan; Chen, Yan; Li, Daliang; Liu, Qing; Xuan, Zhenyu; Li, Wen-Hong

2017-02-01

MicroRNAs are small non-coding RNAs acting as posttranscriptional repressors of gene expression. Identifying mRNA targets of a given miRNA remains an outstanding challenge in the field. We have developed a new experimental approach, TargetLink, that applied locked nucleic acid (LNA) as the affinity probe to enrich target genes of a specific microRNA in intact cells. TargetLink also consists a rigorous and systematic data analysis pipeline to identify target genes by comparing LNA-enriched sequences between experimental and control samples. Using miR-21 as a test microRNA, we identified 12 target genes of miR-21 in a human colorectal cancer cell by this approach. The majority of the identified targets interacted with miR-21 via imperfect seed pairing. Target validation confirmed that miR-21 repressed the expression of the identified targets. The cellular abundance of the identified miR-21 target transcripts varied over a wide range, with some targets expressed at a rather low level, confirming that both abundant and rare transcripts are susceptible to regulation by microRNAs, and that TargetLink is an efficient approach for identifying the target set of a specific microRNA in intact cells. C20orf111, one of the novel targets identified by TargetLink, was found to reside in the nuclear speckle and to be reliably repressed by miR-21 through the interaction at its coding sequence.

Identifying source regions for the atmospheric input of PCDD/Fs to the Baltic Sea

NASA Astrophysics Data System (ADS)

Sellström, Ulla; Egebäck, Anna-Lena; McLachlan, Michael S.

PCDD/F contamination of the Baltic Sea has resulted in the European Union imposing restrictions on the marketing of several fish species. Atmospheric deposition is the major source of PCDD/Fs to the Baltic Sea, and hence there is a need to identify the source regions of the PCDD/Fs in ambient air over the Baltic Sea. A novel monitoring strategy was employed to address this question. During the winter of 2006-2007 air samples were collected in Aspvreten (southern Sweden) and Pallas (northern Finland). Short sampling times (24 h) were employed and only samples with stable air mass back trajectories were selected for analysis of the 2,3,7,8-substituted PCDD/F congeners. The range in the PCDD/F concentrations from 40 samples collected at Aspvreten was a factor of almost 50 (range 0.6-29 fg TEQ/m 3). When the samples were grouped according to air mass origin into seven compass sectors, the variability was much lower (typically less than a factor of 3). This indicates that air mass origin was the primary source of the variability. The contribution of each sector to the PCDD/F contamination over the Baltic Sea during the winter half year of 2006/2007 was calculated from the average PCDD/F concentration for each sector and the frequency with which the air over the Baltic Sea came from that sector. Air masses originating from the south-southwest, south-southeast and east segments contributed 65% of the PCDDs and 75% of the PCDFs. Strong correlations were obtained between the concentrations of most of the PCDD/F congeners and the concentration of soot. These correlations can be used to predict the PCDD/F concentrations during the winter half year from inexpensive soot measurements.

Tissue-enriched expression profiles in Aedes aegypti identify hemocyte-specific transcriptome responses to infection

PubMed Central

Choi, Young-Jun; Fuchs, Jeremy F.; Mayhew, George F.; Yu, Helen E.; Christensen, Bruce M.

2012-01-01

Hemocytes are integral components of mosquito immune mechanisms such as phagocytosis, melanization, and production of antimicrobial peptides. However, our understanding of hemocyte-specific molecular processes and their contribution to shaping the host immune response remains limited. To better understand the immunophysiological features distinctive of hemocytes, we conducted genome-wide analysis of hemocyte-enriched transcripts, and examined how tissue-enriched expression patterns change with the immune status of the host. Our microarray data indicate that the hemocyte-enriched trascriptome is dynamic and context-dependent. Analysis of transcripts enriched after bacterial challenge in circulating hemocytes with respect to carcass added a dimension to evaluating infection-responsive genes and immune-related gene families. We resolved patterns of transcriptional change unique to hemocytes from those that are likely shared by other immune responsive tissues, and identified clusters of genes preferentially induced in hemocytes, likely reflecting their involvement in cell type specific functions. In addition, the study revealed conserved hemocyte-enriched molecular repertoires which might be implicated in core hemocyte function by cross-species meta-analysis of microarray expression data from Anopheles gambiae and Drosophila melanogaster. PMID:22796331

Molecular property diagnostic suite (MPDS): Development of disease-specific open source web portals for drug discovery.

PubMed

Nagamani, S; Gaur, A S; Tanneeru, K; Muneeswaran, G; Madugula, S S; Consortium, Mpds; Druzhilovskiy, D; Poroikov, V V; Sastry, G N

2017-11-01

Molecular property diagnostic suite (MPDS) is a Galaxy-based open source drug discovery and development platform. MPDS web portals are designed for several diseases, such as tuberculosis, diabetes mellitus, and other metabolic disorders, specifically aimed to evaluate and estimate the drug-likeness of a given molecule. MPDS consists of three modules, namely data libraries, data processing, and data analysis tools which are configured and interconnected to assist drug discovery for specific diseases. The data library module encompasses vast information on chemical space, wherein the MPDS compound library comprises 110.31 million unique molecules generated from public domain databases. Every molecule is assigned with a unique ID and card, which provides complete information for the molecule. Some of the modules in the MPDS are specific to the diseases, while others are non-specific. Importantly, a suitably altered protocol can be effectively generated for another disease-specific MPDS web portal by modifying some of the modules. Thus, the MPDS suite of web portals shows great promise to emerge as disease-specific portals of great value, integrating chemoinformatics, bioinformatics, molecular modelling, and structure- and analogue-based drug discovery approaches.

The interprocess NIR sampling as an alternative approach to multivariate statistical process control for identifying sources of product-quality variability.

PubMed

Marković, Snežana; Kerč, Janez; Horvat, Matej

2017-03-01

We are presenting a new approach of identifying sources of variability within a manufacturing process by NIR measurements of samples of intermediate material after each consecutive unit operation (interprocess NIR sampling technique). In addition, we summarize the development of a multivariate statistical process control (MSPC) model for the production of enteric-coated pellet product of the proton-pump inhibitor class. By developing provisional NIR calibration models, the identification of critical process points yields comparable results to the established MSPC modeling procedure. Both approaches are shown to lead to the same conclusion, identifying parameters of extrusion/spheronization and characteristics of lactose that have the greatest influence on the end-product's enteric coating performance. The proposed approach enables quicker and easier identification of variability sources during manufacturing process, especially in cases when historical process data is not straightforwardly available. In the presented case the changes of lactose characteristics are influencing the performance of the extrusion/spheronization process step. The pellet cores produced by using one (considered as less suitable) lactose source were on average larger and more fragile, leading to consequent breakage of the cores during subsequent fluid bed operations. These results were confirmed by additional experimental analyses illuminating the underlying mechanism of fracture of oblong pellets during the pellet coating process leading to compromised film coating.

A new continuous light source for high-speed imaging

NASA Astrophysics Data System (ADS)

Paton, R. T.; Hall, R. E.; Skews, B. W.

2017-02-01

Xenon arc lamps have been identified as a suitable continuous light source for high-speed imaging, specifically high-speed Schlieren and shadowgraphy. One issue when setting us such systems is the time that it takes to reduce a finite source to the approximation of a point source for z-type schlieren. A preliminary design of a compact compound lens for use with a commercial Xenon arc lamp was tested for suitability. While it was found that there is some dimming of the illumination at the spot periphery, the overall spectral and luminance distribution of the compact source is quite acceptable, especially considering the time benefit that it represents.

Sound Sources Identified in High-Speed Jets by Correlating Flow Density Fluctuations With Far-Field Noise

NASA Technical Reports Server (NTRS)

Panda, Jayanta; Seasholtz, Richard G.

2003-01-01

Noise sources in high-speed jets were identified by directly correlating flow density fluctuation (cause) to far-field sound pressure fluctuation (effect). The experimental study was performed in a nozzle facility at the NASA Glenn Research Center in support of NASA s initiative to reduce the noise emitted by commercial airplanes. Previous efforts to use this correlation method have failed because the tools for measuring jet turbulence were intrusive. In the present experiment, a molecular Rayleigh-scattering technique was used that depended on laser light scattering by gas molecules in air. The technique allowed accurate measurement of air density fluctuations from different points in the plume. The study was conducted in shock-free, unheated jets of Mach numbers 0.95, 1.4, and 1.8. The turbulent motion, as evident from density fluctuation spectra was remarkably similar in all three jets, whereas the noise sources were significantly different. The correlation study was conducted by keeping a microphone at a fixed location (at the peak noise emission angle of 30 to the jet axis and 50 nozzle diameters away) while moving the laser probe volume from point to point in the flow. The following figure shows maps of the nondimensional coherence value measured at different Strouhal frequencies ([frequency diameter]/jet speed) in the supersonic Mach 1.8 and subsonic Mach 0.95 jets. The higher the coherence, the stronger the source was.

Identifying natural and anthropogenic sources of metals in urban and rural soils using GIS-based data, PCA, and spatial interpolation

PubMed Central

Davis, Harley T.; Aelion, C. Marjorie; McDermott, Suzanne; Lawson, Andrew B.

2009-01-01

Determining sources of neurotoxic metals in rural and urban soils is important for mitigating human exposure. Surface soil from four areas with significant clusters of mental retardation and developmental delay (MR/DD) in children, and one control site were analyzed for nine metals and characterized by soil type, climate, ecological region, land use and industrial facilities using readily-available GIS-based data. Kriging, principal component analysis (PCA) and cluster analysis (CA) were used to identify commonalities of metal distribution. Three MR/DD areas (one rural and two urban) had similar soil types and significantly higher soil metal concentrations. PCA and CA results suggested that Ba, Be and Mn were consistently from natural sources; Pb and Hg from anthropogenic sources; and As, Cr, Cu, and Ni from both sources. Arsenic had low commonality estimates, was highly associated with a third PCA factor, and had a complex distribution, complicating mitigation strategies to minimize concentrations and exposures. PMID:19361902

Questionable Specificity of Genetic Total Faecal Pollution Markers for Integrated Water Quality Monitoring and Source Tracking

NASA Astrophysics Data System (ADS)

Vierheilig, Julia; Reischer, Georg H.; Farnleitner, Andreas H.

2010-05-01

Characterisation of microbial faecal hazards in water is a fundamental aspect for target-orientated water resources management to achieve appropriate water quality for various purposes like water supply or agriculture and thus to minimize related health risks. Nowadays the management of water resources increasingly demands detailed knowledge on the extent and the origin of microbial pollution. Cultivation of standard faecal indicator bacteria, which has been used for over a century to test the microbiological water quality, cannot sufficiently meet these challenges. The abundant intestinal bacterial populations are very promising alternative targets for modern faecal indication systems. Numerous assays for the detection of genetic markers targeting source-specific populations of the phylum Bacteroidetes have been developed in recent years. In some cases markers for total faecal pollution were also proposed in order to relate source-specific marker concentrations to general faecal pollution levels. However, microbial populations in intestinal and non-intestinal systems exhibit a dazzling array of diversity and molecular analysis of microbial faecal pollution has been based on a fragmentary puzzle of very limited sequence information. The aim of this study was to test the available qPCR-based methods detecting genetic Bacteroidetes markers for total faecal pollution in terms of their value and specificity as indicators of faecal pollution. We applied the AllBac (Layton et al., 2006) the BacUni (Kildare et al., 2007) and the Bacteroidetes (Dick and Field, 2004) assays on soil DNA samples. Samples were collected in well characterised karst spring catchments in Austria's Eastern Calcareous Alps. They were at various levels of altitude between 800 and 1800 meters above sea level and from several different habitats (woodland, alpine pastures, krummholz). In addition we tried to choose sampling sites representing a presumptive gradient of faecal pollution levels. For

Sparse Feature Selection Identifies H2A.Z as a Novel, Pattern-Specific Biomarker for Asymmetrically Self-Renewing Distributed Stem Cells

PubMed Central

Huh, Yang Hoon; Noh, Minsoo; Burden, Frank R.; Chen, Jennifer C.; Winkler, David A.; Sherley, James L.

2015-01-01

There is a long-standing unmet clinical need for biomarkers with high specificity for distributed stem cells (DSCs) in tissues, or for use in diagnostic and therapeutic cell preparations (e.g., bone marrow). Although DSCs are essential for tissue maintenance and repair, accurate determination of their numbers for medical applications has been problematic. Previous searches for biomarkers expressed specifically in DSCs were hampered by difficulty obtaining pure DSCs and by the challenges in mining complex molecular expression data. To identify DSC such useful and specific biomarkers, we combined a novel sparse feature selection method with combinatorial molecular expression data focused on asymmetric self-renewal, a conspicuous property of DSCs. The analysis identified reduced expression of the histone H2A variant H2A.Z as a superior molecular discriminator for DSC asymmetric self-renewal. Subsequent molecular expression studies showed H2A.Z to be a novel “pattern-specific biomarker” for asymmetrically self-renewing cells with sufficient specificity to count asymmetrically self-renewing DSCs in vitro and potentially in situ. PMID:25636161

Luminous Infrared Sources in the Local Group: Identifying the Missing Links in Massive Star Evolution

NASA Astrophysics Data System (ADS)

Britavskiy, N.; Bonanos, A. Z.; Mehner, A.

2015-01-01

We present the first systematic survey of dusty massive stars (RSGs, LBVs, sgB[e]) in nearby galaxies, with the goal of understanding their importance in massive star evolution. Using the fact that these stars are bright in mid-infrared colors due to dust, we provide a technique for selecting and identifying dusty evolved stars based on the results of Bonanos et al. (2009, 2010), Britavskiy et al. (2014), and archival Spitzer/IRAC photometry. We present the results of our spectroscopic follow-up of luminous infrared sources in the Local Group dwarf irregular galaxies: Pegasus, Phoenix, Sextans A and WLM. The survey aims to complete the census of dusty massive stars in the Local Group.

GMRT DISCOVERY OF PSR J1544+4937: AN ECLIPSING BLACK-WIDOW PULSAR IDENTIFIED WITH A FERMI-LAT SOURCE

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

Bhattacharyya, B.; Roy, J.; Gupta, Y.

2013-08-10

Using the Giant Metrewave Radio Telescope, we performed deep observations to search for radio pulsations in the directions of unidentified Fermi-Large Area Telescope {gamma}-ray sources. We report the discovery of an eclipsing black-widow millisecond pulsar, PSR J1544+4937, identified with the uncataloged {gamma}-ray source FERMI J1544.2+4941. This 2.16 ms pulsar is in a 2.9 hr compact circular orbit with a very low mass companion (M{sub c} > 0.017M{sub Sun }). At 322 MHz this pulsar is found to be eclipsing for 13% of its orbit, whereas at 607 MHz the pulsar is detected throughout the low-frequency eclipse phase. Variations in themore » eclipse ingress phase are observed, indicating a clumpy and variable eclipsing medium. Moreover, additional short-duration absorption events are observed around the eclipse boundaries. Using the radio timing ephemeris we were able to detect {gamma}-ray pulsations from this pulsar, confirming it as the source powering the {gamma}-ray emission.« less

Sex-Specific Genetic Loci for Femoral Neck Bone Mass and Strength Identified in Inbred COP and DA Rats

PubMed Central

Alam, Imranul; Sun, Qiwei; Liu, Lixiang; Koller, Daniel L; Carr, Lucinda G; Econs, Michael J; Foroud, Tatiana; Turner, Charles H

2008-01-01

Introduction Hip fracture is the most devastating osteoporotic fracture type with significant morbidity and mortality. Several studies in humans identified chromosomal regions linked to hip size and bone mass. Animal models, particularly the inbred rat, serve as complementary approaches for studying the genetic influence on hip fragility. The purpose of this study is to identify sex-independent and sex-specific quantitative trait loci (QTLs) for femoral neck density, structure, and strength in inbred Copenhagen 2331 (COP) and Dark Agouti (DA) rats. Materials and Methods A total of 828 (405 males and 423 females) F2 progeny derived from the inbred COP and DA strains of rats were phenotyped for femoral neck volumetric BMD (vBMD), cross-sectional area, polar moment of inertia (Ip), neck width, ultimate force, and energy to break. A whole genome screen was performed using 93 microsatellite markers with an average intermarker distance of 20 cM. Recombination-based marker maps were generated using MAPMAKER/EXP from the COP × DA F2 data and compared with published Rat Genome Database (RGD) maps. These maps were used for genome-wide linkage analyses to detect sex-independent and sex-specific QTLs. Results Significant evidence of linkage (p < 0.01) for sex-independent QTLs were detected for (1) femoral neck vBMD on chromosomes (Chrs) 1, 6, 10, and 12, (2) femoral neck structure on Chrs 5, 7, 10, and 18, and (3) biomechanical properties on Chrs 1 and 4. Male-specific QTLs were discovered on Chrs 2, 9, and 18 for total vBMD, on Chr 17 for trabecular vBMD, on Chr 9 for total bone area, and on Chr 15 for ultimate force. A female-specific QTL was discovered on Chr 2 for ultimate force. The effect size of the individual QTL varied between 1% and 4%. Conclusions We detected evidence that sex-independent and sex-specific QTLs contribute to hip fragility in the inbred rat. Several QTLs regions identified in this study are homologous to human chromosomal regions previously linked to

Design specification for the European Spallation Source neutron generating target element

NASA Astrophysics Data System (ADS)

Aguilar, A.; Sordo, F.; Mora, T.; Mena, L.; Mancisidor, M.; Aguilar, J.; Bakedano, G.; Herranz, I.; Luna, P.; Magan, M.; Vivanco, R.; Jimenez-Villacorta, F.; Sjogreen, K.; Oden, U.; Perlado, J. M.; Martinez, J. L.; Bermejo, F. J.

2017-06-01

The paper addresses some of the most relevant issues concerning the thermal hydraulics and radiation damage of the neutron generation target to be built at the European Spallation Source as recently approved after a critical design review. The target unit consists of a set of Tungsten blocks placed inside a wheel of 2.5 m diameter which rotates at some 0.5 Hz in order to distribute the heat generated from incoming protons which reach the target in the radial direction. The spallation material elements are composed of an array of Tungsten pieces which rest on a rotating steel support (the cassette) and are distributed in a cross-flow configuration. The thermal, mechanical and radiation effects resulting from the impact of a 2 GeV proton pulse are analysed in detail as well as an evaluation of the inventory of spallation products. The current design is found to conform to specifications and found to be robust enough to deal with several accident scenarios.

