Measurements of Organic Composition of Aerosol and Rainwater Samples Using Offline Aerosol Mass Spectrometry

NASA Astrophysics Data System (ADS)

OBrien, R. E.; Ridley, K. J.; Canagaratna, M. R.; Croteau, P.; Budisulistiorini, S. H.; Cui, T.; Green, H. S.; Surratt, J. D.; Jayne, J. T.; Kroll, J. H.

2016-12-01

A thorough understanding of the sources, evolution, and budgets of atmospheric organic aerosol requires widespread measurements of the amount and chemical composition of atmospheric organic carbon in the condensed phase (within particles and water droplets). Collecting such datasets requires substantial spatial and temporal (long term) coverage, which can be challenging when relying on online measurements by state-of-the-art research-grade instrumentation (such as those used in atmospheric chemistry field studies). Instead, samples are routinely collected using relatively low-cost techniques, such as aerosol filters, for offline analysis of their chemical composition. However, measurements made by online and offline instruments can be fundamentally different, leading to disparities between data from field studies and those from more routine monitoring. To better connect these two approaches, and take advantage of the benefits of each, we have developed a method to introduce collected samples into online aerosol instruments using nebulization. Because nebulizers typically require tens to hundreds of milliliters of solution, limiting this technique to large samples, we developed a new, ultrasonic micro-nebulizer that requires only small volumes (tens of microliters) of sample for chemical analysis. The nebulized (resuspended) sample is then sent into a high-resolution Aerosol Mass Spectrometer (AMS), a widely-used instrument that provides key information on the chemical composition of aerosol particulate matter (elemental ratios, carbon oxidation state, etc.), measurements that are not typically made for collected atmospheric samples. Here, we compare AMS data collected using standard on-line techniques with our offline analysis, demonstrating the utility of this new technique to aerosol filter samples. We then apply this approach to organic aerosol filter samples collected in remote regions, as well as rainwater samples from across the US. This data provides information on the sample composition and changes in key chemical characteristics across locations and seasons.

Prevalence of TMJ Disorders among the Patients Attending the Dental Clinic of Ajman University of Science and Technology-Fujairah Campus, UAE.

PubMed

AlShaban, Kashef K; Gul Abdul Waheed, Zainab

2018-01-01

The objective of this study was to determine the prevalence of temporomandibular joint (TMJ) disorders (if any) among the patients attending the dental clinic (for routine dental treatment) of Ajman University of Science and Technology (AUST)-Fujairah campus, UAE, and its possible causes. A sample of 100 adult patients attending the dental clinic of AUST for different types of dental treatment were collected; the routine examination of the TMJ and possible disorders such as clicking, crepitation, limitation or deviation during mouth opening, or tenderness reveals that 41% of the sample experience varying degrees of disorders in the TMJ. Radiographs were taken if needed (panoramic radiograph). The information was collected and recorded for each patient through questionnaires.

Large-scale atlas of microarray data reveals biological landscape of gene expression in Arabidopsis

USDA-ARS?s Scientific Manuscript database

Transcriptome datasets from thousands of samples of the model plant Arabidopsis thaliana have been collectively generated by multiple individual labs. Although integration and meta-analysis of these samples has become routine in the plant research community, it is often hampered by the lack of metad...

Evaluation of environmental sampling methods for detection of Salmonella enterica in a large animal veterinary hospital.

PubMed

Goeman, Valerie R; Tinkler, Stacy H; Hammac, G Kenitra; Ruple, Audrey

2018-04-01

Environmental surveillance for Salmonella enterica can be used for early detection of contamination; thus routine sampling is an integral component of infection control programs in hospital environments. At the Purdue University Veterinary Teaching Hospital (PUVTH), the technique regularly employed in the large animal hospital for sample collection uses sterile gauze sponges for environmental sampling, which has proven labor-intensive and time-consuming. Alternative sampling methods use Swiffer brand electrostatic wipes for environmental sample collection, which are reportedly effective and efficient. It was hypothesized that use of Swiffer wipes for sample collection would be more efficient and less costly than the use of gauze sponges. A head-to-head comparison between the 2 sampling methods was conducted in the PUVTH large animal hospital and relative agreement, cost-effectiveness, and sampling efficiency were compared. There was fair agreement in culture results between the 2 sampling methods, but Swiffer wipes required less time and less physical effort to collect samples and were more cost-effective.

Clinical whole-genome sequencing from routine formalin-fixed, paraffin-embedded specimens: pilot study for the 100,000 Genomes Project.

PubMed

Robbe, Pauline; Popitsch, Niko; Knight, Samantha J L; Antoniou, Pavlos; Becq, Jennifer; He, Miao; Kanapin, Alexander; Samsonova, Anastasia; Vavoulis, Dimitrios V; Ross, Mark T; Kingsbury, Zoya; Cabes, Maite; Ramos, Sara D C; Page, Suzanne; Dreau, Helene; Ridout, Kate; Jones, Louise J; Tuff-Lacey, Alice; Henderson, Shirley; Mason, Joanne; Buffa, Francesca M; Verrill, Clare; Maldonado-Perez, David; Roxanis, Ioannis; Collantes, Elena; Browning, Lisa; Dhar, Sunanda; Damato, Stephen; Davies, Susan; Caulfield, Mark; Bentley, David R; Taylor, Jenny C; Turnbull, Clare; Schuh, Anna

2018-02-01

PurposeFresh-frozen (FF) tissue is the optimal source of DNA for whole-genome sequencing (WGS) of cancer patients. However, it is not always available, limiting the widespread application of WGS in clinical practice. We explored the viability of using formalin-fixed, paraffin-embedded (FFPE) tissues, available routinely for cancer patients, as a source of DNA for clinical WGS.MethodsWe conducted a prospective study using DNAs from matched FF, FFPE, and peripheral blood germ-line specimens collected from 52 cancer patients (156 samples) following routine diagnostic protocols. We compared somatic variants detected in FFPE and matching FF samples.ResultsWe found the single-nucleotide variant agreement reached 71% across the genome and somatic copy-number alterations (CNAs) detection from FFPE samples was suboptimal (0.44 median correlation with FF) due to nonuniform coverage. CNA detection was improved significantly with lower reverse crosslinking temperature in FFPE DNA extraction (80 °C or 65 °C depending on the methods). Our final data showed somatic variant detection from FFPE for clinical decision making is possible. We detected 98% of clinically actionable variants (including 30/31 CNAs).ConclusionWe present the first prospective WGS study of cancer patients using FFPE specimens collected in a routine clinical environment proving WGS can be applied in the clinic.GENETICS in MEDICINE advance online publication, 1 February 2018; doi:10.1038/gim.2017.241.

Evaluation of the BD Vacutainer(®) RST blood collection tube for routine chemistry analytes: clinical significance of differences and stability study.

PubMed

Kocijancic, Marija; Cargonja, Jelena; Delic-Knezevic, Alma

2014-01-01

Preanalytical variables account for most of laboratory errors. There is a wide range of factors that affect the reliability of laboratory report. Most convenient sample type for routine laboratory analysis is serum. BD Vacutainer(®) Rapid Serum Tube (RST) (Becton, Dickinson and Company, Franklin Lakes, NJ, USA) blood collection tube provides rapid clotting time allowing fast serum separation. Our aim was to evaluate the comparability of routine chemistry parameters in BD Vacutainer(®) RST blood collection tube in reference with the BD Vacutainer(®) Serum Separating Tubes II Advance Tube (SST) (Becton, Dickinson and Company, Franklin Lakes, NJ, USA). Blood specimens were collected from 90 participants for evaluation on its results, clotting time and stability study of six routine biochemistry parameters: glucose (Glu), aspartate aminotransferase (AST), alanine aminotransferase (ALT), calcium (Ca), lactate dehidrogenase (LD) and potassium (K) measured with Olympus AU2700 analyzer (Beckman Coulter, Tokyo, Japan). The significance of the differences between samples was assessed by paired t-test or Wilcoxon Matched-Pairs Rank test after checking for normality. Clotting process was significantly shorter in the RSTs compared to SSTs (2.49 min vs. 19.47 min, respectively; P < 0.001). There was a statistically significant difference between the RST and SST II tubes for glucose, calcium and LD (P < 0.001). Differences for glucose and LD were also clinically significant. Analyte stability studies showed that all analytes were stable for 24 h at 4 °C. Most results (except LD and glucose) from RST are comparable with those from SST. In addition, RST tube provides shorter clotting time.

Chapter A5. Section 6.1.F. Wastewater, Pharmaceutical, and Antibiotic Compounds

USGS Publications Warehouse

Lewis, Michael Edward; Zaugg, Steven D.

2003-01-01

The USGS differentiates between samples collected for analysis of wastewater compounds and those collected for analysis of pharmaceutical and antibiotic compounds, based on the analytical schedule for the laboratory method. Currently, only the wastewater laboratory method for field-filtered samples (SH1433) is an approved, routine (production) method. (The unfiltered wastewater method LC 8033 also is available but requires a proposal for custom analysis.) At this time, analysis of samples for pharmaceutical and antibiotic compounds is confined to research studies and is available only on a custom basis.

Can routine surveillance samples from tracheal aspirate predict bacterial flora in cases of ventilator-associated pneumonia?

PubMed

Lampati, L; Maggioni, E; Langer, M; Malacarne, P; Mozzo, R; Pesenti, A; Fumagalli, R

2009-10-01

The aim of this study was to investigate the hypothesis that periodical sampling of the tracheo-bronchial tree in the absence of clinical suspicion of pneumonia is useful to identify bacteria responsible for subsequent late ventilator associated pneumonia (VAP). This was a retrospective observational human study carried out in two medical-surgical intensive care units of two different hospitals. From January 1999 to December 2000, 559 patients, who received invasive respiratory support for more than 48 hours, were screened. Tracheal aspiration (TA) was performed once or twice weekly in all mechanically ventilated patients. The microbiological findings from TA surveillance cultures done in the eight days before suspicion of VAP were compared to those isolated from the positive diagnostic samples done for late onset VAP (after more than four days of mechanical ventilation). The sensitivity, specificity, and positive/negative predictive values of the ability of the surveillance sample to anticipate the VAP pathogen were calculated. Among the microorganisms isolated from TA, 68% were retrieved from diagnostic samples. All VAP pathogens previously isolated were from 43% of the TA samples. If TA was collected 2-4 days before the clinical diagnosis of VAP, pathogens were detected in 58% of samples. In contrast, only 27% were collected more than four days earlier (P<0.05). The positive predictive values for Pseudomonas aeruginosa and methicillin resistant Staphylococcus aureus from routine TA samples were 92% and 90%, respectively. The negative predictive values for Pseudomonas aeruginosa and methicillin resistant Staphylococcus aureus from routine TA samples were 75% and 89%, respectively. TA cultures in ventilated patients may help to predict pathogens. Early detection may lead to earlier treatment in long term ventilated patients when VAP is suspected.

K(3)EDTA Vacuum Tubes Validation for Routine Hematological Testing.

PubMed

Lima-Oliveira, Gabriel; Lippi, Giuseppe; Salvagno, Gian Luca; Montagnana, Martina; Poli, Giovanni; Solero, Giovanni Pietro; Picheth, Geraldo; Guidi, Gian Cesare

2012-01-01

Background and Objective. Some in vitro diagnostic devices (e.g, blood collection vacuum tubes and syringes for blood analyses) are not validated before the quality laboratory managers decide to start using or to change the brand. Frequently, the laboratory or hospital managers select the vacuum tubes for blood collection based on cost considerations or on relevance of a brand. The aim of this study was to validate two dry K(3)EDTA vacuum tubes of different brands for routine hematological testing. Methods. Blood specimens from 100 volunteers in two different K(3)EDTA vacuum tubes were collected by a single, expert phlebotomist. The routine hematological testing was done on Advia 2120i hematology system. The significance of the differences between samples was assessed by paired Student's t-test after checking for normality. The level of statistical significance was set at P < 0.05. Results and Conclusions. Different brand's tubes evaluated can represent a clinically relevant source of variations only on mean platelet volume (MPV) and platelet distribution width (PDW). Basically, our validation will permit the laboratory or hospital managers to select the brand's vacuum tubes validated according to him/her technical or economical reasons for routine hematological tests.

K3EDTA Vacuum Tubes Validation for Routine Hematological Testing

PubMed Central

Lima-Oliveira, Gabriel; Lippi, Giuseppe; Salvagno, Gian Luca; Montagnana, Martina; Poli, Giovanni; Solero, Giovanni Pietro; Picheth, Geraldo; Guidi, Gian Cesare

2012-01-01

Background and Objective. Some in vitro diagnostic devices (e.g, blood collection vacuum tubes and syringes for blood analyses) are not validated before the quality laboratory managers decide to start using or to change the brand. Frequently, the laboratory or hospital managers select the vacuum tubes for blood collection based on cost considerations or on relevance of a brand. The aim of this study was to validate two dry K3EDTA vacuum tubes of different brands for routine hematological testing. Methods. Blood specimens from 100 volunteers in two different K3EDTA vacuum tubes were collected by a single, expert phlebotomist. The routine hematological testing was done on Advia 2120i hematology system. The significance of the differences between samples was assessed by paired Student's t-test after checking for normality. The level of statistical significance was set at P < 0.05. Results and Conclusions. Different brand's tubes evaluated can represent a clinically relevant source of variations only on mean platelet volume (MPV) and platelet distribution width (PDW). Basically, our validation will permit the laboratory or hospital managers to select the brand's vacuum tubes validated according to him/her technical or economical reasons for routine hematological tests. PMID:22888448

Isotopic (d18O/d2H) integrity of water samples collected and stored by automatic samplers

USDA-ARS?s Scientific Manuscript database

Stable water isotopes are increasingly becoming part of routine monitoring programs that utilize automatic samplers. The objectives of this study were to quantify the uncertainty in isotope signatures due to the length of sample storage (1-24 d) inside autosamplers over a range of air temperatures (...

A preliminary assessment of the spatial sources of contemporary suspended sediment in the Ohio River basin, United States, using water quality data from the NASQAN programme in a source tracing procedure

USGS Publications Warehouse

Zhang, Y.-S.; Collins, A.L.; Horowitz, A.J.

2012-01-01

Reliable information on catchment scale suspended sediment sources is required to inform the design of management strategies for helping abate the numerous environmental issues associated with enhanced sediment mobilization and off-site loadings. Since sediment fingerprinting techniques avoid many of the logistical constraints associated with using more traditional indirect measurement methods at catchment scale, such approaches have been increasingly reported in the international literature and typically use data sets collected specifically for sediment source apportionment purposes. There remains scope for investigating the potential for using geochemical data sets assembled by routine monitoring programmes to fingerprint sediment provenance. In the United States, routine water quality samples are collected as part of the US Geological Survey's revised National Stream Quality Accounting Network programme. Accordingly, the geochemistry data generated from these samples over a 10-year period (1996-2006) were used as the basis for a fingerprinting exercise to assess the key tributary sub-catchment spatial sources of contemporary suspended sediment transported by the Ohio River. Uncertainty associated with the spatial source estimates was quantified using a Monte Carlo approach in conjunction with mass balance modelling. Relative frequency weighted means were used as an alternative way of summarizing the spatial source contributions, thereby avoiding the need to use confidence limits. The results should be interpreted in the context of the routine, but infrequent nature, of the suspended sediment samples used to assemble geochemistry as a basis for the sourcing exercise. Nonetheless, the study demonstrates how routine monitoring samples can be used to provide some preliminary information on sediment provenance in large drainage basins. ?? 2011 John Wiley & Sons, Ltd.

Monitoring Malaria Vector Control Interventions: Effectiveness of Five Different Adult Mosquito Sampling Methods

PubMed Central

Onyango, Shirley A.; Kitron, Uriel; Mungai, Peter; Muchiri, Eric M.; Kokwaro, Elizabeth; King, Charles H.; Mutuku, Francis M.

2014-01-01

Long-term success of ongoing malaria control efforts based on mosquito bed nets (long-lasting insecticidal net) and indoor residual spraying is dependent on continuous monitoring of mosquito vectors, and thus on effective mosquito sampling tools. The objective of our study was to identify the most efficient mosquito sampling tool(s) for routine vector surveillance for malaria and lymphatic filariasis transmission in coastal Kenya. We evaluated relative efficacy of five collection methods—light traps associated with a person sleeping under a net, pyrethrum spray catches, Prokopack aspirator, clay pots, and urine-baited traps—in four villages representing three ecological settings along the south coast of Kenya. Of the five methods, light traps were the most efficient for collecting female Anopheles gambiae s.l. (Giles) (Diptera: Culicidae) and Anopheles funestus (Giles) (Diptera: Culicidae) mosquitoes, whereas the Prokopack aspirator was most efficient in collecting Culex quinquefasciatus (Say) (Diptera: Culicidae) and other culicines. With the low vector densities here, and across much of sub-Saharan Africa, wherever malaria interventions, long-lasting insecticidal nets, and/or indoor residual spraying are in place, the use of a single mosquito collection method will not be sufficient to achieve a representative sample of mosquito population structure. Light traps will remain a relevant tool for host-seeking mosquitoes, especially in the absence of human landing catches. For a fair representation of the indoor mosquito population, light traps will have to be supplemented with aspirator use, which has potential for routine monitoring of indoor resting mosquitoes, and can substitute the more labor-intensive and intrusive pyrethrum spray catches. There are still no sufficiently efficient mosquito collection methods for sampling outdoor mosquitoes, particularly those that are bloodfed. PMID:24180120

Rainfall, Streamflow, and Water-Quality Data During Stormwater Monitoring, Halawa Stream Drainage Basin, Oahu, Hawaii, July 1, 2003 to June 30, 2004

USGS Publications Warehouse

Young, Stacie T.M.; Ball, Marcael T.J.

2004-01-01

Storm runoff water-quality samples were collected as part of the State of Hawaii Department of Transportation Stormwater Monitoring Program. This program is designed to assess the effects of highway runoff and urban runoff on Halawa Stream. For this program, rainfall data were collected at two sites, continuous streamflow data at three sites, and water-quality data at five sites, which include the three streamflow sites. This report summarizes rainfall, streamflow, and water-quality data collected between July 1, 2003 and June 30, 2004. A total of 30 samples was collected over four storms during July 1, 2003 to June 30, 2004. In general, an attempt was made to collect grab samples nearly simultaneously at all five sites, and flow-weighted time-composite samples were collected at the three sites equipped with automatic samplers. However, all four storms were partially sampled because either not all stations were sampled or only grab samples were collected. Samples were analyzed for total suspended solids, total dissolved solids, nutrients, chemical oxygen demand, and selected trace metals (cadmium, copper, lead, and zinc). Grab samples were additionally analyzed for oil and grease, total petroleum hydrocarbons, fecal coliform, and biological oxygen demand. Quality-assurance/quality-control samples, collected during storms and during routine maintenance, were also collected to verify analytical procedures and check the effectiveness of equipment-cleaning procedures.

Rainfall, Streamflow, and Water-Quality Data During Stormwater Monitoring, Halawa Stream Drainage Basin, Oahu, Hawaii, July 1, 2002 to June 30, 2003

USGS Publications Warehouse

Young, Stacie T.M.; Ball, Marcael T.J.

2003-01-01

Storm runoff water-quality samples were collected as part of the State of Hawaii Department of Transportation Stormwater Monitoring Program. This program is designed to assess the effects of highway runoff and urban runoff on Halawa Stream. For this program, rainfall data was collected at two sites, continuous streamflow data at three sites, and water-quality data at five sites, which include the three streamflow sites. This report summarizes rainfall, streamflow, and water-quality data collected between July 1, 2002 to June 30, 2003. A total of 28 samples were collected over five storms during July 1, 2002 to June 30, 2003. For two of the five storms, five grab samples and three flow-weighted timecomposite samples were collected. Grab samples were collected nearly simultaneously at all five sites, and flow-weighted timecomposite samples were collected at the three sites equipped with automatic samplers. The other three storms were partially sampled, where only flow-weighted time-composite samples were collected and/or not all stations were sampled. Samples were analyzed for total suspended solids, total dissolved solids, nutrients, chemical oxygen demand, and selected trace metals (cadmium, copper, lead, and zinc). Grab samples were additionally analyzed for oil and grease, total petroleum hydrocarbons, fecal coliform, and biological oxygen demand. Quality-assurance/qualitycontrol samples, collected during storms and during routine maintenance, were also collected to verify analytical procedures and insure proper cleaning of equipment.

A precision multi-sampler for deep-sea hydrothermal microbial mat studies

NASA Astrophysics Data System (ADS)

Breier, J. A.; Gomez-Ibanez, D.; Reddington, E.; Huber, J. A.; Emerson, D.

2012-12-01

A new tool was developed for deep-sea microbial mat studies by remotely operated vehicles and was successfully deployed during a cruise to the hydrothermal vent systems of the Mid-Cayman Rise. The Mat Sampler allows for discrete, controlled material collection from complex microbial structures, vertical-profiling within thick microbial mats and particulate and fluid sample collection from venting seafloor fluids. It has a reconfigurable and expandable sample capacity based on magazines of 6 syringes, filters, or water bottles. Multiple magazines can be used such that 12-36 samples can be collected routinely during a single dive; several times more if the dive is dedicated for this purpose. It is capable of hosting in situ physical, electrochemical, and optical sensors, including temperature and oxygen probes in order to guide sampling and to record critical environmental parameters at the time and point of sample collection. The precision sampling capability of this instrument will greatly enhance efforts to understand the structured, delicate, microbial mat communities that grow in diverse benthic habitats.

Validating Analytical Protocols to Determine Selected Pesticides and PCBs Using Routine Samples.

PubMed

Pindado Jiménez, Oscar; García Alonso, Susana; Pérez Pastor, Rosa María

2017-01-01

This study aims at providing recommendations concerning the validation of analytical protocols by using routine samples. It is intended to provide a case-study on how to validate the analytical methods in different environmental matrices. In order to analyze the selected compounds (pesticides and polychlorinated biphenyls) in two different environmental matrices, the current work has performed and validated two analytical procedures by GC-MS. A description is given of the validation of the two protocols by the analysis of more than 30 samples of water and sediments collected along nine months. The present work also scopes the uncertainty associated with both analytical protocols. In detail, uncertainty of water sample was performed through a conventional approach. However, for the sediments matrices, the estimation of proportional/constant bias is also included due to its inhomogeneity. Results for the sediment matrix are reliable, showing a range 25-35% of analytical variability associated with intermediate conditions. The analytical methodology for the water matrix determines the selected compounds with acceptable recoveries and the combined uncertainty ranges between 20 and 30%. Analyzing routine samples is rarely applied to assess trueness of novel analytical methods and up to now this methodology was not focused on organochlorine compounds in environmental matrices.

Laboratory diagnosis of gestational diabetes: An in silico investigation into the effects of pre-analytical processing on the diagnostic sensitivity and specificity of the oral glucose tolerance test.

PubMed

Mansell, Erin; Lunt, Helen; Docherty, Paul

2017-06-01

Delayed separation of red cells from plasma causes pre analytical glucose loss, which in turn results in an under-diagnosis of GDM (gestational diabetes) based on the OGTT (oral glucose tolerance test). In silico investigations may help laboratory decision making, when exploring pragmatic improvements to sample processing. Late pregnancy 0, 1 and 2h 75g OGTT values were obtained from two distinct populations of pregnant women: 1. Values derived from the HAPO (Hyperglycemia and Adverse Pregnancy Outcome) Study and 2. New Zealand women identified as at higher risk of GDM by their caregivers, undergoing OGTT during routine antenatal care. In both populations studied, in silico modelling focussed on the effects of pre-analytical delays in plasma separation, when using fluoride collection tubes. Using a model that 'batched' samples from the three OGTT collection times, diagnostic sensitivity was estimated as follows: 66.1% for HAPO research population and 48.4% for the 1305 women receiving routine antenatal care. If samples were not batched, but processed shortly after each blood sample was collected, then sensitivity increased to 81%. Exploration of a range of clinical and laboratory scenarios using in silico modelling, showed that delaying the processing of pregnancy OGTT samples, using batched sample collection into fluoride tubes, causes unacceptable loss of GDM diagnostic sensitivity across two distinct population groups. This modelling approach will hopefully provide information that helps with final decision making around improved laboratory processing techniques. Copyright © 2017 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Comparative Proteomic Analysis of Whole-Gut Lavage Fluid and Pancreatic Juice Reveals a Less Invasive Method of Sampling Pancreatic Secretions

PubMed Central

Rocker, Jana M; Tan, Marcus C; Thompson, Lee W; Contreras, Carlo M; DiPalma, Jack A; Pannell, Lewis K

2016-01-01

OBJECTIVES: There are currently no reliable, non-invasive screening tests for pancreatic ductal adenocarcinoma. The fluid secreted from the pancreatic ductal system (“pancreatic juice”) has been well-studied as a potential source of cancer biomarkers. However, it is invasive to collect. We recently observed that the proteomic profile of intestinal effluent from the bowel in response to administration of an oral bowel preparation solution (also known as whole-gut lavage fluid, WGLF) contains large amounts of pancreas-derived proteins. We therefore hypothesized that the proteomic profile is similar to that of pancreatic juice. In this study, we compared the proteomic profiles of 77 patients undergoing routine colonoscopy with the profiles of 19 samples of pure pancreatic juice collected during surgery. METHODS: WGLF was collected from patients undergoing routine colonoscopy, and pancreatic juice was collected from patients undergoing pancreatic surgery. Protein was isolated from both samples using an optimized method and analyzed by LC-MS/MS. Identified proteins were compared between samples and groups to determine similarity of the two fluids. We then compared our results with literature reports of pancreatic juice-based studies to determine similarity. RESULTS: We found 104 proteins in our pancreatic juice samples, of which 90% were also found in our WGLF samples. The majority (67%) of the total proteins found in the WGLF were common to pancreatic juice, with intestine-specific proteins making up a smaller proportion. CONCLUSIONS: WGLF and pancreatic juice appear to have similar proteomic profiles. This supports the notion that WGLF is a non-invasive, surrogate bio-fluid for pancreatic juice. Further studies are required to further elucidate its role in the diagnosis of pancreatic cancer. PMID:27228405

Evaluation of PCR for cutaneous leishmaniasis diagnosis and species identification using filter paper samples in Panama, Central America.

PubMed

Miranda, A; Saldaña, A; González, K; Paz, H; Santamaría, G; Samudio, F; Calzada, J E

2012-09-01

Cutaneous leishmaniasis (CL) is a major vectorborne disease in Panama. In this study, the diagnostic performance and usefulness of two DNA extraction procedures from skin scraping samples collected on FTA filter paper for subsequent PCR diagnosis of CL was evaluated. A positive CL laboratory diagnosis was based on a positive parasitological test (Giemsa-stained smears or in vitro culture) and/or positive PCR test performed from skin scrapings collected in TE buffer (PCR-TE). Of 100 patients with skin lesions suggestive of CL, 82 (82%) were confirmed as CL positive. The sensitivity was calculated for each of the PCR approaches from samples collected on filter paper. The highest sensitivity was achieved by PCR-FTA processed by Chelex 100 (PCR-Chelex) (0.94). PCR-FTA extracted using the FTA purification reagent presented a lower sensitivity (0.60). Good concordance between routine PCR-TE and PCR-Chelex was observed (percent agreement=0.88, κ index=0.65). In conclusion, use of FTA filter paper for skin scraping collection combined with PCR is a reliable and convenient method for CL diagnosis in Panama, with comparable performance to the routine PCR method and with improved sensitivity compared with those of conventional parasitological methods. Copyright © 2012 Royal Society of Tropical Medicine and Hygiene. Published by Elsevier Ltd. All rights reserved.

Tank 30 and 37 Supernatant Sample Cross-Check and Evaporator Feed Qualification Analysis-2012

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

Oji, L. N.

2013-03-07

This report summarizes the analytical data reported by the F/H and Savannah River National Laboratories for the 2012 cross-check analysis for high level waste supernatant liquid samples from SRS Tanks 30 and 37. The intent of this Tank 30 and 37 sample analyses was to perform cross-checks against routine F/H Laboratory analyses (corrosion and evaporator feed qualification programs) using samples collected at the same time from both tanks as well as split samples from the tanks.

Colloidal-facilitated transport of inorganic contaminants in ground water: part 1, sampling considerations

USGS Publications Warehouse

Puls, Robert W.; Eychaner, James H.; Powell, Robert M.

1996-01-01

Investigations at Pinal Creek, Arizona, evaluated routine sampling procedures for determination of aqueous inorganic geochemistry and assessment of contaminant transport by colloidal mobility. Sampling variables included pump type and flow rate, collection under air or nitrogen, and filter pore diameter. During well purging and sample collection, suspended particle size and number as well as dissolved oxygen, temperature, specific conductance, pH, and redox potential were monitored. Laboratory analyses of both unfiltered samples and the filtrates were performed by inductively coupled argon plasma, atomic absorption with graphite furnace, and ion chromatography. Scanning electron microscopy with Energy Dispersive X-ray was also used for analysis of filter particulates. Suspended particle counts consistently required approximately twice as long as the other field-monitored indicators to stabilize. High-flow-rate pumps entrained normally nonmobile particles. Difference in elemental concentrations using different filter-pore sizes were generally not large with only two wells having differences greater than 10 percent in most wells. Similar differences (>10%) were observed for some wells when samples were collected under nitrogen rather than in air. Fe2+/Fe3+ ratios for air-collected samples were smaller than for samples collected under a nitrogen atmosphere, reflecting sampling-induced oxidation.

Assessment of Contribution of Contemporary Carbon Sources to Size-Fractionated Particulate Matter and Time-Resolved Bulk Particulate Matter Using the Measurement of Radiocarbon

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

Hwang, H M; Young, T M; Buchholz, B A

2009-04-16

This study was motivated by a desire to improve understanding of the sources contributing to the carbon that is an important component of airborne particulate matter (PM). The ultimate goal of this project was to lay a ground work for future tools that might be easily implemented with archived or routinely collected samples. A key feature of this study was application of radiocarbon measurement that can be interpreted to indicate the relative contributions from fossil and non-fossil carbon sources of atmospheric PM. Size-resolved PM and time-resolved PM{sub 10} collected from a site in Sacramento, CA in November 2007 (Phase I)more » and March 2008 (Phase II) were analyzed for radiocarbon and source markers such as levoglucosan, cholesterol, and elemental carbon. Radiocarbon data indicates that the contributions of non-fossil carbon sources were much greater than that from fossil carbon sources in all samples. Radiocarbon and source marker measurements confirm that a greater contribution of non-fossil carbon sources in Phase I samples was highly likely due to residential wood combustion. The present study proves that measurement of radiocarbon and source markers can be readily applied to archived or routinely collected samples for better characterization of PM sources. More accurate source apportionment will support ARB in developing more efficient control strategies.« less

Surface-water-quality assessment of the Kentucky River Basin, Kentucky; fixed-station network and selected water-quality data, April 1987 through August 1991

USGS Publications Warehouse

Griffin, M.S.; Martin, G.R.; White, K.D.

1994-01-01

This report describes selected data-collection activities and the associated data collected during the Kentucky River Basin pilot study of the U.S. Geological Survey's National Water-Quality Assessment Program. The data are intended to provide a nationally consistent description and improved understanding of current water quality in the basin. The data were collected at seven fixed stations that represent stream cross sections where constituent transport and water-quality trends can be evaluated. The report includes descriptions of (1) the basin; (2) the design of the fixed-station network; (3) the fixed-station sites; (4) the physical and chemical measurements; (5) the methods of sample collection, processing, and analysis; and (6) the quality-assurance and quality-control procedures. Water-quality data collected at the fixed stations during routine periodic sampling and supplemental high-flow sampling from April 1987 to August 1991 are presented.

Performance Evaluation of the Elecsys Syphilis Assay for the Detection of Total Antibodies to Treponema pallidum

PubMed Central

Enders, Martin; Hunjet, Andrea; Gleich, Michael; Imdahl, Roland; Mühlbacher, Annelies; Schennach, Harald; Chaiwong, Kriangsak; Sakuldamrongpanich, Tasanee; Turhan, Ajda; Sertöz, Rüchan; Wolf, Eva; Mayer, Wolfgang; Tao, Chuanmin; Wang, Lan Lan; Semprini, Simona

2014-01-01

Syphilis is a health problem of increasing incidence in recent years that may have severe complications if not diagnosed and treated at an early stage. There are many diagnostic tests available for syphilis, but there is no gold standard, and diagnosis therefore usually relies upon a combination of tests. In this multicenter study, we evaluated the treponemal Elecsys syphilis assay for use in the diagnosis of syphilis in routine samples, i.e., when syphilis is suspected or during antenatal or blood donation screening. The sensitivity and specificity of the Elecsys syphilis assay were compared head to head with those of other treponemal assays used in routine clinical practice and were assessed in potentially cross-reactive samples from patients with Epstein-Barr virus, HIV, and Lyme disease. In a total of 8,063 syphilis-negative samples collected from routine diagnostic requests and blood donations, the Elecsys syphilis assay had a specificity of 99.88%. In 928 samples previously identified as syphilis positive, the sensitivity was 99.57 to 100% (the result is presented as a range depending on whether four initially indeterminate samples are included in the assessment). The specificity of the Elecsys syphilis assay in patients with other infections was 100%; no false-positive samples were identified. PMID:25355799

Post-analytical stability of 23 common chemistry and immunochemistry analytes in incurred samples.