Exome chip meta-analysis identifies novel loci and East Asian-specific coding variants contributing to lipid levels and coronary artery disease

PubMed Central

Lu, Xiangfeng; Peloso, Gina M; Liu, Dajiang J.; Wu, Ying; Zhang, He; Zhou, Wei; Li, Jun; Tang, Clara Sze-man; Dorajoo, Rajkumar; Li, Huaixing; Long, Jirong; Guo, Xiuqing; Xu, Ming; Spracklen, Cassandra N.; Chen, Yang; Liu, Xuezhen; Zhang, Yan; Khor, Chiea Chuen; Liu, Jianjun; Sun, Liang; Wang, Laiyuan; Gao, Yu-Tang; Hu, Yao; Yu, Kuai; Wang, Yiqin; Cheung, Chloe Yu Yan; Wang, Feijie; Huang, Jianfeng; Fan, Qiao; Cai, Qiuyin; Chen, Shufeng; Shi, Jinxiu; Yang, Xueli; Zhao, Wanting; Sheu, Wayne H.-H.; Cherny, Stacey Shawn; He, Meian; Feranil, Alan B.; Adair, Linda S.; Gordon-Larsen, Penny; Du, Shufa; Varma, Rohit; da Chen, Yii-Der I; Shu, XiaoOu; Lam, Karen Siu Ling; Wong, Tien Yin; Ganesh, Santhi K.; Mo, Zengnan; Hveem, Kristian; Fritsche, Lars; Nielsen, Jonas Bille; Tse, Hung-fat; Huo, Yong; Cheng, Ching-Yu; Chen, Y. Eugene; Zheng, Wei; Tai, E Shyong; Gao, Wei; Lin, Xu; Huang, Wei; Abecasis, Goncalo; Consortium, GLGC; Kathiresan, Sekar; Mohlke, Karen L.; Wu, Tangchun; Sham, Pak Chung; Gu, Dongfeng; Willer, Cristen J

2017-01-01

Most genome-wide association studies have been conducted in European individuals, even though most genetic variation in humans is seen only in non-European samples. To search for novel loci associated with blood lipid levels and clarify the mechanism of action at previously identified lipid loci, we examined protein-coding genetic variants in 47,532 East Asian individuals using an exome array. We identified 255 variants at 41 loci reaching chip-wide significance, including 3 novel loci and 14 East Asian-specific coding variant associations. After meta-analysis with > 300,000 European samples, we identified an additional 9 novel loci. The same 16 genes were identified by the protein-altering variants in both East Asians and Europeans, likely pointing to the functional genes. Our data demonstrate that most of the low-frequency or rare coding variants associated with lipids are population-specific, and that examining genomic data across diverse ancestries may facilitate the identification of functional genes at associated loci. PMID:29083407

Quantifying and identifying the sources of fine sediment input in a typical Mongolian river basin, the Kharaa River case study

NASA Astrophysics Data System (ADS)

Theuring, Phillip

2013-04-01

Mongolia is facing a tremendous change of land-use intensification due to expansions in the agricultural sector, an increase of cattle and livestock and a growth of urban settlements by migration of the rural population to the cities. With most of its area located in a semiarid to arid environment, Mongolia is vulnerable to climatic changes that are expected to lead to higher temperatures and increased evapotranspiration. It is expected that this may lead to unfavorable changes in surface water quality caused by increased nutrients and sediment bound pollutants emissions. Increased fine sediment load is associated with nutrient, heavy metal and pollutant input and therefore affects water quality. Previous studies using radionuclide fallout isotope sediment source fingerprinting investigations identified riverbank erosion as the main source of suspended sediment in the Kharaa River. Erosion susceptibility calculations in combination with suspended sediment observations showed strong seasonal and annual variabilities of sediment input and in-stream transport, and a strong connection of erosional behaviour with land-use.The objective of this study is to quantify the current water quality threats by fine sediment inputs in the 15,000 km2 Kharaa River basin in Northern Mongolia by delineating the sources of the fine sediments and estimating the sediment budget.To identify the spatial distribution of sediment sources within the catchment, more than 1000 samples from the river confluences at the outlet of each sub basin into the main tributary were collected during 5 intensive grab sediment sampling campaigns in 2009-11. The fine sediment fraction (<10μm) has been analysed using geochemical tracer techniques for spatial source identification, based on major elements (e.g. Si, Al, Mg, Fe, Na, K, P) and trace elements (e.g. Ba, Pb, Sr, Zn). The contribution of suspended sediment of each sub basin in the main tributary has been evaluated with help of a mixing model. To

A strategy for high specific power pyroelectric energy harvesting from a fluid source

NASA Astrophysics Data System (ADS)

Maheux, E.; Hrebtov, M. Yu.; Sukhorukov, G.; Kozyulin, N. N.; Bobrov, M. S.; Dobroselsky, K. G.; Chikishev, L. M.; Dulin, V. M.; Yudin, P. V.

2017-12-01

Conversion of waste heat into usable electricity is now one of the important strategies for saving natural resources and minimizing impact on the environment. In contrast to Seebeck devices, utilizing a temperature gradient, pyroelectric scavengers use temporal temperature oscillations. Here, optimal strategies for pyroelectric energy harvesting are theoretically investigated from the point of view of non-stationary heat exchange for the application-relevant case of harvesting with a pyroelectric lamella from a fluid heat source. It is shown that for a fixed lamella thickness by choosing appropriate phase shift between the temperature oscillations and the voltage on the pyroelectric lamella, one can effectively operate at high frequencies and achieve a two to three-fold increase in specific power with respect to the classical Olsen cycle. A further increase in specific power is achieved by thinning down the lamella. For devices with a thickness down to a few hundreds of nanometers, specific power linearly increases with the inverse thickness. Further scaling down of the device is hampered with the heat exchange in the boundary layer. Our simulations for a representative pyroelectric Pb(Zr0,5Ti0,5)O3 predict harvestable powers of the order of kW/kg for a device with a thickness in the range from 100 nm to 1 μm, operating at hundreds of Hz.

Multivariate statistical and lead isotopic analyses approach to identify heavy metal sources in topsoil from the industrial zone of Beijing Capital Iron and Steel Factory.

PubMed

Zhu, Guangxu; Guo, Qingjun; Xiao, Huayun; Chen, Tongbin; Yang, Jun

2017-06-01

than the natural sources. Our study could not only reveal the overall situation of heavy metal contamination, but also identify the specific pollution sources.

Identifying Genetic Sources of Phenotypic Heterogeneity in Orofacial Clefts by Targeted Sequencing.

PubMed

Carlson, Jenna C; Taub, Margaret A; Feingold, Eleanor; Beaty, Terri H; Murray, Jeffrey C; Marazita, Mary L; Leslie, Elizabeth J

2017-07-17

Orofacial clefts (OFCs), including nonsyndromic cleft lip with or without cleft palate (NSCL/P), are common birth defects. NSCL/P is highly heterogeneous with multiple phenotypic presentations. Two common subtypes of NSCL/P are cleft lip (CL) and cleft lip with cleft palate (CLP) which have different population prevalence. Similarly, NSCL/P can be divided into bilateral and unilateral clefts, with unilateral being the most common. Individuals with unilateral NSCL/P are more likely to be affected on the left side of the upper lip, but right side affection also occurs. Moreover, NSCL/P is twice as common in males as in females. The goal of this study is to discover genetic variants that have different effects in case subgroups. We conducted both common variant and rare variant analyses in 1034 individuals of Asian ancestry with NSCL/P, examining four sources of heterogeneity within CL/P: cleft type, sex, laterality, and side. We identified several regions associated with subtype differentiation: cleft type differences in 8q24 (p = 1.00 × 10 -4 ), laterality differences in IRF6, a gene previously implicated with wound healing (p = 2.166 × 10 -4 ), sex differences and side of unilateral CL differences in FGFR2 (p = 3.00 × 10 -4 ; p = 6.00 × 10 -4 ), and sex differences in VAX1 (p < 1.00 × 10 -4 ) among others. Many of the regions associated with phenotypic modification were either adjacent to or overlapping functional elements based on ENCODE chromatin marks and published craniofacial enhancers. We have identified multiple common and rare variants as potential phenotypic modifiers of NSCL/P, and suggest plausible elements responsible for phenotypic heterogeneity, further elucidating the complex genetic architecture of OFCs. Birth Defects Research 109:1030-1038, 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Identifying Patterns in the Weather of Europe for Source Term Estimation

NASA Astrophysics Data System (ADS)

Klampanos, Iraklis; Pappas, Charalambos; Andronopoulos, Spyros; Davvetas, Athanasios; Ikonomopoulos, Andreas; Karkaletsis, Vangelis

2017-04-01

During emergencies that involve the release of hazardous substances into the atmosphere the potential health effects on the human population and the environment are of primary concern. Such events have occurred in the past, most notably involving radioactive and toxic substances. Examples of radioactive release events include the Chernobyl accident in 1986, as well as the more recent Fukushima Daiichi accident in 2011. Often, the release of dangerous substances in the atmosphere is detected at locations different from the release origin. The objective of this work is the rapid estimation of such unknown sources shortly after the detection of dangerous substances in the atmosphere, with an initial focus on nuclear or radiological releases. Typically, after the detection of a radioactive substance in the atmosphere indicating the occurrence of an unknown release, the source location is estimated via inverse modelling. However, depending on factors such as the spatial resolution desired, traditional inverse modelling can be computationally time-consuming. This is especially true for cases where complex topography and weather conditions are involved and can therefore be problematic when timing is critical. Making use of machine learning techniques and the Big Data Europe platform1, our approach moves the bulk of the computation before any such event taking place, therefore allowing for rapid initial, albeit rougher, estimations regarding the source location. Our proposed approach is based on the automatic identification of weather patterns within the European continent. Identifying weather patterns has long been an active research field. Our case is differentiated by the fact that it focuses on plume dispersion patterns and these meteorological variables that affect dispersion the most. For a small set of recurrent weather patterns, we simulate hypothetical radioactive releases from a pre-known set of nuclear reactor locations and for different substance and temporal

Public clonotype usage identifies protective Gag-specific CD8+ T cell responses in SIV infection

PubMed Central

Asher, Tedi E.; Wilson, Nancy A.; Nason, Martha C.; Brenchley, Jason M.; Metzler, Ian S.; Venturi, Vanessa; Gostick, Emma; Chattopadhyay, Pratip K.; Roederer, Mario; Davenport, Miles P.; Watkins, David I.; Douek, Daniel C.

2009-01-01

Despite the pressing need for an AIDS vaccine, the determinants of protective immunity to HIV remain concealed within the complexity of adaptive immune responses. We dissected immunodominant virus-specific CD8+ T cell populations in Mamu-A*01+ rhesus macaques with primary SIV infection to elucidate the hallmarks of effective immunity at the level of individual constituent clonotypes, which were identified according to the expression of distinct T cell receptors (TCRs). The number of public clonotypes, defined as those that expressed identical TCR β-chain amino acid sequences and recurred in multiple individuals, contained within the acute phase CD8+ T cell population specific for the biologically constrained Gag CM9 (CTPYDINQM; residues 181–189) epitope correlated negatively with the virus load set point. This independent molecular signature of protection was confirmed in a prospective vaccine trial, in which clonotype engagement was governed by the nature of the antigen rather than the context of exposure and public clonotype usage was associated with enhanced recognition of epitope variants. Thus, the pattern of antigen-specific clonotype recruitment within a protective CD8+ T cell population is a prognostic indicator of vaccine efficacy and biological outcome in an AIDS virus infection. PMID:19349463

Consideration of the Protection Curtain's Shielding Ability after Identifying the Source of Scattered Radiation in the Angiography.

PubMed

Sato, Naoki; Fujibuchi, Toshioh; Toyoda, Takatoshi; Ishida, Takato; Ohura, Hiroki; Miyajima, Ryuichi; Orita, Shinichi; Sueyoshi, Tomonari

2017-06-15

To decrease radiation exposure to medical staff performing angiography, the dose distribution in the angiography was calculated in room using the particle and heavy ion transport code system (PHITS), which is based on Monte Carlo code, and the source of scattered radiation was confirmed using a tungsten sheet by considering the difference shielding performance among different sheet placements. Scattered radiation generated from a flat panel detector, X-ray tube and bed was calculated using the PHITS. In this experiment, the source of scattered radiation was identified as the phantom or acrylic window attached to the X-ray tube thus, a protection curtain was placed on the bed to shield against scattered radiation at low positions. There was an average difference of 20% between the measured and calculated values. The H*(10) value decreased after placing the sheet on the right side of the phantom. Thus, the curtain could decrease scattered radiation. © Crown copyright 2016.

Identifying key sources of uncertainty in the modelling of greenhouse gas emissions from wastewater treatment.

PubMed

Sweetapple, Christine; Fu, Guangtao; Butler, David

2013-09-01

This study investigates sources of uncertainty in the modelling of greenhouse gas emissions from wastewater treatment, through the use of local and global sensitivity analysis tools, and contributes to an in-depth understanding of wastewater treatment modelling by revealing critical parameters and parameter interactions. One-factor-at-a-time sensitivity analysis is used to screen model parameters and identify those with significant individual effects on three performance indicators: total greenhouse gas emissions, effluent quality and operational cost. Sobol's method enables identification of parameters with significant higher order effects and of particular parameter pairs to which model outputs are sensitive. Use of a variance-based global sensitivity analysis tool to investigate parameter interactions enables identification of important parameters not revealed in one-factor-at-a-time sensitivity analysis. These interaction effects have not been considered in previous studies and thus provide a better understanding wastewater treatment plant model characterisation. It was found that uncertainty in modelled nitrous oxide emissions is the primary contributor to uncertainty in total greenhouse gas emissions, due largely to the interaction effects of three nitrogen conversion modelling parameters. The higher order effects of these parameters are also shown to be a key source of uncertainty in effluent quality. Copyright © 2013 Elsevier Ltd. All rights reserved.

Sources of plutonium to the tropical Northwest Pacific Ocean (1943-1999) identified using a natural coral archive

NASA Astrophysics Data System (ADS)

Lindahl, Patric; Asami, Ryuji; Iryu, Yasufumi; Worsfold, Paul; Keith-Roach, Miranda; Choi, Min-Seok

2011-03-01

The Pu isotopes, 239Pu and 240Pu, were determined in annually-banded skeletons of an accurately dated (1943-1999) modern coral ( Porites lobata) from Guam Island to identify historical Pu sources to the tropical Northwest Pacific Ocean. Activity concentrations of 239+240Pu and 240Pu/ 239Pu atom ratios were determined in the dated coral bands using multi-collector inductively coupled plasma mass spectrometry (MC-ICP-MS). Close-in fallout from the former US Pacific Proving Grounds (PPG) in the Marshall Islands and global fallout were identified as the two main sources. The Guam site was dominated by PPG close-in fallout in the 1950s, with an average 240Pu/ 239Pu atom ratio of 0.315 ± 0.005. In addition, a higher 240Pu/ 239Pu atom ratio (0.456 ± 0.020) was observed that could be attributed to fallout from the "Ivy Mike" thermonuclear detonation in 1952. The atom ratio decreased in the 1960s and 1970s due to increase in the global fallout with a low 240Pu/ 239Pu atom ratio (˜0.18). Recent coral bands (1981-1999) are dominated by the transport of remobilised Pu, with high 240Pu/ 239Pu atom ratios, from the Marshall Islands to Guam Island along the North Equatorial Current (NEC). This remobilised Pu was estimated to comprise 69% of the total Pu in the recent coral bands, although its contribution was variable over time.

Airborne Quercus pollen in SW Spain: Identifying favourable conditions for atmospheric transport and potential source areas.

PubMed

Maya-Manzano, José María; Fernández-Rodríguez, Santiago; Smith, Matt; Tormo-Molina, Rafael; Reynolds, Andrew M; Silva-Palacios, Inmaculada; Gonzalo-Garijo, Ángela; Sadyś, Magdalena

2016-11-15

The pollen grains of Quercus spp. (oak trees) are allergenic. This study investigates airborne Quercus pollen in SW Spain with the aim identifying favourable conditions for atmospheric transport and potential sources areas. Two types of Quercus distribution maps were produced. Airborne Quercus pollen concentrations were measured at three sites located in the Extremadura region (SW Spain) for 3 consecutive years. The seasonal occurrence of Quercus pollen in the air was investigated, as well as days with pollen concentrations ≥80Pm(-3). The distance that Quercus pollen can be transported in appreciable numbers was calculated using clusters of back trajectories representing the air mass movement above the source areas (oak woodlands), and by using a state-of-the-art dispersion model. The two main potential sources of Quercus airborne pollen captured in SW Spain are Q. ilex subsp. ballota and Q. suber. The minimum distances between aerobiological stations and Quercus woodlands have been estimated as: 40km (Plasencia), 66km (Don Benito), 62km (Zafra) from the context of this study. Daily mean Quercus pollen concentration can exceed 1,700Pm(-3), levels reached not less than 24 days in a single year. High Quercus pollen concentration were mostly associated with moderate wind speed events (6-10ms(-1)), whereas that a high wind speed (16-20ms(-1)) seems to be associated with low concentrations. Copyright © 2016 Elsevier B.V. All rights reserved.

An exploratory study identifying where local government public health decision makers source their evidence for policy.

PubMed

Stoneham, Melissa; Dodds, James

2014-08-01

The Western Australian (WA) Public Health Bill will replace the antiquated Health Act 1911. One of the proposed clauses of the Bill requires all WA local governments to develop a Public Health Plan. The Bill states that Public Health Plans should be based on evidence from all levels, including national and statewide priorities, community needs, local statistical evidence, and stakeholder data. This exploratory study, which targeted 533 WA local government officers, aimed to identify the sources of evidence used to generate the list of public health risks to be included in local government Public Health Plans. The top four sources identified for informing local policy were: observation of the consequences of the risks in the local community (24.5%), statewide evidence (17.6%), local evidence (17.6%) and coverage in local media (16.2%). This study confirms that both hard and soft data are used to inform policy decisions at the local level. Therefore, the challenge that this study has highlighted is in the definition or constitution of evidence. SO WHAT? Evidence is critical to the process of sound policy development. This study highlights issues associated with what actually constitutes evidence in the policy development process at the local government level. With the exception of those who work in an extremely narrow field, it is difficult for local government officers, whose role includes policymaking, to read the vast amount of information that has been published in their area of expertise. For those who are committed to the notion of evidence-based policymaking, as advocated within the WA Public Health Bill, this presents a considerable challenge.

Simultaneous event-specific estimates of transport, loss, and source rates for relativistic outer radiation belt electrons: Event-Specific 1-D Modeling

DOE PAGES

Schiller, Q.; Tu, W.; Ali, A. F.; ...

2017-03-11

The most significant unknown regarding relativistic electrons in Earth’s outer Van Allen radiation belt is the relative contribution of loss, transport, and acceleration processes within the inner magnetosphere. Detangling each individual process is critical to improve the understanding of radiation belt dynamics, but determining a single component is challenging due to sparse measurements in diverse spatial and temporal regimes. However, there are currently an unprecedented number of spacecraft taking measurements that sample different regions of the inner magnetosphere. With the increasing number of varied observational platforms, system dynamics can begin to be unraveled. In this work, we employ in-situ measurementsmore » during the 13-14 January 2013 enhancement event to isolate transport, loss, and source dynamics in a one dimensional radial diffusion model. We then validate the results by comparing them to Van Allen Probes and THEMIS observations, indicating that the three terms have been accurately and individually quantified for the event. Finally, a direct comparison is performed between the model containing event-specific terms and various models containing terms parameterized by geomagnetic index. Models using a simple 3/Kp loss timescale show deviation from the event specific model of nearly two orders of magnitude within 72 hours of the enhancement event. However, models using alternative loss timescales closely resemble the event specific model.« less

Simultaneous event-specific estimates of transport, loss, and source rates for relativistic outer radiation belt electrons: Event-Specific 1-D Modeling

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

Schiller, Q.; Tu, W.; Ali, A. F.

The most significant unknown regarding relativistic electrons in Earth’s outer Van Allen radiation belt is the relative contribution of loss, transport, and acceleration processes within the inner magnetosphere. Detangling each individual process is critical to improve the understanding of radiation belt dynamics, but determining a single component is challenging due to sparse measurements in diverse spatial and temporal regimes. However, there are currently an unprecedented number of spacecraft taking measurements that sample different regions of the inner magnetosphere. With the increasing number of varied observational platforms, system dynamics can begin to be unraveled. In this work, we employ in-situ measurementsmore » during the 13-14 January 2013 enhancement event to isolate transport, loss, and source dynamics in a one dimensional radial diffusion model. We then validate the results by comparing them to Van Allen Probes and THEMIS observations, indicating that the three terms have been accurately and individually quantified for the event. Finally, a direct comparison is performed between the model containing event-specific terms and various models containing terms parameterized by geomagnetic index. Models using a simple 3/Kp loss timescale show deviation from the event specific model of nearly two orders of magnitude within 72 hours of the enhancement event. However, models using alternative loss timescales closely resemble the event specific model.« less

Identifying Sources of Funding That Contribute to Scholastic Productivity in Academic Plastic Surgeons.

PubMed

Ruan, Qing Zhao; Cohen, Justin B; Baek, Yoonji; Chen, Austin D; Doval, Andres F; Singhal, Dhruv; Fukudome, Eugene Y; Lin, Samuel J; Lee, Bernard T

2018-04-01

Scholastic productivity has previously been shown to be positively associated with National Institute of Health (NIH) grants and industry funding. This study examines whether society, industry, or federal funding contributes toward academic productivity as measured by scholastic output of academic plastic surgeons. Institution Web sites were used to acquire academic attributes of full-time academic plastic surgeons. The Center for Medicare and Medicaid Services Open Payment database, NIH reporter, the Plastic Surgery Foundation (PSF), and American Association of Plastic Surgeons (AAPS) Web sites were accessed for funding and endowment details. Bibliometric data of each surgeon were then collected via Scopus to ascertain strengths of association with each source. Multiple linear regression analysis was used to identify significant contributors to high scholastic output. We identified 935 academic plastic surgeons with 94 (10.1%), 24 (2.6%), 724 (77.4%), and 62 (6.6%) receiving funding from PSF, AAPS, industry, and NIH, respectively. There were positive correlations in receiving NIH, PSF, and/or AAPS funding (P < 0.001), whereas industry funding was found to negatively associate with PSF (r = -0.75, P = 0.022) grants. The NIH R award was consistently found to be the most predictive of academic output across bibliometrics, followed by the AAPS academic scholarship award. Conventional measures of academic seniority remained predictive across all measures used. Our study demonstrates for the first time interactions between industry, federal, and association funding. The NIH R award was the strongest determinant of high scholastic productivity. Recognition through AAPS academic scholarships seemed to associate with subsequent success in NIH funding.