PubMed

Nielsen, Betina Klint; Frederiksen, Tina; Friis-Hansen, Lennart; Larsen, Pia Bükmann

2017-12-01

Storage of blood samples after centrifugation, decapping and initial sampling allows ordering of additional blood tests. The pre-analytic stability of biochemistry and immunochemistry analytes has been studied in detail, but little is known about the post-analytical stability in incurred samples. We examined the stability of 23 routine analytes on the Dimension Vista® (Siemens Healthineers, Denmark): 42-60 routine samples in lithium-heparin gel tubes (Vacutainer, BD, USA) were centrifuged at 3000×g for 10min. Immediately after centrifugation, initial concentration of analytes were measured in duplicate (t=0). The tubes were stored decapped at room temperature and re-analyzed after 2, 4, 6, 8 and 10h in singletons. The concentration from reanalysis were normalized to initial concentration (t=0). Internal acceptance criteria for bias and total error were used to determine stability of each analyte. Additionally, evaporation from the decapped blood collection tubes and the residual platelet count in the plasma after centrifugation were quantified. We report a post-analytical stability of most routine analytes of ≥8h and do therefore - with few exceptions - suggest a standard 8hour-time limit for reordering and reanalysis of analytes in incurred samples. Copyright © 2017 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Evaluation of a multiresidue method for measuring fourteen chemical groups of pesticides in water by use of LC-MS-MS.

PubMed

Carvalho, J J; Jerónimo, P C A; Gonçalves, C; Alpendurada, M F

2008-11-01

European Council Directive 98/83/EC on the quality of water intended for human consumption brought a new challenge for water-quality control routine laboratories, mainly on pesticides analysis. Under the guidelines of ISO/IEC 17025:2005, a multiresidue method was developed, validated, implemented in routine, and studied with real samples during a one-year period. The proposed method enables routine laboratories to handle a large number of samples, since 28 pesticides of 14 different chemical groups can be quantitated in a single procedure. The method comprises a solid-phase extraction step and subsequent analysis by liquid chromatography-mass spectrometry (LC-MS-MS). The accuracy was established on the basis of participation in interlaboratory proficiency tests, with encouraging results (majority |z-score| <2), and the precision was consistently analysed over one year. The limits of quantitation (below 0.050 microg L(-1)) are in agreement with the enforced threshold value for pesticides of 0.10 microg L(-1). Overall method performance is suitable for routine use according to accreditation rules, taking into account the data collected over one year.

Use of proficiency samples to assess diagnostic laboratories in France performing a Trichinella digestion assay.

PubMed

Vallée, Isabelle; Macé, Pauline; Forbes, Lorry; Scandrett, Brad; Durand, Benoit; Gajadhar, Alvin; Boireau, Pascal

2007-07-01

Routine diagnosis of animal trichinellosis for food safety and trade relies on a method of artificial digestion to free Trichinella muscle larvae from meat for subsequent identification by microscopy. As part of a quality control system, the French National Reference Laboratory (NRL) initiated ring trials to determine the sensitivity of the test performed in the 72 routine diagnostic laboratories in France. A method was devised to obtain calibrated meat samples containing known numbers of capsules with Trichinella spiralis muscle larvae. This method was based on an incomplete artificial digestion of Trichinella-infected mice carcasses to allow the collection of intact Trichinella capsules. Capsules were placed into a meatball of 100 +/- 2 g of pork and horsemeat to produce proficiency samples. Three categories of samples were prepared: small (3 to 5 capsules), medium (7 to 10), and large (12 to 15). The sensitivity was expressed as the percentage of muscle larvae recovered from each proficiency sample. Reproducibility was tested with ring trials organized between two NRLs (France and Canada), and a reference sensitivity of 84.9% was established. National ring trials were then organized in France, with the 72 routine diagnostic laboratories each receiving four proficiency samples per session. After five sessions, an improvement in the digest test sensitivity was observed. Results at the fifth session indicated sensitivities of 78.60% +/- 23.70%, 81.19% +/- 19.59%, and 80.52% +/- 14.71% muscle larvae for small, medium, and large samples, respectively. This study supports the use of proficiency samples to accurately evaluate the performance of routine diagnostic laboratories that conduct digestion tests for animal trichinellosis diagnosis.

Water quality of the tidal Potomac River and estuary hydrologic data report, 1980 water year

USGS Publications Warehouse

Blanchard, Stephen; Coupe, R.H.; Woodward, J.C.

1982-01-01

This report contains data on the physical and chemical properties measured in the Tidal Potomac River and Estuary during the 1980 Water Year. Data were collected routinely at five stations, and periodically at 17 stations including three stations near the mouth of the Potomac River in Chesapeake Bay. Each of the five stations represent a cross section through which the transport of selected dissolved and suspended materials can be computed. The remaining stations represent locations at which data were collected for special synoptic studies such as salt water migration, and dissolved oxygen dynamics. Routinely, samples were analyzed for silica, nitrogen, phosphorus, chlorophyll-a, pheophytin, and suspended sediment. Additional samples were analyzed for organic carbon, calcium, manganese, magnesium, sodium, alkalinity, sulfate, iron, potassium, chloride, fluoride, seston, algal growth potential, adenosine triphosphate, nitrifying bacteria and dissolved-solids residue. In addition, solar radiation measurements and in-situ measurements of dissolved oxygen, specific conductance, pH, temperature, and Secchi disk transparency are reported. (USGS)

A novel method for semen collection and artificial insemination in large parrots (Psittaciformes)

PubMed Central

Lierz, Michael; Reinschmidt, Matthias; Müller, Heiner; Wink, Michael; Neumann, Daniel

2013-01-01

The paper described a novel technique for semen collection in large psittacines (patent pending), a procedure which was not routinely possible before. For the first time, a large set of semen samples is now available for analysis as well as for artificial insemination. Semen samples of more than 100 psittacine taxa were collected and analysed; data demonstrate large differences in the spermatological parameters between families, indicating an ecological relationship with breeding behaviour (polygamous versus monogamous birds). Using semen samples for artificial insemination resulted in the production of offspring in various families, such as Macaws and Cockatoos, for the first time ever. The present technique represents a breakthrough in species conservation programs and will enable future research into the ecology and environmental factors influencing endangered species. PMID:23797622

Sequim Marine Research Laboratory routine environmental measurements during CY-1978. [Monitoring for laboratory-related radioactivity and pollutants in environment

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

Houston, J.R.; Blumer, P.J.

1979-03-01

Environmental data collected during 1978 in the vicinity of the Marine Research Laboratory show continued compliance with all applicable state and federal regulations and furthermore show no detectable change from conditions that existed in previous years. Samples collected for radiological analysis included soil, drinking water, bay water, clams, and seaweed. Radiation dose rates at 1 meter aboveground were also measured.

[Laser microdissection for biology and medicine].

PubMed

Podgornyĭ, O V; Lazarev, V N; Govorun, V M

2012-01-01

For routine extraction of DNA, RNA, proteins and metabolites, small tissue pieces are placed into lysing solution. These tissue pieces in general contain different cell types. For this reason, lysate contains components of different cell types, which complicates the interpretation of molecular analysis results. The laser microdissection allows overcoming this trouble. The laser microdissection is a method to procure tissue samples contained defined cell subpopulations, individual cells and even subsellular components under direct microscopic visualization. Collected samples can be undergone to different downstream molecular assays: DNA analysis, RNA transcript profiling, cDNA library generation and gene expression analysis, proteomic analysis and metabolite profiling. The laser microdissection has wide applications in oncology (research and routine), cellular and molecular biology, biochemistry and forensics. This paper reviews the principles of different laser microdissection instruments, examples of laser microdissection application and problems of sample preparation for laser microdissection.

Bacterial contamination and stethoscope disinfection practices: a cross-sectional survey of healthcare workers in Karachi, Pakistan.

PubMed

Rao, Danish Ahmed; Aman, Aiysha; Muhammad Mubeen, Syed; Shah, Ahmed

2017-07-01

Stethoscopes routinely used for clinical examination of patients may potentially transfer micro-organisms and cause iatrogenic infections. This study was undertaken to detect the presence of microorganisms on stethoscopes used clinically in hospitals of Karachi, Pakistan and to ascertain the infection control practices of healthcare workers (HCWs). In a cross-sectional study, 118 samples were collected from public and private institutions. Samples were tested for the presence and sensitivity of pathogenic microorganisms. Microorganisms were found on diaphragms of 33/64 (51.6%) and 19/57 (33.3%) stethoscopes in public and private sector hospitals, respectively. Methycillin resistance was identified in all staphylococcally contaminated samples. Only 33 (18%) respondents reported cleaning their stethoscopes regularly. We highlight the need for more and better on-the-job routines for decontaminating stethoscopes among HCWs in Karachi.

Evaluation of droplet digital PCR for quantification of residual leucocytes in red blood cell concentrates.

PubMed

Doescher, A; Loges, U; Petershofen, E K; Müller, T H

2017-11-01

Enumeration of residual white blood cells in leucoreduced blood components is essential part of quality control. Digital PCR has substantially facilitated quantitative PCR and was thus evaluated for measurements of leucocytes. Target for quantification of leucocytes by digital droplet PCR was the blood group gene RHCE. The SPEF1 gene was added as internal control for the entire assay starting with automated DNA extraction. The sensitivity of the method was determined by serial dilutions of standard samples. Quality control samples were analysed within 24 h, 7 days and 6 months after collection. Routine samples from leucodepleted red blood cell concentrates (n = 150) were evaluated in parallel by flow-cytometry (LeucoCount) and by digital PCR. Digital PCR reliably detected at least 0·4 leucocytes per assay. The mean difference between PCR and flow-cytometric results from 150 units was -0·01 (±1·0). DNA samples were stable for up to at least six months. PCR measurement of leucocytes in samples from plasma and platelet concentrates also provided valid results in a pilot study. Droplet digital PCR to enumerate leucocytes offers an alternative for quality control of leucoreduced blood products. Sensitivity, specificity and reproducibility are comparable to flow-cytometry. The option to collect samples over an extended period of time and the automatization introduce attractive features for routine quality control. © 2017 International Society of Blood Transfusion.

Rainfall, Streamflow, and Water-Quality Data During Stormwater Monitoring, Halawa Stream Drainage Basin, Oahu, Hawaii, July 1, 2006 to June 30, 2007

USGS Publications Warehouse

Young, Stacie T.M.; Jamison, Marcael T.J.

2007-01-01

Storm runoff water-quality samples were collected as part of the State of Hawaii Department of Transportation Stormwater Monitoring Program. This program is designed to assess the effects of highway runoff and urban runoff on Halawa Stream. For this program, rainfall data were collected at two stations, continuous streamflow data at three stations, and water-quality data at five stations, which include the two continuous streamflow stations. This report summarizes rainfall, streamflow, and water-quality data collected between July 1, 2006 and June 30, 2007. A total of 13 samples was collected over two storms during July 1, 2006 to June 30, 2007. The goal was to collect grab samples nearly simultaneously at all five stations and flow-weighted time-composite samples at the three stations equipped with automatic samplers. Samples were analyzed for total suspended solids, total dissolved solids, nutrients, chemical oxygen demand, and selected trace metals (cadmium, chromium, copper, lead, nickel, and zinc). Additionally, grab samples were analyzed for oil and grease, total petroleum hydrocarbons, fecal coliform, and biological oxygen demand. Quality-assurance/quality-control samples were also collected during storms and during routine maintenance to verify analytical procedures and check the effectiveness of equipment-cleaning procedures.

Effects of Packstock Use and Backpackers on Water Quality in Yosemite National Park, California

NASA Astrophysics Data System (ADS)

Forrester, H.; Clow, D. W.; Roche, J. W.; Heyvaert, A.

2016-12-01

Visitor use, primarily backpacker camping, packstock (horse and mule) trail use, and packstock grazing, in designated Wilderness, increases the potential for negative effects on water quality. To determine the effects of visitor use on water quality in Wilderness in Yosemite National Park, we collected and analyzed surface-water samples for water quality indicators, consisting of fecal indicator bacteria (Escherichia coli), nutrients (nitrogen, phosphorus), suspended sediment concentration (SSC), and hormones (e.g. estrogen compounds) during the summers of 2012-2014. We collected samples upstream and downstream from different types of visitor use at routine intervals (weekly or biweekly) and during storms. Additionally, we sampled upstream and downstream from meadows, and targeted different types of visitor use during a park-wide synoptic sampling campaign (n=63). At packstock stream crossings, statistically significant (P≤0.05) increases in Escherichia coli (E. coli) and SSC occurred downstream from crossings compared to upstream conditions during routine sampling (median difference: 3 CFU 100ml-1, and >0.3 mg l-1, respectively) and during storms (median difference: 32 CFU 100ml-1, and 2.9 mg l-1). At backpacker campsites, during routine sampling, significant increases occurred downstream from backpacker camping for E. coli (median difference: 1 CFU 100ml-1), and estrogen hormones were detected. At packstock grazing areas, which are located in meadows, no significant increases were detected for any of the measured water quality indicators downstream from grazing. Most synoptic sample concentrations were near or below detection limits. Our results indicate that under current use levels: 1) packstock trail use and backpacker camping are associated with detectable effects on water quality, which are most pronounced during storms; 2) increases in water quality indicators were not detected downstream from meadows where packstock were grazed; and 3) environmental processes in meadows provide a valuable ecosystem service by reducing human related sources of microbial contamination.

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

None

Volume II of the Site Environmental Report for 2006 is provided by Ernest Orlando Lawrence Berkeley National Laboratory as a supplemental appendix to Volume I, which contains the body of the report. Volume II contains the environmental monitoring and sampling data used to generate summary results of routine and nonroutine activities at the Laboratory (except for groundwater sampling data, which may be found in the reports referred to in Chapter 4). Volume I summarizes the results from analyses of the data. The results from sample collections are more comprehensive in Volume II than in Volume I: For completeness, all resultsmore » from sample collections that began or ended in calendar year (CY) 2006 are included in this volume. However, the samples representing CY 2005 data have not been used in the summary results that are reported in Volume I. (For example, although ambient air samples collected on January 2, 2006, are presented in Volume II, they represent December 2005 data and are not included in Table 4-2 in Volume I.)« less

Feasibility of using routinely collected inpatient data to monitor quality and inform choice: a case study using the UK inflammatory bowel disease audit

PubMed Central

Roberts, Stephen E; Williams, John G; Cohen, David R; Akbari, Ashley; Groves, Sam; Button, Lori A

2011-01-01

Objective To assess the utility and cost of using routinely collected inpatient data for large-scale audit. Design Comparison of audit data items collected nationally in a designed audit of inflammatory bowel disease (UK IBD audit) with routinely collected inpatient data; surveys of audit sites to compare costs. Setting National Health Service hospitals across England, Wales and Northern Ireland that participated in the UK IBD audit. Patients Patients in the UK IBD audit. Interventions None. Main outcome measures Percentage agreement between designed audit data items collected for the UK IBD audit and routine inpatient data items; costs of conducting the designed UK IBD audit and the routine data audit. Results There were very high matching rates between the designed audit data and routine data for a small subset of basic important information collected in the UK IBD audit, including mortality; major surgery; dates of admission, surgery, discharge and death; principal diagnoses; and sociodemographic patient characteristics. There were lower matching rates for other items, including source of admission, primary reason for admission, most comorbidities, colonoscopy and sigmoidoscopy. Routine data did not cover most detailed information collected in the UK IBD audit. Using routine data was much less costly than collecting designed audit data. Conclusion Although valuable for large population-based studies, and less costly than designed data, routine inpatient data are not suitable for the evaluation of individual patient care within a designed audit. PMID:28839601

Rainfall, Streamflow, and Water-Quality Data During Stormwater Monitoring, Halawa Stream Drainage Basin, Oahu, Hawaii, July 1, 2004 to June 30, 2005

USGS Publications Warehouse

Young, Stacie T.M.; Ball, Marcael T.J.

2005-01-01

Storm runoff water-quality samples were collected as part of the State of Hawaii Department of Transportation Stormwater Monitoring Program. This program is designed to assess the effects of highway runoff and urban runoff on Halawa Stream. For this program, rainfall data were collected at two stations, continuous streamflow data at two stations, and water-quality data at five stations, which include the two continuous streamflow stations. This report summarizes rainfall, streamflow, and water-quality data collected between July 1, 2004 and June 30, 2005. A total of 15 samples was collected over three storms during July 1, 2004 to June 30, 2005. In general, an attempt was made to collect grab samples nearly simultaneously at all five stations and flow-weighted time-composite samples at the three stations equipped with automatic samplers. However, all three storms were partially sampled because either not all stations were sampled or not all composite samples were collected. Samples were analyzed for total suspended solids, total dissolved solids, nutrients, chemical oxygen demand, and selected trace metals (cadmium, chromium, copper, lead, nickel, and zinc). Chromium and nickel were added to the analysis starting October 1, 2004. Grab samples were additionally analyzed for oil and grease, total petroleum hydrocarbons, fecal coliform, and biological oxygen demand. Quality-assurance/quality-control samples were also collected during storms and during routine maintenance to verify analytical procedures and check the effectiveness of equipment-cleaning procedures.

Waste-water characterization survey, Whiteman Air Force Base, Missouri. Final report, 28 Oct-7 Nov 91

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

Fields, M.K.; Davis, R.P.

1992-08-01

A wastewater characterization survey was conducted by members of the Armstrong Laboratory Occupational and Environmental Health directorate Water Quality Function from 28 Oct 91 - 7 Nov 91 at Whiteman AFB, MO. The purpose of the survey was to identify and characterize the wastewater, determine the appropriateness of present disposal methods, determine the need for routine sampling or monitoring and recommend parameters for wastewater analysis. Results of the sampling showed metals and volatile organic discharge in varying concentrations throughout the base. Recommendations are: (1) evaluation of industrial operations and chemical disposal procedures at designated sites; (2) routine monitoring of themore » discharge from the Hospital and Audiovisual for silver; (3) excavation and sediment disposal at the Transportation Washrack and WWTP Effluent discharge point; (4) collection and analyses of sludge at oil water separators, to include the oil and water side; (5) evaluation of the sanitary sewer system for corrosion and sediment buildup by a mobile Reveal and Seal Unit; (6) background soil sample collection and analyses; and (7) pretreatment of Aqueous Film Forming Foam discharge and notification of the Base Bioenvironmental Engineer, Environmental Coordinator, and WWTP personnel when discharge occurs.« less

Review of Pre-Analytical Errors in Oral Glucose Tolerance Testing in a Tertiary Care Hospital.

PubMed

Nanda, Rachita; Patel, Suprava; Sahoo, Sibashish; Mohapatra, Eli

2018-03-13

The pre-pre-analytical and pre-analytical phases form a major chunk of the errors in a laboratory. The process has taken into consideration a very common procedure which is the oral glucose tolerance test to identify the pre-pre-analytical errors. Quality indicators provide evidence of quality, support accountability and help in the decision making of laboratory personnel. The aim of this research is to evaluate pre-analytical performance of the oral glucose tolerance test procedure. An observational study that was conducted overa period of three months, in the phlebotomy and accessioning unit of our laboratory using questionnaire that examined the pre-pre-analytical errors through a scoring system. The pre-analytical phase was analyzed for each sample collected as per seven quality indicators. About 25% of the population gave wrong answer with regard to the question that tested the knowledge of patient preparation. The appropriateness of test result QI-1 had the most error. Although QI-5 for sample collection had a low error rate, it is a very important indicator as any wrongly collected sample can alter the test result. Evaluating the pre-analytical and pre-pre-analytical phase is essential and must be conducted routinely on a yearly basis to identify errors and take corrective action and to facilitate their gradual introduction into routine practice.

Highly sensitive serological methods for detecting tomato yellow leaf curl virus in tomato plants and whiteflies.

PubMed

Xie, Yan; Jiao, Xiaoyang; Zhou, Xueping; Liu, Huan; Ni, Yuequn; Wu, Jianxiang

2013-05-06

Tomato yellow leaf curl virus (TYLCV) is a member of the genus Begomovirus in the family Geminiviridae, which causes severe losses in tomato production in tropic and subtropic regions. The purified TYLCV virions were used as the immunogen to produce monoclonal antibodies (MAbs) using the hybridoma technology. MAb-based dot enzyme-linked immunosorbent assay (dot-ELISA) and direct tissue blot immunoassay (DTBIA) were developed for sensitive, simple, and rapid detection of TYLCV in field tomato and whitefly (Bemisia tabaci) samples collected from TYLCV prevalent provinces in China. Using the hybridoma technology, six murine MAbs (1C4, 8D10, 6E3, 2F2, 3F4 and 4G3) against TYLCV were prepared. Using the MAb 1C4, dot-ELISA and DTBIA were then established for detecting TYLCV in field tomato and whitefly samples collected from TYLCV prevalent provinces in China. The dot-ELISA could detect TYLCV in infected tissue crude extract diluted at 1:5,120 (w/v, g mL-1), and in viruliferous whitefly homogenate diluted at 1:128 (individual whitefly/μL), respectively. Field tomato samples (n=487) and whitefly samples (n=110) from TYLCV prevalent districts in China were screened for the presence of TYLCV using the two developed methods, and the results were further confirmed by PCR and nucleotide sequencing. The survey revealed that TYLCV is widespread on tomato plants in Zhejiang, Shandong and Henan provinces in China. The developed dot-ELISA is very suitable for the routine detection of TYLCV in field tomato and whitefly samples, and the DTBIA is more suitable for the routine detection of TYLCV in large-scale tomato plant samples collected from TYLCV prevalent areas.

Self-sampling with HPV mRNA analyses from vagina and urine compared with cervical samples.

PubMed

Asciutto, Katrin Christine; Ernstson, Avalon; Forslund, Ola; Borgfeldt, Christer

2018-04-01

In order to increase coverage in the organized cervical screening program, self-sampling with HPV analyses has been suggested. The aim was to compare human papillomavirus (HPV) mRNA detection in vaginal and urine self-collected samples with clinician-taken cervical samples and the corresponding clinician-taken histological specimens. Self-collected vaginal, urine and clinician-taken cervical samples were analyzed from 209 women with the Aptima mRNA assay (Hologic Inc, MA, USA). Cervical cytology, colposcopy, biopsy and/or the loop electrosurgical excision procedure (LEEP) were performed in every examination. The sensitivity of the HPV mRNA test in detecting high-grade squamous intraepithelial lesions (HSIL)/adenocarcinoma in situ (AIS)/cancer cases was as follows: for the vaginal self-samples 85.5% (95% CI; 75.0-92.8), the urinary samples 44.8% (95% CI; 32.6-57.4), and for routine cytology 81.7% (95% CI; 70.7-89.9). For the clinician-taken cervical HPV samples the sensitivity of the HPV mRNA test in detecting HSIL/AIS/cancer was 100.0% (95% CI; 94.9-100.0). The specificity of the HPV mRNA was similar for the clinician-taken cervical HPV samples and the self-samples: 49.0% vs. 48.1%. The urinary HPV samples had a specificity of 61.9% and cytology had a specificity of 93.3%. The sensitivity of the Aptima HPV mRNA test in detecting HSIL/AIS/cancer from vaginal self-samples was similar to that of routine cytology. The Aptima HPV mRNA vaginal self-sampling analysis may serve as a complement in screening programs. Copyright © 2018 Elsevier B.V. All rights reserved.

Quality of surface water at selected sites in the Suwannee River basin, Florida

USGS Publications Warehouse

Coffin, J.E.

1982-01-01

This report presents the results of analyses of water-quality samples collected from 14 surface-water sites in the Suwannee River basin in Florida from January through December 1980. The analyses of samples collected routinely included: nutrients, total organic carbon, and 5-day biochemical oxygen demand, bimonthly; and trace metals, annually. The array of constituents sampled was expanded in October 1978 at three of the original nine stations to provide quality-of-water information for streams draining an industrial area: Rocky Creek near Belmont, Hunter Creek near Belmont, and Swift Creek at Facil. Data collected at these three sites now include: major chemical constituents, six times per year: radium-226, two times per year; and trace metals, one time per year. These constituents are determined in addition to nutrients, total organic carbon, and bio-chemical oxygen demand which continue to be analyzed six times per year. All results of analyses of the water-quality samples collected from January through December 1980 remained within, or near, previously measured ranges and water-quality fluctuations were similar to those noted from data collected since 1971. (USGS)

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

Paik, Samuel Y.; Epperson, Patrick M.; Kasper, Kenneth M.

Here, this article presents air and surface sampling data collected over the first two years since beryllium was introduced as a target material at the National Ignition Facility. Over this time, 101 experiments with beryllium-containing targets were executed. The data provides an assessment of current conditions in the facility and a baseline for future impacts as new, reduced regulatory limits for beryllium are being proposed by both the Occupational Safety and Health Administration and Department of Energy. This study also investigates how beryllium deposits onto exposed surfaces as a result of x-ray vaporization and the effectiveness of simple decontamination measuresmore » in reducing the amount of removable beryllium from a surface. Based on 1,961 surface wipe samples collected from entrant components (equipment directly exposed to target debris) and their surrounding work areas during routine reconfiguration activities, only one result was above the beryllium release limit of 0.2 µg/100 cm 2 and 27 results were above the analytical reporting limit of 0.01 µg/100 cm 2, for a beryllium detection rate of 1.4%. Surface wipe samples collected from the internal walls of the NIF target chamber, however, showed higher levels of beryllium, with beryllium detected on 73% and 87% of the samples during the first and second target chamber entries (performed annually), respectively, with 23% of the samples above the beryllium release limit during the second target chamber entry. The analysis of a target chamber wall panel exposed during the first 30 beryllium-containing experiments (cumulatively) indicated that 87% of the beryllium contamination remains fixed onto the surface after wet wiping the surface and 92% of the non-fixed contamination was removed by decontaminating the surface using a dry wipe followed by a wet wipe. Personal airborne exposures assessed during access to entrant components and during target chamber entry indicated that airborne beryllium was not present in workers' breathing zones. Finally, all the data thus far have shown that beryllium has been effectively managed to prevent exposures to workers during routine and non-routine work.« less

Assessment of personal airborne exposures and surface contamination from x-ray vaporization of beryllium targets at the National Ignition Facility.

PubMed

Paik, Samuel Y; Epperson, Patrick M; Kasper, Kenneth M

2017-06-01

This article presents air and surface sampling data collected over the first two years since beryllium was introduced as a target material at the National Ignition Facility. Over this time, 101 experiments with beryllium-containing targets were executed. The data provides an assessment of current conditions in the facility and a baseline for future impacts as new, reduced regulatory limits for beryllium are being proposed by both the Occupational Safety and Health Administration and Department of Energy. This study also investigates how beryllium deposits onto exposed surfaces as a result of x-ray vaporization and the effectiveness of simple decontamination measures in reducing the amount of removable beryllium from a surface. Based on 1,961 surface wipe samples collected from entrant components (equipment directly exposed to target debris) and their surrounding work areas during routine reconfiguration activities, only one result was above the beryllium release limit of 0.2 µg/100 cm 2 and 27 results were above the analytical reporting limit of 0.01 µg/100 cm 2 , for a beryllium detection rate of 1.4%. Surface wipe samples collected from the internal walls of the NIF target chamber, however, showed higher levels of beryllium, with beryllium detected on 73% and 87% of the samples during the first and second target chamber entries (performed annually), respectively, with 23% of the samples above the beryllium release limit during the second target chamber entry. The analysis of a target chamber wall panel exposed during the first 30 beryllium-containing experiments (cumulatively) indicated that 87% of the beryllium contamination remains fixed onto the surface after wet wiping the surface and 92% of the non-fixed contamination was removed by decontaminating the surface using a dry wipe followed by a wet wipe. Personal airborne exposures assessed during access to entrant components and during target chamber entry indicated that airborne beryllium was not present in workers' breathing zones. All the data thus far have shown that beryllium has been effectively managed to prevent exposures to workers during routine and non-routine work.

Assessment of personal airborne exposures and surface contamination from x-ray vaporization of beryllium targets at the National Ignition Facility

DOE PAGES

Paik, Samuel Y.; Epperson, Patrick M.; Kasper, Kenneth M.

2017-02-28

Here, this article presents air and surface sampling data collected over the first two years since beryllium was introduced as a target material at the National Ignition Facility. Over this time, 101 experiments with beryllium-containing targets were executed. The data provides an assessment of current conditions in the facility and a baseline for future impacts as new, reduced regulatory limits for beryllium are being proposed by both the Occupational Safety and Health Administration and Department of Energy. This study also investigates how beryllium deposits onto exposed surfaces as a result of x-ray vaporization and the effectiveness of simple decontamination measuresmore » in reducing the amount of removable beryllium from a surface. Based on 1,961 surface wipe samples collected from entrant components (equipment directly exposed to target debris) and their surrounding work areas during routine reconfiguration activities, only one result was above the beryllium release limit of 0.2 µg/100 cm 2 and 27 results were above the analytical reporting limit of 0.01 µg/100 cm 2, for a beryllium detection rate of 1.4%. Surface wipe samples collected from the internal walls of the NIF target chamber, however, showed higher levels of beryllium, with beryllium detected on 73% and 87% of the samples during the first and second target chamber entries (performed annually), respectively, with 23% of the samples above the beryllium release limit during the second target chamber entry. The analysis of a target chamber wall panel exposed during the first 30 beryllium-containing experiments (cumulatively) indicated that 87% of the beryllium contamination remains fixed onto the surface after wet wiping the surface and 92% of the non-fixed contamination was removed by decontaminating the surface using a dry wipe followed by a wet wipe. Personal airborne exposures assessed during access to entrant components and during target chamber entry indicated that airborne beryllium was not present in workers' breathing zones. Finally, all the data thus far have shown that beryllium has been effectively managed to prevent exposures to workers during routine and non-routine work.« less

Urban contributions of glyphosate and its degradate AMPA to streams in the United States

USGS Publications Warehouse

Kolpin, D.W.; Thurman, E.M.; Lee, E.A.; Meyer, M.T.; Furlong, E.T.; Glassmeyer, S.T.

2006-01-01

Glyphosate is the most widely used herbicide in the world, being routinely applied to control weeds in both agricultural and urban settings. Microbial degradation of glyphosate produces aminomethyl phosphonic acid (AMPA). The high polarity and water-solubility of glyphosate and AMPA has, until recently, made their analysis in water samples problematic. Thus, compared to other herbicides (e.g. atrazine) there are relatively few studies on the environmental occurrence of glyphosate and AMPA. In 2002, treated effluent samples were collected from 10 wastewater treatment plants (WWTPs) to study the occurrence of glyphosate and AMPA. Stream samples were collected upstream and downstream of the 10 WWTPs. Two reference streams were also sampled. The results document the apparent contribution of WWTP effluent to stream concentrations of glyphosate and AMPA, with roughly a two-fold increase in their frequencies of detection between stream samples collected upstream and those collected downstream of the WWTPs. Thus, urban use of glyphosate contributes to glyphosate and AMPA concentrations in streams in the United States. Overall, AMPA was detected much more frequently (67.5%) compared to glyphosate (17.5%).

Factors and misperceptions of routine childhood immunization service uptake in Ethiopia: findings from a nationwide qualitative study

PubMed Central

Tadesse, Tefera; Getachew, Kinde; Assefa, Tersit; Ababu, Yohannes; Simireta, Tesfaye; Birhanu, Zewdie; Hailemichael, Yohannes

2017-01-01

Introduction While the routine childhood immunization program might be affected by several factors, its identification using qualitative evidence of caretakers is generally minimal. This article explores the various factors and misperceptions of routine childhood immunization service uptake in Ethiopia and provides possible recommendations to mitigate them. Methods In this study, we used a qualitative multiple case study design collecting primary data from 63 focus group discussions (FGDs) conducted with a purposefully selected sample of children's caretakers (n = 630). Results According to the results of this study, the use of routine childhood immunization is dependent on four major factors: caretakers' behavior, family characteristics, information and communication and immunization service system. In addition, the participants had some misperceptions about routine childhood immunization. For example, immunization should be taken when the child gets sick and a single dose vaccine is enough for a child. These factors and misperceptions are complex and sometimes context-specific and vary between categories of caretakers. Conclusion Our interpretations suggest that no single factor affects immunization service uptake alone in a unique way. Rather, it is the synergy among the factors that has a collective influence on the childhood immunization system. Therefore, intervention efforts should target these multiple factors simultaneously. Importantly, this study recommends improving the quality of existing childhood immunization services and building awareness among caretakers as crucial components. PMID:29675124

Mycobacterium avium subsp. avium in lymph nodes and diaphragms of pigs from one infected herd in the Czech Republic.

PubMed

Kriz, Petr; Kaevska, Marija; Slana, Iva; Bartejsova, Iva; Pavlik, Ivo

2014-01-01

This study was performed on 40 finished pigs from one herd naturally infected with Mycobacterium avium subsp. avium. The aim was to investigate the presence and amount of M. a. avium in samples of lymph nodes and diaphragm tissues collected during routine postmortem inspection using the triplex quantitative real time PCR (qPCR) method. We collected, in total, 107 samples: various lymph nodes affected by gross tuberculosis (TB)-like lesions from 17 pig carcasses, as well as samples of head and mesenteric lymph nodes from 23 carcasses without TB-like lesions. Samples of diaphragm tissues were collected from all carcasses. M. a. avium was detected in one or more tissue samples collected from half of the slaughtered pigs tested. Samples of diaphragm tissues of three pigs with detected TB-like lesions contained M. a. avium (10(2) to 10(3) cells per g of sample); the organism was not detected in diaphragm tissues from pigs without TB-like lesions. The qPCR method may be useful for quantification of M. a. avium in pigs for the purposes of foodborne risk assessment.

Liquid Metering Centrifuge Sticks (LMCS): A Centrifugal Approach to Metering Known Sample Volumes for Colorimetric Solid Phase Extraction (C-SPE)

NASA Technical Reports Server (NTRS)

Gazda, Daniel B.; Schultz, John R.; Clarke, Mark S.

2007-01-01

Phase separation is one of the most significant obstacles encountered during the development of analytical methods for water quality monitoring in spacecraft environments. Removing air bubbles from water samples prior to analysis is a routine task on earth; however, in the absence of gravity, this routine task becomes extremely difficult. This paper details the development and initial ground testing of liquid metering centrifuge sticks (LMCS), devices designed to collect and meter a known volume of bubble-free water in microgravity. The LMCS uses centrifugal force to eliminate entrapped air and reproducibly meter liquid sample volumes for analysis with Colorimetric Solid Phase Extraction (C-SPE). C-SPE is a sorption-spectrophotometric platform that is being developed as a potential spacecraft water quality monitoring system. C-SPE utilizes solid phase extraction membranes impregnated with analyte-specific colorimetric reagents to concentrate and complex target analytes in spacecraft water samples. The mass of analyte extracted from the water sample is determined using diffuse reflectance (DR) data collected from the membrane surface and an analyte-specific calibration curve. The analyte concentration can then be calculated from the mass of extracted analyte and the volume of the sample analyzed. Previous flight experiments conducted in microgravity conditions aboard the NASA KC-135 aircraft demonstrated that the inability to collect and meter a known volume of water using a syringe was a limiting factor in the accuracy of C-SPE measurements. Herein, results obtained from ground based C-SPE experiments using ionic silver as a test analyte and either the LMCS or syringes for sample metering are compared to evaluate the performance of the LMCS. These results indicate very good agreement between the two sample metering methods and clearly illustrate the potential of utilizing centrifugal forces to achieve phase separation and metering of water samples in microgravity.

Reliability of routinely collected hospital data for child maltreatment surveillance.

PubMed

McKenzie, Kirsten; Scott, Debbie A; Waller, Garry S; Campbell, Margaret

2011-01-05

Internationally, research on child maltreatment-related injuries has been hampered by a lack of available routinely collected health data to identify cases, examine causes, identify risk factors and explore health outcomes. Routinely collected hospital separation data coded using the International Classification of Diseases and Related Health Problems (ICD) system provide an internationally standardised data source for classifying and aggregating diseases, injuries, causes of injuries and related health conditions for statistical purposes. However, there has been limited research to examine the reliability of these data for child maltreatment surveillance purposes. This study examined the reliability of coding of child maltreatment in Queensland, Australia. A retrospective medical record review and recoding methodology was used to assess the reliability of coding of child maltreatment. A stratified sample of hospitals across Queensland was selected for this study, and a stratified random sample of cases was selected from within those hospitals. In 3.6% of cases the coders disagreed on whether any maltreatment code could be assigned (definite or possible) versus no maltreatment being assigned (unintentional injury), giving a sensitivity of 0.982 and specificity of 0.948. The review of these cases where discrepancies existed revealed that all cases had some indications of risk documented in the records. 15.5% of cases originally assigned a definite or possible maltreatment code, were recoded to a more or less definite strata. In terms of the number and type of maltreatment codes assigned, the auditor assigned a greater number of maltreatment types based on the medical documentation than the original coder assigned (22% of the auditor coded cases had more than one maltreatment type assigned compared to only 6% of the original coded data). The maltreatment types which were the most 'under-coded' by the original coder were psychological abuse and neglect. Cases coded with a sexual abuse code showed the highest level of reliability. Given the increasing international attention being given to improving the uniformity of reporting of child-maltreatment related injuries and the emphasis on the better utilisation of routinely collected health data, this study provides an estimate of the reliability of maltreatment-specific ICD-10-AM codes assigned in an inpatient setting.

Reliability of Routinely Collected Hospital Data for Child Maltreatment Surveillance

PubMed Central

2011-01-01

Background Internationally, research on child maltreatment-related injuries has been hampered by a lack of available routinely collected health data to identify cases, examine causes, identify risk factors and explore health outcomes. Routinely collected hospital separation data coded using the International Classification of Diseases and Related Health Problems (ICD) system provide an internationally standardised data source for classifying and aggregating diseases, injuries, causes of injuries and related health conditions for statistical purposes. However, there has been limited research to examine the reliability of these data for child maltreatment surveillance purposes. This study examined the reliability of coding of child maltreatment in Queensland, Australia. Methods A retrospective medical record review and recoding methodology was used to assess the reliability of coding of child maltreatment. A stratified sample of hospitals across Queensland was selected for this study, and a stratified random sample of cases was selected from within those hospitals. Results In 3.6% of cases the coders disagreed on whether any maltreatment code could be assigned (definite or possible) versus no maltreatment being assigned (unintentional injury), giving a sensitivity of 0.982 and specificity of 0.948. The review of these cases where discrepancies existed revealed that all cases had some indications of risk documented in the records. 15.5% of cases originally assigned a definite or possible maltreatment code, were recoded to a more or less definite strata. In terms of the number and type of maltreatment codes assigned, the auditor assigned a greater number of maltreatment types based on the medical documentation than the original coder assigned (22% of the auditor coded cases had more than one maltreatment type assigned compared to only 6% of the original coded data). The maltreatment types which were the most 'under-coded' by the original coder were psychological abuse and neglect. Cases coded with a sexual abuse code showed the highest level of reliability. Conclusion Given the increasing international attention being given to improving the uniformity of reporting of child-maltreatment related injuries and the emphasis on the better utilisation of routinely collected health data, this study provides an estimate of the reliability of maltreatment-specific ICD-10-AM codes assigned in an inpatient setting. PMID:21208411

Application of allflex conservation buffer in illumina genotyping.

PubMed

de Groot, M; Ras, T; van Haeringen, W A

2016-12-01

This experiment was designed to study if liquid conservation buffer used in the novel Tissue Sampling Technology (TST) from Allflex can be used for Illumina BeadChip genotyping. Ear punches were collected from 6 bovine samples, using both the Tissue Sampling Unit (TSU) as well as the Total Tagger Universal (TTU) collection system. The stability of the liquid conservation buffer was tested by genotyping samples on Illumina BeadChips, incubated at 0, 3, 15, 24, 48, 72, 168, 336, 720 h after sample collection. Additionally, a replenishment study was designed to test how often the liquid conservation buffer could be completely replenished before a significant call rate drop could be observed. Results from the stability study showed an average call rate of 0.993 for samples collected with the TSU system and 0.953 for samples collected with the TTU system, both exceeding the inclusion threshold call rate of 0.85. As an additional control, the identity of the individual animals was confirmed using the International Society of Animal Genetics (ISAG) recommended SNP panel. The replenishment study revealed a slight drop in the sample call rate after replenishing the conservation buffer for the fourth time for the TSU as well as the TTU samples. In routine analysis, this application allows for multiple experiments to be performed on the liquid conservation buffer, while maintaining the tissue samples for future use. The data collected in this study shows that the liquid conservation buffer used in the TST system can be used for Illumina BeadChip genotyping applications.

Systematic review of discharge coding accuracy

PubMed Central

Burns, E.M.; Rigby, E.; Mamidanna, R.; Bottle, A.; Aylin, P.; Ziprin, P.; Faiz, O.D.

2012-01-01

Introduction Routinely collected data sets are increasingly used for research, financial reimbursement and health service planning. High quality data are necessary for reliable analysis. This study aims to assess the published accuracy of routinely collected data sets in Great Britain. Methods Systematic searches of the EMBASE, PUBMED, OVID and Cochrane databases were performed from 1989 to present using defined search terms. Included studies were those that compared routinely collected data sets with case or operative note review and those that compared routinely collected data with clinical registries. Results Thirty-two studies were included. Twenty-five studies compared routinely collected data with case or operation notes. Seven studies compared routinely collected data with clinical registries. The overall median accuracy (routinely collected data sets versus case notes) was 83.2% (IQR: 67.3–92.1%). The median diagnostic accuracy was 80.3% (IQR: 63.3–94.1%) with a median procedure accuracy of 84.2% (IQR: 68.7–88.7%). There was considerable variation in accuracy rates between studies (50.5–97.8%). Since the 2002 introduction of Payment by Results, accuracy has improved in some respects, for example primary diagnoses accuracy has improved from 73.8% (IQR: 59.3–92.1%) to 96.0% (IQR: 89.3–96.3), P= 0.020. Conclusion Accuracy rates are improving. Current levels of reported accuracy suggest that routinely collected data are sufficiently robust to support their use for research and managerial decision-making. PMID:21795302

A prioritization and analysis strategy for environmental surveillance results.

PubMed

Shyr, L J; Herrera, H; Haaker, R

1997-11-01

DOE facilities are required to conduct environmental surveillance to verify that facility operations are operated within the approved risk envelope and have not caused undue risk to the public and the environment. Given a reduced budget, a strategy for analyzing environmental surveillance data was developed to set priorities for sampling needs. The radiological and metal data collected at Sandia National Laboratories, New Mexico, were used to demonstrate the analysis strategy. Sampling locations were prioritized for further investigation and the needs for routine sampling. The process of data management, analysis, prioritization, and presentation has been automated through a custom-designed computer tool. Data collected over years can be analyzed and summarized in a short table format for prioritization and decision making.

Rainfall, Streamflow, and Water-Quality Data During Stormwater Monitoring, Halawa Stream Drainage Basin, Oahu, Hawaii, July 1, 2005 to June 30, 2006

USGS Publications Warehouse

Presley, Todd K.; Jamison, Marcael T.J.; Young-Smith, Stacie T. M.

2006-01-01

Storm runoff water-quality samples were collected as part of the State of Hawaii Department of Transportation Stormwater Monitoring Program. This program is designed to assess the effects of highway runoff and urban runoff on Halawa Stream. For this program, rainfall data were collected at two stations, continuous discharge data at one station, continuous streamflow data at two stations, and water-quality data at five stations, which include the continuous discharge and streamflow stations. This report summarizes rainfall, discharge, streamflow, and water-quality data collected between July 1, 2005 and June 30, 2006. A total of 23 samples was collected over five storms during July 1, 2005 to June 30, 2006. The goal was to collect grab samples nearly simultaneously at all five stations, and flow-weighted time-composite samples at the three stations equipped with automatic samplers; however, all five storms were partially sampled owing to lack of flow at the time of sampling at some sites, or because some samples collected by the automatic sampler did not represent water from the storm. Samples were analyzed for total suspended solids, total dissolved solids, nutrients, chemical oxygen demand, and selected trace metals (cadmium, chromium, copper, lead, nickel, and zinc). Additionally, grab samples were analyzed for oil and grease, total petroleum hydrocarbons, fecal coliform, and biological oxygen demand. Quality-assurance/quality-control samples were also collected during storms and during routine maintenance to verify analytical procedures and check the effectiveness of equipment-cleaning procedures.

2007 Chicago Regional Household Travel Inventory | Transportation Secure

Science.gov Websites

period. In addition to traditional survey-based data collection, this study featured a sub-sample of processing and filtering routines. Survey Records Survey records include 460 households. More Information For more information about the survey, see the CMAP Regional Travel Survey Final Report. Transportation

Quantitative and mixed analyses to identify factors that affect cervical cancer screening uptake among lesbian and bisexual women and transgender men.

PubMed

Johnson, Michael J; Mueller, Martina; Eliason, Michele J; Stuart, Gail; Nemeth, Lynne S

2016-12-01

The purposes of this study were to measure the prevalence of, and identify factors associated with, cervical cancer screening among a sample of lesbian, bisexual and queer women, and transgender men. Past research has found that lesbian, bisexual and queer women underuse cervical screening service. Because deficient screening remains the most significant risk factor for cervical cancer, it is essential to understand the differences between routine and nonroutine screeners. A convergent-parallel mixed methods design. A convenience sample of 21- to 65-year-old lesbian and bisexual women and transgender men were recruited in the USA from August-December 2014. Quantitative data were collected via a 48-item Internet questionnaire (N = 226), and qualitative data were collected through in-depth telephone interviews (N = 20) and open-ended questions on the Internet questionnaire. Seventy-three per cent of the sample was routine cervical screeners. The results showed that a constellation of factors influence the use of cervical cancer screening among lesbian, bisexual and queer women. Some of those factors overlap with the general female population, whereas others are specific to the lesbian, bisexual or queer identity. Routine screeners reported feeling more welcome in the health care setting, while nonroutine screeners reported more discrimination related to their sexual orientation and gender expression. Routine screeners were also more likely to 'out' to their provider. The quantitative and qualitative factors were also compared and contrasted. Many of the factors identified in this study to influence cervical cancer screening relate to the health care environment and to interactions between the patient and provider. Nurses should be involved with creating welcoming environments for lesbian, bisexual and queer women and their partners. Moreover, nurses play a large role in patient education and should promote self-care behaviours among lesbian women and transgender men. © 2016 John Wiley & Sons Ltd.

Stability and reproducibility of a single-sample urinary C-peptide/creatinine ratio and its correlation with 24-h urinary C-peptide.

PubMed

McDonald, Tim J; Knight, Bridget A; Shields, Beverley M; Bowman, Pamela; Salzmann, Maurice B; Hattersley, Andrew T

2009-11-01

C-peptide measurement in blood or 24-h urine samples provides useful information regarding endogenous insulin secretion, but problems related to the rapid degradation of C-peptide in blood and difficulty of 24-h urine collection have limited widespread routine clinical use of this test. We assessed the feasibility of measuring urinary C-peptide (UCP) with correction for creatinine concentration in single urine samples. We analyzed UCP using a routine electrochemiluminescence immunoassay in samples from 21 healthy volunteers. We investigated the stability of UCP with different preservatives and storage conditions and compared the reproducibility of urinary C-peptide/creatinine ratio (UCPCR) in first- and second-void fasting urines, then assessed correlations with 24-h collections. UCPCR was unchanged at room temperature for 24 h and at 4 degrees C for 72 h even in the absence of preservative. UCPCR collected in boric acid was stable at room temperature for 72 h. UCPCR remained stable after 7 freeze-thaw cycles but decreased with freezer storage time and dropped to 82%-84% of baseline by 90 days at -20 degrees C. Second-void fasting UCPCRs were lower than first-void (median 0.78 vs 1.31, P = 0.0003) and showed less variation (CV 33% vs 52%), as second-void UCPCRs were not influenced by evening food-related insulin secretion. Second-void fasting UCPCR was highly correlated with 24-h UCP (r = 0.8, P = 0.00006). Second-void fasting UCPCR is a reproducible measure that correlates well with 24-h UCP in normal samples. The 3-day stability of UCPCR at room temperature greatly increases its potential clinical utility.

Solid phase microextraction device using aerogel

DOEpatents

Miller, Fred S.; Andresen, Brian D.

2005-06-14

A sample collection substrate of aerogel and/or xerogel materials bound to a support structure is used as a solid phase microextraction (SPME) device. The xerogels and aerogels may be organic or inorganic and doped with metals or other compounds to target specific chemical analytes. The support structure is typically formed of a glass fiber or a metal wire (stainless steel or kovar). The devices are made by applying gel solution to the support structures and drying the solution to form aerogel or xerogel. Aerogel particles may be attached to the wet layer before drying to increase sample collection surface area. These devices are robust, stable in fields of high radiation, and highly effective at collecting gas and liquid samples while maintaining superior mechanical and thermal stability during routine use. Aerogel SPME devices are advantageous for use in GC/MS analyses due to their lack of interfering background and tolerance of GC thermal cycling.

Method for preparing a solid phase microextraction device using aerogel

DOEpatents

Miller, Fred S [Bethel Island, CA; Andresen, Brian D [Livermore, CA

2006-10-24

A sample collection substrate of aerogel and/or xerogel materials bound to a support structure is used as a solid phase microextraction (SPME) device. The xerogels and aerogels may be organic or inorganic and doped with metals or other compounds to target specific chemical analytes. The support structure is typically formed of a glass fiber or a metal wire (stainless steel or kovar). The devices are made by applying gel solution to the support structures and drying the solution to form aerogel or xerogel. Aerogel particles may be attached to the wet layer before drying to increase sample collection surface area. These devices are robust, stable in fields of high radiation, and highly effective at collecting gas and liquid samples while maintaining superior mechanical and thermal stability during routine use. Aerogel SPME devices are advantageous for use in GC/MS analyses due to their lack of interfering background and tolerance of GC thermal cycling.

Genetic and environmental contributions to the inverse association between specific autistic traits and experience seeking in adults.

PubMed

Romero-Martínez, Ángel; Moya-Albiol, Luís; Vinkhuyzen, Anna A E; Polderman, Tinca J C

2016-12-01

Autistic traits are characterized by social and communication problems, restricted, repetitive and stereotyped patterns of behavior, interests and activities. The relation between autistic traits and personality characteristics is largely unknown. This study focused on the relation between five specific autistic traits measured with the abridged version of the Autism Spectrum Quotient ("social problems," "preference for routine," "attentional switching difficulties," "imagination impairments," "fascination for numbers and patterns") and Experience Seeking (ES) in a general population sample of adults, and subsequently investigated the genetic and environmental etiology between these traits. Self-reported data on autistic traits and ES were collected in a population sample (n = 559) of unrelated individuals, and in a population based family sample of twins and siblings (n = 560). Phenotypic, genetic and environmental associations between traits were examined in a bivariate model, accounting for sex and age differences. Phenotypically, ES correlated significantly with "preference for routine" and "imagination impairments" in both samples but was unrelated to the other autistic traits. Genetic analyses in the family sample revealed that the association between ES and "preference for routine" and "imagination impairments" could largely be explained by a shared genetic factor (89% and 70%, respectively). Our analyses demonstrated at a phenotypic and genetic level an inverse relationship between ES and specific autistic traits in adults. ES is associated with risk taking behavior such as substance abuse, antisocial behavior and financial problems. Future research could investigate whether autistic traits, in particular strong routine preference and impaired imagination skills, serve as protective factors for such risky behaviors. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

Circadian temperature rhythms of older people

NASA Technical Reports Server (NTRS)

Monk, T. H.; Buysse, D. J.; Reynolds, C. F. 3rd; Kupfer, D. J.; Houck, P. R.

1995-01-01

This collection of studies had the aim of exploring whether older (77+ years) men and women have circadian body temperature rhythms different from those of younger adults. A total of 20 older men and 28 older women were compared with either 22 young men or 14 middle-aged men in four protocols; all but the first protocol using a subset of the sample. The four protocols were: 1) 24 h, and 2) 72 h data collections on a normal laboratory routine (sleeping at night); 3) between 36 h and 153 h of field data collection at home; and 4) 36 h of a constant conditions routine (wakeful bedrest under temporal isolation) in the laboratory. There was some evidence for an age-related phase advance in temperature rhythm, especially for the older men on a normal routine, though this was not present in the constant conditions protocol, where 5 of the older subjects showed major delays in the timing of the body temperature trough (10:00 or later). There was no statistically significant evidence from any of the protocols that older subjects generally had lower temperature rhythm amplitudes than younger adults. Only when older men were compared with younger men in 24-h rhythm amplitude by simple t-test did any comparison involving amplitude achieve statistical significance (p < 0.05).

Rainfall, Discharge, and Water-Quality Data During Stormwater Monitoring, July 1, 2007, to June 30, 2008; Halawa Stream Drainage Basin and the H-1 Storm Drain, Oahu, Hawaii

USGS Publications Warehouse

Presley, Todd K.; Jamison, Marcael T.J.; Young, Stacie T.M.

2008-01-01

Storm runoff water-quality samples were collected as part of the State of Hawaii Department of Transportation Stormwater Monitoring Program. The program is designed to assess the effects of highway runoff and urban runoff on Halawa Stream and to assess the effects from the H-1 storm drain on Manoa Stream. For this program, rainfall data were collected at three stations, continuous discharge data at four stations, and water-quality data at six stations, which include the four continuous discharge stations. This report summarizes rainfall, discharge, and water-quality data collected between July 1, 2007, and June 30, 2008. A total of 16 environmental samples were collected over two storms during July 1, 2007, to June 30, 2008, within the Halawa Stream drainage area. Samples were analyzed for total suspended solids, total dissolved solids, nutrients, chemical oxygen demand, and selected trace metals (cadmium, chromium, copper, lead, and zinc). Additionally, grab samples were analyzed for oil and grease, total petroleum hydrocarbons, fecal coliform, and biological oxygen demand. Some samples were analyzed for only a partial list of these analytes because an insufficient volume of sample was collected by the automatic samplers. Three additional quality-assurance/quality-control samples were collected concurrently with the storm samples. A total of 16 environmental samples were collected over four storms during July 1, 2007, to June 30, 2008 at the H-1 Storm Drain. All samples at this site were collected using an automatic sampler. Samples generally were analyzed for total suspended solids, nutrients, chemical oxygen demand, oil and grease, total petroleum hydrocarbons, and selected trace metals (cadmium, chromium, copper, lead, nickel, and zinc), although some samples were analyzed for only a partial list of these analytes. During the storm of January 29, 2008, 10 discrete samples were collected. Varying constituent concentrations were detected for the samples collected at different times during this storm event. Two quality-assurance/quality-control samples were collected concurrently with the storm samples. Three additional quality-assurance/quality-control samples were collected during routine sampler maintenance to check the effectiveness of equipment-cleaning procedures.

Informed, advance refusals of treatment by people with severe mental illness in a randomised controlled trial of joint crisis plans: demand, content and correlates.

PubMed

Henderson, Claire; Farrelly, Simone; Flach, Clare; Borschmann, Rohan; Birchwood, Max; Thornicroft, Graham; Waheed, Waquas; Szmukler, George

2017-11-24

In the UK, crisis planning for mental health care should acknowledge the right to make an informed advance treatment refusal under the Mental Capacity Act 2005. Our aims were to estimate the demand for such treatment refusals within a sample of service users who had had a recent hospital admission for psychosis or bipolar disorder, and to examine the relationship between refusals, and service user characteristics. To identify refusals we conducted content analysis of Joint Crisis Plans, which are plans formulated by service users and their clinical team with involvement from an external facilitator, and routine care plans in sub-samples from a multi-centre randomised controlled trial of Joint Crisis Plans (plus routine mental health care) versus routine care alone (CRIMSON) in England. Factors hypothesised to be associated with refusals were identified using the trial data collected through baseline interviews of service users and clinicians and collection of routine clinical data. Ninety-nine of 221 (45%) of the Joint Crisis Plans contained a treatment refusal compared to 10 of 424 (2.4%) baseline routine care plans. No Joint Crisis Plans recorded disagreement with refusals on the part of clinicians. Among those with completed Joint Crisis Plans, adjusted analyses indicated a significant association between treatment refusals and perceived coercion at baseline (odds ratio = 1.21, 95% CI 1.02-1.43), but not with baseline working alliance or a past history of involuntary admission. We demonstrated significant demand for written treatment refusals in line with the Mental Capacity Act 2005, which had not previously been elicited by the process of treatment planning. Future treatment/crisis plans should incorporate the opportunity for service users to record a treatment refusal during the drafting of such plans. ISRCTN11501328 Registered 13th March 2008.

Jack Healy Remembers - Anecdotal Evidence for the Origin of the Approximate 24-hour Urine Sampling Protocol Used for Worker Bioassay Monitoring

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

Carbaugh, Eugene H.

2008-10-01

The origin of the approximate 24-hour urine sampling protocol used at Hanford for routine bioassay is attributed to an informal study done in the mid-1940s. While the actual data were never published and have been lost, anecdotal recollections by staff involved in the initial bioassay program design and administration suggest that the sampling protocol had a solid scientific basis. Numerous alternate methods for normalizing partial day samples to represent a total 24-hour collection have since been proposed and used, but no one method is obviously preferred.

Genetic antimicrobial susceptibility testing in Gram-negative sepsis - impact on time to results in a routine laboratory.

PubMed

Kommedal, Øyvind; Aasen, Johanne Lind; Lindemann, Paul Christoffer

2016-07-01

Diagnostic testing of positive blood cultures is among the most critical tasks performed by clinical microbiology laboratories, and the total analysis time from sampling to results should be kept as short as possible. By providing identification of pelleted bacteria directly from positive blood-cultures, MALDI-TOF MS opens for relatively low-complex species-adjusted genetic susceptibility testing from the same bacterial pellet. In our lab routine, we prospectively evaluated a rapid in-house real-time PCR targeting the most common aminoglycoside and cephalosporin resistance genes in Escherichia coli and Klebsiella pneumoniae and measured time to preliminary susceptibility reporting for 138 samples. The results were compared to direct phenotypic susceptibility testing with interpretation after 6 h and overnight incubation respectively. Results from the genetic susceptibility testing were available for 69.5% (96/138) of the positive blood cultures within 24 h after sample collection. No phenotypic susceptibility results were available at this time. Compared to overnight direct susceptibility testing, the average time from sample collection to preliminary susceptibility reporting was reduced with 43%, from 45 h and 5 min to 25 h and 44 min, providing an earlier adjustment of antimicrobial therapy for 12 patients. Minor logistic adjustments have the potential to save yet another 4 h. © 2016 APMIS. Published by John Wiley & Sons Ltd.

Underutilisation of routinely collected data in the HIV programme in Zambia: a review of quantitatively analysed peer-reviewed articles.

PubMed

Munthali, Tendai; Musonda, Patrick; Mee, Paul; Gumede, Sehlulekile; Schaap, Ab; Mwinga, Alwyn; Phiri, Caroline; Kapata, Nathan; Michelo, Charles; Todd, Jim

2017-06-13

The extent to which routinely collected HIV data from Zambia has been used in peer-reviewed published articles remains unexplored. This paper is an analysis of peer-reviewed articles that utilised routinely collected HIV data from Zambia within six programme areas from 2004 to 2014. Articles on HIV, published in English, listed in the Directory of open access journals, African Journals Online, Google scholar, and PubMed were reviewed. Only articles from peer-reviewed journals, that utilised routinely collected data and included quantitative data analysis methods were included. Multi-country studies involving Zambia and another country, where the specific results for Zambia were not reported, as well as clinical trials and intervention studies that did not take place under routine care conditions were excluded, although community trials which referred patients to the routine clinics were included. Independent extraction was conducted using a predesigned data collection form. Pooled analysis was not possible due to diversity in topics reviewed. A total of 69 articles were extracted for review. Of these, 7 were excluded. From the 62 articles reviewed, 39 focused on HIV treatment and retention in care, 15 addressed prevention of mother-to-child transmission, 4 assessed social behavioural change, and 4 reported on voluntary counselling and testing. In our search, no articles were found on condom programming or voluntary male medical circumcision. The most common outcome measures reported were CD4+ count, clinical failure or mortality. The population analysed was children in 13 articles, women in 16 articles, and both adult men and women in 33 articles. During the 10 year period of review, only 62 articles were published analysing routinely collected HIV data in Zambia. Serious consideration needs to be made to maximise the utility of routinely collected data, and to benefit from the funds and efforts to collect these data. This could be achieved with government support of operational research and publication of findings based on routinely collected Zambian HIV data.

Preoperative Hand Decontamination in Ophthalmic Surgery: A Comparison of the Removal of Bacteria from Surgeons' Hands by Routine Antimicrobial Scrub versus an Alcoholic Hand Rub.

PubMed

Forer, Yaara; Block, Colin; Frenkel, Shahar

2017-09-01

The goal of this experiment was to evaluate and compare the antimicrobial efficacy of routine preoperative hand washing using commercial medicated sponge brushes versus an alcoholic hand rub, by comparing bacterial growth on ophthalmic surgeons' hands after application of each of these methods. Twenty ophthalmic surgeons were recruited at the Hadassah-Hebrew University Medical Center in Jerusalem, Israel. Samples were collected twice from the hands of each surgeon after hand decontamination using two different protocols during routine surgical practice. The routine preparation consisted of a 3-minute surgical scrub using commercial brush-sponges incorporating either 4% chlorhexidine gluconate (CHG) or 1% povidone-iodine (PVP-I) formulations with detergent, followed by drying the hands with a sterile towel, while the 70% ethanol solution was applied for 60-seconds and allowed to air dry. Half of the group was randomly assigned to provide samples first after the routine method and the alcoholic solution a week later, and the other half of the group was sampled in the reverse order. Viable counts of bacteria were evaluated using a modified glove juice method. Bacterial colonies were enumerated after incubation for 24 hours and expressed as colony forming units (CFU)/mL for each pair of hands. Geometric mean counts were 1310 and 39 CFU/mL, in the routine and alcohol rub groups, respectively, representing a mean log 10 reduction in 1.53. The difference between the paired bacterial counts for the routine versus the alcohol rub was statistically significant (p < 0.0001). There was no statistically significant difference between log 10 reductions for CHG and PVP-I (p = 0.97). This study provides evidence that an alcohol rub protocol is more effective in reducing bacterial counts on hands than routine surgical hand preparation with PVP-I and CHG in a population of practicing ophthalmic surgeons in the operative clinical setting. Thus, it provides a safe alternative as a preoperative hand disinfection method.

Blood sample collection and patient identification demand improvement: a questionnaire study of preanalytical practices in hospital wards and laboratories.

PubMed

Wallin, Olof; Söderberg, Johan; Van Guelpen, Bethany; Stenlund, Hans; Grankvist, Kjell; Brulin, Christine

2010-09-01

Scand J Caring Sci; 2010; 24; 581-591 
 Blood sample collection and patient identification demand improvement: a questionnaire study of preanalytical practices in hospital wards and laboratories   Most errors in venous blood testing result from human mistakes occurring before the sample reach the laboratory.   To survey venous blood sampling (VBS) practices in hospital wards and to compare practices with hospital laboratories.   Staff in two hospitals (all wards) and two hospital laboratories (314 respondents, response rate 94%), completed a questionnaire addressing issues relevant to the collection of venous blood samples for clinical chemistry testing.   The findings suggest that instructions for patient identification and the collection of venous blood samples were not always followed. For example, 79% of the respondents reported the undesirable practice (UDP) of not always using wristbands for patient identification. Similarly, 87% of the respondents noted the UDP of removing venous stasis after the sampling is finished. Compared with the ward staff, a significantly higher proportion of the laboratory staff reported desirable practices regarding the collection of venous blood samples. Neither education nor the existence of established sampling routines was clearly associated with VBS practices among the ward staff.   The results of this study, the first of its kind, suggest that a clinically important risk of error is associated with VBS in the surveyed wards. Most important is the risk of misidentification of patients. Quality improvement of blood sample collection is clearly needed, particularly in hospital wards. © 2009 The Authors. Journal compilation © 2009 Nordic College of Caring Science.

A quality-assurance assessment for constituents reported by the national atmospheric deposition program and the national trends network

NASA Astrophysics Data System (ADS)

See, Randolph B.; Schroder, LeRoy J.; Willoughby, Timothy C.

A continuing quality-assurance program has been operated by the U.S. Geological Survey to evaluate any bias introduced by routine handling, shipping, and laboratory analyses of wet-deposition samples collected in the National Atmospheric Deposition Program (NADP) and National Trends Network (NTN). Blind-audit samples having a variety of constituent concentrations and values were selected. Only blind-audit samples with constituent concentrations and values less than the 95th-percentile concentration for natural wet-deposition samples were included in the analysis. Of the major ions, there was a significant increase of Ca 2+, Mg 2+, Na 2+, K +, SO 42- and Cl -1 in samples handled according to standard protocols and shipped in NADP/NTN sample-collection buckets. For 1979-1987, graphs of smoothed data showing the estimated contamination in blind-audit samples indicate a decrease in the median concentration and ranges of Ca 2+, Mg 2+ and SO 42- contamination of blind-audit samples shipped in sample-collection buckets. Part of the contamination detected in blind-audit samples can be attributed to contact with the sample-collection bucket and lid; however, additional sources also seem to contaminate the blind-audit sample. Apparent decreases in the magnitude and range of sample contamination may be caused by differences in sample-collection bucket- and lid-washing procedures by the NADP/NTN Central Analytical Laboratory. Although the degree of bias is minimal for most constituents, summaries of the NADP/NTN data base may contain overestimates of Ca 2+, Mg 2+, Na -, K + and SO 42- and Cl - concentrations, and underestimates of H + concentrations.

A quality-assurance assessment for constituents reported by the National Atmospheric Deposition Program and the National Trends Network

USGS Publications Warehouse

See, R.B.; Schroder, L.J.; Willoughby, T.C.

1989-01-01

A continuing quality-assurance program has been operated by the U.S. Geographical Survey to evaluate any bias introduced by routine handling, shipping, and laboratory analyses of wet-deposition samples collected in the National Atmospheric Deposition Program (NADP) and National Trends Network (NTN). Blind-audit samples having a variety of constituent concentrations and values were selected. Only blind-audit samples with constituent concentrations and values less than the 95th-percentile concentration for natural wet-deposition samples were included in the analysis. Of the major ions, there was a significant increase of Ca2+, Mg2+, K+ SO42+ and Cl- in samples handled according to standard protocols and shipped in NADP/NTN sample-collection buckets. For 1979-1987, graphs of smoothed data showing the estimated contaminations in blind-audit samples indicate a decrease in the median concentration and ranges of Ca2+, Mg2+ and SO42- contamination of blind-audit samples shipped in sample-collection buckets. Part of the contamination detected in blind-audit samples can be attributed to contact with the sample-collection bucket and lid; however, additional sources also seem to contaminate the blind-audit sample. Apparent decreases in the magnitude and range of sample contamination may be caused by differences in sample-collection bucket- and lid-washing procedures by the NADP/NTN Central Analytical Laboratory. Although the degree of bias is minimal for most constituents, summaries of the NADP/NTN data base may contain overestimates of Ca2+, Mg2+, Na-, K+, SO42- and Cl- concentrations, and underestimates of H+ concentrations.

Management of asthma in Australian general practice: care is still not in line with clinical practice guidelines.

PubMed

Barton, Christopher; Proudfoot, Judith; Amoroso, Cheryl; Ramsay, Emmae; Holton, Christine; Bubner, Tanya; Harris, Mark; Beilby, Justin

2009-06-01

We investigated the quality of primary care asthma management in a sample of Australian general practices. 247 general practitioners (GPs) from 97 practices completed a structured interview about management of asthma, diabetes and hypertension/heart disease. A further structured interview with the senior practice principal and practice manager was used to collect information about practice capacity for chronic disease management. Just under half of GPs (47%) had access to an asthma register and the majority (76%) had access to spirometry in their practice. In terms of routine management of asthma, 12% of GPs reported using spirometry routinely, 13% routinely reviewed written asthma action plans, 27% routinely provided education about trigger factors, 30% routinely reviewed inhaler technique, 24% routinely assessed asthma severity, and 29% routinely assessed physical activity. Practice characteristics such as practice size (p=1.0) and locality (rural/metropolitan) (p=0.7) did not predict quality of asthma management nor did indicators of practice capacity including Business maturity, IT/IM maturity, Multidisciplinary teamwork, and Clinical linkages. Gaps remain in the provision of evidence-based care for patients with asthma in general practice. Markers of practice capacity measured here were not associated with guideline-based respiratory care within practices.