Source apportionment of elevated wintertime PAHs by compound-specific radiocarbon analysis

NASA Astrophysics Data System (ADS)

Sheesley, R. J.; Kruså, M.; Krecl, P.; Johansson, C.; Gustafsson, Ã.-.

2008-12-01

Natural abundance radiocarbon analysis facilitates distinct source apportionment between contemporary biomass/biofuel (14C "alive") versus fossil fuel (14C "dead") combustion. Here, the first compound-specific radiocarbon analysis (CSRA) of atmospheric polycylic aromatic hydrocarbons (PAHs) was demonstrated for a set of samples collected in Lycksele, Sweden a small town with frequent episodes of severe atmospheric pollution in the winter. Renewed interest in residential wood combustion means than this type of seasonal pollution is of increasing concern in many areas. Five individual/paired PAH isolates from three pooled fortnight-long filter collections were analyzed by CSRA: phenanthrene, fluoranthene, pyrene, benzo[b+k]fluoranthene and indeno[cd]pyrene plus benzo[ghi]perylene; phenanthrene was the only compound also analyzed in the gas phase. The measured Δ14C for PAHs spanned from -138.3‰ to 58.0‰. A simple isotopic mass balance model was applied to estimate the fraction biomass (fbiomass) contribution that was constrained to a range of 71% for indeno[cd]pyrene+benzo[ghi]perylene to 87% for the gas phase phenanthrene and particulate fluoranthene, respectively. Indeno[cd]pyrene plus benzo[ghi]perylene, known to be enhanced in gasoline-powered motor vehicle exhaust compared to diesel exhaust, had the lowest contribution of biomass combustion of the measured PAHs by 9%. The total organic carbon (TOC, defined as carbon remaining after removal of inorganic carbon) fbiomass was estimated to be 77%, which falls within the range for PAHs. This CSRA data of atmospheric PAHs demonstrate the non-uniformity of biomass combustion contribution to different PAHs even in a location with limited local emission sources and illustrates that regulatory efforts would not evenly reduce all PAHs.

Inventory of Data Sources for Estimating Health Care Costs in the United States

PubMed Central

Lund, Jennifer L.; Yabroff, K. Robin; Ibuka, Yoko; Russell, Louise B.; Barnett, Paul G.; Lipscomb, Joseph; Lawrence, William F.; Brown, Martin L.

2011-01-01

Objective To develop an inventory of data sources for estimating health care costs in the United States and provide information to aid researchers in identifying appropriate data sources for their specific research questions. Methods We identified data sources for estimating health care costs using 3 approaches: (1) a review of the 18 articles included in this supplement, (2) an evaluation of websites of federal government agencies, non profit foundations, and related societies that support health care research or provide health care services, and (3) a systematic review of the recently published literature. Descriptive information was abstracted from each data source, including sponsor, website, lowest level of data aggregation, type of data source, population included, cross-sectional or longitudinal data capture, source of diagnosis information, and cost of obtaining the data source. Details about the cost elements available in each data source were also abstracted. Results We identified 88 data sources that can be used to estimate health care costs in the United States. Most data sources were sponsored by government agencies, national or nationally representative, and cross-sectional. About 40% were surveys, followed by administrative or linked administrative data, fee or cost schedules, discharges, and other types of data. Diagnosis information was available in most data sources through procedure or diagnosis codes, self-report, registry, or chart review. Cost elements included inpatient hospitalizations (42.0%), physician and other outpatient services (45.5%), outpatient pharmacy or laboratory (28.4%), out-of-pocket (22.7%), patient time and other direct nonmedical costs (35.2%), and wages (13.6%). About half were freely available for downloading or available for a nominal fee, and the cost of obtaining the remaining data sources varied by the scope of the project. Conclusions Available data sources vary in population included, type of data source, scope, and

Identifying exposure disparities in air pollution epidemiology specific to adverse birth outcomes

NASA Astrophysics Data System (ADS)

Geer, Laura A.

2014-10-01

More than 147 million people in the US live in areas where pollutant levels are above regulatory limits and pose a risk to health. Most of the vast network of air pollutant monitors in the US are located in places with higher pollution levels and a higher density of pollutant sources (e.g., point sources from industrial pollution). Vulnerable populations are more likely to live closer to pollutant sources, and thus closer to pollutant monitors. These differential exposures have an impact on maternal and child health; maternal air pollutant exposures have been linked to adverse outcomes such as preterm birth and infant low birth weight. Several studies are highlighted that address methodological approaches in the study of air pollution and health disparities.

Distribution and region-specific sources of Dechlorane Plus in marine sediments from the coastal East China Sea.

PubMed

Wang, Guoguang; Peng, Jialin; Hao, Ting; Liu, Yao; Zhang, Dahai; Li, Xianguo

2016-12-15

Dechlorane Plus (DP) is a highly chlorinated flame retardant and found to be ubiquitously present in the environment. We reported here the first record of DP in sediments from the coastal East China Sea (ECS). DP was detected in most of the surface sediments, and the concentrations ranged from 14.8 to 198pg/g dry weight (dw) with a mean value of 64.4pg/g dw. Overall, DP levels exhibited a seaward decreasing trend from the inshore toward outer sea. The fractional abundance of anti-DP (f anti ) showed regional discrepancies, attributing to different environmental behaviors of DP isomers. Depth profiles of DP in a sediment core from estuarine environment showed distinct fluctuation, and the core in open sea had stable deposition environment with two peak values of DP in ~1978 and 2000. The f anti exhibited downward decreasing trend prior to mid-1950s, indicating a preferential degradation of anti-DP and/or a greater adsorption capacity of syn-DP after its burial. Lignin and lipid biomarkers (∑C 27 +C 29 +C 31 n-alkanes) of terrestrial organic matters were introduced to identify region-specific sources of DP, and the results showed that DP in the northern inner shelf, southern inner shelf of 29 °N and mud area southwest of Cheju Island was mainly come from Yangtze River (YR) input, surface runoffs after discharge of local sources close to the Taizhou-Wenzhou Region and the atmospheric deposition from the North China and East Asia, respectively. The coastal ECS was an important reservoir of DP in the world, with mass inventory of approximately 310.7kg in the surface sediments (0-5cm). Copyright © 2016 Elsevier B.V. All rights reserved.

Single measure and gated screening approaches for identifying students at-risk for academic problems: Implications for sensitivity and specificity.

PubMed

Van Norman, Ethan R; Nelson, Peter M; Klingbeil, David A

2017-09-01

Educators need recommendations to improve screening practices without limiting students' instructional opportunities. Repurposing previous years' state test scores has shown promise in identifying at-risk students within multitiered systems of support. However, researchers have not directly compared the diagnostic accuracy of previous years' state test scores with data collected during fall screening periods to identify at-risk students. In addition, the benefit of using previous state test scores in conjunction with data from a separate measure to identify at-risk students has not been explored. The diagnostic accuracy of 3 types of screening approaches were tested to predict proficiency on end-of-year high-stakes assessments: state test data obtained during the previous year, data from a different measure administered in the fall, and both measures combined (i.e., a gated model). Extant reading and math data (N = 2,996) from 10 schools in the Midwest were analyzed. When used alone, both measures yielded similar sensitivity and specificity values. The gated model yielded superior specificity values compared with using either measure alone, at the expense of sensitivity. Implications, limitations, and ideas for future research are discussed. (PsycINFO Database Record (c) 2017 APA, all rights reserved).

Direction of Magnetoencephalography Sources Associated with Feedback and Feedforward Contributions in a Visual Object Recognition Task

PubMed Central

Ahlfors, Seppo P.; Jones, Stephanie R.; Ahveninen, Jyrki; Hämäläinen, Matti S.; Belliveau, John W.; Bar, Moshe

2014-01-01

Identifying inter-area communication in terms of the hierarchical organization of functional brain areas is of considerable interest in human neuroimaging. Previous studies have suggested that the direction of magneto- and electroencephalography (MEG, EEG) source currents depends on the layer-specific input patterns into a cortical area. We examined the direction in MEG source currents in a visual object recognition experiment in which there were specific expectations of activation in the fusiform region being driven by either feedforward or feedback inputs. The source for the early non-specific visual evoked response, presumably corresponding to feedforward driven activity, pointed outward, i.e., away from the white matter. In contrast, the source for the later, object-recognition related signals, expected to be driven by feedback inputs, pointed inward, toward the white matter. Associating specific features of the MEG/EEG source waveforms to feedforward and feedback inputs could provide unique information about the activation patterns within hierarchically organized cortical areas. PMID:25445356

Sulphur and oxygen isotope analysis to identify sources of sulphur in gypsum-rich black crusts developed on granites.

PubMed

Rivas, T; Pozo, S; Paz, M

2014-06-01

We describe the results of sulphur and oxygen isotope analyses used to identify sources of the gypsum present in black crusts that grow on the granite of historical buildings. The crusts were sampled at various locations in and near the city of Vigo (NW Spain) and were analysed for their sulphur content and δ(34)S and δ(18)O isotope ratios. Sampled crusts had δ(34)S values of 7.3‰ to 12.9‰ and δ(18)O values of 6.56‰ to 12.51‰. Sampled as potential sulphur sources were bulk depositions, seawater, foundation, ashlar and construction materials and combustion residues. The results indicated marine and, to a lesser extent, anthropogenic, origins for the sulphur and ruled out the contribution of sub-soil sulphates by capillary rise from building foundations. Isotope analyses would indicate that cement and mortar were enriched in sulphur after their application in buildings. The fact that facade orientation (towards the sea or fossil fuel pollution sources) was correlated with sulphur isotope distribution pointed to various contributions to black crust formation. Copyright © 2014 Elsevier B.V. All rights reserved.

Using the Textpresso Site-Specific Recombinases Web server to identify Cre expressing mouse strains and floxed alleles.

PubMed

Condie, Brian G; Urbanski, William M

2014-01-01

Effective tools for searching the biomedical literature are essential for identifying reagents or mouse strains as well as for effective experimental design and informed interpretation of experimental results. We have built the Textpresso Site Specific Recombinases (Textpresso SSR) Web server to enable researchers who use mice to perform in-depth searches of a rapidly growing and complex part of the mouse literature. Our Textpresso Web server provides an interface for searching the full text of most of the peer-reviewed publications that report the characterization or use of mouse strains that express Cre or Flp recombinase. The database also contains most of the publications that describe the characterization or analysis of strains carrying conditional alleles or transgenes that can be inactivated or activated by site-specific recombinases such as Cre or Flp. Textpresso SSR complements the existing online databases that catalog Cre and Flp expression patterns by providing a unique online interface for the in-depth text mining of the site specific recombinase literature.

Modeling and observations of an elevated, moving infrasonic source: Eigenray methods.

PubMed

Blom, Philip; Waxler, Roger

2017-04-01

The acoustic ray tracing relations are extended by the inclusion of auxiliary parameters describing variations in the spatial ray coordinates and eikonal vector due to changes in the initial conditions. Computation of these parameters allows one to define the geometric spreading factor along individual ray paths and assists in identification of caustic surfaces so that phase shifts can be easily identified. A method is developed leveraging the auxiliary parameters to identify propagation paths connecting specific source-receiver geometries, termed eigenrays. The newly introduced method is found to be highly efficient in cases where propagation is non-planar due to horizontal variations in the propagation medium or the presence of cross winds. The eigenray method is utilized in analysis of infrasonic signals produced by a multi-stage sounding rocket launch with promising results for applications of tracking aeroacoustic sources in the atmosphere and specifically to analysis of motor performance during dynamic tests.

Ancestry-specific and sex-specific risk alleles identified in a genome-wide gene-by-alcohol dependence interaction study of risky sexual behaviors.

PubMed

Polimanti, Renato; Zhao, Hongyu; Farrer, Lindsay A; Kranzler, Henry R; Gelernter, Joel

2017-12-01

We previously mapped loci for the genome-wide association studies (GWAS) and genome-wide gene-by-alcohol dependence interaction (GW-GxAD) analyses of risky sexual behaviors (RSB). This study extends those findings by analyzing the ancestry- and sex-specific AD-stratified effects on RSB. We examined the concordance of findings for the AD-stratified GWAS and the GW-GxAD analysis of RSB, with concordance defined as genome-wide significance in one analysis and at least nominal significance in the second analysis. A total of 2,173 African-American (AA) and 1,751 European-American (EA) subjects were investigated. Information regarding RSB (lifetime experiences of unprotected sex and multiple sexual partners) and DSM-IV diagnosis of lifetime AD were derived from the Semi-Structured Assessment for Drug Dependence and Alcoholism (SSADDA). In our ancestry- and sex-specific analyses, we identified four independent genome-wide significant (GWS) loci (p < 5*10 -8 ) and one suggestive locus (p < 6*10 -8 ). In men, we observed a GWS signal in FAM162A (rs2002594, p = 4.96*10 -8 ). In women, there was a suggestive locus in PLGRKT (rs3824435, p = 5.52*10 -8 ). In AAs, there was a GWS signal in GRK5 (rs1316543, p = 1.25*10 -9 ). In AA men, we observed an intergenic GWS signal (rs12898370, p = 4.49*10 -8 ) near LINGO1. In EA men, there was a GWS signal in CCSER1 (rs62313897; p = 7.93*10 -10 ). The loci identified in this GWAS implicate molecular mechanisms related to psychiatric illness and personality features, suggesting that the interplay between AD and RSB is mediated by alleles associated with behavioral traits. © 2017 Wiley Periodicals, Inc.

A source-specific model for lossless compression of global Earth data

NASA Astrophysics Data System (ADS)

Kess, Barbara Lynne

A Source Specific Model for Global Earth Data (SSM-GED) is a lossless compression method for large images that captures global redundancy in the data and achieves a significant improvement over CALIC and DCXT-BT/CARP, two leading lossless compression schemes. The Global Land 1-Km Advanced Very High Resolution Radiometer (AVHRR) data, which contains 662 Megabytes (MB) per band, is an example of a large data set that requires decompression of regions of the data. For this reason, SSM-GED compresses the AVHRR data as a collection of subwindows. This approach defines the statistical parameters for the model prior to compression. Unlike universal models that assume no a priori knowledge of the data, SSM-GED captures global redundancy that exists among all of the subwindows of data. The overlap in parameters among subwindows of data enables SSM-GED to improve the compression rate by increasing the number of parameters and maintaining a small model cost for each subwindow of data. This lossless compression method is applicable to other large volumes of image data such as video.

Hyperspectral microscopy to identify foodborne bacteria with optimum lighting source

USDA-ARS?s Scientific Manuscript database

Hyperspectral microscopy is an emerging technology for rapid detection of foodborne pathogenic bacteria. Since scattering spectral signatures from hyperspectral microscopic images (HMI) vary with lighting sources, it is important to select optimal lights. The objective of this study is to compare t...

Microbial source tracking in impaired watersheds using PhyloChip and machine-learning classification.

PubMed

Dubinsky, Eric A; Butkus, Steven R; Andersen, Gary L

2016-11-15

Sources of fecal indicator bacteria are difficult to identify in watersheds that are impacted by a variety of non-point sources. We developed a molecular source tracking test using the PhyloChip microarray that detects and distinguishes fecal bacteria from humans, birds, ruminants, horses, pigs and dogs with a single test. The multiplexed assay targets 9001 different 25-mer fragments of 16S rRNA genes that are common to the bacterial community of each source type. Both random forests and SourceTracker were tested as discrimination tools, with SourceTracker classification producing superior specificity and sensitivity for all source types. Validation with 12 different mammalian sources in mixtures found 100% correct identification of the dominant source and 84-100% specificity. The test was applied to identify sources of fecal indicator bacteria in the Russian River watershed in California. We found widespread contamination by human sources during the wet season proximal to settlements with antiquated septic infrastructure and during the dry season at beaches during intense recreational activity. The test was more sensitive than common fecal indicator tests that failed to identify potential risks at these sites. Conversely, upstream beaches and numerous creeks with less reliance on onsite wastewater treatment contained no fecal signal from humans or other animals; however these waters did contain high counts of fecal indicator bacteria after rain. Microbial community analysis revealed that increased E. coli and enterococci at these locations did not co-occur with common fecal bacteria, but rather co-varied with copiotrophic bacteria that are common in freshwaters with high nutrient and carbon loading, suggesting runoff likely promoted the growth of environmental strains of E. coli and enterococci. These results indicate that machine-learning classification of PhyloChip microarray data can outperform conventional single marker tests that are used to assess health

Exome chip meta-analysis identifies novel loci and East Asian-specific coding variants that contribute to lipid levels and coronary artery disease.

PubMed

Lu, Xiangfeng; Peloso, Gina M; Liu, Dajiang J; Wu, Ying; Zhang, He; Zhou, Wei; Li, Jun; Tang, Clara Sze-Man; Dorajoo, Rajkumar; Li, Huaixing; Long, Jirong; Guo, Xiuqing; Xu, Ming; Spracklen, Cassandra N; Chen, Yang; Liu, Xuezhen; Zhang, Yan; Khor, Chiea Chuen; Liu, Jianjun; Sun, Liang; Wang, Laiyuan; Gao, Yu-Tang; Hu, Yao; Yu, Kuai; Wang, Yiqin; Cheung, Chloe Yu Yan; Wang, Feijie; Huang, Jianfeng; Fan, Qiao; Cai, Qiuyin; Chen, Shufeng; Shi, Jinxiu; Yang, Xueli; Zhao, Wanting; Sheu, Wayne H-H; Cherny, Stacey Shawn; He, Meian; Feranil, Alan B; Adair, Linda S; Gordon-Larsen, Penny; Du, Shufa; Varma, Rohit; Chen, Yii-Der Ida; Shu, Xiao-Ou; Lam, Karen Siu Ling; Wong, Tien Yin; Ganesh, Santhi K; Mo, Zengnan; Hveem, Kristian; Fritsche, Lars G; Nielsen, Jonas Bille; Tse, Hung-Fat; Huo, Yong; Cheng, Ching-Yu; Chen, Y Eugene; Zheng, Wei; Tai, E Shyong; Gao, Wei; Lin, Xu; Huang, Wei; Abecasis, Goncalo; Kathiresan, Sekar; Mohlke, Karen L; Wu, Tangchun; Sham, Pak Chung; Gu, Dongfeng; Willer, Cristen J

2017-12-01

Most genome-wide association studies have been of European individuals, even though most genetic variation in humans is seen only in non-European samples. To search for novel loci associated with blood lipid levels and clarify the mechanism of action at previously identified lipid loci, we used an exome array to examine protein-coding genetic variants in 47,532 East Asian individuals. We identified 255 variants at 41 loci that reached chip-wide significance, including 3 novel loci and 14 East Asian-specific coding variant associations. After a meta-analysis including >300,000 European samples, we identified an additional nine novel loci. Sixteen genes were identified by protein-altering variants in both East Asians and Europeans, and thus are likely to be functional genes. Our data demonstrate that most of the low-frequency or rare coding variants associated with lipids are population specific, and that examining genomic data across diverse ancestries may facilitate the identification of functional genes at associated loci.

A Space Experiment to Measure the Atomic Oxygen Erosion of Polymers and Demonstrate a Technique to Identify Sources of Silicone Contamination

NASA Technical Reports Server (NTRS)

Banks, Bruce A.; deGroh, Kim K.; Baney-Barton, Elyse; Sechkar, Edward A.; Hunt, Patricia K.; Willoughby, Alan; Bemer, Meagan; Hope, Stephanie; Koo, Julie; Kaminski, Carolyn;

Source apportionment of airborne particulates through receptor modeling: Indian scenario

NASA Astrophysics Data System (ADS)

Banerjee, Tirthankar; Murari, Vishnu; Kumar, Manish; Raju, M. P.