Detection of BRAF V600 Mutations in Melanoma: Evaluation of Concordance between the Cobas® 4800 BRAF V600 Mutation Test and the Methods Used in French National Cancer Institute (INCa) Platforms in a Real-Life Setting

PubMed Central

Mourah, Samia; Denis, Marc G.; Narducci, Fabienne Escande; Solassol, Jérôme; Merlin, Jean-Louis; Sabourin, Jean-Christophe; Scoazec, Jean-Yves; Ouafik, L’Houcine; Emile, Jean-François; Heller, Remy; Souvignet, Claude; Bergougnoux, Loïc; Merlio, Jean-Philippe

2015-01-01

Vemurafenib is approved for the treatment of metastatic melanoma in patients with BRAF V600 mutation. In pivotal clinical trials, BRAF testing has always been done with the approved cobas 4800 BRAF test. In routine practice, several methods are available and are used according to the laboratories usual procedures. A national, multicenter, non-interventional study was conducted with prospective and consecutive collection of tumor samples. A parallel evaluation was performed in routine practice between the cobas 4800 BRAF V600 mutation test and home brew methods (HBMs) of 12 national laboratories, labelled and funded by the French National Cancer Institute (INCa). For 420 melanoma samples tested, the cobas method versus HBM showed a high concordance (93.3%; kappa = 0.86) in BRAF V600 genotyping with similar mutation rates (34.0% versus 35.7%, respectively). Overall, 97.4% and 98.6% of samples gave valid results using the cobas and HBM, respectively. Of the 185 samples strictly fulfilling the cobas guidelines, the concordance rate was even higher (95.7%; kappa = 0.91; 95%CI [0.85; 0.97]). Out of the 420 samples tested, 28 (6.7%) showed discordance between HBM and cobas. This prospective study shows a high concordance rate between the cobas 4800 BRAF V600 test and home brew methods in the routine detection of BRAF V600E mutations. PMID:25789737

Expanding sexually transmitted infection screening among women and men engaging in transactional sex: the feasibility of field-based self-collection.

PubMed

Roth, A M; Rosenberger, J G; Reece, M; Van Der Pol, B

2013-04-01

Routine screening is a key component of sexually transmitted infection (STI) prevention and control; however, traditional programmes often fail to effectively reach men and women in hidden communities. To reduce prevalence, we must understand the programmatic features that would encourage utilization of services among asymptomatic individuals. Using incentivized snowball sampling, 44 women and men recently engaging in transactional sex were recruited (24 women, 20 men); median age 37 years. Respondents were offered the opportunity to collect genital, oropharyngeal and rectal samples for STI testing and completed a face-to-face interview about their experience with self-obtained sampling. Interviews were analysed using qualitative methods. Participants were unaware of potential risk for STI, but found self-sampling in non-clinical settings to be acceptable and preferable to clinic-based testing. All participants collected genital specimens; 96% and 4% collected oropharyngeal and rectal specimens, respectively. The burden of disease in this population was high: 38% tested positive for at least one STI. We detected multiple concomitant infections. Incorporating field collection of self-obtained samples into STI control programmes may increase utilization among high-risk populations unlikely to access clinic-based services. High infection rates indicate that individuals engaging in transactional sex would benefit from, and be responsive to, community-based self-sampling for STI screening.

Phylogenetic characterisation of circulating, clinical influenza isolates from Bali, Indonesia: preliminary report from the BaliMEI project.

PubMed

Adisasmito, W; Budayanti, S N; Aisyah, D N; Gallo Cassarino, T; Rudge, J W; Watson, S J; Kozlakidis, Z; Smith, G J D; Coker, R

2017-08-23

Human influenza represents a major public health concern, especially in south-east Asia where the risk of emergence and spread of novel influenza viruses is particularly high. The BaliMEI study aims to conduct a five year active surveillance and characterisation of influenza viruses in Bali using an extensive network of participating healthcare facilities. Samples were collected during routine diagnostic treatment in healthcare facilities. In addition to standard clinical and molecular methods for influenza typing, next generation sequencing and subsequent de novo genome assembly were performed to investigate the phylogeny of the collected patient samples. The samples collected are characteristic of the seasonally circulating influenza viruses with indications of phylogenetic links to other samples characterised in neighbouring countries during the same time period. There were some strong phylogenetic links with sequences from samples collected in geographically proximal regions, with some of the samples from the same time-period resulting to small clusters at the tree-end points. However this work, which is the first of its kind completely performed within Indonesia, supports the view that the circulating seasonal influenza in Bali reflects the strains circulating in geographically neighbouring areas as would be expected to occur within a busy regional transit centre.

Identification of Escherichia coli and Trueperella pyogenes isolated from the uterus of dairy cows using routine bacteriological testing and Fourier transform infrared spectroscopy.

PubMed

Jaureguiberry, María; Madoz, Laura Vanina; Giuliodori, Mauricio Javier; Wagener, Karen; Prunner, Isabella; Grunert, Tom; Ehling-Schulz, Monika; Drillich, Marc; de la Sota, Rodolfo Luzbel

2016-11-28

Uterine disorders are common postpartum diseases in dairy cows. In practice, uterine treatment is often based on systemic or locally applied antimicrobials with no previous identification of pathogens. Accurate on-farm diagnostics are not available, and routine testing is time-consuming and cost intensive. An accurate method that could simplify the identification of uterine pathogenic bacteria and improve pathogen-specific treatments could be an important advance to practitioners. The objective of the present study was to evaluate whether a database built with uterine bacteria from European dairy cows could be used to identify bacteria from Argentinean cows by Fourier transformed infrared (FTIR) spectroscopy. Uterine samples from 64 multiparous dairy cows with different types of vaginal discharge (VD) were collected between 5 and 60 days postpartum, analyzed by routine bacteriological testing methods and then re-evaluated by FTIR spectroscopy (n = 27). FTIR spectroscopy identified Escherichia coli in 12 out of 14 samples and Trueperella pyogenes in 8 out of 10 samples. The agreement between the two methods was good with a Kappa coefficient of 0.73. In addition, the likelihood for bacterial growth of common uterine pathogens such as E. coli and T. pyogenes tended to increase with VD score. The odds for a positive result to E. coli or T. pyogenes was 1.88 times higher in cows with fetid VD than in herdmates with clear normal VD. We conclude that the presence of E. coli and T. pyogenes in uterine samples from Argentinean dairy cows can be detected with FTIR with the use of a database built with uterine bacteria from European dairy cows. Future studies are needed to determine if FTIR can be used as an alternative to routine bacteriological testing methods.

Factors affecting access to information on routine immunization among mothers of under 5 children in Kaduna State Nigeria, 2015

PubMed Central

Taiwo, Lydia; Idris, Suleiman; Abubakar, Aisha; Nguku, Patrick; Nsubuga, Peter; Gidado, Saheed; Okeke, Lilian; Emiasegen, Samuel; Waziri, Endie

2017-01-01

Introduction Immunization is one of the most effective interventions to prevent disease and early child death. A substantial number of children worldwide do not complete immunization schedules because neither health services nor conventional communication mechanisms regularly reach their communities. Knowledge and perception of mothers/caregivers regarding VPDs influence demand and utilization of immunization services. We examined the associations between knowledge, perception and information on routine immunization received by mothers/caregivers in Kaduna State. Methods We enrolled 379 eligible caregivers in a community-based cross-sectional study. We sampled respondents using multistage sampling technique. We collected data on socio-demographic characteristics; knowledge and perception on routine immunization using semi-structured interviewer-administered questionnaire. We conducted bivariate analysis and logistic regression using Epi-InfoTM version 7 at 5% level of significance. Results Mean age of respondents was 28.6 years (standard deviation=±6.6 years), 34% completed secondary school, 65% were unemployed, 49% lived in rural settlements. Among respondents' children 53.3% were females and 62.8% fell within 2nd-5th birth order. Only 15.6% of these children were fully immunized. Seventy-five percent of respondent did not obtain information on routine immunization within 12 months prior to the study. About 64% had unsatisfactory knowledge while 55.4% exhibited poor perceptions regarding routine immunization. Commonest source of information was radio (61.61%). On logistic regression educated participants (Adjusted odds ratio (AOR)=1.9, 95% CI: 1.1-3.3), mothers' perception (AOR=2.6, 95% CI: 1.5-4.5) and monogamous family setting (AOR=2.4, 95% CI: 0.2-0.6) were likely to have obtained information on routine immunization. Conclusion There is low access to information, poor maternal knowledge on routine immunization with low vaccination coverage in this community. Efforts should be made by the Governments to scale up sensitization of mothers/caregivers to improve their knowledge on routine immunization through radio jingles. PMID:29187919

Factors affecting access to information on routine immunization among mothers of under 5 children in Kaduna State Nigeria, 2015.

PubMed

Taiwo, Lydia; Idris, Suleiman; Abubakar, Aisha; Nguku, Patrick; Nsubuga, Peter; Gidado, Saheed; Okeke, Lilian; Emiasegen, Samuel; Waziri, Endie

2017-01-01

Immunization is one of the most effective interventions to prevent disease and early child death. A substantial number of children worldwide do not complete immunization schedules because neither health services nor conventional communication mechanisms regularly reach their communities. Knowledge and perception of mothers/caregivers regarding VPDs influence demand and utilization of immunization services. We examined the associations between knowledge, perception and information on routine immunization received by mothers/caregivers in Kaduna State. We enrolled 379 eligible caregivers in a community-based cross-sectional study. We sampled respondents using multistage sampling technique. We collected data on socio-demographic characteristics; knowledge and perception on routine immunization using semi-structured interviewer-administered questionnaire. We conducted bivariate analysis and logistic regression using Epi-InfoTM version 7 at 5% level of significance. Mean age of respondents was 28.6 years (standard deviation=±6.6 years), 34% completed secondary school, 65% were unemployed, 49% lived in rural settlements. Among respondents' children 53.3% were females and 62.8% fell within 2 nd -5 th birth order. Only 15.6% of these children were fully immunized. Seventy-five percent of respondent did not obtain information on routine immunization within 12 months prior to the study. About 64% had unsatisfactory knowledge while 55.4% exhibited poor perceptions regarding routine immunization. Commonest source of information was radio (61.61%). On logistic regression educated participants (Adjusted odds ratio (AOR)=1.9, 95% CI: 1.1-3.3), mothers' perception (AOR=2.6, 95% CI: 1.5-4.5) and monogamous family setting (AOR=2.4, 95% CI: 0.2-0.6) were likely to have obtained information on routine immunization. There is low access to information, poor maternal knowledge on routine immunization with low vaccination coverage in this community. Efforts should be made by the Governments to scale up sensitization of mothers/caregivers to improve their knowledge on routine immunization through radio jingles.

Long-term frozen storage of urine samples: a trouble to get PCR results in Schistosoma spp. DNA detection?

PubMed

Fernández-Soto, Pedro; Velasco Tirado, Virginia; Carranza Rodríguez, Cristina; Pérez-Arellano, José Luis; Muro, Antonio

2013-01-01

Human schistosomiasis remains a serious worldwide public health problem. At present, a sensitive and specific assay for routine diagnosis of schistosome infection is not yet available. The potential for detecting schistosome-derived DNA by PCR-based methods in human clinical samples is currently being investigated as a diagnostic tool with potential application in routine schistosomiasis diagnosis. Collection of diagnostic samples such as stool or blood is usually difficult in some populations. However, urine is a biological sample that can be collected in a non-invasive method, easy to get from people of all ages and easy in management, but as a sample for PCR diagnosis is still not widely used. This could be due to the high variability in the reported efficiency of detection as a result of the high variation in urine samples' storage or conditions for handling and DNA preservation and extraction methods. We evaluate different commercial DNA extraction methods from a series of long-term frozen storage human urine samples from patients with parasitological confirmed schistosomiasis in order to assess the PCR effectiveness for Schistosoma spp. detection. Patients urine samples were frozen for 18 months up to 7 years until use. Results were compared with those obtained in PCR assays using fresh healthy human urine artificially contaminated with Schistosoma mansoni DNA and urine samples from mice experimentally infected with S. mansoni cercariae stored frozen for at least 12 months before use. PCR results in fresh human artificial urine samples using different DNA based extraction methods were much more effective than those obtained when long-term frozen human urine samples were used as the source of DNA template. Long-term frozen human urine samples are probably not a good source for DNA extraction for use as a template in PCR detection of Schistosoma spp., regardless of the DNA method of extraction used.

Analysis of water from the Space Shuttle and Mir Space Station by ion chromatography and capillary electrophoresis

NASA Technical Reports Server (NTRS)

Orta, D.; Mudgett, P. D.; Ding, L.; Drybread, M.; Schultz, J. R.; Sauer, R. L.

1998-01-01

Drinking water and condensate samples collected from the US Space Shuttle and the Russian Mir Space Station are analyzed routinely at the NASA-Johnson Space Center as part of an ongoing effort to verify water quality and monitor the environment of the spacecraft. Water quality monitoring is particularly important for the Mir water supply because approximately half of the water consumed is recovered from humidity condensate. Drinking water on Shuttle is derived from the fuel cells. Because there is little equipment on board the spacecraft for monitoring the water quality, samples collected by the crew are transported to Earth on Shuttle or Soyuz vehicles, and analyzed exhaustively. As part of the test battery, anions and cations are measured by ion chromatography, and carboxylates and amines by capillary electrophoresis. Analytical data from Shuttle water samples collected before and after several missions, and Mir condensate and potable recovered water samples representing several recent missions are presented and discussed. Results show that Shuttle water is of distilled quality, and Mir recovered water contains various levels of minerals imparted during the recovery processes as designed. Organic ions are rarely detected in potable water samples, but were present in humidity condensate samples.

Delivering Vitamin A Supplements to Children Aged 6 to 59 Months: Comparing Delivery Through Mass Campaign and Through Routine Health Services in Ethiopia.

PubMed

Gatobu, Sospeter; Horton, Susan; Kiflie Aleyamehu, Yibeltal; Abraham, Gelila; Birhanu, Negalign; Greig, Alison

2017-12-01

The delivery of vitamin A supplements in Ethiopia has been shifting from Child Health Days (campaigns) to routine delivery via the community health services. The objective of this study was to compare the cost and effectiveness of these 2 delivery methods. No previous studies have done this. A mixed method approach was used. Quantitative data on costs were collected from interviews with key staff and coverage data from health facility records. Qualitative data on the 2 modalities were collected from key informants and community members from purposefully sampled communities using the 2 modalities. Communities appreciated the provision of vitamin A supplements to their under 5-year-old children. The small drop in coverage that occurred as a result of the change in modality can be attributed to normal changes that occur with any system change. Advantages of campaigns included greater ease of mobilization and better coverage of older children from more remote communities. Advantages of routine delivery included not omitting children who happened to miss the 1 day per round that supplementation occurred and not disrupting the availability of other health services for the 5 to 6 days each campaign requires. The cost of routine delivery is not easy to measure nor is the cost of disruption to normal services entailed by campaigns. Cost-effectiveness likely depends more on effectiveness than on cost. Overall, the routine approach can achieve good coverage and is sustainable in the long run, as long as the transition is well planned and implemented.

A Diaper Pad for Diaper-Based Urine Collection and Colorimetric Screening of Urinary Biomarkers.

PubMed

Karlsen, Haakon; Dong, Tao; Suo, Zhenhe

2018-05-01

The high prevalence of urinary tract infection in aging adults is a challenging aspect of geriatric care. Incontinence and cognitive/functional impairment make collection of urine samples difficult and often require either catheterization for sample collection, which is a risk factor for infections, or more lenient criteria for initiating antibiotic treatment. We report the development of a diaper inlay with absorbent materials, superabsorbent polymer-based valve and chemical reaction pads for rapid screening of urinary tract infection of incontinent diaper-wearing elderly receivers of home care services. The developed diaper inlay was capable of collecting, isolating, analyzing samples and retaining results > 8 h. The diaper inlay can therefore be compatible with the diaper changing routines of nurses in home care services, without requiring much time or effort. A nurse can insert a diaper inlay in a diaper and the results can be recorded during a later diaper change. Although the research focuses on tools for home care services, the nursing home sector has similar problems and may benefit from technological development for rapid screening to avoid unnecessary catheterization and overuse of antibiotics.

Fluorescein: a Photo-CIDNP Sensitizer Enabling Hyper-Sensitive NMR Data Collection in Liquids at Low Micromolar Concentration

PubMed Central

Okuno, Yusuke; Cavagnero, Silvia

2016-01-01

Photochemically induced dynamic nuclear polarization (photo-CIDNP) is a powerful approach for sensitivity enhancement in NMR spectroscopy. In liquids, inter-molecular photo-CIDNP depends on the transient bimolecular reaction between photoexcited dye and sample of interest. Hence the extent of polarization is sample-concentration dependent. This study introduces fluorescein (FL) as a photo-CIDNP dye whose performance is exquisitely tailored to data collection at extremely low sample concentrations. The photo-CIDNP resonance intensities of tryptophan in the presence of either FL or FMN (i.e., the routinely employed flavin mononucleotide photosensitizer) in the liquid state show that FL yields superior sensitivity and enables rapid data collection down to an unprecedented 1 micromolar concentration. This result was achieved on a conventional spectrometer operating at 14.1 Tesla, and equipped with a room-temperature probe (i.e., non-cryogenic). Kinetic simulations show that the excellent behavior of FL arises from its long excited-state triplet lifetime and superior photostability relative to conventional photo-CIDNP sensitizers. PMID:26744790

Investigation of a systematic offset in the measurement of organic carbon with a semicontinuous analyzer.

PubMed

Offenberg, John H; Lewandowski, Michael; Edney, Edward O; Kleindienst, Tadeusz E; Jaoui, Mohammed

2007-05-01

Organic carbon (OC) was measured semicontinuously in laboratory experiments of steady-state secondary organic aerosol formed by hydrocarbon + nitrogen oxide irradiations. Examination of the mass of carbon measured on the filter for various sample volumes reveals a systematic offset that is not observed when performing an instrumental blank. These findings suggest that simple subtraction of instrumental blanks determined as the standard analysis without sample collection (i.e., by cycling the pump and valves yet filtering zero liters of air followed by routine chemical analysis) from measured concentrations may be inadequate. This may be especially true for samples collected through the filtration of small air volumes wherein the influence of the systematic offset is greatest. All of the experiments show that filtering a larger volume of air minimizes the influence of contributions from the systematic offset. Application of these results to measurements of ambient concentrations of carbonaceous aerosol suggests a need for collection of sufficient carbon mass to minimize the relative influence of the offset signal.

Semen collection and ejaculate characteristics of the Leopard Tortoise (Stigmochelys pardalis)

PubMed Central

Mitchell, Mark A

2017-01-01

Abstract The preservation of spermatozoa is an important tool used in conservation programs to increase the genetic diversity of threatened and endangered species. Although routinely used to manage conservation programs for higher vertebrates, there have been limited attempts to establish reproductive assistance programs for tortoises. The purpose of this study was to develop a model for collecting and characterizing semen in Testudinidae. Semen was collected from 13/16 (81.2%, 95% CI: 62–100) adult male leopard tortoises (Stigmochelys pardalis) via electroejaculation under propofol anesthesia. Semen samples were collected most frequently after the second series of electrostimulations (6/13, 46.1%), with fewer animals producing semen after the first (5/13, 38.5%) or third (2/13, 15.4%) electrostimulations. The average volume of a semen sample in the tortoises was 0.26 ml (standard deviation: 0.16, minimum–maximum: 0.1–0.6), the average spermatozoal concentration was 101.62 × 106/ml, and the average motility at time of collection was 57.3%. A rapid decrease in motility was observed in refrigerated samples over 24 h resulting in a median motility of 0% at 24 h post-collection. The results of this study suggest that electroejaculation is a safe and efficient method for collecting semen from leopard tortoises. PMID:29230293

Long-Term Frozen Storage of Urine Samples: A Trouble to Get PCR Results in Schistosoma spp. DNA Detection?

PubMed Central

Fernández-Soto, Pedro; Velasco Tirado, Virginia; Carranza Rodríguez, Cristina; Pérez-Arellano, José Luis; Muro, Antonio

2013-01-01

Background Human schistosomiasis remains a serious worldwide public health problem. At present, a sensitive and specific assay for routine diagnosis of schistosome infection is not yet available. The potential for detecting schistosome-derived DNA by PCR-based methods in human clinical samples is currently being investigated as a diagnostic tool with potential application in routine schistosomiasis diagnosis. Collection of diagnostic samples such as stool or blood is usually difficult in some populations. However, urine is a biological sample that can be collected in a non-invasive method, easy to get from people of all ages and easy in management, but as a sample for PCR diagnosis is still not widely used. This could be due to the high variability in the reported efficiency of detection as a result of the high variation in urine samples’ storage or conditions for handling and DNA preservation and extraction methods. Methodology/Principal Findings We evaluate different commercial DNA extraction methods from a series of long-term frozen storage human urine samples from patients with parasitological confirmed schistosomiasis in order to assess the PCR effectiveness for Schistosoma spp. detection. Patientś urine samples were frozen for 18 months up to 7 years until use. Results were compared with those obtained in PCR assays using fresh healthy human urine artificially contaminated with Schistosoma mansoni DNA and urine samples from mice experimentally infected with S. mansoni cercariae stored frozen for at least 12 months before use. PCR results in fresh human artificial urine samples using different DNA based extraction methods were much more effective than those obtained when long-term frozen human urine samples were used as the source of DNA template. Conclusions/Significance Long-term frozen human urine samples are probably not a good source for DNA extraction for use as a template in PCR detection of Schistosoma spp., regardless of the DNA method of extraction used. PMID:23613907

A problem-solving routine for improving hospital operations.

PubMed

Ghosh, Manimay; Sobek Ii, Durward K

2015-01-01

The purpose of this paper is to examine empirically why a systematic problem-solving routine can play an important role in the process improvement efforts of hospitals. Data on 18 process improvement cases were collected through semi-structured interviews, reports and other documents, and artifacts associated with the cases. The data were analyzed using a grounded theory approach. Adherence to all the steps of the problem-solving routine correlated to greater degrees of improvement across the sample. Analysis resulted in two models. The first partially explains why hospital workers tended to enact short-term solutions when faced with process-related problems; and tended not seek longer-term solutions that prevent problems from recurring. The second model highlights a set of self-reinforcing behaviors that are more likely to address problem recurrence and result in sustained process improvement. The study was conducted in one hospital setting. Hospital managers can improve patient care and increase operational efficiency by adopting and diffusing problem-solving routines that embody three key characteristics. This paper offers new insights on why caregivers adopt short-term approaches to problem solving. Three characteristics of an effective problem-solving routine in a healthcare setting are proposed.

Variations in achievement of evidence-based, high-impact quality indicators in general practice: An observational study

PubMed Central

West, Robert; Rushforth, Bruno; Stokes, Tim; Glidewell, Liz; Carder, Paul; Faulkner, Simon; Foy, Robbie

2017-01-01

Background There are widely recognised variations in the delivery and outcomes of healthcare but an incomplete understanding of their causes. There is a growing interest in using routinely collected ‘big data’ in the evaluation of healthcare. We developed a set of evidence-based ‘high impact’ quality indicators (QIs) for primary care and examined variations in achievement of these indicators using routinely collected data in the United Kingdom (UK). Methods Cross-sectional analysis of routinely collected, electronic primary care data from a sample of general practices in West Yorkshire, UK (n = 89). The QIs covered aspects of care (including processes and intermediate clinical outcomes) in relation to diabetes, hypertension, atrial fibrillation, myocardial infarction, chronic kidney disease (CKD) and ‘risky’ prescribing combinations. Regression models explored the impact of practice and patient characteristics. Clustering within practice was accounted for by including a random intercept for practice. Results Median practice achievement of the QIs ranged from 43.2% (diabetes control) to 72.2% (blood pressure control in CKD). Considerable between-practice variation existed for all indicators: the difference between the highest and lowest performing practices was 26.3 percentage points for risky prescribing and 100 percentage points for anticoagulation in atrial fibrillation. Odds ratios associated with the random effects for practices emphasised this; there was a greater than ten-fold difference in the likelihood of achieving the hypertension indicator between the lowest and highest performing practices. Patient characteristics, in particular age, gender and comorbidity, were consistently but modestly associated with indicator achievement. Statistically significant practice characteristics were identified less frequently in adjusted models. Conclusions Despite various policy and improvement initiatives, there are enduring inappropriate variations in the delivery of evidence-based care. Much of this variation is not explained by routinely collected patient or practice variables, and is likely to be attributable to differences in clinical and organisational behaviour. PMID:28704407

Comparison of dementia recorded in routinely collected hospital admission data in England with dementia recorded in primary care.

PubMed

Brown, Anna; Kirichek, Oksana; Balkwill, Angela; Reeves, Gillian; Beral, Valerie; Sudlow, Cathie; Gallacher, John; Green, Jane

2016-01-01

Electronic linkage of UK cohorts to routinely collected National Health Service (NHS) records provides virtually complete follow-up for cause-specific hospital admissions and deaths. The reliability of dementia diagnoses recorded in NHS hospital data is not well documented. For a sample of Million Women Study participants in England we compared dementia recorded in routinely collected NHS hospital data (Hospital Episode Statistics: HES) with dementia recorded in two separate sources of primary care information: a primary care database [Clinical Practice Research Datalink (CPRD), n = 340] and a survey of study participants' General Practitioners (GPs, n = 244). Dementia recorded in HES fully agreed both with CPRD and with GP survey data for 85% of women; it did not agree for 1 and 4%, respectively. Agreement was uncertain for the remaining 14 and 11%, respectively; and among those classified as having uncertain agreement in CPRD, non-specific terms compatible with dementia, such as 'memory loss', were recorded in the CPRD database for 79% of the women. Agreement was significantly better (p < 0.05 for all comparisons) for women with HES diagnoses for Alzheimer's disease (95 and 94% agreement with any dementia for CPRD and GP survey, respectively) and for vascular dementia (88 and 88%, respectively) than for women with a record only of dementia not otherwise specified (70 and 72%, respectively). Dementia in the same woman was first mentioned an average 1.6 (SD 2.6) years earlier in primary care (CPRD) than in hospital (HES) data. Age-specific rates for dementia based on the hospital admission data were lower than the rates based on the primary care data, but were similar if the delay in recording in HES was taken into account. Dementia recorded in routinely collected NHS hospital admission data for women in England agrees well with primary care records of dementia assessed separately from two different sources, and is sufficiently reliable for epidemiological research.

Blood Substrate Collection and Handling Procedures under Pseudo-Field Conditions: Evaluation of Suitability for Inflammatory Biomarker Measurement.

PubMed

Sugden, Karen; Danese, Andrea; Shalev, Idan; Williams, Benjamin S; Caspi, Avshalom

2015-01-01

Routine incorporation of blood-based biomarker measurements in population studies has been hampered by challenges in obtaining samples suitable for biomarker assessment outside of laboratory settings. Here, we assessed the suitability of venous blood left unprocessed for 4, 24, or 48 hours post-collection at either room temperature or 4°C for quantification of two biomarkers, Interleukin-6 (IL-6) and C-reactive protein (CRP). Blood samples were collected in both K2EDTA tubes and a dedicated plasma-preservation tube, P100. Dried blood spot (DBS) samples from the same subjects were also collected in order to compare delayed-processing plasma performance against a popular alternative collection method. We found that K2EDTA mean plasma concentrations of both IL-6 and CRP were not significantly different from concentrations in plasma processed immediately; this was observed for tubes stored up to 48 hours pre-processing at either temperature. Concentrations of IL-6 measured in P100 tubes showed significant time-dependent increases when stored at room temperature; otherwise, levels of IL-6 and CRP were similar to those found in samples processed immediately. Levels of CRP in DBS were correlated with plasma CRP levels, even when pre-processed blood was stored for up to 48 hours. These data indicate that plasma is suitable for IL-6 and CRP estimation under data collection conditions that involve processing delays.

GROWTH AND DEVELOPMENT OF NEGRO INFANTS. IX, STUDIES ON WEIGHT, HEIGHT, PELVIC BREADTH, HEAD AND CHEST CIRCUMFERENCES DURING THE FIRST YEAR OF LIFE.

ERIC Educational Resources Information Center

SCOTT, ROLAND B.; AND OTHERS

THIS ARTICLE PRESENTS SIZE AND GROWTH VELOCITY DATA COLLECTED DURING A LONGITUDINAL STUDY OF 111 NORMAL, HEALTHY NEGRO INFANTS FROM LOWER-MIDDLE-CLASS FAMILIES. DATA WERE OBTAINED FROM BIRTH RECORDS AND MEASUREMENTS TAKEN DURING ROUTINE PHYSICAL EXAMINATIONS. WHEN THIS NEGRO SAMPLE WAS COMPARED WITH WHITE INFANTS IN SIMILAR STUDIES IT WAS FOUND…

Estimated Prevalence of Cryptococcus Antigenemia (CrAg) among HIV-Infected Adults with Advanced Immunosuppression in Namibia Justifies Routine Screening and Preemptive Treatment.

PubMed

Sawadogo, Souleymane; Makumbi, Boniface; Purfield, Anne; Ndjavera, Christophine; Mutandi, Gram; Maher, Andrew; Kaindjee-Tjituka, Francina; Kaplan, Jonathan E; Park, Benjamin J; Lowrance, David W

2016-01-01

Cryptococcal meningitis is common and associated with high mortality among HIV infected persons. The World Health Organization recommends that routine Cryptococcal antigen (CrAg) screening in ART-naïve adults with a CD4+ count <100 cells/μL followed by pre-emptive antifungal therapy for CrAg-positive patients be considered where CrAg prevalence is ≥3%. The prevalence of CrAg among HIV adults in Namibia is unknown. We estimated CrAg prevalence among HIV-infected adults receiving care in Namibia for the purpose of informing routine screening strategies. The study design was cross-sectional. De-identified plasma specimens collected for routine CD4+ testing from HIV-infected adults enrolled in HIV care at 181 public health facilities from November 2013 to January 2014 were identified at the national reference laboratory. Remnant plasma from specimens with CD4+ counts <200 cells/μL were sampled and tested for CrAg using the IMMY® Lateral Flow Assay. CrAg prevalence was estimated and assessed for associations with age, sex, and CD4+ count. A total of 825 specimens were tested for CrAg. The median (IQR) age of patients from whom specimens were collected was 38 (32-46) years, 45.9% were female and 62.9% of the specimens had CD4 <100 cells/μL. CrAg prevalence was 3.3% overall and 3.9% and 2.3% among samples with CD4+ counts of CD4+<100 cells/μL and 100-200 cells/μL, respectively. CrAg positivity was significantly higher among patients with CD4+ cells/μL < 50 (7.2%, P = 0.001) relative to those with CD4 cells/μL 50-200 (2.2%). This is the first study to estimate CrAg prevalence among HIV-infected patients in Namibia. CrAg prevalence of ≥3.0% among patients with CD4+<100 cells/μL justifies routine CrAg screening and preemptive treatment among HIV-infected in Namibia in line with WHO recommendations. Patients with CD4+<100 cells/μL have a significantly greater risk for CrAg positivity. Revised guidelines for ART in Namibia now recommend routine screening for CrAg.

Statistical analysis of environmental monitoring data: does a worst case time for monitoring clean rooms exist?

PubMed

Cundell, A M; Bean, R; Massimore, L; Maier, C

1998-01-01

To determine the relationship between the sampling time of the environmental monitoring, i.e., viable counts, in aseptic filling areas and the microbial count and frequency of alerts for air, surface and personnel microbial monitoring, statistical analyses were conducted on 1) the frequency of alerts versus the time of day for routine environmental sampling conducted in calendar year 1994, and 2) environmental monitoring data collected at 30-minute intervals during routine aseptic filling operations over two separate days in four different clean rooms with multiple shifts and equipment set-ups at a parenteral manufacturing facility. Statistical analyses showed, except for one floor location that had significantly higher number of counts but no alert or action level samplings in the first two hours of operation, there was no relationship between the number of counts and the time of sampling. Further studies over a 30-day period at the floor location showed no relationship between time of sampling and microbial counts. The conclusion reached in the study was that there is no worst case time for environmental monitoring at that facility and that sampling any time during the aseptic filling operation will give a satisfactory measure of the microbial cleanliness in the clean room during the set-up and aseptic filling operation.

Fully automatic characterization and data collection from crystals of biological macromolecules.

PubMed

Svensson, Olof; Malbet-Monaco, Stéphanie; Popov, Alexander; Nurizzo, Didier; Bowler, Matthew W

2015-08-01

Considerable effort is dedicated to evaluating macromolecular crystals at synchrotron sources, even for well established and robust systems. Much of this work is repetitive, and the time spent could be better invested in the interpretation of the results. In order to decrease the need for manual intervention in the most repetitive steps of structural biology projects, initial screening and data collection, a fully automatic system has been developed to mount, locate, centre to the optimal diffraction volume, characterize and, if possible, collect data from multiple cryocooled crystals. Using the capabilities of pixel-array detectors, the system is as fast as a human operator, taking an average of 6 min per sample depending on the sample size and the level of characterization required. Using a fast X-ray-based routine, samples are located and centred systematically at the position of highest diffraction signal and important parameters for sample characterization, such as flux, beam size and crystal volume, are automatically taken into account, ensuring the calculation of optimal data-collection strategies. The system is now in operation at the new ESRF beamline MASSIF-1 and has been used by both industrial and academic users for many different sample types, including crystals of less than 20 µm in the smallest dimension. To date, over 8000 samples have been evaluated on MASSIF-1 without any human intervention.

Image analysis library software development

NASA Technical Reports Server (NTRS)

Guseman, L. F., Jr.; Bryant, J.

1977-01-01

The Image Analysis Library consists of a collection of general purpose mathematical/statistical routines and special purpose data analysis/pattern recognition routines basic to the development of image analysis techniques for support of current and future Earth Resources Programs. Work was done to provide a collection of computer routines and associated documentation which form a part of the Image Analysis Library.

Computer Program For Linear Algebra

NASA Technical Reports Server (NTRS)

Krogh, F. T.; Hanson, R. J.

1987-01-01

Collection of routines provided for basic vector operations. Basic Linear Algebra Subprogram (BLAS) library is collection from FORTRAN-callable routines for employing standard techniques to perform basic operations of numerical linear algebra.

Impact of routine Bacillus thuringiensis israelensis (Bti) treatment on the availability of flying insects as prey for aerial feeding predators.

PubMed

Timmermann, Ute; Becker, Norbert

2017-12-01

Since 1980, mosquito breeding habitats in the Upper Rhine Valley were routinely treated with Bacillus thuringiensis var. israelensis (Bti). Bti is considered to significantly reduce the number of mosquitoes, and - especially when used in higher dosages - to be toxic to other Nematocera species, e.g. Chironomidae, which could be food sources for aerial feeding predators. To investigate direct and indirect effects of routine Bti treatment on food sources for aerial feeding predators, the availability of flying insects in treated and untreated areas was compared. A car trap was used for insect collection, which allowed their exact spatiotemporal assignment. The statistical analysis revealed that insect taxa abundance was influenced differently by the factors season, temperature and time of day. Nematocera (Diptera) were the most frequently collected insects in all areas. Chironomidae were the predominant aquatic Nematocera. The comparison of treated and untreated sites did not show significant differences that would indicate any direct or indirect effect of routine Bti treatment on the availability of flying insects. Additional to food availability, food selection must be considered when investigating food resources for aerial feeding predators. In this study, food selection of Delichon urbicum (House Martin) as an example was investigated with the help of neck ring samples. The preferred prey of the investigated D. urbicum colony consisted of diurnal insects with terrestrial larvae (Aphidina, Brachycera, Coleoptera). Chironomidae were consumed, but not preferred.

Spectral signature selection for mapping unvegetated soils

NASA Technical Reports Server (NTRS)

May, G. A.; Petersen, G. W.

1975-01-01

Airborne multispectral scanner data covering the wavelength interval from 0.40-2.60 microns were collected at an altitude of 1000 m above the terrain in southeastern Pennsylvania. Uniform training areas were selected within three sites from this flightline. Soil samples were collected from each site and a procedure developed to allow assignment of scan line and element number from the multispectral scanner data to each sampling location. These soil samples were analyzed on a spectrophotometer and laboratory spectral signatures were derived. After correcting for solar radiation and atmospheric attenuation, the laboratory signatures were compared to the spectral signatures derived from these same soils using multispectral scanner data. Both signatures were used in supervised and unsupervised classification routines. Computer-generated maps using the laboratory and multispectral scanner derived signatures resulted in maps that were similar to maps resulting from field surveys. Approximately 90% agreement was obtained between classification maps produced using multispectral scanner derived signatures and laboratory derived signatures.

The analysis of tire rubber traces collected after braking incidents using Pyrolysis-GasChromatography/Mass Spectrometry.

PubMed

Sarkissian, Garry

2007-09-01

Automobile tire marks can routinely be found at the scenes of crime, particularly hit-and-run accidents and are left on road surfaces because of sudden braking or the wheels spinning. The tire marks are left due to the friction between the tire rubber and the solid road surface, and do not always demonstrate the tire tread pattern. However, the tire mark will contain traces of the tire. In this study, Pyrolysis Gas Chromatography/Mass Spectrometry was used to analyze 12 tires from different manufacturer's and their traces collected after braking incidents. Tire marks were left on a conglomerate road surface with sudden braking. The samples were pyrolysed without removal of contaminant in a micro-furnace type pyrolyser. Quantitative and qualitative analysis were performed on all the samples. All 12 samples were distinguished from each other. Each of the tire traces were identified as coming from there original source.

Recent (2008-10) concentrations and isotopic compositions of nitrate and concentrations of wastewater compounds in the Barton Springs zone, south-central Texas, and their potential relation to urban development in the contributing zone

USGS Publications Warehouse

Mahler, Barbara J.; Musgrove, MaryLynn; Herrington, Chris; Sample, Thomas L.

2011-01-01

During 2008–10, the U.S. Geological Survey, in cooperation with the City of Austin, the City of Dripping Springs, the Barton Springs/Edwards Aquifer Conservation District, the Lower Colorado River Authority, Hays County, and Travis County, collected and analyzed water samples from five streams (Barton, Williamson, Slaughter, Bear, and Onion Creeks), two groundwater wells (Marbridge well [YD–58–50–704] and Buda well [LR–58–58–403]), and the main orifice of Barton Springs in Austin, Texas, with the objective of characterizing concentrations and isotopic compositions of nitrate and concentrations of wastewater compounds in the Barton Springs zone. The Barton Springs zone is in south-central Texas, an area undergoing rapid growth in population and in land area affected by development, with associated increases in wastewater generation. Over a period of 17 months, during which the hydrologic conditions transitioned from dry to wet, samples were collected routinely from the streams, wells, and spring and, in response to storms, from the streams and spring; some or all samples were analyzed for nitrate, nitrogen and oxygen isotopes of nitrate, and waste­water compounds. The median nitrate concentrations in routine samples from all sites were higher in samples collected during the wet period than in samples collected during the dry period, with the greatest difference for stream samples (0.05 milligram per liter during the dry period to 0.96 milligram per liter for the wet period). Nitrate concentrations in recent (2008–10) samples were elevated relative to concentrations in historical (1990–2008) samples from streams and from Barton Springs under medium- and high-flow conditions. Recent nitrate concentrations were higher than historical concentrations at the Marbridge well but the reverse was true at the Buda well. The elevated concentrations likely are related to the cessation of dry conditions coupled with increased nitrogen loading in the contributing watersheds. An isotopic composition of nitrate (delta nitrogen–15) greater than 8 per mil in many of the samples indicated there was a contribution of nitrate with a biogenic (human and or animal waste, or both) origin. Wastewater compounds measured in routine samples were detected infrequently (3 percent of cases), and concentrations were very low (less than the method reporting level in most cases). There was no correlation between nitrate concentrations and the frequency of detection of wastewater compounds, indicating that wastewater compounds might be undergoing removal during such processes as infiltration through soil. Three potential sources of biogenic nitrate to the contributing zone were considered: septic systems, land application of treated wastewater, and domesticated dogs and cats. During 2001–10, the estimated densities of septic systems and domesticated dogs and cats (number per acre) increased in the watersheds of all five creeks, and the rate of land application of treated wastewater (gallons per day per acre) increased in the watersheds of Barton, Bear, and Onion Creeks. Considering the timing and location of the increases in the three sources, septic systems were considered a likely source of increased nitrate to Bear Creek; land application of treated wastewater a likely source to Barton, Bear, and Onion Creeks; and domestic dogs and cats a potential source principally to Williamson Creek. The results of this investigation indicate that baseline water quality, in terms of nitrate, has shifted upward between 2001 and 2010, even without any direct discharges of treated wastewater to the creeks.

Chemical and radiochemical constituents in water from wells in the vicinity of the naval reactors facility, Idaho National Engineering and Environmental Laboratory, Idaho, 1997-98

USGS Publications Warehouse

Bartholomay, Roy C.; Knobel, LeRoy L.; Tucker, Betty J.; Twining, Brian V.

2000-01-01

The U.S. Geological Survey, in response to a request from the U.S. Department of Energy?s Phtsburgh Naval Reactors Ofilce, Idaho Branch Office, sampled water from 13 wells during 1997?98 as part of a long-term project to monitor water quality of the Snake River Plain aquifer in the vicinity of the Naval Reactors Facility, Idaho National Engineering and Environmental Laboratory, Idaho. Water samples were analyzed for naturally occurring constituents and man-made contaminants. A totalof91 samples were collected from the 13 monitoring wells. The routine samples contained detectable concentrations of total cations and dissolved anions, and nitrite plus nitrate as nitrogen. Most of the samples also had detectable concentrations of gross alpha- and gross beta-particle radioactivity and tritium. Fourteen qualityassurance samples also were collected and analyze~ seven were field-blank samples, and seven were replicate samples. Most of the field blank samples contained less than detectable concentrations of target constituents; however, some blank samples did contain detectable concentrations of calcium, magnesium, barium, copper, manganese, nickel, zinc, nitrite plus nitrate, total organic halogens, tritium, and selected volatile organic compounds.

Evaluation of field sampling and preservation methods for strontium-90 in ground water at the Idaho National Engineering Laboratory, Idaho

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

Cecil, L.D.; Knobel, L.L.; Wegner, S.J.

1989-09-01

From 1952 to 1988, about 140 curies of strontium-90 have been discharged in liquid waste to disposal ponds and wells at the INEL (Idaho National Engineering Laboratory). The US Geological Survey routinely samples ground water from the Snake River Plain aquifer and from discontinuous perched-water zones for selected radionuclides, major and minor ions, and chemical and physical characteristics. Water samples for strontium-90 analyses collected in the field are unfiltered and preserved to an approximate 2-percent solution with reagent-grade hydrochloric acid. Water from four wells completed in the Snake River Plain aquifer was sampled as part of the US Geological Survey'smore » quality-assurance program to evaluate the effect of filtration and preservation methods on strontium-90 concentrations in ground water at the INEL. The wells were selected for sampling on the basis of historical concentrations of strontium-90 in ground water. Water from each well was filtered through either a 0.45- or a 0.1-micrometer membrane filter; unfiltered samples also were collected. Two sets of filtered and two sets of unfiltered water samples were collected at each well. One set of water samples was preserved in the field to an approximate 2-percent solution with reagent-grade hydrochloric acid and the other set of samples was not acidified. 13 refs., 2 figs., 6 tabs.« less

Influence of centrifugation conditions on the results of 77 routine clinical chemistry analytes using standard vacuum blood collection tubes and the new BD-Barricor tubes

PubMed Central

Cadamuro, Janne; Mrazek, Cornelia; Leichtle, Alexander B.; Kipman, Ulrike; Felder, Thomas K.; Wiedemann, Helmut; Oberkofler, Hannes; Fiedler, Georg M.; Haschke-Becher, Elisabeth

2017-01-01

Introduction Although centrifugation is performed in almost every blood sample, recommendations on duration and g-force are heterogeneous and mostly based on expert opinions. In order to unify this step in a fully automated laboratory, we aimed to evaluate different centrifugation settings and their influence on the results of routine clinical chemistry analytes. Materials and methods We collected blood from 41 healthy volunteers into BD Vacutainer PST II-heparin-gel- (LiHepGel), BD Vacutainer SST II-serum-, and BD Vacutainer Barricor heparin-tubes with a mechanical separator (LiHepBar). Tubes were centrifuged at 2000xg for 10 minutes and 3000xg for 7 and 5 minutes, respectively. Subsequently 60 and 21 clinical chemistry analytes were measured in plasma and serum samples, respectively, using a Roche COBAS instrument. Results High sensitive Troponin T, pregnancy-associated plasma protein A, ß human chorionic gonadotropin and rheumatoid factor had to be excluded from statistical evaluation as many of the respective results were below the measuring range. Except of free haemoglobin (fHb) measurements, no analyte result was altered by the use of shorter centrifugation times at higher g-forces. Comparing LiHepBar to LiHepGel tubes at different centrifugation setting, we found higher lactate-dehydrogenase (LD) (P = 0.003 to < 0.001) and lower bicarbonate values (P = 0.049 to 0.008) in the latter. Conclusions Serum and heparin samples may be centrifuged at higher speed (3000xg) for a shorter amount of time (5 minutes) without alteration of the analytes tested in this study. When using LiHepBar tubes for blood collection, a separate LD reference value might be needed. PMID:29187797

Influence of centrifugation conditions on the results of 77 routine clinical chemistry analytes using standard vacuum blood collection tubes and the new BD-Barricor tubes.

PubMed

Cadamuro, Janne; Mrazek, Cornelia; Leichtle, Alexander B; Kipman, Ulrike; Felder, Thomas K; Wiedemann, Helmut; Oberkofler, Hannes; Fiedler, Georg M; Haschke-Becher, Elisabeth

2018-02-15

Although centrifugation is performed in almost every blood sample, recommendations on duration and g-force are heterogeneous and mostly based on expert opinions. In order to unify this step in a fully automated laboratory, we aimed to evaluate different centrifugation settings and their influence on the results of routine clinical chemistry analytes. We collected blood from 41 healthy volunteers into BD Vacutainer PST II-heparin-gel- (LiHepGel), BD Vacutainer SST II-serum-, and BD Vacutainer Barricor heparin-tubes with a mechanical separator (LiHepBar). Tubes were centrifuged at 2000xg for 10 minutes and 3000xg for 7 and 5 minutes, respectively. Subsequently 60 and 21 clinical chemistry analytes were measured in plasma and serum samples, respectively, using a Roche COBAS instrument. High sensitive Troponin T, pregnancy-associated plasma protein A, ß human chorionic gonadotropin and rheumatoid factor had to be excluded from statistical evaluation as many of the respective results were below the measuring range. Except of free haemoglobin (fHb) measurements, no analyte result was altered by the use of shorter centrifugation times at higher g-forces. Comparing LiHepBar to LiHepGel tubes at different centrifugation setting, we found higher lactate-dehydrogenase (LD) (P = 0.003 to < 0.001) and lower bicarbonate values (P = 0.049 to 0.008) in the latter. Serum and heparin samples may be centrifuged at higher speed (3000xg) for a shorter amount of time (5 minutes) without alteration of the analytes tested in this study. When using LiHepBar tubes for blood collection, a separate LD reference value might be needed.

Better research reporting to improve the utility of routine data for making better treatment decisions.

PubMed

Hemkens, Lars G; Langan, Sinéad M; Benchimol, Eric I

2016-03-01

The availability of routinely collected health data, such as health administrative data, electronic health records, prescription records and disease registries, has increased in the information age. This has led to an explosion of reports of comparativeness effectiveness research using such data. Guidelines for the REporting of studies Conducted using Observational Routinely-collected Data (RECORD) will improve the completeness and transparency of reporting of research using routinely collected health data. The Journal of Comparative Effectiveness Research has endorsed these guidelines. In this commentary, the RECORD checklist is reprinted and members of the RECORD working committee reflect on the importance of these reporting guidelines for the field of comparative effectiveness research.

Attentional switching forms a genetic link between attention problems and autistic traits in adults.

PubMed

Polderman, T J C; Hoekstra, R A; Vinkhuyzen, A A E; Sullivan, P F; van der Sluis, S; Posthuma, D

2013-09-01

Attention deficit hyperactivity disorder (ADHD) symptoms and autistic traits often occur together. The pattern and etiology of co-occurrence are largely unknown, particularly in adults. This study investigated the co-occurrence between both traits in detail, and subsequently examined the etiology of the co-occurrence, using two independent adult population samples. Method Data on ADHD traits (Inattention and Hyperactivity/Impulsivity) were collected in a population sample (S1, n = 559) of unrelated individuals. Data on Attention Problems (AP) were collected in a population-based family sample of twins and siblings (S2, n = 560). In both samples five dimensions of autistic traits were assessed (social skills, routine, attentional switching, imagination, patterns). Hyperactive traits (S1) did not correlate substantially with the autistic trait dimensions. For Inattention (S1) and AP (S2), the correlations with the autistic trait dimensions were low, apart from a prominent correlation with the attentional switching scale (0.47 and 0.32 respectively). Analyses in the genetically informative S2 revealed that this association could be explained by a shared genetic factor. Our findings suggest that the co-occurrence of ADHD traits and autistic traits in adults is not determined by problems with hyperactivity, social skills, imagination or routine preferences. Instead, the association between those traits is due primarily to shared attention-related problems (inattention and attentional switching capacity). As the etiology of this association is purely genetic, biological pathways involving attentional control could be a promising focus of future studies aimed at unraveling the genetic causes of these disorders.

Murine norovirus detection in the exhaust air of IVCs is more sensitive than serological analysis of soiled bedding sentinels.

PubMed

Zorn, Julia; Ritter, Bärbel; Miller, Manuel; Kraus, Monika; Northrup, Emily; Brielmeier, Markus

2017-06-01

One limitation to housing rodents in individually ventilated cages (IVCs) is the ineffectiveness of traditional health monitoring programs that test soiled bedding sentinels every quarter. Aerogen transmission does not occur with this method. Moreover, the transmission of numerous pathogens in bedding is uncertain, and sentinel susceptibility to various pathogens varies. A novel method using particle collection from samples of exhaust air was developed in this study which was also systematically compared with routine health monitoring using soiled bedding sentinels. We used our method to screen these samples for the presence of murine norovirus (MNV), a mouse pathogen highly prevalent in laboratory animal facilities. Exhaust air particles from prefilters of IVC racks with known MNV prevalence were tested by quantitative reverse transcription polymerase chain reaction (RT-qPCR). MNV was detected in exhaust air as early as one week with one MNV-positive cage per rack, while sentinels discharged MNV RNA without seroconverting. MNV was reliably and repeatedly detected in particles collected from samples of exhaust air in all seven of the three-month sampling rounds, with increasing MNV prevalence, while sentinels only seroconverted in one round. Under field conditions, routine soiled bedding sentinel health monitoring in our animal facility failed to identify 67% ( n = 85) of positive samples by RT-qPCR of exhaust air particles. Thus, this method proved to be highly sensitive and superior to soiled bedding sentinels in the reliable detection of MNV. These results represent a major breakthrough in hygiene monitoring of rodent IVC systems and contribute to the 3R principles by reducing the number of animals used and by improving experimental conditions.

Exhaled breath condensate methods adapted from human studies using longitudinal metabolomics for predicting early health alterations in dolphins.

PubMed

Borras, Eva; Aksenov, Alexander A; Baird, Mark; Novick, Brittany; Schivo, Michael; Zamuruyev, Konstantin O; Pasamontes, Alberto; Parry, Celeste; Foutouhi, Soraya; Venn-Watson, Stephanie; Weimer, Bart C; Davis, Cristina E

2017-11-01

Monitoring health conditions is essential to detect early asymptomatic stages of a disease. To achieve this, blood, urine and breath samples are commonly used as a routine clinical diagnostic. These samples offer the opportunity to detect specific metabolites related to diseases and provide a better understanding of their development. Although blood samples are commonly used routinely to monitor health, the implementation of a relatively noninvasive technique, such as exhaled breath condensate (EBC) analysis, may further benefit the well-being of both humans and other animals. EBC analysis can be used to track possible physical or biochemical alterations caused by common diseases of the bottlenose dolphin (Tursiops truncatus), such as infections or inflammatory-mediated processes. We have used an untargeted metabolomic method with liquid chromatography-mass spectrometry analysis of EBC samples to determine biomarkers related to disease development. In this study, five dolphins under human care were followed up for 1 year. We collected paired blood, physical examination information, and EBC samples. We then statistically correlated this information to predict specific health alterations. Three dolphins provided promising case study information about biomarkers related to cutaneous infections, respiratory infections, dental disease, or hormonal changes (pregnancy). The use of complementary liquid chromatography platforms, with hydrophilic interaction chromatography and reverse-phased columns, allowed us to detect a wide spectrum of EBC biomarker compounds that could be related to these health alterations. Moreover, these two analytical techniques not only provided complementary metabolite information but in both cases they also provided promising diagnostic information for these health conditions. Graphical abstract Collection of the exhaled condensed breath from a bottlenose dolphin from U.S. Navy Marine Mammal Program (MMP).

Insights into PM10 sources in Houston, Texas: Role of petroleum refineries in enriching lanthanoid metals during episodic emission events

NASA Astrophysics Data System (ADS)

Bozlaker, Ayşe; Buzcu-Güven, Birnur; Fraser, Matthew P.; Chellam, Shankararaman

2013-04-01

Petroleum refineries may emit large quantities of pollutants during non-routine operations that include start-ups and shutdowns, planned maintenance, and unplanned equipment failures. The Texas Commission on Environmental Quality (TCEQ) tracks such events by requiring industries to self-report estimates of these emissions because they often have a detrimental impact on local air quality and potentially, public health. An inventory of non-routine episodic emission events is available via TCEQ's website. However, there is on-going concern that such episodic emissions are sometimes under-reported or even not cataloged. Herein, we present concentrations of 42 main group, transition, and lanthanoid elements in 114 time-resolved (3 or 6 h) samples collected over a 1-month period. We also develop strategies to identify aerosol sources using elemental tracers and compare source apportionment (performed by positive matrix factorization) based on ambient measurements to inventoried non-routine emission events. Through interpretation of key marker elements, five sources impacting concentrations of metals in PM10 were identified and calculated to contribute 73% of the measured PM10 mass. On average, primary emissions from fluidized-bed catalytic cracking (FCC) units negligibly contributed to apportioned PM10 mass. However, 35 samples were identified as impacted by transient PM10 emissions from FCC units because of elevated levels of lanthanoid metals and their ratios. Only 31 of these 35 samples coincided with self-reported non-routine emission events. Further, roughly half of the emission event self-reports detailed only emissions of gaseous pollutants. Based on this, we posit that not all PM10 emission events are reported and even self-reported emission events are incomplete - those that only catalog gaseous pollutants may also include unreported PM emissions.

The influence of contrast media on kidney function in patients with stable coronary artery disease.

PubMed

Reuter, Simon Bertram; Harutyunyan, Marina; Mygind, Naja Dam; Jørgensen, Erik; Kastrup, Jens

2014-08-01

To investigate the incidence of contrast media-induced nephropathy (CIN) in patients with stable coronary artery disease (CAD) referred for elective coronary intervention following hydration routines. The reversibility of CIN was followed in a 6 month-period. A total of 447 patients referred for elective coronary intervention due to suspected CAD were included. Blood samples were collected before and 24 h after intervention and medical records were obtained. Patients had no drinking fluid restrictions and were routinely treated with a 1000 ml saline infusion. All patients were invited to a 6-month examination and collection of blood samples. A total of 19 patients (4.3%) developed CIN. CIN patients had a pre-investigation higher estimated glomerular filtration rate (eGRF), lower level of kidney failure and lower creatinine level than non-CIN patients. Kidney function was not normalized in CIN patients 6 months after the intervention. Two patients still met the definition of CIN. With no restriction in fluid intake and supplementary infusion of saline, only a few patients with stable CAD developed early indications of CIN during elective coronary interventions. Kidney function and the amount of contrast media used was not a predictor of CIN development. The induced CIN was not completely normalized in a 6-month follow-up period.

Prevalent emm types and superantigen gene patterns of group A Streptococcus in Thailand.

PubMed

Paveenkittiporn, W; Nozawa, T; Dejsirilert, S; Nakagawa, I; Hamada, S

2016-03-01

Group A Streptococcus (GAS) are globally distributed bacterial pathogens. We examined the emm genotypes, which are important indicators of virulence, of 349 clinical GAS isolates collected using two surveillance systems, i.e. Invasive Bacterial Infection Surveillance (IBIS) from 2010 to 2011 (234 isolates) and routine surveillance of clinically isolated bacteria from various hospitals during 1996-2011 (115 isolates) in Thailand. The major emm genotypes in IBIS samples were emm44 (12·0%), emm104 (6·8%), emm22 (5·6%), and emm81 (5·6%), whereas only one isolate (0·4%) had the emm1 genotype, which is significantly more common in invasive cases in the Western world. In samples collected during routine surveillance, emm238 (10·4%), emm44 (8·7%), and emm165 (7·0%) were dominant. The major superantigen gene profiles were similar between the groups, and 30·1% of isolates did not possess the phage-encoded superantigens (speA, speC, speH, speI, speK, speL, speM, ssa). Although most isolates exhibited limited gene profiles, emm44 isolates had highly variable gene profiles (15 patterns). We conclude that emm44 is the predominant GAS genotype in Thailand, and isolates varied in superantigen gene profiles.

Ground-Based Aerosol Measurements | Science Inventory ...

EPA Pesticide Factsheets

Atmospheric particulate matter (PM) is a complex chemical mixture of liquid and solid particles suspended in air (Seinfeld and Pandis 2016). Measurements of this complex mixture form the basis of our knowledge regarding particle formation, source-receptor relationships, data to test and verify complex air quality models, and how PM impacts human health, visibility, global warming, and ecological systems (EPA 2009). Historically, PM samples have been collected on filters or other substrates with subsequent chemical analysis in the laboratory and this is still the major approach for routine networks (Chow 2005; Solomon et al. 2014) as well as in research studies. In this approach, air, at a specified flow rate and time period, is typically drawn through an inlet, usually a size selective inlet, and then drawn through filters, 1 INTRODUCTION Atmospheric particulate matter (PM) is a complex chemical mixture of liquid and solid particles suspended in air (Seinfeld and Pandis 2016). Measurements of this complex mixture form the basis of our knowledge regarding particle formation, source-receptor relationships, data to test and verify complex air quality models, and how PM impacts human health, visibility, global warming, and ecological systems (EPA 2009). Historically, PM samples have been collected on filters or other substrates with subsequent chemical analysis in the laboratory and this is still the major approach for routine networks (Chow 2005; Solomo

Evaluation of FTA cards as a laboratory and field sampling device for the detection of foot-and-mouth disease virus and serotyping by RT-PCR and real-time RT-PCR.

PubMed

Muthukrishnan, Madhanmohan; Singanallur, Nagendrakumar B; Ralla, Kumar; Villuppanoor, Srinivasan A

2008-08-01

Foot-and-mouth disease virus (FMDV) samples transported to the laboratory from far and inaccessible areas for serodiagnosis pose a major problem in a tropical country like India, where there is maximum temperature fluctuation. Inadequate storage methods lead to spoilage of FMDV samples collected from clinically positive animals in the field. Such samples are declared as non-typeable by the typing laboratories with the consequent loss of valuable epidemiological data. The present study evaluated the usefulness of FTA Classic Cards for the collection, shipment, storage and identification of the FMDV genome by RT-PCR and real-time RT-PCR. The stability of the viral RNA, the absence of infectivity and ease of processing the sample for molecular methods make the FTA cards a useful option for transport of FMDV genome for identification and serotyping. The method can be used routinely for FMDV research as it is economical and the cards can be transported easily in envelopes by regular document transport methods. Live virus cannot be isolated from samples collected in FTA cards, which is a limitation. This property can be viewed as an advantage as it limits the risk of transmission of live virus.

Family History Collection Practices: National Survey of Pediatric Primary Care Providers.

PubMed

Tarini, Beth A; Gornick, Michele C; Zikmund-Fisher, Brian J; Saal, Howard M; Edmondson, Laurie; Uhlmann, Wendy R

2018-05-01

While family history (FH) collection is a core responsibility of pediatric primary care providers (PCPs), few details about this practice are known. We surveyed a random national sample of 1200 pediatricians and family medicine physicians about FH collection practices. A total of 86% of respondents (n = 289 pediatricians; n = 152 family medicine physicians) indicated that they collect a FH "always" or "most of the time" with 77% reporting collection at the first visit, regardless of whether it is a health maintenance or problem-focused visit. Less than half ask about relatives other than parents, siblings, or grandparents (36.3%). Among respondents, 42% routinely update the FH at every health maintenance visit while 6% updated FH at every visit. Pediatric PCPs use a variety of methods to collect a FH that is limited in scope and variably updated. Our results suggest that interventions are needed to help pediatric PCPs collect a systematic, efficient, and updated FH.

Establishing an EGFR mutation screening service for non-small cell lung cancer - sample quality criteria and candidate histological predictors.

PubMed

Leary, Alexandra F; Castro, David Gonzalez de; Nicholson, Andrew G; Ashley, Sue; Wotherspoon, Andrew; O'Brien, Mary E R; Popat, Sanjay

2012-01-01

EGFR screening requires good quality tissue, sensitivity and turn-around time (TAT). We report our experience of routine screening, describing sample type, TAT, specimen quality (cellularity and DNA yield), histopathological description, mutation result and clinical outcome. Non-small cell lung cancer (NSCLC) sections were screened for EGFR mutations (M+) in exons 18-21. Clinical, pathological and screening outcome data were collected for year 1 of testing. Screening outcome alone was collected for year 2. In year 1, 152 samples were tested, most (72%) were diagnostic. TAT was 4.9 days (95%confidence interval (CI)=4.5-5.5). EGFR-M+ prevalence was 11% and higher (20%) among never-smoking women with adenocarcinomas (ADCs), but 30% of mutations occurred in current/ex-smoking men. EGFR-M+ tumours were non-mucinous ADCs and 100% thyroid transcription factor (TTF1+). No mutations were detected in poorly differentiated NSCLC-not otherwise specified (NOS). There was a trend for improved overall survival (OS) among EGFR-M+ versus EGFR-M- patients (median OS=78 versus 17 months). In year 1, test failure rate was 19%, and associated with scant cellularity and low DNA concentrations. However 75% of samples with poor cellularity but representative of tumour were informative and mutation prevalence was 9%. In year 2, 755 samples were tested; mutation prevalence was 13% and test failure only 5.4%. Although samples with low DNA concentration (<2 ng/μL) had more test failures (30% versus 3.9% for [DNA]>2.2 ng/μL), the mutation rate was 9.2%. Routine epidermal growth factor receptor (EGFR) screening using diagnostic samples is fast and feasible even on samples with poor cellularity and DNA content. Mutations tend to occur in better-differentiated non-mucinous TTF1+ ADCs. Whether these histological criteria may be useful to select patients for EGFR testing merits further investigation. Copyright © 2011 Elsevier Ltd. All rights reserved.

Soils element activities for the period October 1973--September 1974

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

Fowler, E.B.; Essington, E.H.; White, M.G.

Soils Element activities were conducted on behalf of the U. S. Atomic Energy Commission's Nevada Applied Ecology Group (NAEG) program to provide source term information for the other program elements and maintain continuous cognizance of program requirements for sampling, sample preparation, and analysis. Activities included presentation of papers; participation in workshops; analysis of soil, vegetation, and animal tissue samples for $sup 238$Pu, $sup 239-240$Pu, $sup 241$Am, $sup 137$Cs, $sup 60$Co, and gamma scan for routine and laboratory quality control purposes; preparation and analysis of animal tissue samples for NAEG laboratory certification; studies on a number of analytical, sample preparation, andmore » sample collection procedures; and contributions to the evaluation of procedures for calculation of specialized counting statistics. (auth)« less

[Comparison of the determination of cyclosporin-A in blood samples collected on filter paper and by the ordinary technique].

PubMed

Azevedo, L S; Manrique, R; Sabbaga, E

1995-01-01

Monitoring cyclosporin-A (CsA) blood levels is of utmost importance for the rational use of this drug. Although many centers perform transplants, in Brazil there are few laboratories able to measure CsA blood levels. Therefore making blood samples reach the laboratory emerged as a problem. Collection of blood on filter paper has been a technique used for a long time in special cases. PURPOSE--To confirm the usefulness of measuring CsA blood levels in blood samples collected on filter paper and in the usual way. METHOD--We studied twenty renal cadaver kidney recipients who were receiving CsA, azathioprine and prednisone. Ninety five blood samples were collected and divided into two aliquots. One of them was sent routinely to one laboratory to perform whole blood CsA measurements. From the other aliquot, 20 microliters were pipetted on filter paper. When dried they were mailed to the other laboratory, where, after elution, CsA was measured. In both cases radioimmunoassay with polyclonal antibody was used. RESULTS--Linear correlation between both measurements revealed r = 0.81 with no statistical difference. CONCLUSION--The technique showed to be useful in clinical practice. In countries with continental size, as Brazil, it may be very helpful.

Making sense of the shadows: priorities for creating a learning healthcare system based on routinely collected data

PubMed Central

Deeny, Sarah R; Steventon, Adam

2015-01-01

Socrates described a group of people chained up inside a cave, who mistook shadows of objects on a wall for reality. This allegory comes to mind when considering ‘routinely collected data’—the massive data sets, generated as part of the routine operation of the modern healthcare service. There is keen interest in routine data and the seemingly comprehensive view of healthcare they offer, and we outline a number of examples in which they were used successfully, including the Birmingham OwnHealth study, in which routine data were used with matched control groups to assess the effect of telephone health coaching on hospital utilisation. Routine data differ from data collected primarily for the purposes of research, and this means that analysts cannot assume that they provide the full or accurate clinical picture, let alone a full description of the health of the population. We show that major methodological challenges in using routine data arise from the difficulty of understanding the gap between patient and their ‘data shadow’. Strategies to overcome this challenge include more extensive data linkage, developing analytical methods and collecting more data on a routine basis, including from the patient while away from the clinic. In addition, creating a learning health system will require greater alignment between the analysis and the decisions that will be taken; between analysts and people interested in quality improvement; and between the analysis undertaken and public attitudes regarding appropriate use of data. PMID:26065466

Epidemiology of hepatitis E virus infection during pregnancy in Benin.