2015-10-01

Airborne particulate chemistry mostly governed by associated sources and apportionment of specific sources is extremely essential to delineate explicit control strategies. The present submission initially deals with the publications (1980s-2010s) of Indian origin which report regional heterogeneities of particulate concentrations with reference to associated species. Such meta-analyses clearly indicate the presence of reservoir of both primary and secondary aerosols in different geographical regions. Further, identification of specific signatory molecules for individual source category was also evaluated in terms of their scientific merit and repeatability. Source signatures mostly resemble international profile while, in selected cases lack appropriateness. In India, source apportionment (SA) of airborne particulates was initiated way back in 1985 through factor analysis, however, principal component analysis (PCA) shares a major proportion of applications (34%) followed by enrichment factor (EF, 27%), chemical mass balance (CMB, 15%) and positive matrix factorization (PMF, 9%). Mainstream SA analyses identify earth crust and road dust resuspensions (traced by Al, Ca, Fe, Na and Mg) as a principal source (6-73%) followed by vehicular emissions (traced by Fe, Cu, Pb, Cr, Ni, Mn, Ba and Zn; 5-65%), industrial emissions (traced by Co, Cr, Zn, V, Ni, Mn, Cd; 0-60%), fuel combustion (traced by K, NH4+, SO4-, As, Te, S, Mn; 4-42%), marine aerosols (traced by Na, Mg, K; 0-15%) and biomass/refuse burning (traced by Cd, V, K, Cr, As, TC, Na, K, NH4+, NO3-, OC; 1-42%). In most of the cases, temporal variations of individual source contribution for a specific geographic region exhibit radical heterogeneity possibly due to unscientific orientation of individual tracers for specific source and well exaggerated by methodological weakness, inappropriate sample size, implications of secondary aerosols and inadequate emission inventories. Conclusively, a number of challenging

Genome-wide Association Study Identifies African-Specific Susceptibility Loci in African Americans with Inflammatory Bowel Disease

PubMed Central

Brant, Steven R.; Okou, David T.; Simpson, Claire L.; Cutler, David J.; Haritunians, Talin; Bradfield, Jonathan P.; Chopra, Pankaj; Prince, Jarod; Begum, Ferdouse; Kumar, Archana; Huang, Chengrui; Venkateswaran, Suresh; Datta, Lisa W.; Wei, Zhi; Thomas, Kelly; Herrinton, Lisa J.; Klapproth, Jan-Micheal A.; Quiros, Antonio J.; Seminerio, Jenifer; Liu, Zhenqiu; Alexander, Jonathan S.; Baldassano, Robert N.; Dudley-Brown, Sharon; Cross, Raymond K.; Dassopoulos, Themistocles; Denson, Lee A.; Dhere, Tanvi A.; Dryden, Gerald W.; Hanson, John S.; Hou, Jason K.; Hussain, Sunny Z.; Hyams, Jeffrey S.; Isaacs, Kim L.; Kader, Howard; Kappelman, Michael D.; Katz, Jeffry; Kellermayer, Richard; Kirschner, Barbara S.; Kuemmerle, John F.; Kwon, John H.; Lazarev, Mark; Li, Ellen; Mack, David; Mannon, Peter; Moulton, Dedrick E.; Newberry, Rodney D.; Osuntokun, Bankole O.; Patel, Ashish S.; Saeed, Shehzad A.; Targan, Stephan R.; Valentine, John F.; Wang, Ming-Hsi; Zonca, Martin; Rioux, John D.; Duerr, Richard H.; Silverberg, Mark S.; Cho, Judy H.; Hakonarson, Hakon; Zwick, Michael E.; McGovern, Dermot P.B.; Kugathasan, Subra

2016-01-01

Background & Aims The inflammatory bowel diseases (IBD) ulcerative colitis (UC) and Crohn’s disease (CD) cause significant morbidity and are increasing in prevalence among all populations, including African Americans. More than 200 susceptibility loci have been identified in populations of predominantly European ancestry, but few loci have been associated with IBD in other ethnicities. Methods We performed 2 high-density, genome-wide scans comprising 2345 cases of African Americans with IBD (1646 with CD, 583 with UC, and 116 inflammatory bowel disease unclassified [IBD-U]) and 5002 individuals without IBD (controls, identified from the Health Retirement Study and Kaiser Permanente database). Single-nucleotide polymorphisms (SNPs) associated at P<5.0×10−8 in meta-analysis with a nominal evidence (P<.05) in each scan were considered to have genome-wide significance. Results We detected SNPs at HLA-DRB1, and African-specific SNPs at ZNF649 and LSAMP, with associations of genome-wide significance for UC. We detected SNPs at USP25 with associations of genome-wide significance associations for IBD. No associations of genome-wide significance were detected for CD. In addition, 9 genes previously associated with IBD contained SNPs with significant evidence for replication (P<1.6×10−6): ADCY3, CXCR6, HLA-DRB1 to HLA-DQA1 (genome-wide significance on conditioning), IL12B, PTGER4, and TNC for IBD; IL23R, PTGER4, and SNX20 (in strong linkage disequilibrium with NOD2) for CD; and KCNQ2 (near TNFRSF6B) for UC. Several of these genes, such as TNC (near TNFSF15), CXCR6, and genes associated with IBD at the HLA locus, contained SNPs with unique association patterns with African-specific alleles. Conclusions We performed a genome-wide association study of African Americans with IBD and identified loci associated with CD and UC in only this population; we also replicated loci identified in European populations. The detection of variants associated with IBD risk in only

Genome-Wide Association Study Identifies African-Specific Susceptibility Loci in African Americans With Inflammatory Bowel Disease.

PubMed

Brant, Steven R; Okou, David T; Simpson, Claire L; Cutler, David J; Haritunians, Talin; Bradfield, Jonathan P; Chopra, Pankaj; Prince, Jarod; Begum, Ferdouse; Kumar, Archana; Huang, Chengrui; Venkateswaran, Suresh; Datta, Lisa W; Wei, Zhi; Thomas, Kelly; Herrinton, Lisa J; Klapproth, Jan-Micheal A; Quiros, Antonio J; Seminerio, Jenifer; Liu, Zhenqiu; Alexander, Jonathan S; Baldassano, Robert N; Dudley-Brown, Sharon; Cross, Raymond K; Dassopoulos, Themistocles; Denson, Lee A; Dhere, Tanvi A; Dryden, Gerald W; Hanson, John S; Hou, Jason K; Hussain, Sunny Z; Hyams, Jeffrey S; Isaacs, Kim L; Kader, Howard; Kappelman, Michael D; Katz, Jeffry; Kellermayer, Richard; Kirschner, Barbara S; Kuemmerle, John F; Kwon, John H; Lazarev, Mark; Li, Ellen; Mack, David; Mannon, Peter; Moulton, Dedrick E; Newberry, Rodney D; Osuntokun, Bankole O; Patel, Ashish S; Saeed, Shehzad A; Targan, Stephan R; Valentine, John F; Wang, Ming-Hsi; Zonca, Martin; Rioux, John D; Duerr, Richard H; Silverberg, Mark S; Cho, Judy H; Hakonarson, Hakon; Zwick, Michael E; McGovern, Dermot P B; Kugathasan, Subra

2017-01-01

The inflammatory bowel diseases (IBD) ulcerative colitis (UC) and Crohn's disease (CD) cause significant morbidity and are increasing in prevalence among all populations, including African Americans. More than 200 susceptibility loci have been identified in populations of predominantly European ancestry, but few loci have been associated with IBD in other ethnicities. We performed 2 high-density, genome-wide scans comprising 2345 cases of African Americans with IBD (1646 with CD, 583 with UC, and 116 inflammatory bowel disease unclassified) and 5002 individuals without IBD (controls, identified from the Health Retirement Study and Kaiser Permanente database). Single-nucleotide polymorphisms (SNPs) associated at P < 5.0 × 10 -8 in meta-analysis with a nominal evidence (P < .05) in each scan were considered to have genome-wide significance. We detected SNPs at HLA-DRB1, and African-specific SNPs at ZNF649 and LSAMP, with associations of genome-wide significance for UC. We detected SNPs at USP25 with associations of genome-wide significance for IBD. No associations of genome-wide significance were detected for CD. In addition, 9 genes previously associated with IBD contained SNPs with significant evidence for replication (P < 1.6 × 10 -6 ): ADCY3, CXCR6, HLA-DRB1 to HLA-DQA1 (genome-wide significance on conditioning), IL12B,PTGER4, and TNC for IBD; IL23R, PTGER4, and SNX20 (in strong linkage disequilibrium with NOD2) for CD; and KCNQ2 (near TNFRSF6B) for UC. Several of these genes, such as TNC (near TNFSF15), CXCR6, and genes associated with IBD at the HLA locus, contained SNPs with unique association patterns with African-specific alleles. We performed a genome-wide association study of African Americans with IBD and identified loci associated with UC in only this population; we also replicated IBD, CD, and UC loci identified in European populations. The detection of variants associated with IBD risk in only people of African descent demonstrates the

Next-generation DNA sequencing identifies novel gene variants and pathways involved in specific language impairment.

PubMed

Chen, Xiaowei Sylvia; Reader, Rose H; Hoischen, Alexander; Veltman, Joris A; Simpson, Nuala H; Francks, Clyde; Newbury, Dianne F; Fisher, Simon E

2017-04-25

A significant proportion of children have unexplained problems acquiring proficient linguistic skills despite adequate intelligence and opportunity. Developmental language disorders are highly heritable with substantial societal impact. Molecular studies have begun to identify candidate loci, but much of the underlying genetic architecture remains undetermined. We performed whole-exome sequencing of 43 unrelated probands affected by severe specific language impairment, followed by independent validations with Sanger sequencing, and analyses of segregation patterns in parents and siblings, to shed new light on aetiology. By first focusing on a pre-defined set of known candidates from the literature, we identified potentially pathogenic variants in genes already implicated in diverse language-related syndromes, including ERC1, GRIN2A, and SRPX2. Complementary analyses suggested novel putative candidates carrying validated variants which were predicted to have functional effects, such as OXR1, SCN9A and KMT2D. We also searched for potential "multiple-hit" cases; one proband carried a rare AUTS2 variant in combination with a rare inherited haplotype affecting STARD9, while another carried a novel nonsynonymous variant in SEMA6D together with a rare stop-gain in SYNPR. On broadening scope to all rare and novel variants throughout the exomes, we identified biological themes that were enriched for such variants, including microtubule transport and cytoskeletal regulation.

Next-generation DNA sequencing identifies novel gene variants and pathways involved in specific language impairment

PubMed Central

Chen, Xiaowei Sylvia; Reader, Rose H.; Hoischen, Alexander; Veltman, Joris A.; Simpson, Nuala H.; Francks, Clyde; Newbury, Dianne F.; Fisher, Simon E.

2017-01-01

A significant proportion of children have unexplained problems acquiring proficient linguistic skills despite adequate intelligence and opportunity. Developmental language disorders are highly heritable with substantial societal impact. Molecular studies have begun to identify candidate loci, but much of the underlying genetic architecture remains undetermined. We performed whole-exome sequencing of 43 unrelated probands affected by severe specific language impairment, followed by independent validations with Sanger sequencing, and analyses of segregation patterns in parents and siblings, to shed new light on aetiology. By first focusing on a pre-defined set of known candidates from the literature, we identified potentially pathogenic variants in genes already implicated in diverse language-related syndromes, including ERC1, GRIN2A, and SRPX2. Complementary analyses suggested novel putative candidates carrying validated variants which were predicted to have functional effects, such as OXR1, SCN9A and KMT2D. We also searched for potential “multiple-hit” cases; one proband carried a rare AUTS2 variant in combination with a rare inherited haplotype affecting STARD9, while another carried a novel nonsynonymous variant in SEMA6D together with a rare stop-gain in SYNPR. On broadening scope to all rare and novel variants throughout the exomes, we identified biological themes that were enriched for such variants, including microtubule transport and cytoskeletal regulation. PMID:28440294

Meta-analysis of lipid-traits in Hispanics identifies novel loci, population-specific effects, and tissue-specific enrichment of eQTLs

PubMed Central

Below, Jennifer E.; Parra, Esteban J.; Gamazon, Eric R.; Torres, Jason; Krithika, S.; Candille, Sophie; Lu, Yingchang; Manichakul, Ani; Peralta-Romero, Jesus; Duan, Qing; Li, Yun; Morris, Andrew P.; Gottesman, Omri; Bottinger, Erwin; Wang, Xin-Qun; Taylor, Kent D.; Ida Chen, Y.-D.; Rotter, Jerome I.; Rich, Stephen S.; Loos, Ruth J. F.; Tang, Hua; Cox, Nancy J.; Cruz, Miguel; Hanis, Craig L.; Valladares-Salgado, Adan

2016-01-01

We performed genome-wide meta-analysis of lipid traits on three samples of Mexican and Mexican American ancestry comprising 4,383 individuals, and followed up significant and highly suggestive associations in three additional Hispanic samples comprising 7,876 individuals. Genome-wide significant signals were observed in or near CELSR2, ZNF259/APOA5, KANK2/DOCK6 and NCAN/MAU2 for total cholesterol, LPL, ABCA1, ZNF259/APOA5, LIPC and CETP for HDL cholesterol, CELSR2, APOB and NCAN/MAU2 for LDL cholesterol, and GCKR, TRIB1, ZNF259/APOA5 and NCAN/MAU2 for triglycerides. Linkage disequilibrium and conditional analyses indicate that signals observed at ABCA1 and LIPC for HDL cholesterol and NCAN/MAU2 for triglycerides are independent of previously reported lead SNP associations. Analyses of lead SNPs from the European Global Lipids Genetics Consortium (GLGC) dataset in our Hispanic samples show remarkable concordance of direction of effects as well as strong correlation in effect sizes. A meta-analysis of the European GLGC and our Hispanic datasets identified five novel regions reaching genome-wide significance: two for total cholesterol (FN1 and SAMM50), two for HDL cholesterol (LOC100996634 and COPB1) and one for LDL cholesterol (LINC00324/CTC1/PFAS). The top meta-analysis signals were found to be enriched for SNPs associated with gene expression in a tissue-specific fashion, suggesting an enrichment of tissue-specific function in lipid-associated loci. PMID:26780889

Quantitative Analysis of Localized Sources Identified by Focal Impulse and Rotor Modulation Mapping in Atrial Fibrillation

PubMed Central

Benharash, Peyman; Buch, Eric; Frank, Paul; Share, Michael; Tung, Roderick; Shivkumar, Kalyanam; Mandapati, Ravi

2015-01-01

Background New approaches to ablation of atrial fibrillation (AF) include focal impulse and rotor modulation (FIRM) mapping, and initial results reported with this technique have been favorable. We sought to independently evaluate the approach by analyzing quantitative characteristics of atrial electrograms used to identify rotors and describe acute procedural outcomes of FIRM-guided ablation. Methods and Results All FIRM-guided ablation procedures (n=24; 50% paroxysmal) at University of California, Los Angeles Medical Center were included for analysis. During AF, unipolar atrial electrograms collected from a 64-pole basket catheter were used to construct phase maps and identify putative AF sources. These sites were targeted for ablation, in conjunction with pulmonary vein isolation in most patients (n=19; 79%). All patients had rotors identified (mean, 2.3±0.9 per patient; 72% in left atrium). Prespecified acute procedural end point was achieved in 12 of 24 (50%) patients: AF termination (n=1), organization (n=3), or >10% slowing of AF cycle length (n=8). Basket electrodes were within 1 cm of 54% of left atrial surface area, and a mean of 31 electrodes per patient showed interpretable atrial electrograms. Offline analysis revealed no differences between rotor and distant sites in dominant frequency or Shannon entropy. Electroanatomic mapping showed no rotational activation at FIRM-identified rotor sites in 23 of 24 patients (96%). Conclusions FIRM-identified rotor sites did not exhibit quantitative atrial electrogram characteristics expected from rotors and did not differ quantitatively from surrounding tissue. Catheter ablation at these sites, in conjunction with pulmonary vein isolation, resulted in AF termination or organization in a minority of patients (4/24; 17%). Further validation of this approach is necessary. PMID:25873718

WORKER INHALATION DOSE COEFFICIENTS FOR RADIONUCLIDES NOT PREVIOUSLY IDENTIFIED IN ICRP PUBLICATION 68

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

McLaughlin, David A; Schwahn, Scott O

2011-01-01

While inhalation dose coefficients are provided for about 800 radionuclides in International Commission on Radiological Protection (ICRP) Publication 68, many radionuclides of practical dosimetric interest for facilities such as high-energy proton accelerators are not specifically addressed, nor are organ-specific dose coefficients tabulated. The ICRP Publication 68 methodology is used, along with updated radiological decay data and metabolic data, to identify committed equivalent dose coefficients [hT(50)] and committed effective dose coefficients [e(50)] for radionuclides produced at the Oak Ridge National Laboratory s Spallation Neutron Source.

[Identifying the specific causes of kidney allograft loss: A population-based study].

PubMed

Lohéac, Charlotte; Aubert, Olivier; Loupy, Alexandre; Legendre, Christophe

2018-04-01

Results of kidney transplantation have been improving but long-term allograft survival remains disappointing. The objective of the present study was to identify the specific causes of renal allograft loss, to assess their incidence and long-term outcomes. A total of 4783 patients from four French centres, transplanted between January 2004 and January 2014 were prospectively included. A total of 9959 kidney biopsies (protocol and for cause) performed between January 2004 and March 2015 were included. Donor and recipient clinical and biological parameters as well as anti-HLA antibody directed against the donor were included. The main outcome was the long-term kidney allograft survival, including the study of the associated causes of graft loss, the delay of graft loss according to their causes and the determinants of graft loss. There were 732 graft losses during the follow-up period (median time: 4.51 years) with an identified cause in 95.08 %. Kidney allograft survival at 9 years post-transplant was 78 %. The causes of allograft loss were: antibody-mediated rejection (31.69 %), thrombosis (25.55 %), medical intercurrent disease (14.62 %), recurrence of primary renal disease (7.1 %), BK- or CMV-associated nephropathy (n=35, 4.78 %), T cell-mediated rejection (4.78 %), urological disease (2.46 %) and calcineurin inhibitor nephrotoxicity (1.09 %). The main causes of allograft loss were antibody-mediated rejection and thrombosis. These results encourage efforts to prevent and detect these complications earlier in order to improve allograft survival. Copyright © 2018 Association Société de néphrologie. Published by Elsevier Masson SAS. All rights reserved.

Gastric Cancer-Specific Protein Profile Identified Using Endoscopic Biopsy Samples via MALDI Mass Spectrometry

PubMed Central

Kim, Hark Kyun; Reyzer, Michelle L.; Choi, Il Ju; Kim, Chan Gyoo; Kim, Hee Sung; Oshima, Akira; Chertov, Oleg; Colantonio, Simona; Fisher, Robert J.; Allen, Jamie L.; Caprioli, Richard M.; Green, Jeffrey E.

2012-01-01

To date, proteomic analyses on gastrointestinal cancer tissue samples have been performed using surgical specimens only, which are obtained after a diagnosis is made. To determine if a proteomic signature obtained from endoscopic biopsy samples could be found to assist with diagnosis, frozen endoscopic biopsy samples collected from 63 gastric cancer patients and 43 healthy volunteers were analyzed using matrix-assisted laser desorption/ionization (MALDI) mass spectrometry. A statistical classification model was developed to distinguish tumor from normal tissues using half the samples and validated with the other half. A protein profile was discovered consisting of 73 signals that could classify 32 cancer and 22 normal samples in the validation set with high predictive values (positive and negative predictive values for cancer, 96.8% and 91.3%; sensitivity, 93.8%; specificity, 95.5%). Signals overexpressed in tumors were identified as α-defensin-1, α-defensin-2, calgranulin A, and calgranulin B. A protein profile was also found to distinguish pathologic stage Ia (pT1N0M0) samples (n = 10) from more advanced stage (Ib or higher) tumors (n = 48). Thus, protein profiles obtained from endoscopic biopsy samples may be useful in assisting with the diagnosis of gastric cancer and, possibly, in identifying early stage disease. PMID:20557134

A Novel Semi-Supervised Methodology for Extracting Tumor Type-Specific MRS Sources in Human Brain Data

PubMed Central

Ortega-Martorell, Sandra; Ruiz, Héctor; Vellido, Alfredo; Olier, Iván; Romero, Enrique; Julià-Sapé, Margarida; Martín, José D.; Jarman, Ian H.; Arús, Carles; Lisboa, Paulo J. G.