PubMed

De Paschale, Massimo; Ceriani, Cristina; Romanò, Luisa; Cerulli, Teresa; Cagnin, Debora; Cavallari, Serena; Ndayake, Joseph; Zaongo, Dieudonné; Diombo, Kouma; Priuli, Gianbattista; Viganò, Paolo; Clerici, Pierangelo

2016-01-01

Hepatitis E virus (HEV) is the cause of enterically transmitted non-A, non-C hepatitis (an infection that is particularly severe during pregnancy) in tropical and subtropical countries. As there are no published data concerning the prevalence of HEV antibodies in Benin, their presence was investigated in pregnant women undergoing routine HIV screening in a rural area in northern Benin and in pregnant women with acute non-A, non-C hepatitis. A total of 278 serum samples were collected from asymptomatic pregnant women in 2011 were tested for HEV and hepatitis A virus (HAV) antibodies, and the HEV IgM-positive samples were further tested for HEV-RNA. A further seven samples of pregnant women with acute non-A, non-C hepatitis collected during episodes of acute hepatitis in 2005 were also analysed. Of the 278 samples collected in 2011, 16.19% were positive for HEV IgG and 1.44% for HEV IgM (none positive for HEV-RNA), and 99.64% were positive for total HAV antibodies (none positive for HAV IgM). Six of the seven samples collected in 2005 were positive for HEV IgG and IgM, and two were also positive for HEV-RNA. The circulation of HEV infection is significant among pregnant women in Benin, in whom the consequences may be fatal. © 2015 John Wiley & Sons Ltd.

Stability of 35 biochemical and immunological routine tests after 10 hours storage and transport of human whole blood at 21°C.

PubMed

Henriksen, Linda O; Faber, Nina R; Moller, Mette F; Nexo, Ebba; Hansen, Annebirthe B

2014-10-01

Suitable procedures for transport of blood samples from general practitioners to hospital laboratories are requested. Here we explore routine testing on samples stored and transported as whole blood in lithium-heparin or serum tubes. Blood samples were collected from 106 hospitalized patients, and analyzed on Architect c8000 or Advia Centaur XP for 35 analytes at base line, and after storage and transport of whole blood in lithium-heparin or serum tubes at 21 ± 1°C for 10 h. Bias and imprecision (representing variation from analysis and storage) were calculated from values at baseline and after storage, and differences tested by paired t-tests. Results were compared to goals set by the laboratory. We observed no statistically significant bias and results within the goal for imprecision between baseline samples and 10-h samples for albumin, alkaline phosphatase, antitrypsin, bilirubin, creatinine, free triiodothyronine, γ-glutamyl transferase, haptoglobin, immunoglobulin G, lactate dehydrogenase, prostate specific antigen, total carbon dioxide, and urea. Alanine aminotransferase, amylase, C-reactive protein, calcium, cholesterol, creatine kinase, ferritin, free thyroxine, immunoglobulin A, immunoglobulin M, orosomucoid, sodium, transferrin, and triglycerides met goals for imprecision, though they showed a minor, but statistically significant bias in results after storage. Cobalamin, folate, HDL-cholesterol, iron, phosphate, potassium, thyroid stimulating hormone and urate warranted concern, but only folate and phosphate showed deviations of clinical importance. We conclude that whole blood in lithium-heparin or serum tubes stored for 10 h at 21 ± 1°C, may be used for routine analysis without restrictions for all investigated analytes but folate and phosphate.

Results of calendar year 1994 monitor well inspection and maintenance program, Y-12 Plant, Oak Ridge, Tennessee

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

McMaster, B.W.; Jones, S.B.; Sitzler, J.L.

1995-06-01

This document is a compendium of results of the calendar year 1994 Monitor Well Inspection and Maintenance Program at the Department of Energy Y-12 Plant in Oak Ridge, Tennessee. This report documents the work relating to well inspections and maintenance requests. Inspections are implemented in order to better assess the condition and maintenance needs of wells that are actively being monitored. Currently this approach calls for inspecting all wells on a routine (annual or triennial) basis which are: (1) in an active sampling program; (2) included in a hydrologic study; or (3) not in service, but not scheduled for pluggingmore » and abandonment. Routine inspections help to ensure that representative groundwater samples and hydrologic data are being collected, and contribute to the life expectancy of each well. This report formally presents well inspection and maintenance activities that were conducted at the Y-12 Plant during 1994. All inspections were conducted between April and December.« less

Signal Peptide and Denaturing Temperature are Critical Factors for Efficient Mammalian Expression and Immunoblotting of Cannabinoid Receptors*

PubMed Central

WANG, Chenyun; WANG, Yingying; WANG, Miao; CHEN, Jiankui; YU, Nong; SONG, Shiping; KAMINSKI, Norbert E.; ZHANG, Wei

2013-01-01

Summary Many researchers employed mammalian expression system to artificially express cannabinoid receptors, but immunoblot data that directly prove efficient protein expression can hardly be seen in related research reports. In present study, we demonstrated cannabinoid receptor protein was not able to be properly expressed with routine mammalian expression system. This inefficient expression was rescued by endowing an exogenous signal peptide ahead of cannabinoid receptor peptide. In addition, the artificially synthesized cannabinoid receptor was found to aggregate under routine sample denaturing temperatures (i.e., ≥95°C), forming a large molecular weight band when analyzed by immunoblotting. Only denaturing temperatures ≤75°C yielded a clear band at the predicted molecular weight. Collectively, we showed that efficient mammalian expression of cannabinoid receptors need a signal peptide sequence, and described the requirement for a low sample denaturing temperature in immunoblot analysis. These findings provide very useful information for efficient mammalian expression and immunoblotting of membrane receptors. PMID:22528237

Airborne Detection of H5N8 Highly Pathogenic Avian Influenza Virus Genome in Poultry Farms, France.

PubMed

Scoizec, Axelle; Niqueux, Eric; Thomas, Rodolphe; Daniel, Patrick; Schmitz, Audrey; Le Bouquin, Sophie

2018-01-01

In southwestern France, during the winter of 2016-2017, the rapid spread of highly pathogenic avian influenza H5N8 outbreaks despite the implementation of routine control measures, raised the question about the potential role of airborne transmission in viral spread. As a first step to investigate the plausibility of that transmission, air samples were collected inside, outside and downwind from infected duck and chicken facilities. H5 avian influenza virus RNA was detected in all samples collected inside poultry houses, at external exhaust fans and at 5 m distance from poultry houses. For three of the five flocks studied, in the sample collected at 50-110 m distance, viral genomic RNA was detected. The measured viral air concentrations ranged between 4.3 and 6.4 log 10 RNA copies per m 3 , and their geometric mean decreased from external exhaust fans to the downwind measurement point. These findings are in accordance with the possibility of airborne transmission and question the procedures for outbreak depopulation.

Airborne Detection of H5N8 Highly Pathogenic Avian Influenza Virus Genome in Poultry Farms, France

PubMed Central

Scoizec, Axelle; Niqueux, Eric; Thomas, Rodolphe; Daniel, Patrick; Schmitz, Audrey; Le Bouquin, Sophie

2018-01-01

In southwestern France, during the winter of 2016–2017, the rapid spread of highly pathogenic avian influenza H5N8 outbreaks despite the implementation of routine control measures, raised the question about the potential role of airborne transmission in viral spread. As a first step to investigate the plausibility of that transmission, air samples were collected inside, outside and downwind from infected duck and chicken facilities. H5 avian influenza virus RNA was detected in all samples collected inside poultry houses, at external exhaust fans and at 5 m distance from poultry houses. For three of the five flocks studied, in the sample collected at 50–110 m distance, viral genomic RNA was detected. The measured viral air concentrations ranged between 4.3 and 6.4 log10 RNA copies per m3, and their geometric mean decreased from external exhaust fans to the downwind measurement point. These findings are in accordance with the possibility of airborne transmission and question the procedures for outbreak depopulation. PMID:29487857

Public attitudes to the storage of blood left over from routine general practice tests and its use in research.

PubMed

Treweek, Shaun; Doney, Alex; Leiman, David

2009-01-01

There is increasing international interest in DNA biobanks but relatively little evidence concerning appropriate recruitment methods for these repositories of genetic information linked to patient-specific phenotypic data. To this end, our study aimed to investigate the attitudes of members of the public recruited through general practices to the donation and storage of blood left over from routine clinical tests in general practice. A questionnaire was mailed to 2600 individuals randomly selected from two general practice patient lists in Dundee, Scotland. Using a 7-point Likert scale, respondents rated their attitudes toward DNA biobanks in general, and procurement of blood samples specifically. Overall, 841 (34%) of 2471 delivered questionnaires were returned. Compared with patients on the practice lists, respondents were older and more likely to be women. A majority of respondents (61%) were unequivocally positive about storing blood left over from routine tests. Despite general support for this collection method, when asked about open-ended consent, respondents expressed concern about future uses. Respondents' increasing age and level of deprivation had significant adverse effects on attitudes towards making leftover routine biological samples available for research (P = 0.013 and P = 0.034, respectively). The study had three main limitations: there was a low response rate (34%) such that respondents were not entirely respresentative of the survey population; some respondents had difficulty with the questionnaire; and the study was somewhat underpowered for some comparisons. Despite its limitations, this first survey of a general practice population suggests that the majority would be willing to consider giving open-ended consent for the use of blood left over from routine clinical tests in general practice to be stored and used later for medical research.

Suspected seminal vesiculitis in an Asian elephant (Elephas maximus).

PubMed

Kilburn, Jennifer J; Velguth, Karen E; Backues, Kay A

2011-09-01

A 32-year-old male Asian elephant (Elephas maximus) underwent routine transrectal stimulation for semen collection as part of an artificial insemination program. The procedure consisted of a preinsemination semen collection followed by two consecutive days of semen collections for artificial insemination. The second day's sample contained large numbers of inflammatory cells, intracellular bacteria, and phagocytized sperm. Semen was submitted for culture and sensitivity. Culture revealed Acinetobacter lwoffii, Staphylococcus intermedius, Kocuria roseus, and an unidentified gram-positive organism. Empirical antibiotic therapy with trimethoprim sulfa was initiated and then changed to enrofloxacin based on sensitivity panel results for a total of 28 days of treatment. Diagnostic semen collections were performed during treatment and 2 wk posttreatment to determine the success of therapy. Posttreatment collections revealed resolution of the inflammation. The origin of the infection was suspected to be the seminal vesicles.

mHealth Series: Measuring maternal newborn and child health coverage by text messaging – a county–level model for China

PubMed Central

Zhang, Yanfeng; Chen, Li; van Velthoven, Michelle H. M. M. T.; Wang, Wei; Liu, Li; Du, Xiaozhen; Wu, Qiong; Li, Ye; Car, Josip

2013-01-01

Background Effective interventions in maternal, newborn and child health (MNCH), if achieving high level of population coverage, could prevent most of deaths in children under five years of age. High–quality measurements of MNCH coverage are essential for tracking progress and making evidence–based decisions. Methods MNCH coverage data are mainly collected through fieldworkers’ interview with preselected households in standard programs of Demographic and Health Surveys (DHS) or Multiple Indicator Cluster Surveys (MICS) in most low– and middle–income countries. Household surveys will continue to be the major data source for MNCH coverage in the foreseeable future. However, face–to–face data collection broadly used in household surveys is labor–intensive, time–consuming and expensive. Mobile phones are drawing more and more interest in medical research with the rapid increase in usage and text messaging could be an innovative way of data collection, that is, we could collect DHS data through mHealth method. We refer to it as “mDHS”. Finding We propose in this paper a conceptual model for measuring MNCH coverage by text messaging in China. In developing this model, we considered resource constraints, sample representativeness, sample size and survey bias. The components of the model are text messaging platform, routine health information system, health facilities, communities and households. Conclusions Measuring MNCH interventions coverage by text messaging could be advantageous in many ways and establish a much larger evidence–base for MNCH health policies in China. Before mDHS could indeed be launched, research priorities would include a systematic assessment of routine health information systems and exploring feasibility to collect name lists, mobile phone numbers and general demographic and socio–economic data; qualitative interviews with health workers and caregivers; assessment of data validity of all indicators to be collected by text messaging; and exploring approaches to increase participation rate. PMID:24363920

To mix or not to mix venous blood samples collected in vacuum tubes?

PubMed

Parenmark, Anna; Landberg, Eva

2011-09-08

There are recommendations to mix venous blood samples by inverting the tubes immediately after venipuncture. Though mixing allows efficient anticoagulation in plasma tubes and fast initiation of coagulation in serum tubes, the effect on laboratory analyses and risk of haemolysis has not been thoroughly evaluated. Venous blood samples were collected by venipuncture in vacuum tubes from 50 patients (10 or 20 patients in each group). Four types of tubes and 18 parameters used in routine clinical chemistry were evaluated. For each patient and tube, three types of mixing strategies were used: instant mixing, no mixing and 5 min of rest followed by mixing. Most analyses did not differ significantly in samples admitted to different mixing strategies. Plasma lactate dehydrogenase and haemolysis index showed a small but significant increase in samples omitted to instant mixing compared to samples without mixing. However, in one out of twenty non-mixed samples, activated partial thromboplastin time was seriously affected. These results indicate that mixing blood samples after venipuncture is not mandatory for all types of tubes. Instant mixing may introduce interference for those analyses susceptible to haemolysis. However, tubes with liquid-based citrate buffer for coagulation testing should be mixed to avoid clotting.

[Phantoms for the collection of genital secretions in stallions].

PubMed

Klug, E; Brinkhoff, D; Flüge, A; Scherbarth, R; Essich, G; Kienzler, M

1977-10-05

Practical experiences of the phantom method for collection of genital secretions from stallions are reported. Taking a phantom used in the Richard-Götze-Haus Tierärztliche Hochschule Hannover as a prototype two further models slightly modified have been constructed, baring a flat hollow in the right side of the caudal phantom body for manual inserting of the Artificial Vagina. These three models fulfill four important conditions for routine use: (1) sufficient sexual attractivity for the stallions; 80-85% successful collections of presecretions out of a total of 1050 using the dummy and 70% successful semen collections from more than 240 in total; (2) solid and resistant construction; (3) easy cleaning and desinfection of the surface of the phantom to get representative samples; (4) firm installation on a hygienic floor.

Fully automatic characterization and data collection from crystals of biological macromolecules

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

Svensson, Olof; Malbet-Monaco, Stéphanie; Popov, Alexander

A fully automatic system has been developed that performs X-ray centring and characterization of, and data collection from, large numbers of cryocooled crystals without human intervention. Considerable effort is dedicated to evaluating macromolecular crystals at synchrotron sources, even for well established and robust systems. Much of this work is repetitive, and the time spent could be better invested in the interpretation of the results. In order to decrease the need for manual intervention in the most repetitive steps of structural biology projects, initial screening and data collection, a fully automatic system has been developed to mount, locate, centre to themore » optimal diffraction volume, characterize and, if possible, collect data from multiple cryocooled crystals. Using the capabilities of pixel-array detectors, the system is as fast as a human operator, taking an average of 6 min per sample depending on the sample size and the level of characterization required. Using a fast X-ray-based routine, samples are located and centred systematically at the position of highest diffraction signal and important parameters for sample characterization, such as flux, beam size and crystal volume, are automatically taken into account, ensuring the calculation of optimal data-collection strategies. The system is now in operation at the new ESRF beamline MASSIF-1 and has been used by both industrial and academic users for many different sample types, including crystals of less than 20 µm in the smallest dimension. To date, over 8000 samples have been evaluated on MASSIF-1 without any human intervention.« less

Organic Contamination Baseline Study: In NASA JSC Astromaterials Curation Laboratories. Summary Report

NASA Technical Reports Server (NTRS)

Calaway, Michael J.

2013-01-01

In preparation for OSIRIS-REx and other future sample return missions concerned with analyzing organics, we conducted an Organic Contamination Baseline Study for JSC Curation Labsoratories in FY12. For FY12 testing, organic baseline study focused only on molecular organic contamination in JSC curation gloveboxes: presumably future collections (i.e. Lunar, Mars, asteroid missions) would use isolation containment systems over only cleanrooms for primary sample storage. This decision was made due to limit historical data on curation gloveboxes, limited IR&D funds and Genesis routinely monitors organics in their ISO class 4 cleanrooms.

Hepatitis B Virus Genotyping: Is the Time Ripe for Routine Clinical Use?

PubMed Central

Madan, Kaushal; Tyagi, Pankaj

2012-01-01

Hepatitis B is one of the major causes of end-stage liver disease and liver cancer worldwide. A number of host and viral factors influence the disease course and outcomes. One such viral factor is hepatitis B virus (HBV) genotypes. There are eight major HBV genotypes described from various geographic regions of the world. Although direct sequencing appears to be the gold standard for HBV genotyping, it is expensive and laborintensive and therefore cannot be applied for routine clinical use. The newer molecular methods including serotyping have made genotyping easier and simple to apply to large number of samples rapidly. The data collected mainly over the last decade have suggested that HBV genotypes may have a bearing over the natural course of the disease and its response to therapy. This review summarizes the available literature and highlights how genotyping could be incorporated into routine clinical practice in order to improve delivery of care to HBV-infected individuals. PMID:25755425

An estimation of the clinical mastitis incidence per 100 cows per year based on routinely collected herd data.

PubMed

Santman-Berends, I M G A; Lam, T J G M; Keurentjes, J; van Schaik, G

2015-10-01

The aim of this study was to evaluate whether it was possible to (1) estimate the clinical mastitis incidence rate (CMI) for all Dutch dairy herds and (2) to detect farms with a high CMI based on routinely collected herd data. For this study, 240 dairy farms with a conventional milking system that participated in the milk recording program every 4 to 6 wk were randomly selected and agreed to participate. From the initial 240 herds, data of clinical mastitis (CM) registrations and routinely collected herd data of 227 herds were complete and could be used for analysis. Routinely collected herd data consisted of identification and registration records, antimicrobial usage, test-day records from the milk recording program, bulk tank milk (BTM) somatic cell count data and results of diagnostic tests on BTM samples. For each of the 227 herds, the CMI per 100 cows per year was calculated per quarter of the year and was combined with the available herd data. Two models were developed to predict the CMI for all dairy herds and to detect individual herds that belonged to the 25% herds with the highest CMI. Records of 156 (67%) herds were used for development of the models and the remaining 71 (33%) were used for validation. The model that estimated the CMI in all herds consisted of 11 explanatory variables. The observed and predicted averages of the validation herds were not significantly different. The model estimated a CMI per 100 cows per year of 32.5 cases (95% confidence interval=30.2-34.8), whereas the farmers registered 33.4 cases (95% confidence interval=29.5-37.4). The model that aimed at detecting individual herds with a high CMI contained 6 explanatory variables and could correctly classify 77% of all validation herds at the quarter-year level. The most important variables in the model were antibiotic usage for treating CM and BTM somatic cell count. In conclusion, models based on routinely collected herd data gave an accurate prediction of CMI for all Dutch dairy herds and could detect individual dairy herds with a high CMI. With these models it is possible to periodically monitor CMI both at the herd and at the national level, which is valuable for monitoring purposes and can motivate farmers to continuously improve udder health in their herds. Copyright © 2015 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

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

Anheier, Norman C.; Cannon, Bret D.; Martinez, Alonzo

The International Atomic Energy Agency’s (IAEA’s) long-term research and development plan calls for more cost-effective and efficient safeguard methods to detect and deter misuse of gaseous centrifuge enrichment plants (GCEPs). The IAEA’s current safeguards approaches at GCEPs are based on a combination of routine and random inspections that include environmental sampling and destructive assay (DA) sample collection from UF6 in-process material and selected cylinders. Samples are then shipped offsite for subsequent laboratory analysis. In this paper, a new DA sample collection and onsite analysis approach that could help to meet challenges in transportation and chain of custody for UF6 DAmore » samples is introduced. This approach uses a handheld sampler concept and a Laser Ablation, Laser Absorbance Spectrometry (LAARS) analysis instrument, both currently under development at the Pacific Northwest National Laboratory. A LAARS analysis instrument could be temporarily or permanently deployed in the IAEA control room of the facility, in the IAEA data acquisition cabinet, for example. The handheld PNNL DA sampler design collects and stabilizes a much smaller DA sample mass compared to current sampling methods. The significantly lower uranium mass reduces the sample radioactivity and the stabilization approach diminishes the risk of uranium and hydrogen fluoride release. These attributes enable safe sample handling needed during onsite LAARS assay and may help ease shipping challenges for samples to be processed at the IAEA’s offsite laboratory. The LAARS and DA sampler implementation concepts will be described and preliminary technical viability results presented.« less

Primary productivity by phytoplankton in the tidal, fresh Potomac River, Maryland, May 1980 to August 1981

USGS Publications Warehouse

Cohen, R.R.; Pollock, S.O.

1983-01-01

Primary productivity by phytoplankton was measured on samples collected from the Potomac Tidal River, Maryland. The studies were performed monthly from May 1980 to September 1981. Additional studies were done once a week in August 1980, twice a week from August 4 to 8, 1980 and twice in September 1980. Depth-integrated samples were collected at five stations and incubated in boxes that were exposed to natural sunlight. The boxes were covered with neutral density filters transmitting 100 , 65, 32, 16, and 6 percent surface light. River water was pumped continuously over the samples. The extinction of light in the water column by phytoplankton was measured when samples were collected. Experiments were performed to select a method for routine productivity analysis. No difference was found between productivity: (1) determined in situ and in boxes; (2) measured in 300 ml and (4) calculated from short term (4 hours) and long term (10-24 hours) incubations. There were higher productivity differences in samples that were rotated among different light intensities every 15 minutes (simulating mixing) than those remaining stationary. Respiration was significantly less in samples pumped through a hose from those collected using a depth-integrating sampler. Depth-integrated primary productivity was determined from the productivity data using an equation modified from one reported in the literature. Depth-integrated gross primary productivity was highest in August 1980 and 1981 and lowest in January 1980. (USGS)

Measuring myokines with cardiovascular functions: pre-analytical variables affecting the analytical output.

PubMed

Lombardi, Giovanni; Sansoni, Veronica; Banfi, Giuseppe

2017-08-01

In the last few years, a growing number of molecules have been associated to an endocrine function of the skeletal muscle. Circulating myokine levels, in turn, have been associated with several pathophysiological conditions including the cardiovascular ones. However, data from different studies are often not completely comparable or even discordant. This would be due, at least in part, to the whole set of situations related to the preparation of the patient prior to blood sampling, blood sampling procedure, processing and/or store. This entire process constitutes the pre-analytical phase. The importance of the pre-analytical phase is often not considered. However, in routine diagnostics, the 70% of the errors are in this phase. Moreover, errors during the pre-analytical phase are carried over in the analytical phase and affects the final output. In research, for example, when samples are collected over a long time and by different laboratories, a standardized procedure for sample collecting and the correct procedure for sample storage are acknowledged. In this review, we discuss the pre-analytical variables potentially affecting the measurement of myokines with cardiovascular functions.

Blood Substrate Collection and Handling Procedures under Pseudo-Field Conditions: Evaluation of Suitability for Inflammatory Biomarker Measurement

PubMed Central

Danese, Andrea; Shalev, Idan; Williams, Benjamin S.; Caspi, Avshalom

2015-01-01

Routine incorporation of blood-based biomarker measurements in population studies has been hampered by challenges in obtaining samples suitable for biomarker assessment outside of laboratory settings. Here, we assessed the suitability of venous blood left unprocessed for four, 24 or 48 hours post-collection at either room temperature or 4°C for quantification of two biomarkers, Interleukin-6 (IL-6) and C-Reactive Protein (CRP). Blood samples were collected in both K2EDTA tubes and a dedicated plasma-preservation tube, P100. Dried Blood Spot (DBS) samples from the same subjects were also collected in order to compare delayed-processing plasma performance against a popular alternative collection method. K2EDTA mean plasma concentrations of both IL-6 and CRP were not significantly different from concentrations in plasma processed immediately; this was observed for tubes stored up to 48 hours pre-processing at either temperature. Concentrations of IL-6 measured in P100 tubes showed significant time-dependent increases when stored at room temperature; otherwise, levels of IL-6 and CRP were similar to those processed immediately. Levels of CRP in DBS were correlated with plasma CRP levels, even when pre-processed blood was stored for up to 48 hours. These data indicate that plasma is suitable for IL-6 and CRP estimation under data-collection conditions that involve processing delays. PMID:26652682

Comparison of PIXE and XRF analysis of airborne particulate matter samples collected on Teflon and quartz fibre filters

NASA Astrophysics Data System (ADS)

Chiari, M.; Yubero, E.; Calzolai, G.; Lucarelli, F.; Crespo, J.; Galindo, N.; Nicolás, J. F.; Giannoni, M.; Nava, S.

2018-02-01

Within the framework of research projects focusing on the sampling and analysis of airborne particulate matter, Particle Induced X-ray Emission (PIXE) and Energy Dispersive X-ray Fluorescence (ED-XRF) techniques are routinely used in many laboratories throughout the world to determine the elemental concentration of the particulate matter samples. In this work an inter-laboratory comparison of the results obtained from analysing several samples (collected on both Teflon and quartz fibre filters) using both techniques is presented. The samples were analysed by PIXE (in Florence, at the 3 MV Tandetron accelerator of INFN-LABEC laboratory) and by XRF (in Elche, using the ARL Quant'X EDXRF spectrometer with specific conditions optimized for specific groups of elements). The results from the two sets of measurements are in good agreement for all the analysed samples, thus validating the use of the ARL Quant'X EDXRF spectrometer and the selected measurement protocol for the analysis of aerosol samples. Moreover, thanks to the comparison of PIXE and XRF results on Teflon and quartz fibre filters, possible self-absorption effects due to the penetration of the aerosol particles inside the quartz fibre-filters were quantified.

Educational Module Intervention for Radiographers to Reduce Repetition Rate of Routine Digital Chest Radiography in Makkah Region of Saudi Arabia Tertiary Hospitals: Protocol of a Quasi-Experimental Study.

PubMed

Almalki, Abdullah A; Abdul Manaf, Rosliza; Hanafiah Juni, Muhamad; Kadir Shahar, Hayati; Noor, Noramaliza Mohd; Gabbad, Abdelsafi

2017-09-26

Repetition of an image is a critical event in any radiology department. When the repetition rate of routine digital chest radiographs is high, radiation exposure of staff and patients is increased. In addition, repetition consumes the equipment's life span, thus affecting the annual budget of the department. The aim of this study is to determine the impact of a printed educational module on reducing the repetition rate of routine digital chest radiography among radiographers in Makkah Region tertiary hospitals. A quasi-experimental time series with a control group will be conducted in Makkah Region tertiary hospitals for 8 months starting in the second quarter of 2017. Four hospitals out of 5 in the region will be selected; 2 of them will be selected as the control group and the other 2 as the intervention group. Stratification and a simple random sampling technique will be used to sample 56 radiographers in each group. Pre- and postintervention assessments will be conducted to determine the radiographer knowledge, motivation, and skills and repetition rate of chest radiographs. Radiographs of the chest performed by sampled radiographers in the selected hospitals will be collected for 2 weeks before and after the intervention. A piloted questionnaire will be distributed and collected by a researcher in both groups. One-way multivariate analysis of variance and 2-way repeated multivariate analysis of variance will be used to analyze the data. It is expected that the repetition rate in the intervention group will decline after implementing the intervention and the change will be statistically significant (P<.05). Furthermore, it is expected that the knowledge, motivation, and skill levels in the intervention group will increase significantly among radiographers after implementation of the intervention (P<.05). Meanwhile, knowledge, motivation, and skills in the control group will not change. A quasi-experimental time series with a control will be conducted to investigate the effect of printed educational material in reducing the repetition rate of routine digital chest radiographs among radiographers in tertiary hospitals in the Makkah Region of Saudi Arabia. ©Abdullah A. Almalki, Rosliza Abdul Manaf, Muhamad Hanafiah Juni, Hayati Kadir Shahar, Noramaliza Mohd Noor, Abdelsafi Gabbad. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 26.09.2017.

Current Trend of Antimicrobial Prescription for Oral Implant Surgery Among Dentists in India.

PubMed

Datta, Rahul; Grewal, Yasmin; Batth, J S; Singh, Amandeep

2014-12-01

The aim of our study was to evaluate antimicrobial prescription behaviour amongst dentists performing oral implant surgery in India. Dentists performing oral implant surgery from different parts of India were personally approached during various national events such as conferences and academic meetings and information regarding their prescription habits for antimicrobial agents in routine oral implant surgery was collected using a structured questionnaire. Out of a total sample of 332 dentists, 85.5 % prescribed 17 different groups or combinations of antibiotics routinely for oral implant surgery in the normal healthy patient. Majority preferred the peri-operative protocol of drug therapy (72.2 %) with variable and prolonged duration of therapy after surgery, ranging from 3 to 10 days. An antimicrobial mouthwash was routinely prescribed by all the doctors (14.5 %) not in favour of prescribing antimicrobials in a normal healthy patient. Our findings suggest that there is a trend of antimicrobial agent misuse by dentists performing oral implant surgery in India, both in terms of drugs used and the protocols prescribed. The majority of these dentists prescribed a variety of antimicrobial agents for prolonged durations routinely even in the normal, healthy patients.

Sulfate and nitrate collected by filter sampling near the tropopause

NASA Technical Reports Server (NTRS)

Humenik, F. M.; Lezberg, E. A.; Otterson, D. A.

1980-01-01

Filter samples collected near the tropopause with an F-106 aircraft and two Boeing 747 aircraft were analyzed for sulfate and nitrate ion content. Within the range of routine commercial flight altitudes (at or below 12.5 km), stratospheric mass mixing ratios for the winter-spring group averaged 0.26 ppbm for sulfate and 0.35 ppbm for nitrate. For the summer-fall group, stratosphere mixing ratios averaged 0.13 ppbm and 0.25 ppbm for sulfate and nitrate, respectively. Winter-spring group tropospheric mass mixing ratios averaged 0.08 ppbm for sulfate and 0.10 ppbm for nitrate, while summer-fall group tropospheric mixing ratios averaged 0.05 ppbm for sulfate and 0.08 ppbm for nitrate. Correlations of the filter data with available ozone data suggest that the sulfate and nitrate are transported from the stratosphere to the troposphere.

BASIC Programming In Water And Wastewater Analysis

NASA Technical Reports Server (NTRS)

Dreschel, Thomas

1988-01-01

Collection of computer programs assembled for use in water-analysis laboratories. First program calculates quality-control parameters used in routine water analysis. Second calculates line of best fit for standard concentrations and absorbances entered. Third calculates specific conductance from conductivity measurement and temperature at which measurement taken. Fourth calculates any one of four types of residue measured in water. Fifth, sixth, and seventh calculate results of titrations commonly performed on water samples. Eighth converts measurements, to actual dissolved-oxygen concentration using oxygen-saturation values for fresh and salt water. Ninth and tenth perform calculations of two other common titrimetric analyses. Eleventh calculates oil and grease residue from water sample. Last two use spectro-photometric measurements of absorbance at different wavelengths and residue measurements. Programs included in collection written for Hewlett-Packard 2647F in H-P BASIC.

Bio-repository of post-clinical test samples at the national cancer center hospital (NCCH) in Tokyo.

PubMed

Furuta, Koh; Yokozawa, Karin; Takada, Takako; Kato, Hoichi

2009-08-01

We established the Bio-repository at the National Cancer Center Hospital in October 2002. The main purpose of this article is to show the importance and usefulness of a bio-repository of post-clinical test samples not only for translational cancer research but also for routine clinical oncology by introducing the experience of setting up such a facility. Our basic concept of a post-clinical test sample is not as left-over waste, but rather as frozen evidence of a patient's pathological condition at a particular point. We can decode, if not all, most of the laboratory data from a post-clinical test sample. As a result, the bio-repository is able to provide not only the samples, but potentially all related laboratory data upon request. The areas of sample coverage are the following: sera after routine blood tests; sera after cross-match tests for transfusion; serum or plasma submitted at a patient's clinically important time period by the physician; and samples collected by the individual investigator. The formats of stored samples are plasma or serum, dried blood spot (DBS) and buffy coat. So far, 150 218 plasmas or sera, 35 253 DBS and 536 buffy coats have been registered for our bio-repository system. We arranged to provide samples to various concerned parties under strict legal and ethical agreements. Although the number of the utilized samples was initially limited, the inquiries for sample utilization are now increasing steadily from both research and clinical sources. Further efforts to increase the benefits of the repository are intended.

On the Lipid Composition of Human Meibum and Tears: Comparative Analysis of Nonpolar Lipids

PubMed Central

Butovich, Igor A.

2009-01-01

PURPOSE To qualitatively compare the nonpolar lipids present in meibomian gland (MG) secretions (samples T1) with aqueous tears (AT) collected from the lower tear menisci of healthy, non-dry eye volunteers using either glass microcapillaries (samples T2) or Schirmer test strips (samples T3). METHODS Samples T1 to T3 were analyzed with the use of high-pressure liquid chromatography/positive ion mode atmospheric pressure chemical ionization mass spectrometry. Where possible, the unknown lipids were compared with known standards. RESULTS Samples T1 had the simplest lipid composition among all the tested specimens. Samples T2 and T3 were similar to each other but were noticeably different from samples T1. In addition to all the compounds detected in samples T1, lower molecular weight wax esters and other compounds were found in samples T2 and T3. No appreciable amounts of fatty acid amides (e.g., oleamide), ceramides, or monoacyl glycerols were routinely detected. The occasionally observed minor signals of oleamide (m/z 282) in samples T3 were attributed to the contamination of the samples with common plasticizers routinely found in plastic ware extractives and organic solvents. CONCLUSIONS The MG is a prominent source of lipids for the tear film. However, it would have been a mistake to exclude from consideration other likely sources of lipids such as conjunctiva, cornea, and tears produced by the lacrimal glands. These data showed that lipids in AT are more complex than MG secretions, which necessitates more cautious interpretation of the functions of the latter in the tear film. PMID:18487374

On the lipid composition of human meibum and tears: comparative analysis of nonpolar lipids.