2013-01-01

Background The clinical investigation of human brain tumors often starts with a non-invasive imaging study, providing information about the tumor extent and location, but little insight into the biochemistry of the analyzed tissue. Magnetic Resonance Spectroscopy can complement imaging by supplying a metabolic fingerprint of the tissue. This study analyzes single-voxel magnetic resonance spectra, which represent signal information in the frequency domain. Given that a single voxel may contain a heterogeneous mix of tissues, signal source identification is a relevant challenge for the problem of tumor type classification from the spectroscopic signal. Methodology/Principal Findings Non-negative matrix factorization techniques have recently shown their potential for the identification of meaningful sources from brain tissue spectroscopy data. In this study, we use a convex variant of these methods that is capable of handling negatively-valued data and generating sources that can be interpreted as tumor class prototypes. A novel approach to convex non-negative matrix factorization is proposed, in which prior knowledge about class information is utilized in model optimization. Class-specific information is integrated into this semi-supervised process by setting the metric of a latent variable space where the matrix factorization is carried out. The reported experimental study comprises 196 cases from different tumor types drawn from two international, multi-center databases. The results indicate that the proposed approach outperforms a purely unsupervised process by achieving near perfect correlation of the extracted sources with the mean spectra of the tumor types. It also improves tissue type classification. Conclusions/Significance We show that source extraction by unsupervised matrix factorization benefits from the integration of the available class information, so operating in a semi-supervised learning manner, for discriminative source identification and brain

Source Water Protection Basics

EPA Pesticide Factsheets

Defines drinking water sources (source water), identifies drinking water sources, and describes source water assessments and protection, roles of government and organizations in drinking water source protection

Comparison of seven protocols to identify fecal contamination sources using Escherichia coli

USGS Publications Warehouse

Stoeckel, D.M.; Mathes, M.V.; Hyer, K.E.; Hagedorn, C.; Kator, H.; Lukasik, J.; O'Brien, T. L.; Fenger, T.W.; Samadpour, M.; Strickler, K.M.; Wiggins, B.A.

2004-01-01

Microbial source tracking (MST) uses various approaches to classify fecal-indicator microorganisms to source hosts. Reproducibility, accuracy, and robustness of seven phenotypic and genotypic MST protocols were evaluated by use of Escherichia coli from an eight-host library of known-source isolates and a separate, blinded challenge library. In reproducibility tests, measuring each protocol's ability to reclassify blinded replicates, only one (pulsed-field gel electrophoresis; PFGE) correctly classified all test replicates to host species; three protocols classified 48-62% correctly, and the remaining three classified fewer than 25% correctly. In accuracy tests, measuring each protocol's ability to correctly classify new isolates, ribotyping with EcoRI and PvuII approached 100% correct classification but only 6% of isolates were classified; four of the other six protocols (antibiotic resistance analysis, PFGE, and two repetitive-element PCR protocols) achieved better than random accuracy rates when 30-100% of challenge isolates were classified. In robustness tests, measuring each protocol's ability to recognize isolates from nonlibrary hosts, three protocols correctly classified 33-100% of isolates as "unknown origin," whereas four protocols classified all isolates to a source category. A relevance test, summarizing interpretations for a hypothetical water sample containing 30 challenge isolates, indicated that false-positive classifications would hinder interpretations for most protocols. Study results indicate that more representation in known-source libraries and better classification accuracy would be needed before field application. Thorough reliability assessment of classification results is crucial before and during application of MST protocols.

Cross-reactivity among non-specific lipid-transfer proteins from food and pollen allergenic sources.

PubMed

Morales, María; López-Matas, M Ángeles; Moya, Raquel; Carnés, Jerónimo

2014-12-15

Non-specific lipid-transfer proteins (nsLTPs) are a family of pan-allergens present in foods and pollen. However, sequence homology among them is limited. The objective of this study was to evaluate the IgE-mediated cross-reactivity between nsLTPs from different sources and evaluate the allergenic properties of LTPs from peach (Pru p 3) and pellitory (Par j 1/Par j 2), major fruit and pollen allergens. Both proteins were purified and characterised. Cross-reactivity studies among nsLTPs from different foods and pollens were performed by immunoblot inhibition using sera specific to peach or pellitory pollen. Cross-reactivity with Pru p 3 was observed in hazelnut, onion, corn, peanut and apple while in pollens, none of the extracts was inhibited with Par j 1/2. In conclusion, Pru p 3 did not inhibit LTPs from most fruits. Therefore, although Pru p 3 covers the largest number of epitopes, diagnosis with only this allergen may not detect all LTP sensitivities. Copyright © 2014 Elsevier Ltd. All rights reserved.

Combining structured and unstructured data to identify a cohort of ICU patients who received dialysis

PubMed Central

Abhyankar, Swapna; Demner-Fushman, Dina; Callaghan, Fiona M; McDonald, Clement J

2014-01-01

Objective To develop a generalizable method for identifying patient cohorts from electronic health record (EHR) data—in this case, patients having dialysis—that uses simple information retrieval (IR) tools. Methods We used the coded data and clinical notes from the 24 506 adult patients in the Multiparameter Intelligent Monitoring in Intensive Care database to identify patients who had dialysis. We used SQL queries to search the procedure, diagnosis, and coded nursing observations tables based on ICD-9 and local codes. We used a domain-specific search engine to find clinical notes containing terms related to dialysis. We manually validated the available records for a 10% random sample of patients who potentially had dialysis and a random sample of 200 patients who were not identified as having dialysis based on any of the sources. Results We identified 1844 patients that potentially had dialysis: 1481 from the three coded sources and 1624 from the clinical notes. Precision for identifying dialysis patients based on available data was estimated to be 78.4% (95% CI 71.9% to 84.2%) and recall was 100% (95% CI 86% to 100%). Conclusions Combining structured EHR data with information from clinical notes using simple queries increases the utility of both types of data for cohort identification. Patients identified by more than one source are more likely to meet the inclusion criteria; however, including patients found in any of the sources increases recall. This method is attractive because it is available to researchers with access to EHR data and off-the-shelf IR tools. PMID:24384230

sourceR: Classification and source attribution of infectious agents among heterogeneous populations

PubMed Central

French, Nigel

2017-01-01

Zoonotic diseases are a major cause of morbidity, and productivity losses in both human and animal populations. Identifying the source of food-borne zoonoses (e.g. an animal reservoir or food product) is crucial for the identification and prioritisation of food safety interventions. For many zoonotic diseases it is difficult to attribute human cases to sources of infection because there is little epidemiological information on the cases. However, microbial strain typing allows zoonotic pathogens to be categorised, and the relative frequencies of the strain types among the sources and in human cases allows inference on the likely source of each infection. We introduce sourceR, an R package for quantitative source attribution, aimed at food-borne diseases. It implements a Bayesian model using strain-typed surveillance data from both human cases and source samples, capable of identifying important sources of infection. The model measures the force of infection from each source, allowing for varying survivability, pathogenicity and virulence of pathogen strains, and varying abilities of the sources to act as vehicles of infection. A Bayesian non-parametric (Dirichlet process) approach is used to cluster pathogen strain types by epidemiological behaviour, avoiding model overfitting and allowing detection of strain types associated with potentially high “virulence”. sourceR is demonstrated using Campylobacter jejuni isolate data collected in New Zealand between 2005 and 2008. Chicken from a particular poultry supplier was identified as the major source of campylobacteriosis, which is qualitatively similar to results of previous studies using the same dataset. Additionally, the software identifies a cluster of 9 multilocus sequence types with abnormally high ‘virulence’ in humans. sourceR enables straightforward attribution of cases of zoonotic infection to putative sources of infection. As sourceR develops, we intend it to become an important and flexible

Identifying organic aerosol sources by comparing functional group composition in chamber and atmospheric particles

PubMed Central

Russell, Lynn M.; Bahadur, Ranjit; Ziemann, Paul J.

2011-01-01

Measurements of submicron particles by Fourier transform infrared spectroscopy in 14 campaigns in North America, Asia, South America, and Europe were used to identify characteristic organic functional group compositions of fuel combustion, terrestrial vegetation, and ocean bubble bursting sources, each of which often accounts for more than a third of organic mass (OM), and some of which is secondary organic aerosol (SOA) from gas-phase precursors. The majority of the OM consists of alkane, carboxylic acid, hydroxyl, and carbonyl groups. The organic functional groups formed from combustion and vegetation emissions are similar to the secondary products identified in chamber studies. The near absence of carbonyl groups in the observed SOA associated with combustion is consistent with alkane rather than aromatic precursors, and the absence of organonitrate groups can be explained by their hydrolysis in humid ambient conditions. The remote forest observations have ratios of carboxylic acid, organic hydroxyl, and nonacid carbonyl groups similar to those observed for isoprene and monoterpene chamber studies, but in biogenic aerosols transported downwind of urban areas the formation of esters replaces the acid and hydroxyl groups and leaves only nonacid carbonyl groups. The carbonyl groups in SOA associated with vegetation emissions provides striking evidence for the mechanism of esterification as the pathway for possible oligomerization reactions in the atmosphere. Forest fires include biogenic emissions that produce SOA with organic components similar to isoprene and monoterpene chamber studies, also resulting in nonacid carbonyl groups in SOA. PMID:21317360

Sensitivity and specificity of the Chinese version of the Schizotypal Personality Questionnaire-Brief for identifying undergraduate students susceptible to psychosis.

PubMed

Ma, Wei-Fen; Wu, Po-Lun; Yang, Shu-Ju; Cheng, Kuang-Fu; Chiu, Hsien-Tsai; Lane, Hsien-Yuan

2010-12-01

Early interventions can improve treatment outcomes for individuals with major psychiatric disorders and with nonspecific symptoms but increasingly impaired cognitive perception, emotions, and behaviour. One way used to identify people susceptible to psychosis is through the schizotypal personality trait. Persons with schizotypal characteristics have been identified with the widely used Schizotypal Personality Questionnaire-Brief. However, no suitable instruments are available to screen individuals in the Taiwanese population for evidence of early psychotic symptoms. The purpose of this study was to test the sensitivity and specificity of the Chinese version of the Schizotypal Personality Questionnaire-Brief for identifying undergraduate students' susceptibility to psychosis. Two-stage, cross-sectional survey design. The self-administered scale was tested in a convenience sample of 618 undergraduate students at a medical university in Taiwan. Among these students, 54 completed the scale 2 weeks apart for test-retest reliability, and 80 were tested to identify their susceptibility to psychosis. In Stage I, participants with scores in the top 6.5% were classified as the high-score group (n=40). The control group (n=40) was randomly selected from the remaining participants with scores <15 and matched by gender. These 80 students were asked to participate in psychiatric interviews in Stage II. The instrument was tested for reliability using intraclass correlation coefficients and the Kuder-Richardson formula 20. The instrument was analysed for optimal sensitivity and specificity using odds-ratio analysis and receiver operating characteristic curves. The 22-item Chinese version of the Schizotypal Personality Questionnaire-Brief had a 2-week test-retest reliability of 0.82 and internal consistency of 0.76. The optimal cut-off score was 17, with odds ratios of 24.4 and an area under the receiver operating characteristic curves of 0.83. The instrument had a sensitivity of

Dynamic Metabolic Profiles and Tissue-Specific Source Effects on the Metabolome of Developing Seeds of Brassica napus.

PubMed

Tan, Helin; Xie, Qingjun; Xiang, Xiaoe; Li, Jianqiao; Zheng, Suning; Xu, Xinying; Guo, Haolun; Ye, Wenxue

2015-01-01

Canola (Brassica napus) is one of several important oil-producing crops, and the physiological processes, enzymes, and genes involved in oil synthesis in canola seeds have been well characterized. However, relatively little is known about the dynamic metabolic changes that occur during oil accumulation in seeds, as well as the mechanistic origins of metabolic changes. To explore the metabolic changes that occur during oil accumulation, we isolated metabolites from both seed and silique wall and identified and characterized them by using gas chromatography coupled with mass spectrometry (GC-MS). The results showed that a total of 443 metabolites were identified from four developmental stages. Dozens of these metabolites were differentially expressed during seed ripening, including 20 known to be involved in seed development. To investigate the contribution of tissue-specific carbon sources to the biosynthesis of these metabolites, we examined the metabolic changes of silique walls and seeds under three treatments: leaf-detachment (Ld), phloem-peeling (Pe), and selective silique darkening (Sd). Our study demonstrated that the oil content was independent of leaf photosynthesis and phloem transport during oil accumulation, but required the metabolic influx from the silique wall. Notably, Sd treatment resulted in seed senescence, which eventually led to a severe reduction of the oil content. Sd treatment also caused a significant accumulation of fatty acids (FA), organic acids and amino acids. Furthermore, an unexpected accumulation of sugar derivatives and organic acid was observed in the Pe- and Sd-treated seeds. Consistent with this, the expression of a subset of genes involved in FA metabolism, sugar and oil storage was significantly altered in Pe and Sd treated seeds. Taken together, our studies suggest the metabolite profiles of canola seeds dynamically varied during the course of oil accumulation, which may provide a new insight into the mechanisms of the oil

Information and Source Preferences of a Student Market in Higher Education

ERIC Educational Resources Information Center

Bonnema, J.; Van der Waldt, D. L. R.

2008-01-01

Purpose: Marketing communication practitioners in higher education have not yet identified specific subgroups with similar characteristics within the prospective student (target) market, and do not always know which preferred sources learners consult when deciding on a tertiary institution for further or higher education. In addition, little is…

Source apportionment of airborne particulate matter using organic compounds as tracers

NASA Astrophysics Data System (ADS)

Schauer, James J.; Rogge, Wolfgang F.; Hildemann, Lynn M.; Mazurek, Monica A.; Cass, Glen R.; Simoneit, Bernd R. T.

A chemical mass balance receptor model based on organic compounds has been developed that relates source contributions to airborne fine particle mass concentrations. Source contributions to the concentrations of specific organic compounds are revealed as well. The model is applied to four air quality monitoring sites in southern California using atmospheric organic compound concentration data and source test data collected specifically for the purpose of testing this model. The contributions of up to nine primary particle source types can be separately identified in ambient samples based on this method, and approximately 85% of the organic fine aerosol is assigned to primary sources on an annual average basis. The model provides information on source contributions to fine mass concentrations, fine organic aerosol concentrations and individual organic compound concentrations. The largest primary source contributors to fine particle mass concentrations in Los Angeles are found to include diesel engine exhaust, paved road dust, gasoline-powered vehicle exhaust, plus emissions from food cooking and wood smoke, with smaller contribution from tire dust, plant fragments, natural gas combustion aerosol, and cigarette smoke. Once these primary aerosol source contributions are added to the secondary sulfates, nitrates and organics present, virtually all of the annual average fine particle mass at Los Angeles area monitoring sites can be assigned to its source.

Monitoring Lead (Pb) Pollution and Identifying Pb Pollution Sources in Japan Using Stable Pb Isotope Analysis with Kidneys of Wild Rats.

PubMed

Nakata, Hokuto; Nakayama, Shouta M M; Oroszlany, Balazs; Ikenaka, Yoshinori; Mizukawa, Hazuki; Tanaka, Kazuyuki; Harunari, Tsunehito; Tanikawa, Tsutomu; Darwish, Wageh Sobhy; Yohannes, Yared B; Saengtienchai, Aksorn; Ishizuka, Mayumi

2017-01-10

Although Japan has been considered to have little lead (Pb) pollution in modern times, the actual pollution situation is unclear. The present study aims to investigate the extent of Pb pollution and to identify the pollution sources in Japan using stable Pb isotope analysis with kidneys of wild rats. Wild brown ( Rattus norvegicus , n = 43) and black ( R. rattus , n = 98) rats were trapped from various sites in Japan. Mean Pb concentrations in the kidneys of rats from Okinawa (15.58 mg/kg, dry weight), Aichi (10.83), Niigata (10.62), Fukuoka (8.09), Ibaraki (5.06), Kyoto (4.58), Osaka (4.57), Kanagawa (3.42), and Tokyo (3.40) were above the threshold (2.50) for histological kidney changes. Similarly, compared with the previous report, it was regarded that even structural and functional kidney damage as well as neurotoxicity have spread among rats in Japan. Additionally, the possibility of human exposure to a high level of Pb was assumed. In regard to stable Pb isotope analysis, distinctive values of stable Pb isotope ratios (Pb-IRs) were detected in some kidney samples with Pb levels above 5.0 mg/kg. This result indicated that composite factors are involved in Pb pollution. However, the identification of a concrete pollution source has not been accomplished due to limited differences among previously reported values of Pb isotope composition in circulating Pb products. Namely, the current study established the limit of Pb isotope analysis for source identification. Further detailed research about monitoring Pb pollution in Japan and the demonstration of a novel method to identify Pb sources are needed.

Monitoring Lead (Pb) Pollution and Identifying Pb Pollution Sources in Japan Using Stable Pb Isotope Analysis with Kidneys of Wild Rats

PubMed Central

Nakata, Hokuto; Nakayama, Shouta M. M.; Oroszlany, Balazs; Ikenaka, Yoshinori; Mizukawa, Hazuki; Tanaka, Kazuyuki; Harunari, Tsunehito; Tanikawa, Tsutomu; Darwish, Wageh Sobhy; Yohannes, Yared B.; Saengtienchai, Aksorn; Ishizuka, Mayumi

2017-01-01

Although Japan has been considered to have little lead (Pb) pollution in modern times, the actual pollution situation is unclear. The present study aims to investigate the extent of Pb pollution and to identify the pollution sources in Japan using stable Pb isotope analysis with kidneys of wild rats. Wild brown (Rattus norvegicus, n = 43) and black (R. rattus, n = 98) rats were trapped from various sites in Japan. Mean Pb concentrations in the kidneys of rats from Okinawa (15.58 mg/kg, dry weight), Aichi (10.83), Niigata (10.62), Fukuoka (8.09), Ibaraki (5.06), Kyoto (4.58), Osaka (4.57), Kanagawa (3.42), and Tokyo (3.40) were above the threshold (2.50) for histological kidney changes. Similarly, compared with the previous report, it was regarded that even structural and functional kidney damage as well as neurotoxicity have spread among rats in Japan. Additionally, the possibility of human exposure to a high level of Pb was assumed. In regard to stable Pb isotope analysis, distinctive values of stable Pb isotope ratios (Pb-IRs) were detected in some kidney samples with Pb levels above 5.0 mg/kg. This result indicated that composite factors are involved in Pb pollution. However, the identification of a concrete pollution source has not been accomplished due to limited differences among previously reported values of Pb isotope composition in circulating Pb products. Namely, the current study established the limit of Pb isotope analysis for source identification. Further detailed research about monitoring Pb pollution in Japan and the demonstration of a novel method to identify Pb sources are needed. PMID:28075384

Fluorescently labeled dengue viruses as probes to identify antigen-specific memory B cells by multiparametric flow cytometry.

PubMed

Woda, Marcia; Mathew, Anuja

2015-01-01

Low frequencies of memory B cells in the peripheral blood make it challenging to measure the functional and phenotypic characteristics of this antigen experienced subset of B cells without in vitro culture. To date, reagents are lacking to measure ex vivo frequencies of dengue virus (DENV)-specific memory B cells. We wanted to explore the possibility of using fluorescently labeled DENV as probes to detect antigen-specific memory B cells in the peripheral blood of DENV immune individuals. Alexa Fluor dye-labeled DENV yielded viable virus that could be stored at -80°C for long periods of time. Using a careful gating strategy and methods to decrease non-specific binding, we were able to identify a small frequency of B cells from dengue immune individuals that bound labeled DENV. Sorted DENV(+) B cells from immune, but not naïve donors secreted antibodies that bound DENV after in vitro stimulation. Overall, Alexa Fluor dye-labeled DENVs are useful reagents to enable the detection and characterization of memory B cells in DENV immune individuals. Copyright © 2014 Elsevier B.V. All rights reserved.

Fluorescently labeled dengue viruses as probes to identify antigen-specific memory B cells by multiparametric flow cytometry

PubMed Central

Woda, Marcia; Mathew, Anuja

2015-01-01

Low frequencies of memory B cells in the peripheral blood make it challenging to measure the functional and phenotypic characteristics of this antigen experienced subset of B cells without in vitro culture. To date, reagents are lacking to measure ex vivo frequencies of dengue virus (DENV)-specific memory B cells. We wanted to explore the possibility of using fluorescently labeled DENV as probes to detect antigen-specific memory B cells in the peripheral blood of DENV immune individuals. Alexa Fluor dye-labeled DENV yielded viable virus that could be stored at −80°C for long periods of time. Using a careful gating strategy and methods to decrease non-specific binding, we were able to identify a small frequency of B cells from dengue immune individuals that bound labeled DENV. Sorted DENV+ B cells from immune, but not naïve donors secreted antibodies that bound intact virions after in vitro stimulation. Overall, Alexa Fluor dye labeled -DENV are useful reagents to enable the detection and characterization of memory B cells in DENV immune individuals. PMID:25497702

Specific PCR primers directed to identify cryI and cryIII genes within a Bacillus thuringiensis strain collection.

PubMed Central

Cerón, J; Ortíz, A; Quintero, R; Güereca, L; Bravo, A

1995-01-01

In this paper we describe a PCR strategy that can be used to rapidly identify Bacillus thuringiensis strains that harbor any of the known cryI or cryIII genes. Four general PCR primers which amplify DNA fragments from the known cryI or cryIII genes were selected from conserved regions. Once a strain was identified as an organism that contains a particular type of cry gene, it could be easily characterized by performing additional PCR with specific cryI and cryIII primers selected from variable regions. The method described in this paper can be used to identify the 10 different cryI genes and the five different cryIII genes. One feature of this screening method is that each cry gene is expected to produce a PCR product having a precise molecular weight. The genes which produce PCR products having different sizes probably represent strains that harbor a potentially novel cry gene. Finally, we present evidence that novel crystal genes can be identified by the method described in this paper. PMID:8526493

Genome-wide Association Study Identifies Peanut Allergy-Specific Loci and Evidence of Epigenetic Mediation in U.S. Children

PubMed Central

Hong, Xiumei; Hao, Ke; Ladd-Acosta, Christine; Hansen, Kasper D; Tsai, Hui-Ju; Liu, Xin; Xu, Xin; Thornton, Timothy A.; Caruso, Deanna; Keet, Corinne A; Sun, Yifei; Wang, Guoying; Luo, Wei; Kumar, Rajesh; Fuleihan, Ramsay; Singh, Anne Marie; Kim, Jennifer S; Story, Rachel E; Gupta, Ruchi S; Gao, Peisong; Chen, Zhu; Walker, Sheila O.; Bartell, Tami R; Beaty, Terri H; Fallin, M Daniele; Schleimer, Robert; Holt, Patrick G; Nadeau, Kari Christine; Wood, Robert A; Pongracic, Jacqueline A; Weeks, Daniel E; Wang, Xiaobin

2015-01-01

Food allergy (FA) affects 2–10% of U.S. children and is a growing clinical and public health problem. Here we conduct the first genome-wide association study of well-defined FA, including specific subtypes (peanut, milk, and egg) in 2,759 U.S. participants (1,315 children; 1,444 parents) from the Chicago Food Allergy Study; and identify peanut allergy (PA)-specific loci in the HLA-DR and -DQ gene region at 6p21.32, tagged by rs7192 (p=5.5×10−8) and rs9275596 (p=6.8×10−10), in 2,197 participants of European ancestry. We replicate these associations in an independent sample of European ancestry. These associations are further supported by meta-analyses across the discovery and replication samples. Both single-nucleotide polymorphisms (SNPs) are associated with differential DNA methylation levels at multiple CpG sites (p<5×10−8); and differential DNA methylation of the HLA-DQB1 and HLA-DRB1 genes partially mediate the identified SNP-PA associations. This study suggests that the HLA-DR and -DQ gene region likely poses significant genetic risk for PA. PMID:25710614

Identifying Specific Learning Disabilities: Legislation, Regulation, and Court Decisions

ERIC Educational Resources Information Center

Zumeta, Rebecca O.; Zirkel, Perry A.; Danielson, Louis

2014-01-01

Specific learning disability (SLD) identification and eligibility practices are evolving and sometimes contentious. This article describes the historical context and current status of the SLD definition, legislation, regulation, and case law related to the identification of students eligible for special education services. The first part traces…

The Use of Neural Networks in Identifying Error Sources in Satellite-Derived Tropical SST Estimates

PubMed Central

Lee, Yung-Hsiang; Ho, Chung-Ru; Su, Feng-Chun; Kuo, Nan-Jung; Cheng, Yu-Hsin

2011-01-01

An neural network model of data mining is used to identify error sources in satellite-derived tropical sea surface temperature (SST) estimates from thermal infrared sensors onboard the Geostationary Operational Environmental Satellite (GOES). By using the Back Propagation Network (BPN) algorithm, it is found that air temperature, relative humidity, and wind speed variation are the major factors causing the errors of GOES SST products in the tropical Pacific. The accuracy of SST estimates is also improved by the model. The root mean square error (RMSE) for the daily SST estimate is reduced from 0.58 K to 0.38 K and mean absolute percentage error (MAPE) is 1.03%. For the hourly mean SST estimate, its RMSE is also reduced from 0.66 K to 0.44 K and the MAPE is 1.3%. PMID:22164030

Source diagnostics of polycyclic aromatic hydrocarbons in urban road runoff, dust, rain and canopy throughfall.

PubMed

Zhang, Wei; Zhang, Shucai; Wan, Chao; Yue, Dapan; Ye, Youbin; Wang, Xuejun

2008-06-01

Diagnostic ratios and multivariate analysis were utilized to apportion polycyclic aromatic hydrocarbon (PAH) sources for road runoff, road dust, rain and canopy throughfall based on samples collected in an urban area of Beijing, China. Three sampling sites representing vehicle lane, bicycle lane and branch road were selected. For road runoff and road dust, vehicular emission and coal combustion were identified as major sources, and the source contributions varied among the sampling sites. For rain, three principal components were apportioned representing coal/oil combustion (54%), vehicular emission (34%) and coking (12%). For canopy throughfall, vehicular emission (56%), coal combustion (30%) and oil combustion (14%) were identified as major sources. Overall, the PAH's source for road runoff mainly reflected that for road dust. Despite site-specific sources, the findings at the study area provided a general picture of PAHs sources for the road runoff system in urban area of Beijing.

Genetic Screening Identifies Cyanogenesis-Deficient Mutants of Lotus japonicus and Reveals Enzymatic Specificity in Hydroxynitrile Glucoside Metabolism[W][OA

PubMed Central

Takos, Adam; Lai, Daniela; Mikkelsen, Lisbeth; Abou Hachem, Maher; Shelton, Dale; Motawia, Mohammed Saddik; Olsen, Carl Erik; Wang, Trevor L.; Martin, Cathie; Rook, Fred

2010-01-01

Cyanogenesis, the release of hydrogen cyanide from damaged plant tissues, involves the enzymatic degradation of amino acid–derived cyanogenic glucosides (α-hydroxynitrile glucosides) by specific β-glucosidases. Release of cyanide functions as a defense mechanism against generalist herbivores. We developed a high-throughput screening method and used it to identify cyanogenesis deficient (cyd) mutants in the model legume Lotus japonicus. Mutants in both biosynthesis and catabolism of cyanogenic glucosides were isolated and classified following metabolic profiling of cyanogenic glucoside content. L. japonicus produces two cyanogenic glucosides: linamarin (derived from Val) and lotaustralin (derived from Ile). Their biosynthesis may involve the same set of enzymes for both amino acid precursors. However, in one class of mutants, accumulation of lotaustralin and linamarin was uncoupled. Catabolic mutants could be placed in two complementation groups, one of which, cyd2, encoded the β-glucosidase BGD2. Despite the identification of nine independent cyd2 alleles, no mutants involving the gene encoding a closely related β-glucosidase, BGD4, were identified. This indicated that BGD4 plays no role in cyanogenesis in L. japonicus in vivo. Biochemical analysis confirmed that BGD4 cannot hydrolyze linamarin or lotaustralin and in L. japonicus is specific for breakdown of related hydroxynitrile glucosides, such as rhodiocyanoside A. By contrast, BGD2 can hydrolyze both cyanogenic glucosides and rhodiocyanosides. Our genetic analysis demonstrated specificity in the catabolic pathways for hydroxynitrile glucosides and implied specificity in their biosynthetic pathways as well. In addition, it has provided important tools for elucidating and potentially modifying cyanogenesis pathways in plants. PMID:20453117

Identifying PM2.5 and PM0.1 sources for epidemiological studies in California.

PubMed

Hu, Jianlin; Zhang, Hongliang; Chen, Shuhua; Ying, Qi; Wiedinmyer, Christine; Vandenberghe, Francois; Kleeman, Michael J

2014-05-06

The University of California-Davis_Primary (UCD_P) model was applied to simultaneously track ∼ 900 source contributions to primary particulate matter (PM) in California for seven continuous years (January 1st, 2000 to December 31st, 2006). Predicted source contributions to primary PM2.5 mass, PM1.8 elemental carbon (EC), PM1.8 organic carbon (OC), PM0.1 EC, and PM0.1 OC were in general agreement with the results from previous source apportionment studies using receptor-based techniques. All sources were further subjected to a constraint check based on model performance for PM trace elemental composition. A total of 151 PM2.5 sources and 71 PM0.1 sources contained PM elements that were predicted at concentrations in general agreement with measured values at nearby monitoring sites. Significant spatial heterogeneity was predicted among the 151 PM2.5 and 71 PM0.1 source concentrations, and significantly different seasonal profiles were predicted for PM2.5 and PM0.1 in central California vs southern California. Population-weighted concentrations of PM emitted from various sources calculated using the UCD_P model spatial information differed from the central monitor estimates by up to 77% for primary PM2.5 mass and 148% for PM2.5 EC because the central monitor concentration is not representative of exposure for nearby population. The results from the UCD_P model provide enhanced source apportionment information for epidemiological studies to examine the relationship between health effects and concentrations of primary PM from individual sources.

Identifying sex-specific risk factors for low bone mineral density in adolescent runners.

PubMed

Tenforde, Adam Sebastian; Fredericson, Michael; Sayres, Lauren Carter; Cutti, Phil; Sainani, Kristin Lynn

2015-06-01

Adolescent runners may be at risk for low bone mineral density (BMD) associated with sports participation. Few prior investigations have evaluated bone health in young runners, particularly males. To characterize sex-specific risk factors for low BMD in adolescent runners. Cross-sectional study; Level of evidence, 3. Training characteristics, fracture history, eating behaviors and attitudes, and menstrual history were measured using online questionnaires. A food frequency questionnaire was used to identify dietary patterns and measure calcium intake. Runners (female: n = 94, male: n = 42) completed dual-energy x-ray absorptiometry (DXA) to measure lumbar spine (LS) and total body less head (TBLH) BMD and body composition values, including android-to-gynoid (A:G) fat mass ratio. The BMD was standardized to Z-scores using age, sex, and race/ethnicity reference values. Questionnaire values were combined with DXA values to determine risk factors associated with differences in BMD Z-scores in LS and TBLH and low bone mass (defined as BMD Z-score ≤-1). In multivariable analyses, risk factors for lower LS BMD Z-scores in girls included lower A:G ratio, being shorter, and the combination of (interaction between) current menstrual irregularity and a history of fracture (all P < .01). Later age of menarche, lower A:G ratio, lower lean mass, and drinking less milk were associated with lower TBLH BMD Z-scores (P < .01). In boys, lower body mass index (BMI) Z-scores and the belief that being thinner improves performance were associated with lower LS and TBLH BMD Z-scores (all P < .05); lower A:G ratio was additionally associated with lower TBLH Z-scores (P < .01). Thirteen girls (14%) and 9 boys (21%) had low bone mass. Girls with a BMI ≤17.5 kg/m(2) or both menstrual irregularity and a history of fracture were significantly more likely to have low bone mass. Boys with a BMI ≤17.5 kg/m(2) and belief that thinness improves performance were significantly more likely to have

Omics of Brucella: Species-Specific sRNA-Mediated Gene Ontology Regulatory Networks Identified by Computational Biology.

PubMed

Vishnu, Udayakumar S; Sankarasubramanian, Jagadesan; Gunasekaran, Paramasamy; Sridhar, Jayavel; Rajendhran, Jeyaprakash

2016-06-01

Brucella is an intracellular bacterium that causes the zoonotic infectious disease, brucellosis. Brucella species are currently intensively studied with a view to developing novel global health diagnostics and therapeutics. In this context, small RNAs (sRNAs) are one of the emerging topical areas; they play significant roles in regulating gene expression and cellular processes in bacteria. In the present study, we forecast sRNAs in three Brucella species that infect humans, namely Brucella melitensis, Brucella abortus, and Brucella suis, using a computational biology analysis. We combined two bioinformatic algorithms, SIPHT and sRNAscanner. In B. melitensis 16M, 21 sRNA candidates were identified, of which 14 were novel. Similarly, 14 sRNAs were identified in B. abortus, of which four were novel. In B. suis, 16 sRNAs were identified, and five of them were novel. TargetRNA2 software predicted the putative target genes that could be regulated by the identified sRNAs. The identified mRNA targets are involved in carbohydrate, amino acid, lipid, nucleotide, and coenzyme metabolism and transport, energy production and conversion, replication, recombination, repair, and transcription. Additionally, the Gene Ontology (GO) network analysis revealed the species-specific, sRNA-based regulatory networks in B. melitensis, B. abortus, and B. suis. Taken together, although sRNAs are veritable modulators of gene expression in prokaryotes, there are few reports on the significance of sRNAs in Brucella. This report begins to address this literature gap by offering a series of initial observations based on computational biology to pave the way for future experimental analysis of sRNAs and their targets to explain the complex pathogenesis of Brucella.

Potential sources of precipitation in Lake Baikal basin

NASA Astrophysics Data System (ADS)

Shukurov, K. A.; Mokhov, I. I.

2017-11-01

Based on the data of long-term measurements at 23 meteorological stations in the Russian part of the Lake Baikal basin the probabilities of daily precipitation with different intensity and their contribution to the total precipitation are estimated. Using the trajectory model HYSPLIT_4 for each meteorological station for the period 1948-2016 the 10-day backward trajectories of air parcels, the height of these trajectories and distribution of specific humidity along the trajectories are calculated. The average field of power of potential sources of daily precipitation (less than 10 mm) for all meteorological stations in the Russian part of the Lake Baikal basin was obtained using the CWT (concentration weighted trajectory) method. The areas have been identified from which within 10 days water vapor can be transported to the Lake Baikal basin, as well as regions of the most and least powerful potential sources. The fields of the mean height of air parcels trajectories and the mean specific humidity along the trajectories are compared with the field of mean power of potential sources.

Atmospheric aerosol source identification and estimates of source contributions to air pollution in Dundee, UK

NASA Astrophysics Data System (ADS)

Qin, Y.; Oduyemi, K.

Anthropogenic aerosol (PM 10) emission sources sampled at an air quality monitoring station in Dundee have been analysed. However, the information on local natural aerosol emission sources was unavailable. A method that combines receptor model and atmospheric dispersion model was used to identify aerosol sources and estimate source contributions to air pollution. The receptor model identified five sources. These are aged marine aerosol source with some chlorine replaced by sulphate, secondary aerosol source of ammonium sulphate, secondary aerosol source of ammonium nitrate, soil and construction dust source, and incinerator and fuel oil burning emission source. For the vehicle emission source, which has been comprehensively described in the atmospheric emission inventory but cannot be identified by the receptor model, an atmospheric dispersion model was used to estimate its contributions. In Dundee, a significant percentage, 67.5%, of the aerosol mass sampled at the study station could be attributed to the six sources named above.

Identifying fecal pollution sources using 3M(™) Petrifilm (™) count plates and antibiotic resistance analysis in the Horse Creek Watershed in Aiken County, SC (USA).

PubMed

Harmon, S Michele; West, Ryan T; Yates, James R

2014-12-01

Sources of fecal coliform pollution in a small South Carolina (USA) watershed were identified using inexpensive methods and commonly available equipment. Samples from the upper reaches of the watershed were analyzed with 3M(™) Petrifilm(™) count plates. We were able to narrow down the study's focus to one particular tributary, Sand River, that was the major contributor of the coliform pollution (both fecal and total) to a downstream reservoir that is heavily used for recreation purposes. Concentrations of total coliforms ranged from 2,400 to 120,333 cfu/100 mL, with sharp increases in coliform counts observed in samples taken after rain events. Positive correlations between turbidity and fecal coliform counts suggested a relationship between fecal pollution and stormwater runoff. Antibiotic resistance analysis (ARA) compared antibiotic resistance profiles of fecal coliform isolates from the stream to those of a watershed-specific fecal source library (equine, waterfowl, canines, and untreated sewage). Known fecal source isolates and unknown isolates from the stream were exposed to six antibiotics at three concentrations each. Discriminant analysis grouped known isolates with an overall average rate of correct classification (ARCC) of 84.3 %. A total of 401 isolates from the first stream location were classified as equine (45.9 %), sewage (39.4 %), waterfowl (6.2 %), and feline (8.5 %). A similar pattern was observed at the second sampling location, with 42.6 % equine, 45.2 % sewage, 2.8 % waterfowl, 0.6 % canine, and 8.8 % feline. While there were slight weather-dependent differences, the vast majority of the coliform pollution in this stream appeared to be from two sources, equine and sewage. This information will contribute to better land use decisions and further justify implementation of low-impact development practices within this urban watershed.

Assessment of Equine Fecal Contamination: The Search for Alternative Bacterial Source-tracking Targets

EPA Science Inventory

16S rDNA clone libraries were evaluated for detection of fecal source-identifying bacteria from a collapsed equine manure pile. Libraries were constructed using universal eubacterial primers and Bacteroides-Prevotella group-specific primers. Eubacterial sequences indicat...

PM₁₀ and PM₂.₅ sources at an insular location in the western Mediterranean by using source apportionment techniques.

PubMed

Pey, Jorge; Alastuey, Andrés; Querol, Xavier

2013-07-01

PM₁₀ and PM₂.₅ chemical composition has been determined at a suburban insular site in the Balearic Islands (Spain) during almost one and a half year. As a result, 200 samples with more than 50 chemical parameters analyzed have been obtained. The whole database has been analyzed by two receptor modelling techniques (Principal Component Analysis and Positive Matrix Factorisation) in order to identify the main PM sources. After that, regression analyses with respect to the PM mass concentrations were conducted to quantify the daily contributions of each source. Four common sources were identified by both receptor models: secondary nitrate coupled with vehicular emissions, secondary sulphate influenced by fuel-oil combustion, aged marine aerosols and mineral dust. In addition, PCA isolated harbour emissions and a mixed anthropogenic factor containing industrial emissions; whereas PMF isolated an additional mineral factor interpreted as road dust+harbour emissions, and a vehicular abrasion products factor. The use of both methodologies appeared complementary. Nevertheless, PMF sources by themselves were better differentiated. Besides these receptor models, a specific methodology to quantify African dust was also applied. The combination of these three source apportionment tools allowed the identification of 8 sources, being 4 of them mineral (African, regional, urban and harbour dusts). As a summary, 29% of PM₁₀ was attributed to natural sources (African dust, regional dust and sea spray), whereas the proportion diminished to 11% in PM₂.₅. Furthermore, the secondary sulphate source, which accounted for about 22 and 32% of PM₁₀ and PM₂.₅, is strongly linked to the aged polluted air masses residing over the western Mediterranean in the warm period. Copyright © 2013 Elsevier B.V. All rights reserved.

Task-specific Aspects of Goal-directed Word Generation Identified via Simultaneous EEG-fMRI.

PubMed

Shapira-Lichter, Irit; Klovatch, Ilana; Nathan, Dana; Oren, Noga; Hendler, Talma

2016-09-01

Generating words according to a given rule relies on retrieval-related search and postretrieval control processes. Using fMRI, we recently characterized neural patterns of word generation in response to episodic, semantic, and phonemic cues by comparing free recall of wordlists, category fluency, and letter fluency [Shapira-Lichter, I., Oren, N., Jacob, Y., Gruberger, M., & Hendler, T. Portraying the unique contribution of the default mode network to internally driven mnemonic processes. Proceedings of the National Academy of Sciences, U.S.A., 110, 4950-4955, 2013]. Distinct selectivity for each condition was evident, representing discrete aspects of word generation-related memory retrieval. For example, the precuneus, implicated in processing spatiotemporal information, emerged as a key contributor to the episodic condition, which uniquely requires this information. Gamma band is known to play a central role in memory, and increased gamma power has been observed before word generation. Yet, gamma modulation in response to task demands has not been investigated. To capture the task-specific modulation of gamma power, we analyzed the EEG data recorded simultaneously with the aforementioned fMRI, focusing on the activity locked to and immediately preceding word articulation. Transient increases in gamma power were identified in a parietal electrode immediately before episodic and semantic word generation, however, within a different time frame relative to articulation. Gamma increases were followed by an alpha-theta decrease in the episodic condition, a gamma decrease in the semantic condition. This pattern indicates a task-specific modulation of the gamma signal corresponding to the specific demands of each word generation task. The gamma power and fMRI signal from the precuneus were correlated during the episodic condition, implying the existence of a common cognitive construct uniquely required for this task, possibly the reactivation or processing of

Comprehensive, Multi-Source Cyber-Security Events Data Set

DOE Data Explorer

Kent, Alexander D. [Los Alamos National Lab. (LANL), Los Alamos, NM (United States)

2015-05-21

This data set represents 58 consecutive days of de-identified event data collected from five sources within Los Alamos National Laboratory’s corporate, internal computer network. The data sources include Windows-based authentication events from both individual computers and centralized Active Directory domain controller servers; process start and stop events from individual Windows computers; Domain Name Service (DNS) lookups as collected on internal DNS servers; network flow data as collected on at several key router locations; and a set of well-defined red teaming events that present bad behavior within the 58 days. In total, the data set is approximately 12 gigabytes compressed across the five data elements and presents 1,648,275,307 events in total for 12,425 users, 17,684 computers, and 62,974 processes. Specific users that are well known system related (SYSTEM, Local Service) were not de-identified though any well-known administrators account were still de-identified. In the network flow data, well-known ports (e.g. 80, 443, etc) were not de-identified. All other users, computers, process, ports, times, and other details were de-identified as a unified set across all the data elements (e.g. U1 is the same U1 in all of the data). The specific timeframe used is not disclosed for security purposes. In addition, no data that allows association outside of LANL’s network is included. All data starts with a time epoch of 1 using a time resolution of 1 second. In the authentication data, failed authentication events are only included for users that had a successful authentication event somewhere within the data set.