PubMed

Butovich, Igor A

2008-09-01

To qualitatively compare the nonpolar lipids present in meibomian gland (MG) secretions (samples T1) with aqueous tears (AT) collected from the lower tear menisci of healthy, non-dry eye volunteers using either glass microcapillaries (samples T2) or Schirmer test strips (samples T3). Samples T1 to T3 were analyzed with the use of high-pressure liquid chromatography/positive ion mode atmospheric pressure chemical ionization mass spectrometry. Where possible, the unknown lipids were compared with known standards. Samples T1 had the simplest lipid composition among all the tested specimens. Samples T2 and T3 were similar to each other but were noticeably different from samples T1. In addition to all the compounds detected in samples T1, lower molecular weight wax esters and other compounds were found in samples T2 and T3. No appreciable amounts of fatty acid amides (e.g., oleamide), ceramides, or monoacyl glycerols were routinely detected. The occasionally observed minor signals of oleamide (m/z 282) in samples T3 were attributed to the contamination of the samples with common plasticizers routinely found in plastic ware extractives and organic solvents. The MG is a prominent source of lipids for the tear film. However, it would have been a mistake to exclude from consideration other likely sources of lipids such as conjunctiva, cornea, and tears produced by the lacrimal glands. These data showed that lipids in AT are more complex than MG secretions, which necessitates more cautious interpretation of the functions of the latter in the tear film.

Uniform data collection in routine clinical practice in cardiovascular patients for optimal care, quality control and research: The Utrecht Cardiovascular Cohort.

PubMed

Asselbergs, Folkert W; Visseren, Frank Lj; Bots, Michiel L; de Borst, Gert J; Buijsrogge, Marc P; Dieleman, Jan M; van Dinther, Baukje Gf; Doevendans, Pieter A; Hoefer, Imo E; Hollander, Monika; de Jong, Pim A; Koenen, Steven V; Pasterkamp, Gerard; Ruigrok, Ynte M; van der Schouw, Yvonne T; Verhaar, Marianne C; Grobbee, Diederick E

2017-05-01

Background Cardiovascular disease remains the major contributor to morbidity and mortality. In routine care for patients with an elevated cardiovascular risk or with symptomatic cardiovascular disease information is mostly collected in an unstructured manner, making the data of limited use for structural feedback, quality control, learning and scientific research. Objective The Utrecht Cardiovascular Cohort (UCC) initiative aims to create an infrastructure for uniform registration of cardiovascular information in routine clinical practice for patients referred for cardiovascular care at the University Medical Center Utrecht, the Netherlands. This infrastructure will promote optimal care according to guidelines, continuous quality control in a learning healthcare system and creation of a research database. Methods The UCC comprises three parts. UCC-1 comprises enrolment of all eligible cardiovascular patients in whom the same information will be collected, based on the Dutch cardiovascular management guideline. A sample of UCC-1 will be invited for UCC-2. UCC-2 involves an enrichment through extensive clinical measurements with emphasis on heart failure, cerebral ischaemia, arterial aneurysms, diabetes mellitus and elevated blood pressure. UCC-3 comprises on-top studies, with in-depth measurements in smaller groups of participants typically based on dedicated project grants. All participants are followed up for morbidity and mortality through linkage with national registries. Conclusion In a multidisciplinary effort with physicians, patients and researchers the UCC sets a benchmark for a learning cardiovascular healthcare system. UCC offers an invaluable resource for future high quality care as well as for first-class research for investigators.

Cardiac peptide stability, aprotinin and room temperature: importance for assessing cardiac function in clinical practice.

PubMed

Buckley, M G; Marcus, N J; Yacoub, M H

1999-12-01

Brain natriuretic peptide (BNP), atrial natriuretic peptide (ANP) and N-terminal ANP are good research indices of the severity of heart failure. The stability of these peptides at room temperature has become an important factor in assessing their use as indicators of cardiac function in routine clinical practice. Inhibitors such as aprotinin are routinely added in the blood collection process, but may provide no benefit in sample collection and routine clinical practice. We assessed the stability of BNP, ANP and N-terminal ANP in blood samples collected in either the presence or the absence of the protease inhibitor aprotinin. Blood, either with or without aprotinin, was processed immediately (initial; 0 h) and after blood samples had been left for 3 h, 2 days or 3 days at room temperature. These times were chosen to reflect processing in a hospital outpatient clinic (2-3 h), or when posted from general practice (2-3 days). Initial plasma BNP, ANP and N-terminal ANP levels in the absence of aprotinin were 28.2+/-5.4, 44.2+/-7.9 and 1997+/-608 pg/ml respectively, and were not significantly different from initial values in the presence of aprotinin (29.0+/-5.9, 45.2+/-8.0 and 2009+/-579 pg/ml respectively). After 3 h at room temperature, there was a significant fall in ANP in the absence of aprotinin (36. 7+/-7.9 pg/ml; P<0.005), but not in the presence of aprotinin (41. 2+/-7.6 pg/ml). Both BNP and N-terminal ANP were unchanged in either the absence (BNP, 27.6+/-5.5 pg/ml; N-terminal ANP, 2099+/-613 pg/ml) or the presence (BNP, 29.4+/-5.6 pg/ml; N-terminal ANP, 1988+/-600 pg/ml) of aprotinin. After 2 days at room temperature, ANP had fallen significantly in both the absence (16.9+/-3.4 pg/ml) and the presence (24.0+/-5.0 pg/ml) of aprotinin compared with initial values, and there was a significant difference in ANP levels in the absence and presence of aprotinin (P<0.001). ANP levels had decreased further after 3 days at room temperature, to 11.9+/-3.4 pg/ml (no aprotinin) and 20.3+/-5.0 pg/ml (aprotinin added); these values were significantly different (P=0.002). In contrast, there was no change in the levels of BNP or N-terminal ANP after 2 or 3 days at room temperature, in either the absence or the presence of aprotinin. These studies indicate that aprotinin adds little benefit to the stability of cardiac peptides at room temperature. Blood samples for BNP and N-terminal ANP measurement used as a test of heart function in hospital clinics and by general practitioners in the community could be taken into blood tubes containing only EDTA as anticoagulant and without the additional step of adding the routinely used inhibitor aprotinin.

Evaluating the feasibility of using insecticide quantification kits (IQK) for estimating cyanopyrethroid levels for indoor residual spraying in Vanuatu

PubMed Central

2014-01-01

Background The quality of routine indoor residual spraying (IRS) operations is rarely assessed because of the limited choice of methods available for quantifying insecticide content in the field. This study, therefore, evaluated a user-friendly, rapid colorimetric assay for detecting insecticide content after routine IRS operations were conducted. Methods This study was conducted in Tafea Province, Vanuatu. Routine IRS was conducted with lambda cyhalothrin. Two methods were used to quantify the IRS activities: 1) pre-spray application of small felt pads and 2) post-spray removal of insecticide with adhesive. The insecticide content was quantified using a colorimetric assay (Insecticide Quantification Kit [IQK]), which involved exposing each sample to the test reagents for 15 mins. The concentration of insecticide was indicated by the depth of red colour. Results The IQK proved simple to perform in the field and results could be immediately interpreted by the programme staff. The insecticide content was successfully sampled by attaching felt pads to the house walls prior to spraying. The IRS operation was well conducted, with 83% of houses being sprayed at the target dose (20 – 30 mg AI/m2). The average reading across all houses was 24.4 ± 1.5 mg AI/m2. The results from the felt pads applied pre-spray were used as a base to compare methods for sampling insecticide from walls post-spray. The adhesive of Sellotape did not collect adequate samples. However, the adhesive of the felt pads provided accurate samples of the insecticide content on walls. Conclusion The IQK colorimetric assay proved to be a useful tool that was simple to use under realistic field conditions. The assay provided rapid information on IRS spray dynamics and spray team performance, facilitating timely decision making and reporting for programme managers. The IQK colorimetric assay will have direct applications for routine quality control in malaria control programmes globally and has the potential to improve the efficacy of vector control operations. PMID:24885084

Unreliable alcohol testing in a shipping safety programme.

PubMed

Helander, Anders; Hagelberg, Charlotte Asker; Beck, Olof; Petrini, Björn

2009-08-10

Within a maritime alcohol and drug testing programme, a case showing an unphysiological urine ethanol concentration (235 mmol/L, 10.8 g/L) was found. The sample contained low levels of the ethanol metabolites ethyl glucuronide (EtG) and ethyl sulphate (EtS) which confirmed prior drinking, but also tested positive for the fermenting yeast Candida albicans which suggested post-sampling ethanol formation. This and other questionable cases prompted investigation of the suitability of urine alcohol testing for the intended application. Besides the routine measurements of ethanol, illicit drugs and creatinine, randomly selected ethanol-positive and ethanol-negative urines collected within the maritime programme were checked for the presence of EtG and EtS and for fungal and bacterial growth. Data on sample handling and storage was also gathered. Ten of 15 (67%) ethanol-positive and 4 of 9 (44%) ethanol-negative urines contained yeast and/or bacteria. Among the ethanol-positive cases, 4 (27%) were obviously false positives because EtG and EtS were not detected. Microbial action as the reason for false-high ethanol concentrations was indicated in other cases. When 17 bacteria-infected but fungi-negative urines were supplemented with glucose and stored for 1 week at 21 degrees C, ethanol was formed in 2 specimens containing Escherichia coli and E. coli plus P. aeruginosa. In these samples, EtG was also formed on storage while EtS was not. The routines employed for urine collection and handling within this substance abuse programme caused many false-positive identifications of alcohol use with unintended medico-legal consequences. Unpreserved urines stored without cooling should not be used for alcohol testing, given the high risk for microbial interference.

A laboratory procedure for measuring and georeferencing soil colour

NASA Astrophysics Data System (ADS)

Marques-Mateu, A.; Balaguer-Puig, M.; Moreno-Ramon, H.; Ibanez-Asensio, S.

2015-04-01

Remote sensing and geospatial applications very often require ground truth data to assess outcomes from spatial analyses or environmental models. Those data sets, however, may be difficult to collect in proper format or may even be unavailable. In the particular case of soil colour the collection of reliable ground data can be cumbersome due to measuring methods, colour communication issues, and other practical factors which lead to a lack of standard procedure for soil colour measurement and georeferencing. In this paper we present a laboratory procedure that provides colour coordinates of georeferenced soil samples which become useful in later processing stages of soil mapping and classification from digital images. The procedure requires a laboratory setup consisting of a light booth and a trichromatic colorimeter, together with a computer program that performs colour measurement, storage, and colour space transformation tasks. Measurement tasks are automated by means of specific data logging routines which allow storing recorded colour data in a spatial format. A key feature of the system is the ability of transforming between physically-based colour spaces and the Munsell system which is still the standard in soil science. The working scheme pursues the automation of routine tasks whenever possible and the avoidance of input mistakes by means of a convenient layout of the user interface. The program can readily manage colour and coordinate data sets which eventually allow creating spatial data sets. All the tasks regarding data joining between colorimeter measurements and samples locations are executed by the software in the background, allowing users to concentrate on samples processing. As a result, we obtained a robust and fully functional computer-based procedure which has proven a very useful tool for sample classification or cataloging purposes as well as for integrating soil colour data with other remote sensed and spatial data sets.

Monitoring iCCM: a feasibility study of the indicator guide for monitoring and evaluating integrated community case management.

PubMed

Roberton, Timothy; Kasungami, Dyness; Guenther, Tanya; Hazel, Elizabeth

2016-07-01

Most countries in sub-Saharan Africa have now adopted integrated community case management (iCCM) of common childhood illnesses as a strategy to improve child health. In March 2014, the iCCM Task Force published an Indicator Guide for Monitoring and Evaluating iCCM: a 'menu' of recommended indicators with globally agreed definitions and methodology, to guide countries in developing robust iCCM monitoring systems. The Indicator Guide was conceived as an evolving document that would incorporate collective experience and learning as iCCM programmes themselves evolve. This article presents findings from two studies that examined the feasibility of collecting the Indicator Guide's 18 routine monitoring indicators with the iCCM monitoring systems that countries currently have in place. We reviewed iCCM monitoring tools, protocols and reports from a purposive sample of 10 countries in sub-Saharan Africa. We developed a scorecard system to assess which of the Indicator Guide's 18 routine monitoring indicators could be calculated with the given monitoring tools, and at which level of the health system the relevant information would be available. We found that the data needed to calculate many of the Indicator Guide's routine monitoring indicators are already being collected through existing monitoring systems, although much of these data are only available at health facility level and not aggregated to district or national levels. Our results highlight challenge of using supervision checklists as a data source, and the need for countries to maintain accurate deployment data for CHWs and CHW supervisors. We suggest that some of the recommended indicators need revising. Routine monitoring will be more feasible, effective and efficient if iCCM programmes focus on a smaller set of high-value indicators that are easy to measure, reliably interpreted and useful both for global and national stakeholders and for frontline health workers themselves. © The Author 2016. Published by Oxford University Press in association with The London School of Hygiene and Tropical Medicine.

Microbiological sampling of swine carcasses: a comparison of data obtained by swabbing with medical gauze and data collected routinely by excision at Swedish abattoirs.

PubMed

Lindblad, M

2007-09-15

Swab sample data from a 13-month microbiological baseline study of swine carcasses at Swedish abattoirs were combined with excision sample data collected routinely at five abattoirs. The aim was to compare the numbers of total aerobic counts, Enterobacteriaceae, and Escherichia coli, recovered by swabbing four carcass sites with gauze (total area 400 cm2) with those obtained by excision at equivalent sites (total area 20 cm2). The results are considered in relation to the process hygiene criteria that are stated in Commission Regulation (EC) No 2073/2005. These criteria apply only to destructive sampling of total aerobic counts and Enterobacteriaceae, but alternative sampling schemes, as well as alternative indicator organisms such as E. coli, are allowed if equivalent guarantees of food safety can be provided. Swab sampling resulted in higher mean log numbers of total aerobic counts at four of the five abattoirs, compared with excision, and lower or equal standard deviations at all abattoirs. The percentage of swab and excision samples positive for Enterobacteriaceae at the different abattoirs ranged from 68 to 100% and 15 to 24%, respectively. Similarly, the percentages of swab samples that were positive for E. coli were higher than the percentages of positive excision samples (range 52 to 84% and 3 to 14%, respectively). Due to the low percentage of positive excision results, the mean log numbers of Enterobacteriaceae and E. coli were only compared at two and one abattoirs, respectively, using log probability regression to substitute censored observations. Higher mean log numbers of Enterobacteriaceae were recovered by swabbing compared with excision at one abattoir, whereas the numbers of Enterobacteriaceae and E. coli did not differ significantly between sampling methods at one abattoir. This study suggests that the same process hygiene criteria as those stipulated for excision can be used for swabbing with gauze without compromising food safety. For monitoring of low numbers of Enterobacteriaceae and E. coli, like those found on swine carcasses at Swedish abattoirs, the results also show that swabbing of a relatively large area is superior to excision of a smaller area.

Instrumentation for time-resolved dynamic and static dichroic measurements of polymers with a near-IR acoustooptic tunable filter

NASA Astrophysics Data System (ADS)

Sweat, Joseph Allen

1999-11-01

The optical measurement of the orientational response of chemical functional groups of a polymer as it is subjected to conventional dynamic mechanical analysis can give insight into the rheological behavior of the polymer while under repetitive strain based on the chemical structure. Instrumentation used in the mid infrared has included the use of grating monochromators and interferometers. The use of a multiply modulated optical signal has decreased the level of noise to observe the small amplitude changes (typically >10-3 absorbance units) associated with the repetitive oscillatory strain. The use of digital signal processing to replace phase sensitive detection for demodulation of the optical signal has greatly reduced the spectral collection time. In addition, multiplexing gained with the use of step-scan interferometry in making time resolved measurements has aided in making the procedure more practical. However, instrumental complexity and expense are drawbacks. By incorporating the high throughput, polarized tuned beam, and rapid wavelength switching capability of an acousto-optic tunable filter (AOTF), a dynamic instrument with integrated centralized control by a single microprocessor has been built. it operates in the near infrared with a rapid dynamic data collection time and requires the use of only a single modulation in the form of the sample oscillatory strain. The near infrared permits thicker samples to reduce sample preparation tune or allows polymers to be tested without pretreatment. The use of Fourier based digital filtering improves the signal to noise ratio of the dynamic differential spectra. The instrument is cost effective and rugged in comparison to step-scan interferometers yet has a rapid data collection rate allowing use in a routine industrial setting. Information from these measurements can aid in determining the rheological properties necessary for the end use functionality of a polymer. Additionally, AOTF instrumentation can be used for static dichroic measurements of polymers for routine testing. An example of this is the routine measurement of the dichroic ratio of a natural protein biopolymer, wheat gluten (film), as an indication of the gluten strength. This type of measurement has the potential to be useful in the improvement of wheat varieties and in the indication of wheat quality for end use.

Use of mammal manure by nesting burrowing owls: a test of four functional hypotheses

USGS Publications Warehouse

Smith, M.D.; Conway, C.J.

2007-01-01

Animals have evolved an impressive array of behavioural traits to avoid depredation. Olfactory camouflage of conspicuous odours is a strategy to avoid depredation that has been implicated only in a few species of birds. Burrowing owls, Athene cunicularia, routinely collect dried manure from mammals and scatter it in their nest chamber, in the tunnel leading to their nest and at the entrance to their nesting burrow. This unusual behaviour was thought to reduce nest depredation by concealing the scent of adults and juveniles, but a recent study suggests that manure functions to attract arthropod prey. However, burrowing owls routinely scatter other materials in the same way that they scatter manure, and this fact seems to be at odds with both of these hypotheses. Thus, we examined the function of this behaviour by testing four alternative hypotheses. We found no support for the widely cited olfactory-camouflage hypothesis (manure did not lower the probability of depredation), or for the mate-attraction hypothesis (males collected manure after, not before, pair formation). Predictions of the burrow-occupied hypothesis (manure indicates occupancy to conspecifics and thereby reduces agonistic interactions) were supported, but results were not statistically significant. Our results also supported several predictions of the prey-attraction hypothesis. Pitfall traps at sampling sites with manure collected more arthropod biomass (of taxa common in the diet of burrowing owls) than pitfall traps at sampling sites without manure. Scattering behaviour of burrowing owls appears to function to attract arthropod prey, but may also signal occupancy of a burrow to conspecifics. ?? 2006 The Association for the Study of Animal Behaviour.

Data for Program Management: An Accuracy Assessment of Data Collected in Household Registers by Community Health Workers in Southern Kayonza, Rwanda.

PubMed

Mitsunaga, Tisha; Hedt-Gauthier, Bethany L; Ngizwenayo, Elias; Farmer, Didi Bertrand; Gaju, Erick; Drobac, Peter; Basinga, Paulin; Hirschhorn, Lisa; Rich, Michael L; Winch, Peter J; Ngabo, Fidele; Mugeni, Cathy

2015-08-01

Community health workers (CHWs) collect data for routine services, surveys and research in their communities. However, quality of these data is largely unknown. Utilizing poor quality data can result in inefficient resource use, misinformation about system gaps, and poor program management and effectiveness. This study aims to measure CHW data accuracy, defined as agreement between household registers compared to household member interview and client records in one district in Eastern province, Rwanda. We used cluster-lot quality assurance sampling to randomly sample six CHWs per cell and six households per CHW. We classified cells as having 'poor' or 'good' accuracy for household registers for five indicators, calculating point estimates of percent of households with accurate data by health center. We evaluated 204 CHW registers and 1,224 households for accuracy across 34 cells in southern Kayonza. Point estimates across health centers ranged from 79 to 100% for individual indicators and 61 to 72% for the composite indicator. Recording error appeared random for all but the widely under-reported number of women on modern family planning method. Overall, accuracy was largely 'good' across cells, with varying results by indicator. Program managers should identify optimum thresholds for 'good' data quality and interventions to reach them according to data use. Decreasing variability and improving quality will facilitate potential of these routinely-collected data to be more meaningful for community health program management. We encourage further studies assessing CHW data quality and the impact training, supervision and other strategies have on improving it.

Assessment of the Effects of Holding Time and Temperature on Escherichia coli Densities in Surface Water Samples

PubMed Central

Pope, Misty L.; Bussen, Michelle; Feige, Mary Ann; Shadix, Lois; Gonder, Sharon; Rodgers, Crystal; Chambers, Yildiz; Pulz, Jessica; Miller, Ken; Connell, Kevin; Standridge, Jon

2003-01-01

Escherichia coli is a routinely used microbiological indicator of water quality. To determine whether holding time and storage conditions had an effect on E. coli densities in surface water, studies were conducted in three phases, encompassing 24 sites across the United States and four commonly used monitoring methods. During all three phases of the study, E. coli samples were analyzed at time 0 and at 8, 24, 30, and 48 h after sample collection. During phase 1, when 4°C samples were evaluated by Colilert or by placing a membrane onto mFC medium followed by transfer to nutrient agar containing 4-methylumbelliferyl-β-d-glucuronide (mFC/NA-MUG), three of four sites showed no significant differences throughout the 48-h study. During phase 2, five of seven sites showed no significant difference between time 0 and 24 h by membrane filtration (mFC/NA-MUG). When evaluated by the Colilert method, five of seven sites showed no significant difference in E. coli density between time 0 and 48 h. During phase 3, 8 of 13 sites showed no significant differences in E. coli densities between time 0 and the 48-h holding time, regardless of method. Based on the results of these studies, it appears that if samples are held below 10°C and are not allowed to freeze, most surface water E. coli samples analyzed by commonly used methods beyond 8 h after sample collection can generate E. coli data comparable to those generated within 8 h of sample collection. Notwithstanding this conclusion, E. coli samples collected from surface waters should always be analyzed as soon as possible. PMID:14532081

Soil forensics: How far can soil clay analysis distinguish between soil vestiges?

PubMed

Corrêa, R S; Melo, V F; Abreu, G G F; Sousa, M H; Chaker, J A; Gomes, J A

2018-03-01

Soil traces are useful as forensic evidences because they frequently adhere to individuals and objects associated with crimes and can place or discard a suspect at/from a crime scene. Soil is a mixture of organic and inorganic components and among them soil clay contains signatures that make it reliable as forensic evidence. In this study, we hypothesized that soils can be forensically distinguished through the analysis of their clay fraction alone, and that samples of the same soil type can be consistently distinguished according to the distance they were collected from each other. To test these hypotheses 16 Oxisol samples were collected at distances of between 2m and 1.000m, and 16 Inceptisol samples were collected at distances of between 2m and 300m from each other. Clay fractions were extracted from soil samples and analyzed for hyperspectral color reflectance (HSI), X-ray diffraction crystallographic (XRD), and for contents of iron oxides, kaolinite and gibbsite. The dataset was submitted to multivariate analysis and results were from 65% to 100% effective to distinguish between samples from the two soil types. Both soil types could be consistently distinguished for forensic purposes according to the distance that samples were collected from each other: 1000m for Oxisol and 10m for Inceptisol. Clay color and XRD analysis were the most effective techniques to distinguish clay samples, and Inceptisol samples were more easily distinguished than Oxisol samples. Soil forensics seems a promising field for soil scientists as soil clay can be useful as forensic evidence by using routine analytical techniques from soil science. Copyright © 2017 The Chartered Society of Forensic Sciences. Published by Elsevier B.V. All rights reserved.

Evaluation of diagnostic procedures for subclinical mastitis in meat-producing sheep.

PubMed

Clements, Archie C A; Taylor, David J; Fitzpatrick, Julie L

2003-05-01

Samples of foremilk were collected from 261 clinically normal glands of 150 ewes, and tested using the California mastitis test (CMT). Further samples were collected from 195 of these glands for determination of automated somatic cell counts (SCC), and from 60 of these glands for bacteriological assessment. The sensitivity and specificity of CMT for detecting samples with SCC above different threshold levels and for CMT and SCC in determining bacteriological status were evaluated using two-graph receiver operating characteristics (TG-ROC). Milk samples were obtained subsequently from ten CMT positive, and five CMT negative first- and second-lactation ewes. Samples were cultured using a variety of media, incubation temperatures and atmospheric conditions, immediately after collection, and 1 week after storage at 4 degrees C and -21 degrees C. Results suggested that CMT is best used as a diagnostic test for ovine subclinical mastitis (SCM) with a cut-off of 3 (distinct gel formation), and that automated SCC thresholds of > 1200 x 10(3) cells/ml are appropriate, especially where low prevalences are expected (e.g. < 5%). Additionally, this study showed that routine bacteriological methods were appropriate for isolation of most species of pathogen responsible for ovine SCM, but storage of samples prior to culture, either at 4 degrees C or -21 degrees C, was detrimental to the isolation of several of these organisms.

25OHD analogues and vacuum blood collection tubes dramatically affect the accuracy of automated immunoassays

PubMed Central

Yu, Songlin; Cheng, Xinqi; Fang, Huiling; Zhang, Ruiping; Han, Jianhua; Qin, Xuzhen; Cheng, Qian; Su, Wei; Hou, Li’an; Xia, Liangyu; Qiu, Ling

2015-01-01

Variations in vitamin D quantification methods are large, and influences of vitamin D analogues and blood collection methods have not been systematically examined. We evaluated the effects of vitamin D analogues 25OHD2 and 3-epi 25OHD3 and blood collection methods on vitamin D measurement, using five immunoassay systems and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Serum samples (332) were selected from routine vitamin D assay requests, including samples with or without 25OHD2 or 3-epi 25OHD3, and analysed using various immunoassay systems. In samples with no 25OHD2 or 3-epi 25OHD3, all immunoassays correlated well with LC-MS/MS. However, the Siemens system produced a large positive mean bias of 12.5 ng/mL and a poor Kappa value when using tubes with clot activator and gel separator. When 25OHD2 or 3-epi 25OHD3 was present, correlations and clinical agreement decreased for all immunoassays. Serum 25OHD in VACUETTE tubes with gel and clot activator, as measured by the Siemens system, produced significantly higher values than did samples collected in VACUETTE tubes with no additives. Bias decreased and clinical agreement improved significantly when using tubes with no additives. In conclusion, most automated immunoassays showed acceptable correlation and agreement with LC-MS/MS; however, 25OHD analogues and blood collection tubes dramatically affected accuracy. PMID:26420221

25OHD analogues and vacuum blood collection tubes dramatically affect the accuracy of automated immunoassays.

PubMed

Yu, Songlin; Cheng, Xinqi; Fang, Huiling; Zhang, Ruiping; Han, Jianhua; Qin, Xuzhen; Cheng, Qian; Su, Wei; Hou, Li'an; Xia, Liangyu; Qiu, Ling

2015-09-30

Variations in vitamin D quantification methods are large, and influences of vitamin D analogues and blood collection methods have not been systematically examined. We evaluated the effects of vitamin D analogues 25OHD2 and 3-epi 25OHD3 and blood collection methods on vitamin D measurement, using five immunoassay systems and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Serum samples (332) were selected from routine vitamin D assay requests, including samples with or without 25OHD2 or 3-epi 25OHD3, and analysed using various immunoassay systems. In samples with no 25OHD2 or 3-epi 25OHD3, all immunoassays correlated well with LC-MS/MS. However, the Siemens system produced a large positive mean bias of 12.5 ng/mL and a poor Kappa value when using tubes with clot activator and gel separator. When 25OHD2 or 3-epi 25OHD3 was present, correlations and clinical agreement decreased for all immunoassays. Serum 25OHD in VACUETTE tubes with gel and clot activator, as measured by the Siemens system, produced significantly higher values than did samples collected in VACUETTE tubes with no additives. Bias decreased and clinical agreement improved significantly when using tubes with no additives. In conclusion, most automated immunoassays showed acceptable correlation and agreement with LC-MS/MS; however, 25OHD analogues and blood collection tubes dramatically affected accuracy.

High-density grids for efficient data collection from multiple crystals

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

Baxter, Elizabeth L.; Aguila, Laura; Alonso-Mori, Roberto

Higher throughput methods to mount and collect data from multiple small and radiation-sensitive crystals are important to support challenging structural investigations using microfocus synchrotron beamlines. Furthermore, efficient sample-delivery methods are essential to carry out productive femtosecond crystallography experiments at X-ray free-electron laser (XFEL) sources such as the Linac Coherent Light Source (LCLS). To address these needs, a high-density sample grid useful as a scaffold for both crystal growth and diffraction data collection has been developed and utilized for efficient goniometer-based sample delivery at synchrotron and XFEL sources. A single grid contains 75 mounting ports and fits inside an SSRL cassettemore » or uni-puck storage container. The use of grids with an SSRL cassette expands the cassette capacity up to 7200 samples. Grids may also be covered with a polymer film or sleeve for efficient room-temperature data collection from multiple samples. New automated routines have been incorporated into theBlu-Ice/DCSSexperimental control system to support grids, including semi-automated grid alignment, fully automated positioning of grid ports, rastering and automated data collection. Specialized tools have been developed to support crystallization experiments on grids, including a universal adaptor, which allows grids to be filled by commercial liquid-handling robots, as well as incubation chambers, which support vapor-diffusion and lipidic cubic phase crystallization experiments. Experiments in which crystals were loaded into grids or grown on grids using liquid-handling robots and incubation chambers are described. As a result, crystals were screened at LCLS-XPP and SSRL BL12-2 at room temperature and cryogenic temperatures.« less

High-density grids for efficient data collection from multiple crystals

PubMed Central

Baxter, Elizabeth L.; Aguila, Laura; Alonso-Mori, Roberto; Barnes, Christopher O.; Bonagura, Christopher A.; Brehmer, Winnie; Brunger, Axel T.; Calero, Guillermo; Caradoc-Davies, Tom T.; Chatterjee, Ruchira; Degrado, William F.; Fraser, James S.; Ibrahim, Mohamed; Kern, Jan; Kobilka, Brian K.; Kruse, Andrew C.; Larsson, Karl M.; Lemke, Heinrik T.; Lyubimov, Artem Y.; Manglik, Aashish; McPhillips, Scott E.; Norgren, Erik; Pang, Siew S.; Soltis, S. M.; Song, Jinhu; Thomaston, Jessica; Tsai, Yingssu; Weis, William I.; Woldeyes, Rahel A.; Yachandra, Vittal; Yano, Junko; Zouni, Athina; Cohen, Aina E.

2016-01-01

Higher throughput methods to mount and collect data from multiple small and radiation-sensitive crystals are important to support challenging structural investigations using microfocus synchrotron beamlines. Furthermore, efficient sample-delivery methods are essential to carry out productive femtosecond crystallography experiments at X-ray free-electron laser (XFEL) sources such as the Linac Coherent Light Source (LCLS). To address these needs, a high-density sample grid useful as a scaffold for both crystal growth and diffraction data collection has been developed and utilized for efficient goniometer-based sample delivery at synchrotron and XFEL sources. A single grid contains 75 mounting ports and fits inside an SSRL cassette or uni-puck storage container. The use of grids with an SSRL cassette expands the cassette capacity up to 7200 samples. Grids may also be covered with a polymer film or sleeve for efficient room-temperature data collection from multiple samples. New automated routines have been incorporated into the Blu-Ice/DCSS experimental control system to support grids, including semi-automated grid alignment, fully automated positioning of grid ports, rastering and automated data collection. Specialized tools have been developed to support crystallization experiments on grids, including a universal adaptor, which allows grids to be filled by commercial liquid-handling robots, as well as incubation chambers, which support vapor-diffusion and lipidic cubic phase crystallization experiments. Experiments in which crystals were loaded into grids or grown on grids using liquid-handling robots and incubation chambers are described. Crystals were screened at LCLS-XPP and SSRL BL12-2 at room temperature and cryogenic temperatures. PMID:26894529

High-density grids for efficient data collection from multiple crystals

DOE PAGES

Baxter, Elizabeth L.; Aguila, Laura; Alonso-Mori, Roberto; ...

2015-11-03

Higher throughput methods to mount and collect data from multiple small and radiation-sensitive crystals are important to support challenging structural investigations using microfocus synchrotron beamlines. Furthermore, efficient sample-delivery methods are essential to carry out productive femtosecond crystallography experiments at X-ray free-electron laser (XFEL) sources such as the Linac Coherent Light Source (LCLS). To address these needs, a high-density sample grid useful as a scaffold for both crystal growth and diffraction data collection has been developed and utilized for efficient goniometer-based sample delivery at synchrotron and XFEL sources. A single grid contains 75 mounting ports and fits inside an SSRL cassettemore » or uni-puck storage container. The use of grids with an SSRL cassette expands the cassette capacity up to 7200 samples. Grids may also be covered with a polymer film or sleeve for efficient room-temperature data collection from multiple samples. New automated routines have been incorporated into theBlu-Ice/DCSSexperimental control system to support grids, including semi-automated grid alignment, fully automated positioning of grid ports, rastering and automated data collection. Specialized tools have been developed to support crystallization experiments on grids, including a universal adaptor, which allows grids to be filled by commercial liquid-handling robots, as well as incubation chambers, which support vapor-diffusion and lipidic cubic phase crystallization experiments. Experiments in which crystals were loaded into grids or grown on grids using liquid-handling robots and incubation chambers are described. As a result, crystals were screened at LCLS-XPP and SSRL BL12-2 at room temperature and cryogenic temperatures.« less

Site Environmental Report for 2009, Volume 2

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

Xu, Suying

2010-08-19

Volume II of the Site Environmental Report for 2009 is provided by Ernest Orlando Lawrence Berkeley National Laboratory as a supplemental appendix to Volume I, which contains the body of the report. Volume II contains the environmental monitoring and sampling data used to generate summary results of routine and nonroutine sampling at the Laboratory, except for groundwater sampling data, which may be found in the reports referred to in Chapter 4 of Volume I. The results from sample collections are more comprehensive in Volume II than in Volume I: for completeness, all results from sample collections that began or endedmore » in calendar year (CY) 2009 are included in this volume. However, the samples representing CY 2008 data have not been used in the summary results that are reported in Volume I. (For example, although ambient air samples collected on January 6, 2009, are presented in Volume II, they represent December 2008 data and are not included in Table 4-2 in Volume I.) When appropriate, sampling results are reported in both conventional and International System (SI) units. For some results, the rounding procedure used in data reporting may result in apparent differences between the numbers reported in SI and conventional units. (For example, stack air tritium results reported as < 1.5 Bq/m3 are shown variously as < 39 and < 41 pCi/m3. Both of these results are rounded correctly to two significant digits.)« less

Making sense of the shadows: priorities for creating a learning healthcare system based on routinely collected data.