Source apportionment of airborne particulate matter using organic compounds as tracers

NASA Astrophysics Data System (ADS)

Schauer, James J.; Rogge, Wolfgang F.; Hildemann, Lynn M.; Mazurek, Monica A.; Cass, Glen R.; Simoneit, Bernd R. T.

A chemical mass balance receptor model based on organic compounds has been developed that relates sours; contributions to airborne fine particle mass concentrations. Source contributions to the concentrations of specific organic compounds are revealed as well. The model is applied to four air quality monitoring sites in southern California using atmospheric organic compound concentration data and source test data collected specifically for the purpose of testing this model. The contributions of up to nine primary particle source types can be separately identified in ambient samples based on this method, and approximately 85% of the organic fine aerosol is assigned to primary sources on an annual average basis. The model provides information on source contributions to fine mass concentrations, fine organic aerosol concentrations and individual organic compound concentrations. The largest primary source contributors to fine particle mass concentrations in Los Angeles are found to include diesel engine exhaust, paved road dust, gasoline-powered vehicle exhaust, plus emissions from food cooking and wood smoke, with smaller contribution:; from tire dust, plant fragments, natural gas combustion aerosol, and cigarette smoke. Once these primary aerosol source contributions are added to the secondary sulfates, nitrates and organics present, virtually all of the annual average fine particle mass at Los Angeles area monitoring sites can be assigned to its source.

Genome-wide histone state profiling of fibroblasts from the opossum, Monodelphis domestica, identifies the first marsupial-specific imprinted gene

PubMed Central

2014-01-01

Background Imprinted genes have been extensively documented in eutherian mammals and found to exhibit significant interspecific variation in the suites of genes that are imprinted and in their regulation between tissues and developmental stages. Much less is known about imprinted loci in metatherian (marsupial) mammals, wherein studies have been limited to a small number of genes previously known to be imprinted in eutherians. We describe the first ab initio search for imprinted marsupial genes, in fibroblasts from the opossum, Monodelphis domestica, based on a genome-wide ChIP-seq strategy to identify promoters that are simultaneously marked by mutually exclusive, transcriptionally opposing histone modifications. Results We identified a novel imprinted gene (Meis1) and two additional monoallelically expressed genes, one of which (Cstb) showed allele-specific, but non-imprinted expression. Imprinted vs. allele-specific expression could not be resolved for the third monoallelically expressed gene (Rpl17). Transcriptionally opposing histone modifications H3K4me3, H3K9Ac, and H3K9me3 were found at the promoters of all three genes, but differential DNA methylation was not detected at CpG islands at any of these promoters. Conclusions In generating the first genome-wide histone modification profiles for a marsupial, we identified the first gene that is imprinted in a marsupial but not in eutherian mammals. This outcome demonstrates the practicality of an ab initio discovery strategy and implicates histone modification, but not differential DNA methylation, as a conserved mechanism for marking imprinted genes in all therian mammals. Our findings suggest that marsupials use multiple epigenetic mechanisms for imprinting and support the concept that lineage-specific selective forces can produce sets of imprinted genes that differ between metatherian and eutherian lines. PMID:24484454

An integrated chemical biology approach identifies specific vulnerability of Ewing's sarcoma to combined inhibition of Aurora kinases A and B.

PubMed

Winter, Georg E; Rix, Uwe; Lissat, Andrej; Stukalov, Alexey; Müllner, Markus K; Bennett, Keiryn L; Colinge, Jacques; Nijman, Sebastian M; Kubicek, Stefan; Kovar, Heinrich; Kontny, Udo; Superti-Furga, Giulio

2011-10-01

Ewing's sarcoma is a pediatric cancer of the bone that is characterized by the expression of the chimeric transcription factor EWS-FLI1 that confers a highly malignant phenotype and results from the chromosomal translocation t(11;22)(q24;q12). Poor overall survival and pronounced long-term side effects associated with traditional chemotherapy necessitate the development of novel, targeted, therapeutic strategies. We therefore conducted a focused viability screen with 200 small molecule kinase inhibitors in 2 different Ewing's sarcoma cell lines. This resulted in the identification of several potential molecular intervention points. Most notably, tozasertib (VX-680, MK-0457) displayed unique nanomolar efficacy, which extended to other cell lines, but was specific for Ewing's sarcoma. Furthermore, tozasertib showed strong synergies with the chemotherapeutic drugs etoposide and doxorubicin, the current standard agents for Ewing's sarcoma. To identify the relevant targets underlying the specific vulnerability toward tozasertib, we determined its cellular target profile by chemical proteomics. We identified 20 known and unknown serine/threonine and tyrosine protein kinase targets. Additional target deconvolution and functional validation by RNAi showed simultaneous inhibition of Aurora kinases A and B to be responsible for the observed tozasertib sensitivity, thereby revealing a new mechanism for targeting Ewing's sarcoma. We further corroborated our cellular observations with xenograft mouse models. In summary, the multilayered chemical biology approach presented here identified a specific vulnerability of Ewing's sarcoma to concomitant inhibition of Aurora kinases A and B by tozasertib and danusertib, which has the potential to become a new therapeutic option.

ETD in a traveling wave ion guide at tuned Z-spray ion source conditions allows for site-specific hydrogen/deuterium exchange measurements.

PubMed

Rand, Kasper D; Pringle, Steven D; Morris, Michael; Engen, John R; Brown, Jeffery M

2011-10-01

The recent application of electron transfer dissociation (ETD) to measure the hydrogen exchange of proteins in solution at single-residue resolution (HX-ETD) paves the way for mass spectrometry-based analyses of biomolecular structure at an unprecedented level of detail. The approach requires that activation of polypeptide ions prior to ETD is minimal so as to prevent undesirable gas-phase randomization of the deuterium label from solution (i.e., hydrogen scrambling). Here we explore the use of ETD in a traveling wave ion guide of a quadrupole-time-of-flight (Q-TOF) mass spectrometer with a "Z-spray" type ion source, to measure the deuterium content of individual residues in peptides. We systematically identify key parameters of the Z-spray ion source that contribute to collisional activation and define conditions that allow ETD experiments to be performed in the traveling wave ion guide without gas-phase hydrogen scrambling. We show that ETD and supplemental collisional activation in a subsequent traveling wave ion guide allows for improved extraction of residue-specific deuterium contents in peptides with low charge. Our results demonstrate the feasibility, and illustrate the advantages of performing HX-ETD experiments on a high-resolution Q-TOF instrument equipped with traveling wave ion guides. Determination of parameters of the Z-spray ion source that contribute to ion heating are similarly pertinent to a growing number of MS applications that also rely on an energetically gentle transfer of ions into the gas-phase, such as the analysis of biomolecular structure by native mass spectrometry in combination with gas-phase ion-ion/ion-neutral reactions or ion mobility spectrometry. © American Society for Mass Spectrometry, 2011

Specific Proteins in Nontuberculous Mycobacteria: New Potential Tools

PubMed Central

Orduña, Patricia; Castillo-Rodal, Antonia I.; Mercado, Martha E.; Ponce de León, Samuel; López-Vidal, Yolanda

2015-01-01

Nontuberculous mycobacteria (NTM) have been isolated from water, soil, air, food, protozoa, plants, animals, and humans. Although most NTM are saprophytes, approximately one-third of NTM have been associated with human diseases. In this study, we did a comparative proteomic analysis among five NTM strains isolated from several sources. There were different numbers of protein spots from M. gordonae (1,264), M. nonchromogenicum type I (894), M. nonchromogenicum type II (935), M. peregrinum (806), and M. scrofulaceum/Mycobacterium mantenii (1,486) strains, respectively. We identified 141 proteins common to all strains and specific proteins to each NTM strain. A total of 23 proteins were selected for its identification. Two of the common proteins identified (short-chain dehydrogenase/reductase SDR and diguanylate cyclase) did not align with M. tuberculosis complex protein sequences, which suggest that these proteins are found only in the NTM strains. Some of the proteins identified as common to all strains can be used as markers of NTM exposure and for the development of new diagnostic tools. Additionally, the specific proteins to NTM strains identified may represent potential candidates for the diagnosis of diseases caused by these mycobacteria. PMID:26106621

Specific Proteins in Nontuberculous Mycobacteria: New Potential Tools.

PubMed

Orduña, Patricia; Castillo-Rodal, Antonia I; Mercado, Martha E; Ponce de León, Samuel; López-Vidal, Yolanda

2015-01-01

Nontuberculous mycobacteria (NTM) have been isolated from water, soil, air, food, protozoa, plants, animals, and humans. Although most NTM are saprophytes, approximately one-third of NTM have been associated with human diseases. In this study, we did a comparative proteomic analysis among five NTM strains isolated from several sources. There were different numbers of protein spots from M. gordonae (1,264), M. nonchromogenicum type I (894), M. nonchromogenicum type II (935), M. peregrinum (806), and M. scrofulaceum/Mycobacterium mantenii (1,486) strains, respectively. We identified 141 proteins common to all strains and specific proteins to each NTM strain. A total of 23 proteins were selected for its identification. Two of the common proteins identified (short-chain dehydrogenase/reductase SDR and diguanylate cyclase) did not align with M. tuberculosis complex protein sequences, which suggest that these proteins are found only in the NTM strains. Some of the proteins identified as common to all strains can be used as markers of NTM exposure and for the development of new diagnostic tools. Additionally, the specific proteins to NTM strains identified may represent potential candidates for the diagnosis of diseases caused by these mycobacteria.

Identifying and tracing potential energy surfaces of electronic excitations with specific character via their transition origins: application to oxirane.

PubMed

Li, Jian-Hao; Zuehlsdorff, T J; Payne, M C; Hine, N D M

2015-05-14

We show that the transition origins of electronic excitations identified by quantified natural transition orbital (QNTO) analysis can be employed to connect potential energy surfaces (PESs) according to their character across a wide range of molecular geometries. This is achieved by locating the switching of transition origins of adiabatic potential surfaces as the geometry changes. The transition vectors for analysing transition origins are provided by linear response time-dependent density functional theory (TDDFT) calculations under the Tamm-Dancoff approximation. We study the photochemical CO ring opening of oxirane as an example and show that the results corroborate the traditional Gomer-Noyes mechanism derived experimentally. The knowledge of specific states for the reaction also agrees well with that given by previous theoretical work using TDDFT surface-hopping dynamics that was validated by high-quality quantum Monte Carlo calculations. We also show that QNTO can be useful for considerably larger and more complex systems: by projecting the excitations to those of a reference oxirane molecule, the approach is able to identify and analyse specific excitations of a trans-2,3-diphenyloxirane molecule.

Bioaccumulation of photoprotective compounds in copepods: environmental triggers and sources of intra-specific variability

NASA Astrophysics Data System (ADS)

Zagarese, H. E.; García, P.; Diéguez, M. D.; Ferraro, M. A.

2012-12-01

Ultraviolet radiation (UVR) and temperature are two globally important abiotic factors affecting freshwater ecosystems. Planktonic organisms have developed a battery of counteracting mechanisms to minimize the risk of being damaged by UVR, which respond to three basic principles: avoid, protect, repair. Copepods are among the most successful zooplankton groups. They are highly adaptable animals, capable of displaying flexible behaviors, physiologies, and life strategies. In particular, they are well equipped to cope with harmful UVR. Their arsenal includes vertical migration, accumulation of photoprotective compounds, and photorepair. The preference for a particular strategy is affected by a plethora of environmental (extrinsic) parameters, such as the existence of a depth refuge, the risk of visual predation, and temperature. Temperature modifies the environment (e.g. the lake thermal structure), and animal metabolism (e.g., swimming speed, bioaccumulation of photoprotective compounds). In addition, the relative weight of UVR-coping strategies is also influenced by the organism (intrinsic) characteristics (e.g., inter- and intra-specific variability). The UV absorbing compounds, mycosporine-like amino acids (MAAs), are widely distributed among freshwater copepods. Animals are unable to synthesize MAAs, and therefore depend on external sources for accumulating these compounds. Although copepods may acquire MAAs from their food, for the few centropagic species investigated so far, the main source of MAAs are microbial (most likely prokaryotic) organisms living in close association with the copepods. Boeckella gracilipes is a common centropagic copepod in Patagonian lakes. We suspected that its occurrence in different types of lakes, hydrologically unconnected, but within close geographical proximity, could have resulted in different microbial-copepod associations (i.e., different MAAs sources) that could translate into intra-specific differences in the accumulation

Reducing mortality risk by targeting specific air pollution sources: Suva, Fiji.

PubMed

Isley, C F; Nelson, P F; Taylor, M P; Stelcer, E; Atanacio, A J; Cohen, D D; Mani, F S; Maata, M

2018-01-15

Health implications of air pollution vary dependent upon pollutant sources. This work determines the value, in terms of reduced mortality, of reducing ambient particulate matter (PM 2.5 : effective aerodynamic diameter 2.5μm or less) concentration due to different emission sources. Suva, a Pacific Island city with substantial input from combustion sources, is used as a case-study. Elemental concentration was determined, by ion beam analysis, for PM 2.5 samples from Suva, spanning one year. Sources of PM 2.5 have been quantified by positive matrix factorisation. A review of recent literature has been carried out to delineate the mortality risk associated with these sources. Risk factors have then been applied for Suva, to calculate the possible mortality reduction that may be achieved through reduction in pollutant levels. Higher risk ratios for black carbon and sulphur resulted in mortality predictions for PM 2.5 from fossil fuel combustion, road vehicle emissions and waste burning that surpass predictions for these sources based on health risk of PM 2.5 mass alone. Predicted mortality for Suva from fossil fuel smoke exceeds the national toll from road accidents in Fiji. The greatest benefit for Suva, in terms of reduced mortality, is likely to be accomplished by reducing emissions from fossil fuel combustion (diesel), vehicles and waste burning. Copyright © 2017. Published by Elsevier B.V.

A modification of the Regional Nutrient Management model (ReNuMa) to identify long-term changes in riverine nitrogen sources

NASA Astrophysics Data System (ADS)

Hu, Minpeng; Liu, Yanmei; Wang, Jiahui; Dahlgren, Randy A.; Chen, Dingjiang

2018-06-01

Source apportionment is critical for guiding development of efficient watershed nitrogen (N) pollution control measures. The ReNuMa (Regional Nutrient Management) model, a semi-empirical, semi-process-oriented model with modest data requirements, has been widely used for riverine N source apportionment. However, the ReNuMa model contains limitations for addressing long-term N dynamics by ignoring temporal changes in atmospheric N deposition rates and N-leaching lag effects. This work modified the ReNuMa model by revising the source code to allow yearly changes in atmospheric N deposition and incorporation of N-leaching lag effects into N transport processes. The appropriate N-leaching lag time was determined from cross-correlation analysis between annual watershed individual N source inputs and riverine N export. Accuracy of the modified ReNuMa model was demonstrated through analysis of a 31-year water quality record (1980-2010) from the Yongan watershed in eastern China. The revisions considerably improved the accuracy (Nash-Sutcliff coefficient increased by ∼0.2) of the modified ReNuMa model for predicting riverine N loads. The modified model explicitly identified annual and seasonal changes in contributions of various N sources (i.e., point vs. nonpoint source, surface runoff vs. groundwater) to riverine N loads as well as the fate of watershed anthropogenic N inputs. Model results were consistent with previously modeled or observed lag time length as well as changes in riverine chloride and nitrate concentrations during the low-flow regime and available N levels in agricultural soils of this watershed. The modified ReNuMa model is applicable for addressing long-term changes in riverine N sources, providing decision-makers with critical information for guiding watershed N pollution control strategies.

Identifying Specific Reading Disability Subtypes for Effective Educational Remediation

ERIC Educational Resources Information Center

Feifer, Steven G.; Nader, Rebecca Gerhardstein; Flanagan, Dawn P.; Fitzer, Kim R.; Hicks, Kelly

2014-01-01

The primary purpose of this study was to investigate the various neurocognitive processes concomitant to reading by attempting to identify various subtypes of reading disorders in a referred sample. Participants were 216 elementary school students in grades two through five who were given select subtests of the Woodcock Johnson-III Tests of…

RandSpg: An open-source program for generating atomistic crystal structures with specific spacegroups

NASA Astrophysics Data System (ADS)

Avery, Patrick; Zurek, Eva

2017-04-01

A new algorithm, RANDSPG, that can be used to generate trial crystal structures with specific space groups and compositions is described. The program has been designed for systems where the atoms are independent of one another, and it is therefore primarily suited towards inorganic systems. The structures that are generated adhere to user-defined constraints such as: the lattice shape and size, stoichiometry, set of space groups to be generated, and factors that influence the minimum interatomic separations. In addition, the user can optionally specify if the most general Wyckoff position is to be occupied or constrain select atoms to specific Wyckoff positions. Extensive testing indicates that the algorithm is efficient and reliable. The library is lightweight, portable, dependency-free and is published under a license recognized by the Open Source Initiative. A web interface for the algorithm is publicly accessible at http://xtalopt.openmolecules.net/randSpg/randSpg.html. RANDSPG has also been interfaced with the XTALOPT evolutionary algorithm for crystal structure prediction, and it is illustrated that the use of symmetric lattices in the first generation of randomly created individuals decreases the number of structures that need to be optimized to find the global energy minimum.

Identifying Specific Combinations of Multimorbidity that Contribute to Health Care Resource Utilization: An Analytic Approach.

PubMed

Schiltz, Nicholas K; Warner, David F; Sun, Jiayang; Bakaki, Paul M; Dor, Avi; Given, Charles W; Stange, Kurt C; Koroukian, Siran M

2017-03-01

Multimorbidity affects the majority of elderly adults and is associated with higher health costs and utilization, but how specific patterns of morbidity influence resource use is less understood. The objective was to identify specific combinations of chronic conditions, functional limitations, and geriatric syndromes associated with direct medical costs and inpatient utilization. Retrospective cohort study using the Health and Retirement Study (2008-2010) linked to Medicare claims. Analysis used machine-learning techniques: classification and regression trees and random forest. A population-based sample of 5771 Medicare-enrolled adults aged 65 and older in the United States. Main covariates: self-reported chronic conditions (measured as none, mild, or severe), geriatric syndromes, and functional limitations. Secondary covariates: demographic, social, economic, behavioral, and health status measures. Medicare expenditures in the top quartile and inpatient utilization. Median annual expenditures were $4354, and 41% were hospitalized within 2 years. The tree model shows some notable combinations: 64% of those with self-rated poor health plus activities of daily living and instrumental activities of daily living disabilities had expenditures in the top quartile. Inpatient utilization was highest (70%) in those aged 77-83 with mild to severe heart disease plus mild to severe diabetes. Functional limitations were more important than many chronic diseases in explaining resource use. The multimorbid population is heterogeneous and there is considerable variation in how specific combinations of morbidity influence resource use. Modeling the conjoint effects of chronic conditions, functional limitations, and geriatric syndromes can advance understanding of groups at greatest risk and inform targeted tailored interventions aimed at cost containment.

A formal method for identifying distinct states of variability in time-varying sources: SGR A* as an example

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

Meyer, L.; Witzel, G.; Ghez, A. M.

2014-08-10

Continuously time variable sources are often characterized by their power spectral density and flux distribution. These quantities can undergo dramatic changes over time if the underlying physical processes change. However, some changes can be subtle and not distinguishable using standard statistical approaches. Here, we report a methodology that aims to identify distinct but similar states of time variability. We apply this method to the Galactic supermassive black hole, where 2.2 μm flux is observed from a source associated with Sgr A* and where two distinct states have recently been suggested. Our approach is taken from mathematical finance and works withmore » conditional flux density distributions that depend on the previous flux value. The discrete, unobserved (hidden) state variable is modeled as a stochastic process and the transition probabilities are inferred from the flux density time series. Using the most comprehensive data set to date, in which all Keck and a majority of the publicly available Very Large Telescope data have been merged, we show that Sgr A* is sufficiently described by a single intrinsic state. However, the observed flux densities exhibit two states: noise dominated and source dominated. Our methodology reported here will prove extremely useful to assess the effects of the putative gas cloud G2 that is on its way toward the black hole and might create a new state of variability.« less

Using c-Jun to identify fear extinction learning-specific patterns of neural activity that are affected by single prolonged stress.

PubMed

Knox, Dayan; Stanfield, Briana R; Staib, Jennifer M; David, Nina P; DePietro, Thomas; Chamness, Marisa; Schneider, Elizabeth K; Keller, Samantha M; Lawless, Caroline

2018-04-02

Neural circuits via which stress leads to disruptions in fear extinction is often explored in animal stress models. Using the single prolonged stress (SPS) model of post traumatic stress disorder and the immediate early gene (IEG) c-Fos as a measure of neural activity, we previously identified patterns of neural activity through which SPS disrupts extinction retention. However, none of these stress effects were specific to fear or extinction learning and memory. C-Jun is another IEG that is sometimes regulated in a different manner to c-Fos and could be used to identify emotional learning/memory specific patterns of neural activity that are sensitive to SPS. Animals were either fear conditioned (CS-fear) or presented with CSs only (CS-only) then subjected to extinction training and testing. C-Jun was then assayed within neural substrates critical for extinction memory. Inhibited c-Jun levels in the hippocampus (Hipp) and enhanced functional connectivity between the ventromedial prefrontal cortex (vmPFC) and basolateral amygdala (BLA) during extinction training was disrupted by SPS in the CS-fear group only. As a result, these effects were specific to emotional learning/memory. SPS also disrupted inhibited Hipp c-Jun levels, enhanced BLA c-Jun levels, and altered functional connectivity among the vmPFC, BLA, and Hipp during extinction testing in SPS rats in the CS-fear and CS-only groups. As a result, these effects were not specific to emotional learning/memory. Our findings suggest that SPS disrupts neural activity specific to extinction memory, but may also disrupt the retention of fear extinction by mechanisms that do not involve emotional learning/memory. Copyright © 2017 Elsevier B.V. All rights reserved.

Association of fine particulate matter from different sources with daily mortality in six U.S. cities.

PubMed Central

Laden, F; Neas, L M; Dockery, D W; Schwartz, J

2000-01-01

Previously we reported that fine particle mass (particulate matter [less than and equal to] 2.5 microm; PM(2.5)), which is primarily from combustion sources, but not coarse particle mass, which is primarily from crustal sources, was associated with daily mortality in six eastern U.S. cities (1). In this study, we used the elemental composition of size-fractionated particles to identify several distinct source-related fractions of fine particles and examined the association of these fractions with daily mortality in each of the six cities. Using specific rotation factor analysis for each city, we identified a silicon factor classified as soil and crustal material, a lead factor classified as motor vehicle exhaust, a selenium factor representing coal combustion, and up to two additional factors. We extracted daily counts of deaths from National Center for Health Statistics records and estimated city-specific associations of mortality with each source factor by Poisson regression, adjusting for time trends, weather, and the other source factors. Combined effect estimates were calculated as the inverse variance weighted mean of the city-specific estimates. In the combined analysis, a 10 microg/m(3) increase in PM(2.5) from mobile sources accounted for a 3.4% increase in daily mortality [95% confidence interval (CI), 1.7-5.2%], and the equivalent increase in fine particles from coal combustion sources accounted for a 1.1% increase [CI, 0.3-2.0%). PM(2.5) crustal particles were not associated with daily mortality. These results indicate that combustion particles in the fine fraction from mobile and coal combustion sources, but not fine crustal particles, are associated with increased mortality. PMID:11049813

40 CFR 63.1103 - Source category-specific applicability, definitions, and requirements.

Code of Federal Regulations, 2014 CFR

2014-07-01

... compliance schedule for the carbon black production and acetylene decomposition carbon black production... AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) NATIONAL EMISSION STANDARDS FOR HAZARDOUS AIR POLLUTANTS FOR SOURCE CATEGORIES (CONTINUED) National Emission Standards for Hazardous Air Pollutants for Source...

40 CFR 63.1103 - Source category-specific applicability, definitions, and requirements.

Code of Federal Regulations, 2013 CFR

2013-07-01

... compliance schedule for the carbon black production and acetylene decomposition carbon black production... AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) NATIONAL EMISSION STANDARDS FOR HAZARDOUS AIR POLLUTANTS FOR SOURCE CATEGORIES (CONTINUED) National Emission Standards for Hazardous Air Pollutants for Source...

40 CFR 63.1103 - Source category-specific applicability, definitions, and requirements.

Code of Federal Regulations, 2012 CFR

2012-07-01

... compliance schedule for the carbon black production and acetylene decomposition carbon black production... AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) NATIONAL EMISSION STANDARDS FOR HAZARDOUS AIR POLLUTANTS FOR SOURCE CATEGORIES (CONTINUED) National Emission Standards for Hazardous Air Pollutants for Source...

40 CFR 63.1103 - Source category-specific applicability, definitions, and requirements.

Code of Federal Regulations, 2011 CFR

2011-07-01

... compliance schedule for the carbon black production and acetylene decomposition carbon black production... AGENCY (CONTINUED) AIR PROGRAMS (CONTINUED) NATIONAL EMISSION STANDARDS FOR HAZARDOUS AIR POLLUTANTS FOR SOURCE CATEGORIES (CONTINUED) National Emission Standards for Hazardous Air Pollutants for Source...

Dietary Protein Sources and All-Cause and Cause-Specific Mortality: The Golestan Cohort Study in Iran.

PubMed

Farvid, Maryam S; Malekshah, Akbar F; Pourshams, Akram; Poustchi, Hossein; Sepanlou, Sadaf G; Sharafkhah, Maryam; Khoshnia, Masoud; Farvid, Mojtaba; Abnet, Christian C; Kamangar, Farin; Dawsey, Sanford M; Brennan, Paul; Pharoah, Paul D; Boffetta, Paolo; Willett, Walter C; Malekzadeh, Reza

2017-02-01

Dietary protein comes from foods with greatly different compositions that may not relate equally with mortality risk. Few cohort studies from non-Western countries have examined the association between various dietary protein sources and cause-specific mortality. Therefore, the associations between dietary protein sources and all-cause, cardiovascular disease, and cancer mortality were evaluated in the Golestan Cohort Study in Iran. Among 42,403 men and women who completed a dietary questionnaire at baseline, 3,291 deaths were documented during 11 years of follow up (2004-2015). Cox proportional hazards models estimated age-adjusted and multivariate-adjusted hazard ratios (HRs) and 95% CIs for all-cause and disease-specific mortality in relation to dietary protein sources. Data were analyzed from 2015 to 2016. Comparing the highest versus the lowest quartile, egg consumption was associated with lower all-cause mortality risk (HR=0.88, 95% CI=0.79, 0.97, p trend =0.03). In multivariate analysis, the highest versus the lowest quartile of fish consumption was associated with reduced risk of total cancer (HR=0.79, 95% CI=0.64, 0.98, p trend =0.03) and gastrointestinal cancer (HR=0.75, 95% CI=0.56, 1.00, p trend =0.02) mortality. The highest versus the lowest quintile of legume consumption was associated with reduced total cancer (HR=0.72, 95% CI=0.58, 0.89, p trend =0.004), gastrointestinal cancer (HR=0.76, 95% CI=0.58, 1.01, p trend =0.05), and other cancer (HR=0.66, 95% CI=0.47, 0.93, p trend =0.04) mortality. Significant associations between total red meat and poultry intake and all-cause, cardiovascular disease, or cancer mortality rate were not observed among all participants. These findings support an association of higher fish and legume consumption with lower cancer mortality, and higher egg consumption with lower all-cause mortality. Copyright © 2016 American Journal of Preventive Medicine. All rights reserved.

Dietary Protein Sources and All-Cause and Cause-Specific Mortality: The Golestan Cohort Study in Iran

PubMed Central

Farvid, Maryam S.; Malekshah, Akbar F.; Pourshams, Akram; Poustchi, Hossein; Sepanlou, Sadaf G.; Sharafkhah, Maryam; Khoshnia, Masoud; Farvid, Mojtaba; Abnet, Christian C.; Kamangar, Farin; Dawsey, Sanford M.; Brennan, Paul; Pharoah, Paul D.; Boffetta, Paolo; Willett, Walter C.; Malekzadeh, Reza

2016-01-01

Introduction Dietary protein comes from foods with greatly different compositions that may not relate equally with mortality risk. Few cohort studies from non-Western countries have examined the association between various dietary protein sources and cause-specific mortality. Therefore, the associations between dietary protein sources and all-cause, cardiovascular disease, and cancer mortality were evaluated in the Golestan Cohort Study in Iran. Methods Among 42,403 men and women who completed a dietary questionnaire at baseline, 3,291 deaths were documented during 11 years of follow up (2004–2015). Cox proportional hazards models estimated age-adjusted and multivariate-adjusted hazard ratios (HRs) and 95% CIs for all- cause and disease-specific mortality in relation to dietary protein sources. Data were analyzed from 2015 to 2016. Results Comparing the highest versus the lowest quartile, egg consumption was associated with lower all-cause mortality risk (HR=0.88, 95% CI=0.79, 0.97, ptrend=0.03). In multivariate analysis, the highest versus the lowest quartile of fish consumption was associated with reduced risk of total cancer (HR=0.79, 95% CI=0.64, 0.98, ptrend=0.03) and gastrointestinal cancer (HR=0.75, 95% CI=0.56, 1.00, ptrend=0.02) mortality. The highest versus the lowest quintile of legume consumption was associated with reduced total cancer (HR=0.72, 95% CI=0.58, 0.89, ptrend=0.004), gastrointestinal cancer (HR=0.76, 95% CI=0.58, 1.01, ptrend=0.05), and other cancer (HR=0.66, 95% CI=0.47, 0.93, ptrend=0.04) mortality. Significant associations between total red meat and poultry intake and all- cause, cardiovascular disease, or cancer mortality rate were not observed among all participants. Conclusions These findings support an association of higher fish and legume consumption with lower cancer mortality, and higher egg consumption with lower all-cause mortality. PMID:28109460

Bovine milk as a source of functional oligosaccharides for improving human health.

PubMed

Zivkovic, Angela M; Barile, Daniela

2011-05-01

Human milk oligosaccharides are complex sugars that function as selective growth substrates for specific beneficial bacteria in the gastrointestinal system. Bovine milk is a potentially excellent source of commercially viable analogs of these unique molecules. However, bovine milk has a much lower concentration of these oligosaccharides than human milk, and the majority of the molecules are simpler in structure than those found in human milk. Specific structural characteristics of milk-derived oligosaccharides are crucial to their ability to selectively enrich beneficial bacteria while inhibiting or being less than ideal substrates for undesirable and pathogenic bacteria. Thus, if bovine milk products are to provide human milk-like benefits, it is important to identify specific dairy streams that can be processed commercially and cost-effectively and that can yield specific oligosaccharide compositions that will be beneficial as new food ingredients or supplements to improve human health. Whey streams have the potential to be commercially viable sources of complex oligosaccharides that have the structural resemblance and diversity of the bioactive oligosaccharides in human milk. With further refinements to dairy stream processing techniques and functional testing to identify streams that are particularly suitable for enriching beneficial intestinal bacteria, the future of oligosaccharides isolated from dairy streams as a food category with substantiated health claims is promising.

Gambogic acid identifies an isoform-specific druggable pocket in the middle domain of Hsp90β

PubMed Central

Yim, Kendrick H.; Prince, Thomas L.; Qu, Shiwei; Bai, Fang; Jennings, Patricia A.; Onuchic, José N.; Theodorakis, Emmanuel A.; Neckers, Leonard

2016-01-01

Because of their importance in maintaining protein homeostasis, molecular chaperones, including heat-shock protein 90 (Hsp90), represent attractive drug targets. Although a number of Hsp90 inhibitors are in preclinical/clinical development, none strongly differentiate between constitutively expressed Hsp90β and stress-induced Hsp90α, the two cytosolic paralogs of this molecular chaperone. Thus, the importance of inhibiting one or the other paralog in different disease states remains unknown. We show that the natural product, gambogic acid (GBA), binds selectively to a site in the middle domain of Hsp90β, identifying GBA as an Hsp90β-specific Hsp90 inhibitor. Furthermore, using computational and medicinal chemistry, we identified a GBA analog, referred to as DAP-19, which binds potently and selectively to Hsp90β. Because of its unprecedented selectivity for Hsp90β among all Hsp90 paralogs, GBA thus provides a new chemical tool to study the unique biological role of this abundantly expressed molecular chaperone in health and disease. PMID:27466407

Geriatric-specific triage criteria are more sensitive than standard adult criteria in identifying need for trauma center care in injured older adults.

PubMed

Ichwan, Brian; Darbha, Subrahmanyam; Shah, Manish N; Thompson, Laura; Evans, David C; Boulger, Creagh T; Caterino, Jeffrey M

2015-01-01

We evaluate the sensitivity of Ohio's 2009 emergency medical services (EMS) geriatric trauma triage criteria compared with the previous adult triage criteria in identifying need for trauma center care among older adults. We studied a retrospective cohort of injured patients aged 16 years or older in the 2006 to 2011 Ohio Trauma Registry. Patients aged 70 years or older were considered geriatric. We identified whether each patient met the geriatric and the adult triage criteria. The outcome measure was need for trauma center care, defined by surrogate markers: Injury Severity Score greater than 15, operating room in fewer than 48 hours, any ICU stay, and inhospital mortality. We calculated sensitivity and specificity of both triage criteria for both age groups. We included 101,577 patients; 33,379 (33%) were geriatric. Overall, 57% of patients met adult criteria and 68% met geriatric criteria. Using Injury Severity Score, for older adults geriatric criteria were more sensitive for need for trauma center care (93%; 95% confidence interval [CI] 92% to 93%) than adult criteria (61%; 95% CI 60% to 62%). Geriatric criteria decreased specificity in older adults from 61% (95% CI 61% to 62%) to 49% (95% CI 48% to 49%). Geriatric criteria in older adults (93% sensitivity, 49% specificity) performed similarly to the adult criteria in younger adults (sensitivity 87% and specificity 44%). Similar patterns were observed for other outcomes. Standard adult EMS triage guidelines provide poor sensitivity in older adults. Ohio's geriatric trauma triage guidelines significantly improve sensitivity in identifying Injury Severity Score and other surrogate markers of the need for trauma center care, with modest decreases in specificity for older adults. Copyright © 2014 American College of Emergency Physicians. Published by Elsevier Inc. All rights reserved.

PROMISE: a tool to identify genomic features with a specific biologically interesting pattern of associations with multiple endpoint variables.

PubMed

Pounds, Stan; Cheng, Cheng; Cao, Xueyuan; Crews, Kristine R; Plunkett, William; Gandhi, Varsha; Rubnitz, Jeffrey; Ribeiro, Raul C; Downing, James R; Lamba, Jatinder

2009-08-15

In some applications, prior biological knowledge can be used to define a specific pattern of association of multiple endpoint variables with a genomic variable that is biologically most interesting. However, to our knowledge, there is no statistical procedure designed to detect specific patterns of association with multiple endpoint variables. Projection onto the most interesting statistical evidence (PROMISE) is proposed as a general procedure to identify genomic variables that exhibit a specific biologically interesting pattern of association with multiple endpoint variables. Biological knowledge of the endpoint variables is used to define a vector that represents the biologically most interesting values for statistics that characterize the associations of the endpoint variables with a genomic variable. A test statistic is defined as the dot-product of the vector of the observed association statistics and the vector of the most interesting values of the association statistics. By definition, this test statistic is proportional to the length of the projection of the observed vector of correlations onto the vector of most interesting associations. Statistical significance is determined via permutation. In simulation studies and an example application, PROMISE shows greater statistical power to identify genes with the interesting pattern of associations than classical multivariate procedures, individual endpoint analyses or listing genes that have the pattern of interest and are significant in more than one individual endpoint analysis. Documented R routines are freely available from www.stjuderesearch.org/depts/biostats and will soon be available as a Bioconductor package from www.bioconductor.org.

Attribution of human infections with Shiga toxin-producing Escherichia coli (STEC) to livestock sources and identification of source-specific risk factors, The Netherlands (2010-2014).

PubMed

Mughini-Gras, L; van Pelt, W; van der Voort, M; Heck, M; Friesema, I; Franz, E

2018-02-01

Shiga toxin-producing Escherichia coli (STEC) is a zoonotic pathogen of public health concern whose sources and transmission routes are difficult to trace. Using a combined source attribution and case-control analysis, we determined the relative contributions of four putative livestock sources (cattle, small ruminants, pigs, poultry) to human STEC infections and their associated dietary, animal contact, temporal and socio-econo-demographic risk factors in the Netherlands in 2010/2011-2014. Dutch source data were supplemented with those from other European countries with similar STEC epidemiology. Human STEC infections were attributed to sources using both the modified Dutch model (mDM) and the modified Hald model (mHM) supplied with the same O-serotyping data. Cattle accounted for 48.6% (mDM) and 53.1% (mHM) of the 1,183 human cases attributed, followed by small ruminants (mDM: 23.5%; mHM: 25.4%), pigs (mDM: 12.5%; mHM: 5.7%) and poultry (mDM: 2.7%; mHM: 3.1%), whereas the sources of the remaining 12.8% of cases could not be attributed. Of the top five O-serotypes infecting humans, O157, O26, O91 and O103 were mainly attributed to cattle (61%-75%) and O146 to small ruminants (71%-77%). Significant risk factors for human STEC infection as a whole were the consumption of beef, raw/undercooked meat or cured meat/cold cuts. For cattle-attributed STEC infections, specific risk factors were consuming raw meat spreads and beef. Consuming raw/undercooked or minced meat were risk factors for STEC infections attributed to small ruminants. For STEC infections attributed to pigs, only consuming raw/undercooked meat was significant. Consuming minced meat, raw/undercooked meat or cured meat/cold cuts were associated with poultry-attributed STEC infections. Consuming raw vegetables was protective for all STEC infections. We concluded that domestic ruminants account for approximately three-quarters of reported human STEC infections, whereas pigs and poultry play a minor role and

FECAL BACTERIA SOURCE TRACKING AND BACTEROIDES SPP. HOST SPECIES SPECIFICITY ANALYSIS

EPA Science Inventory

Point and non-point pollution sources of fecal pollution on a watershed adversely impact the quality of drinking source waters and recreational waters. States are required to develop total maximum daily loads (TMDLs) and devise best management practices (BMPs) to reduce the po...

Identifying the effective evidence sources to use in developing Clinical Guidelines for Acute Stroke Management: lived experiences of the search specialist and project manager.

PubMed

Parkhill, Anne; Hill, Kelvin

2009-03-01

The Australian National Stroke Foundation appointed a search specialist to find the best available evidence for the second edition of its Clinical Guidelines for Acute Stroke Management. To identify the relative effectiveness of differing evidence sources for the guideline update. We searched and reviewed references from five valid evidence sources for clinical and economic questions: (i) electronic databases; (ii) reference lists of relevant systematic reviews, guidelines, and/or primary studies; (iii) table of contents of a number of key journals for the last 6 months; (iv) internet/grey literature; and (v) experts. Reference sources were recorded, quantified, and analysed. In the clinical portion of the guidelines document, there was a greater use of previous knowledge and sources other than electronic databases for evidence, while there was a greater use of electronic databases for the economic section. The results confirmed that searchers need to be aware of the context and range of sources for evidence searches. For best available evidence, searchers cannot rely solely on electronic databases and need to encompass many different media and sources.

On - road mobile source pollutant emissions : identifying hotspots and ranking roads.