PubMed

Deeny, Sarah R; Steventon, Adam

2015-08-01

Socrates described a group of people chained up inside a cave, who mistook shadows of objects on a wall for reality. This allegory comes to mind when considering 'routinely collected data'-the massive data sets, generated as part of the routine operation of the modern healthcare service. There is keen interest in routine data and the seemingly comprehensive view of healthcare they offer, and we outline a number of examples in which they were used successfully, including the Birmingham OwnHealth study, in which routine data were used with matched control groups to assess the effect of telephone health coaching on hospital utilisation.Routine data differ from data collected primarily for the purposes of research, and this means that analysts cannot assume that they provide the full or accurate clinical picture, let alone a full description of the health of the population. We show that major methodological challenges in using routine data arise from the difficulty of understanding the gap between patient and their 'data shadow'. Strategies to overcome this challenge include more extensive data linkage, developing analytical methods and collecting more data on a routine basis, including from the patient while away from the clinic. In addition, creating a learning health system will require greater alignment between the analysis and the decisions that will be taken; between analysts and people interested in quality improvement; and between the analysis undertaken and public attitudes regarding appropriate use of data. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Effect of peripheral IV based blood collection on catheter dwell time, blood collection, and patient response.

PubMed

Mulloy, Deborah F; Lee, Susan M; Gregas, Matthew; Hoffman, Kate E; Ashley, Stanley W

2018-04-01

To evaluate the effect of daily PIV-based phlebotomy using the PIVO device on PIVC dwell times and replacement rates, as well as the reliability of blood sample collection, and patient response to this method of blood collection. Blood draws which are also known as phlebotomy for laboratory analyses are one of the most common experiences for hospitalized patients. When performed by venipuncture, they are often associated with pain and anxiety for patients. Most hospitals avoid phlebotomy from peripheral IV catheters due to sample hemolysis, sample dilution by fluids in PIVC line or infused medications, PIVC dislodgement or infiltration, and increased rates of phlebitis. A prospective, randomized- controlled study of 160 GI surgery patients was enrolled. Patients were randomized to either control evaluation of PIVC dwell or to receive daily PIVO blood collections in addition to evaluation of PIVC dwell. Daily PIVO blood collections did not negatively affect PIVC dwell or replacement rates. Overall 81% of blood collection attempts were successful and the likelihood of success was strongly associated with PIVC condition. Patients reported 0.7/10 pain for PIVO blood collection on a 0-10 pain scale and a 9.1/10 preference for PIVO on a 0 (strongly prefer needle) to 10 (strongly prefer PIVO) preference scale. Results suggest that use of a PIV based blood collection was a reliable and valid approach and was superior to routine phlebotomy in self-reported responses from patients. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Native SAD is maturing.

PubMed

Rose, John P; Wang, Bi-Cheng; Weiss, Manfred S

2015-07-01

Native SAD phasing uses the anomalous scattering signal of light atoms in the crystalline, native samples of macromolecules collected from single-wavelength X-ray diffraction experiments. These atoms include sodium, magnesium, phosphorus, sulfur, chlorine, potassium and calcium. Native SAD phasing is challenging and is critically dependent on the collection of accurate data. Over the past five years, advances in diffraction hardware, crystallographic software, data-collection methods and strategies, and the use of data statistics have been witnessed which allow 'highly accurate data' to be routinely collected. Today, native SAD sits on the verge of becoming a 'first-choice' method for both de novo and molecular-replacement structure determination. This article will focus on advances that have caught the attention of the community over the past five years. It will also highlight both de novo native SAD structures and recent structures that were key to methods development.

General administrative rulings and decisions; amendment to the examination and investigation sample requirements; companion document to direct final rule--FDA. Proposed rule.

PubMed

1998-09-25

The Food and Drug Administration (FDA) is proposing to amend its regulations regarding the collection of twice the quantity of food, drug, or cosmetic estimated to be sufficient for analysis. This action increases the dollar amount that FDA will consider to determine whether to routinely collect a reserve sample of a food, drug, or cosmetic product in addition to the quantity sufficient for analysis. Experience has demonstrated that the current dollar amount does not adequately cover the cost of most quantities sufficient for analysis plus reserve samples. This proposed rule is a companion to the direct final rule published elsewhere in this issue of the Federal Register. This action is part of FDA's continuing effort to achieve the objectives of the President's "Reinventing Government" initiative, and it is intended to reduce the burden of unnecessary regulations on food, drugs, and cosmetics without diminishing the protection of the public health.

Routinely collected data as a strategic resource for research: priorities for methods and workforce.

PubMed

Jorm, Louisa

2015-09-30

In the era of 'big data', research using routinely collected data offers greater potential than ever before to drive health system effectiveness and efficiency, and population health improvement. In Australia, the policy environment, and emerging frameworks and processes for data governance and access, increasingly support the use of routinely collected data for research. Capitalising on this strategic resource requires investment in both research methods and research workforce. Priorities for methods development include validation studies, techniques for analysing complex longitudinal data, exploration of bias introduced through linkage error, and a robust toolkit to evaluate policies and programs using 'natural experiments'. Priorities for workforce development include broadening the skills base of the existing research workforce, and the formation of new, larger, interdisciplinary research teams to incorporate capabilities in computer science, partnership research, research translation and the 'business' aspects of research. Large-scale, long-term partnership approaches involving government, industry and researchers offer the most promising way to maximise returns on investment in research using routinely collected data.

Determining health personnel's application trends of new guidelines for preoperative fasting: findings from a survey.

PubMed

Karadağ, Mevlüde; Pekin İşeri, Ozge

2014-06-01

For over a century, the discontinuation of oral food intake preoperatively after midnight has been routinely applied. Although routine fasting during the night before elective surgery has been abandoned by many modern centers, preoperative fasting after midnight continues as a routine practice. The purpose of this study was to determine trends in health personnel's application of new guidelines for preoperative fasting. The research sample of this descriptive study consisted of 73 nurses and physicians who were working in the surgical clinics during the time when the study was conducted and who agreed to participate in the study. The data of the study were collected using a questionnaire designed by the researchers. Of the health personnel included in the study group, 43.8% routinely kept adult patients fasting after midnight, 34.2% discontinued solid food intake 8 hours preoperatively, 5.5% discontinued solid food intake 6 hours preoperatively, and 34.2% discontinued the intake of clear and particulate liquids 4 to 8 hours preoperatively. Compliance of the American Society of Anesthesiologists' "2-4-6-8 rule" by health staff was very low. This study was carried out in a hospital and based on the statements of health staff. Therefore, the findings of the study are suggestive in nature and cannot be generalized. We recommend that the study should be conducted with larger sample groups and that actual preoperative fasting periods of the patients should be determined. Copyright © 2014 American Society of PeriAnesthesia Nurses. Published by Elsevier Inc. All rights reserved.

Evaluating ethanol-based sample preservation to facilitate use of DNA barcoding in routine freshwater biomonitoring programs using benthic macroinvertebrates.

PubMed

Stein, Eric D; White, Bryan P; Mazor, Raphael D; Miller, Peter E; Pilgrim, Erik M

2013-01-01

Molecular methods, such as DNA barcoding, have the potential to enhance biomonitoring programs worldwide. Altering routinely used sample preservation methods to protect DNA from degradation may pose a potential impediment to application of DNA barcoding and metagenomics for biomonitoring using benthic macroinvertebrates. Using higher volumes or concentrations of ethanol, requirements for shorter holding times, or the need to include additional filtering may increase cost and logistical constraints to existing biomonitoring programs. To address this issue we evaluated the efficacy of various ethanol-based sample preservation methods at maintaining DNA integrity. We evaluated a series of methods that were minimally modified from typical field protocols in order to identify an approach that can be readily incorporated into existing monitoring programs. Benthic macroinvertebrates were collected from a minimally disturbed stream in southern California, USA and subjected to one of six preservation treatments. Ten individuals from five taxa were selected from each treatment and processed to produce DNA barcodes from the mitochondrial gene cytochrome c oxidase I (COI). On average, we obtained successful COI sequences (i.e. either full or partial barcodes) for between 93-99% of all specimens across all six treatments. As long as samples were initially preserved in 95% ethanol, successful sequencing of COI barcodes was not affected by a low dilution ratio of 2∶1, transfer to 70% ethanol, presence of abundant organic matter, or holding times of up to six months. Barcoding success varied by taxa, with Leptohyphidae (Ephemeroptera) producing the lowest barcode success rate, most likely due to poor PCR primer efficiency. Differential barcoding success rates have the potential to introduce spurious results. However, routine preservation methods can largely be used without adverse effects on DNA integrity.

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

PubMed Central

Stein, Eric D.; White, Bryan P.; Mazor, Raphael D.; Miller, Peter E.; Pilgrim, Erik M.

2013-01-01

Molecular methods, such as DNA barcoding, have the potential to enhance biomonitoring programs worldwide. Altering routinely used sample preservation methods to protect DNA from degradation may pose a potential impediment to application of DNA barcoding and metagenomics for biomonitoring using benthic macroinvertebrates. Using higher volumes or concentrations of ethanol, requirements for shorter holding times, or the need to include additional filtering may increase cost and logistical constraints to existing biomonitoring programs. To address this issue we evaluated the efficacy of various ethanol-based sample preservation methods at maintaining DNA integrity. We evaluated a series of methods that were minimally modified from typical field protocols in order to identify an approach that can be readily incorporated into existing monitoring programs. Benthic macroinvertebrates were collected from a minimally disturbed stream in southern California, USA and subjected to one of six preservation treatments. Ten individuals from five taxa were selected from each treatment and processed to produce DNA barcodes from the mitochondrial gene cytochrome c oxidase I (COI). On average, we obtained successful COI sequences (i.e. either full or partial barcodes) for between 93–99% of all specimens across all six treatments. As long as samples were initially preserved in 95% ethanol, successful sequencing of COI barcodes was not affected by a low dilution ratio of 2∶1, transfer to 70% ethanol, presence of abundant organic matter, or holding times of up to six months. Barcoding success varied by taxa, with Leptohyphidae (Ephemeroptera) producing the lowest barcode success rate, most likely due to poor PCR primer efficiency. Differential barcoding success rates have the potential to introduce spurious results. However, routine preservation methods can largely be used without adverse effects on DNA integrity. PMID:23308097

Application of drug testing using exhaled breath for compliance monitoring of drug addicts in treatment.

PubMed

Carlsson, Sten; Olsson, Robert; Lindkvist, Irene; Beck, Olof

2015-04-01

Exhaled breath has recently been identified as a possible matrix for drug testing. This study explored the potential of this new method for compliance monitoring of patients being treated for dependence disorders. Outpatients in treatment programs were recruited for this study. Urine was collected as part of clinical routine and a breath sample was collected in parallel together with a questionnaire about their views of the testing procedure. Urine was analyzed for amphetamines, benzodiazepines, cannabis, cocaine, buprenorphine, methadone and opiates using CEDIA immunochemical screening and mass spectrometry confirmation. The exhaled breath was collected using the SensAbues device and analyzed by mass spectrometry for amphetamine, methamphetamine, diazepam, oxazepam, tetrahydrocannabinol, cocaine, benzoylecgonine, buprenorphine, methadone, morphine, codeine and 6-acetylmorphine. A total of 122 cases with parallel urine and breath samples were collected; 34 of these were negative both in urine and breath. Out of 88 cases with positive urine samples 51 (58%) were also positive in breath. Among the patients on methadone treatment, all were positive for methadone in urine and 83% were positive in breath. Among patients in treatment with buprenorphine, 92% were positive in urine and among those 80% were also positive in breath. The questionnaire response documented that in general, patients accepted drug testing well and that the breath sampling procedure was preferred. Compliance testing for the intake of prescribed and unprescribed drugs among patients in treatment for dependence disorders using the exhaled breath sampling technique is a viable method and deserves future attention.

The Savannah River Site's Groundwater Monitoring Program

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

Not Available

1989-01-01

The Environmental Monitoring Section of the Environmental and Health Protection (EHP) Department administers the Savannah River Site's Groundwater Monitoring Program. During fourth quarter 1989 (October--December), EHP conducted routine sampling of monitoring wells and drinking water locations. EHP collected the drinking water samples from Savannah River Site (SRS) drinking water systems supplied by wells. EHP established two sets of flagging criteria in 1986 to assist in the management of sample results. The flagging criteria aid personnel in sample scheduling, interpretation of data, and trend identification. An explanation of flagging criteria for the fourth quarter is presented in the Flagging Criteria sectionmore » of this document. All analytical results from fourth quarter 1989 are listed in this report, which is distributed to all waste-site custodians.« less

The Savannah River Site`s Groundwater Monitoring Program. Fourth quarter, 1989

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

Not Available

1989-12-31

The Environmental Monitoring Section of the Environmental and Health Protection (EHP) Department administers the Savannah River Site`s Groundwater Monitoring Program. During fourth quarter 1989 (October--December), EHP conducted routine sampling of monitoring wells and drinking water locations. EHP collected the drinking water samples from Savannah River Site (SRS) drinking water systems supplied by wells. EHP established two sets of flagging criteria in 1986 to assist in the management of sample results. The flagging criteria aid personnel in sample scheduling, interpretation of data, and trend identification. An explanation of flagging criteria for the fourth quarter is presented in the Flagging Criteria sectionmore » of this document. All analytical results from fourth quarter 1989 are listed in this report, which is distributed to all waste-site custodians.« less

Biobanking of fresh frozen tissue from clinical surgical specimens: transport logistics, sample selection, and histologic characterization.

PubMed

Botling, Johan; Micke, Patrick

2011-01-01

Access to high-quality fresh frozen tissue is critical for translational cancer research and molecular -diagnostics. Here we describe a workflow for the collection of frozen solid tissue samples derived from fresh human patient specimens after surgery. The routines have been in operation at Uppsala University Hospital since 2001. We have integrated cryosection and histopathologic examination of each biobank sample into the biobank manual. In this way, even small, macroscopically ill-defined lesions can be -procured without a diagnostic hazard due to the removal of uncharacterized tissue from a clinical -specimen. Also, knowledge of the histomorphology of the frozen tissue sample - tumor cell content, stromal components, and presence of necrosis - is pivotal before entering a biobank case into costly molecular profiling studies.

Effect of ambient temperature storage on potable water coliform population estimations.

PubMed Central

Standridge, J H; Delfino, J J

1983-01-01

The effect of the length of time between sampling potable water and performing coliform analyses has been a long-standing controversial issue in environmental microbiology. The issue is of practical importance since reducing the sample-to-analysis time may substantially increase costs for water analysis programs. Randomly selected samples (from those routinely collected throughout the State of Wisconsin) were analyzed for total coliforms after being held at room temperature (20 +/- 2 degrees C) for 24 and 48 h. Differences in results for the two holding times were compared with differences predicted by probability calculations. The study showed that storage of the potable water for up to 48 h had little effect on the public health significance of most samples containing more than two coliforms per 100 ml. PMID:6651296

[An epidemic risk of yellow fever in Burkina Faso despite a rapid immunisation riposte: role of a multidisciplinary investigation team].

PubMed

Barennes, H; Baldet, T; Cassel, A-M; Kabiré, C; Kambou, C

2002-01-01

On October 8, 1999, one yellow fever (YF) case is confirmed in the South West of Burkina Faso by the Centre Muraz' virology unit. Epidemic extension is suspected as large movements of population are occurring due to troubles in Côte d'Ivoire nearby and as the Aedes vector is endemic in the region. On October 23, the Gaoua's Health Regional Head immunizes 1,000 people around the detected YF case, i.e. 70% of the estimated population and requests an epidemiological investigation. A multidisciplinary team (epidemiologist, entomologist, virologist) from the Centre Muraz, a medical research centre based in Bobo Dioulasso investigate in order to answer the following questions: are there any other or asymptomatic cases of YF? How far is the epidemic risk? Is a paper filter a valuable method for collecting blood samples? What benefit can be gained from a multidisciplinary team? An epidemiological analysis of the patient, a research of asymptomatic or ignored patient is performed (Health Centre registers, interview of the population). This includes the research of people missing the immunisation campaign. Blood samples are collected through 5 ml EDTA glass tubes or through filter paper in order to measure immunoglobuline M. A classical entomological prospecting completes the investigation. Two possible cases are suspected in the patient's home. History of the patient's is in agreement with a local contamination. In the village 110 people missed the immunisation campaign and samples were collected in 58 people including 26 children. Among them, four (15.3%) were positive with immunoglobuline M, while there were none in the adults. Aedes Luteocephalus, a potential vector is collected through night-captures but is absent of home-water collection. Paper filter assays shows a 100% concordance with classical method. The team could determine the persistency of a yellow fever epidemic risk in the region despite a rapid and adequate immunisation riposte. Due to iterative sporadic cases and due to population movement, a routine survey of YF has to be promoted as the immune status of the population, particularly in the youth, do not protect them. Collection of blood through paper filter will greatly help the routine survey and shall be confirmed during the following investigations.

Screening for microplastic particles in plankton samples: How to integrate marine litter assessment into existing monitoring programs?

PubMed

Gorokhova, Elena

2015-10-15

Microplastics (MPs) are a newly recognized type of environmental pollution in aquatic systems; however no monitoring of these contaminants is conducted, mostly due to the lack of routine quantification. In the net samples collected with a 90-μm WP2 net, pelagic MP abundance was quantified by light microscopy and evaluated as a function of inshore-offshore gradient, depth, and season; the same samples were used for zooplankton analysis. The MP abundance was ∼10(2)-10(4)particlesm(-3), with no significant inshore-offshore gradient during summer but increasing offshore in winter. MP abundance in deeper layers was positively affected by zooplankton abundance in the upper layers and significantly lower during winter compared to summer. These findings indicate heterogeneity of MP distribution due to biotic and abiotic factors and suggest that samples collected for other purposes can be used for quantification of MPs in the Baltic Sea, thus facilitating integration of MP assessment into existing monitoring schemes. Copyright © 2015 Elsevier Ltd. All rights reserved.

90-kilobar diamond-anvil high-pressure cell for use on an automatic diffractometer.

PubMed

Schiferl, D; Jamieson, J C; Lenko, J E

1978-03-01

A gasketed diamond-anvil high-pressure cell is described which can be used on a four-circle automatic diffractometer to collect x-ray intensity data from single-crystal samples subjected to truly hydrostatic pressures of over 90 kilobars. The force generating system exerts only forces normal to the diamond faces to obtain maximum reliability. A unique design allows exceptionally large open areas for maximum x-ray access and is particularly well suited for highly absorbing materials, as the x rays are not transmitted through the sample. Studies on ruby show that high-pressure crystal structure determinations may be done rapidly, reliably, and routinely with this system.

External quality-assurance results for the National Atmospheric Deposition Program/National Trends Network, 1995-96

USGS Publications Warehouse

Gordon, John D.

1999-01-01

The U.S. Geological Survey operated four external quality-assurance programs for the National Atmospheric Deposition Program/National Trends Network (NADP/NTN) in 1995 and 1996: the intersite-comparison program, the blind-audit program, the interlaboratory- comparison program, and the collocated-sampler program. The intersite-comparison program assessed the precision and bias of pH and specific-conductance determinations made by NADP/NTN site operators. The analytical bias introduced during routine handling, processing, and shipping of wet-deposition samples and precision of analyte values was estimated using a blind-audit program. An interlaboratory-comparison program was used to evaluate differences between analytical results and to estimate the analytical precision of five North American laboratories that routinely analyzed wet deposition. A collocated-sampler program estimated the precision of the overall precipitation collection and analysis system from initial sample collection through final storage of the data. Results of two intersite-comparison studies completed in 1995 indicated 94.6 and 94.4 percent of the onsite pH determinations met the NADP/NTN accuracy goals, whereas 97.2 and 98.3 percent of the specific-conductance determinations were within the established limits. The percentages of onsite determinations that met the accuracy goals in 1996 were slightly less for both pH and specific-conductance than in 1995. In 1996, 93.2 and 87.5 percent of onsite pH determinations met the accuracy goals, whereas the percentage of onsite specific-conductance measurements that met the goals was 93.9 and 94.9 percent.The blind audit program utilizes a paired sample design to evaluate the effects of routine sample handling, processing and shipping on the chemistry of weekly precipitation samples. The portion of the blind audit sample subject to all of the normal onsite handling and processing steps of a regular weekly precipitation sample is referred to as the bucket portion, whereas the portion receiving only minimal handling is referred to as the bottle portion. Throughout the report, the term positive bias in regard to blind-audit results indicates that the bucket portion had a higher concentration than the bottle portion. The paired t-test of 1995 blind-audit data indicated that routine sample handling, processing, and shipping introduced a very small positive bias (a=0.05) for hydrogen ion and specific conductance and a slight negative bias (a =0.05) for ammonium and sodium. In 1995, the median paired differences between the bucket and bottle portions ranged from -0.02 milligram per liter for both ammonium and nitrate to +0.002 milligram per liter for calcium. Although the paired t-test indicated a very small positive bias for hydrogen ion, the median paired difference between the bucket and bottle portions was 0.00 microequivalents per liter, whereas for specific conductance, the median paired difference between the bucket and bottle portions was 0.200 microsiemens per centimeter in 1995. The paired t-test of blind-audit results in 1996 indicated statistically significant bias for 6 of the 10 analytes. Only chloride, nitrate, hydrogen ion, and specific conductance were not biased in 1996. However, the magnitude of the bias in 1996 was very small and only of limited importance from the viewpoint of an analytical chemist or data user. The median paired differences between the bucket and bottle portions ranged from -0.02 milligram per liter for both ammonium and chloride to +0.006 milligram per liter for calcium. For hydrogen ion, the median paired difference between the bucket and bottle portions was -0.357 microequivalent per liter; for specific conductance, the median paired difference between the bucket and bottle portions was 0.00 microsiemens per centimeter in 1996. Surface-chemistry effects due to different amounts of precipitation contacting the sample collection and shipping container surfac

Nevada Applied Ecology Group procedures handbook for environmental transuranics

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

White, M.G.; Dunaway, P.B.

The activities of the Nevada Applied Ecology Group (NAEG) integrated research studies of environmental plutonium and other transuranics at the Nevada Test Site have required many standardized field and laboratory procedures. These include sampling techniques, collection and preparation, radiochemical and wet chemistry analysis, data bank storage and reporting, and statistical considerations for environmental samples of soil, vegetation, resuspended particles, animals, and others. This document, printed in two volumes, includes most of the Nevada Applied Ecology Group standard procedures, with explanations as to the specific applications involved in the environmental studies. Where there is more than one document concerning a procedure,more » it has been included to indicate special studies or applications perhaps more complex than the routine standard sampling procedures utilized.« less

Nevada Applied Ecology Group procedures handbook for environmental transuranics

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

White, M.G.; Dunaway, P.B.

The activities of the Nevada Applied Ecology Group (NAEG) integrated research studies of environmental plutonium and other transuranics at the Nevada Test Site have required many standardized field and laboratory procedures. These include sampling techniques, collection and preparation, radiochemical and wet chemistry analysis, data bank storage and reporting, and statistical considerations for environmental samples of soil, vegetation, resuspended particles, animals, and other biological material. This document, printed in two volumes, includes most of the Nevada Applied Ecology Group standard procedures, with explanations as to the specific applications involved in the environmental studies. Where there is more than one document concerningmore » a procedure, it has been included to indicate special studies or applications more complex than the routine standard sampling procedures utilized.« less

A portable cryo-plunger for on-site intact cryogenic microscopy sample preparation in natural environments.

PubMed

Comolli, Luis R; Duarte, Robert; Baum, Dennis; Luef, Birgit; Downing, Kenneth H; Larson, David M; Csencsits, Roseann; Banfield, Jillian F

2012-06-01

We present a modern, light portable device specifically designed for environmental samples for cryogenic transmission-electron microscopy (cryo-TEM) by on-site cryo-plunging. The power of cryo-TEM comes from preparation of artifact-free samples. However, in many studies, the samples must be collected at remote field locations, and the time involved in transporting samples back to the laboratory for cryogenic preservation can lead to severe degradation artifacts. Thus, going back to the basics, we developed a simple mechanical device that is light and easy to transport on foot yet effective. With the system design presented here we are able to obtain cryo-samples of microbes and microbial communities not possible to culture, in their near-intact environmental conditions as well as in routine laboratory work, and in real time. This methodology thus enables us to bring the power of cryo-TEM to microbial ecology. Copyright © 2011 Wiley Periodicals, Inc.

[Standardization of Blastocystis hominis diagnosis using different staining techniques].

PubMed

Eymael, Dayane; Schuh, Graziela Maria; Tavares, Rejane Giacomelli

2010-01-01

The present study was carried out from March to May 2008, with the aim of evaluating the effectiveness of different techniques for diagnosing Blastocystis hominis in a sample of the population attended at the Biomedicine Laboratory of Feevale University, Novo Hamburgo, Rio Grande do Sul. On hundred feces samples from children and adults were evaluated. After collection, the samples were subjected to the techniques of spontaneous sedimentation (HPJ), sedimentation in formalin-ether (Ritchie) and staining by means of Gram and May-Grünwald-Giemsa (MGG). The presence of Blastocystis hominis was observed in 40 samples, when staining techniques were used (MGG and Gram), while sedimentation techniques were less efficient (32 positive samples using the Ritchie technique and 20 positive samples using the HPJ technique). Our results demonstrate that HPJ was less efficient than the other methods, thus indicating the need to include laboratory techniques that enable parasite identification on a routine basis.

Ecological Congruence Assessment for Classroom Activities and Routines: Identifying Goals and Intervention Practices in Childcare.

ERIC Educational Resources Information Center

Wolery, Mark; Brashers, Margaret Sigalove; Neitzel, Jennifer C.

2002-01-01

This article explains how educators can use the ecological congruence assessment process for identifying functional goals for young children with disabilities. Process steps include: teacher collects information about functioning in usual classroom activities, routines, and transitions; summarizes the collected information; and shares the…

Whooping cough in Pakistan: Bordetella pertussis vs Bordetella parapertussis in 2005-2009.

PubMed

Bokhari, Habib; Said, Fahad; Syed, Muhammad A; Mughal, Amjad; Kazi, Yasmeen F; Heuvelman, Kees; Mooi, Frits R

2011-10-01

Pertussis, or whooping cough, is an acute respiratory disease mainly affecting infants and children and is caused by Bordetella pertussis and Bordetella parapertussis. The aim of this study was to investigate the share of Bordetella species from potential whooping cough cases during 2005-2009. Eight hundred and two samples from suspected pertussis cases were collected, mainly from 2 provinces of Pakistan. Bacterial culture, identification, DNA extraction and routinely used polymerase chain reaction (PCR) methods using IS1001, IS1002 and IS481 were used to identify the Bordetella species. The results were unexpected, because all of the isolates collected from the different cities were identified as B. parapertussis (7.4%); B. pertussis was not isolated from any sample. However, PCR results indicated the presence of a small percentage (0.6%) of B. pertussis among the total cases studied. This study suggests that vaccines to protect against both B. pertussis and B. parapertussis should be considered.

Water quality in the tidal Potomac River and Estuary, hydrologic data report, 1979 water year

USGS Publications Warehouse

Blanchard, Stephen F.; Hahl, D.C.

1981-01-01

This report contains data on the physical and chemical properties measured during the 1979 water year for the tidal Potomac River and estuary. Data were collected routinely at five major stations and periodically at 14 intervening stations. Each major station represents a cross section through which the transport of selected dissolved and suspended materials will be computed. The intervening stations represent locations at which data were collected for special studies such as: salt water migration, dissolved oxygen dynamics, and other synoptic studies. About 960 samples were analyzed for silicate, Kjeldhal nitrogen, nitrite, phosphorus, chlorophyll and suspended sediment, with additional samples analyzed for organic carbon, calcium, magnesium, sodium, bicarbonate, sulfate, potassium, chloride, fluoride, seston and dissolved solids residue. In addition, about 1400 in-situ measurements of dissolved oxygen, specific conductance, temperature, and Secchi disk transparency are reported. (USGS)

Significance of microcystin production by benthic communities in water treatment systems of arid zones.

PubMed

Hurtado, I; Aboal, M; Zafra, E; Campillo, D

2008-02-01

The study of the dynamics of phytobenthic and phytoplankton communities was undertaken, during a year, in the regulation reservoir associated with a water treatment plant (WTP), which provides the city of Murcia (Spain) with drinking water. Water samples were collected in different stages of the treatment. In the reservoir, the presence of dissolved and intracellular microcystins is constant, both in benthos and in plankton. The collected samples show a positive correlation between the dissolved microcystins and the benthic ones in the reservoir itself, as well as in an upstream reservoir (Ojós Reservoir). The treatment process (ozone+clarification+ozone+activated carbon) is very effective in the removal of toxins, and the drinking water produced is totally free of microcystins. The incorporation of the benthic communities in the routine check for the presence of microcystins is recommended, since it is not compulsory according to the current legislation.

Is It Okay To Ask: Transgender Patient Perspectives on Sexual Orientation and Gender Identity Collection in Healthcare.

PubMed

Maragh-Bass, Allysha C; Torain, Maya; Adler, Rachel; Ranjit, Anju; Schneider, Eric; Shields, Ryan Y; Kodadek, Lisa M; Snyder, Claire F; German, Danielle; Peterson, Susan; Schuur, Jeremiah; Lau, Brandyn D; Haider, Adil H

2017-06-01

The National Academy of Medicine and Joint Commission recommend routine documentation of sexual orientation (SO) and gender identity (GI) in healthcare to address lesbian, gay, bisexual, or transgender (LGBT) health disparities. We explored transgender patient-reported views on the importance on SO/GI collection, their willingness to disclose, and their perceived facilitators of SO/GI collection in primary care and emergency department (ED) settings. We recruited a national sample of self-identified transgender patients. Participants completed demographic questions, survey questions, and free-response comments regarding their views on SO/GI collection. Data were analyzed using descriptive statistics; inductive content analysis was conducted with open-ended responses. Patients mostly self-identified as male gender (54.5%), white (58.4%), and SO other than heterosexual or LGB (33.7%; N = 101). Patients felt that it was more important for primary care providers to know their GI than SO (89.1% vs. 57%; p < 0.001); there was no difference among reported importance for ED providers to know the patients' SO versus GI. Females were more likely than males to report medical relevance to chief complaint as a facilitator to SO disclosure (89.1% vs. 80%; p = 0.02) and less likely to identify routine collection from all patients as a facilitator to GI disclosure (67.4% vs. 78.2%; p = 0.09). Qualitatively, many patients reported that medical relevance to chief complaint and an LGBT-friendly environment would increase willingness to disclose their SO/GI. Patients also reported need for educating providers in LGBT health prior to implementing routine SO/GI collection. Patients see the importance of providing GI more than SO to providers; nonetheless they are willing to disclose SO/GI in general.. Findings also suggest that gender differences may exist in facilitators of SO/GI disclosure. Given the underrepresentation of transgender patients in healthcare, it is crucial for providers to address their concerns with SO/GI disclosure, which include LGBT education for medical staff and provision of a safe environment. © 2017 by the Society for Academic Emergency Medicine.

Emergency Department Query for Patient-Centered Approaches to Sexual Orientation and Gender Identity : The EQUALITY Study.

PubMed

Haider, Adil H; Schneider, Eric B; Kodadek, Lisa M; Adler, Rachel R; Ranjit, Anju; Torain, Maya; Shields, Ryan Y; Snyder, Claire; Schuur, Jeremiah D; Vail, Laura; German, Danielle; Peterson, Susan; Lau, Brandyn D

2017-06-01

The Institute of Medicine and The Joint Commission recommend routine documentation of patients' sexual orientation in health care settings. Currently, very few health care systems collect these data since patient preferences and health care professionals' support regarding collection of data about patient sexual orientation are unknown. To identify the optimal patient-centered approach to collect sexual orientation data in the emergency department (ED) in the Emergency Department Query for Patient-Centered Approaches to Sexual Orientation and Gender Identity study. An exploratory, sequential, mixed-methods design was used first to evaluate qualitative interviews conducted in the Baltimore, Maryland, and Washington, DC, areas. Fifty-three patients and 26 health care professionals participated in the qualitative interviews. Interviews were followed by a national online survey, in which 1516 (potential) patients (244 lesbian, 289 gay, 179 bisexual, and 804 straight) and 429 ED health care professionals (209 physicians and 220 nurses) participated. Survey participants were recruited using random digit dialing and address-based sampling techniques. Qualitative interviews were used to obtain the perspectives of patients and health care professionals on sexual orientation data collection, and a quantitative survey was used to gauge patients' and health care professionals' willingness to provide or obtain sexual orientation information. Mean (SD) age of patient and clinician participants was 49 (16.4) and 51 (9.4) years, respectively. Qualitative interviews suggested that patients were less likely to refuse to provide sexual orientation than providers expected. Nationally, 154 patients (10.3%) reported that they would refuse to provide sexual orientation; however, 333 (77.8%) of all clinicians thought patients would refuse to provide sexual orientation. After adjustment for demographic characteristics, only bisexual patients had increased odds of refusing to provide sexual orientation compared with heterosexual patients (odds ratio, 2.40; 95% CI, 1.26-4.56). Patients and health care professionals have discordant views on routine collection of data on sexual orientation. A minority of patients would refuse to provide sexual orientation. Implementation of a standardized, patient-centered approach for routine collection of sexual orientation data is required on a national scale to help to identify and address health disparities among lesbian, gay, and bisexual populations.

Routine testing of Mycoplasma genitalium and Trichomonas vaginalis.

PubMed

Jenniskens, Marieke L M; Veerbeek, Jan H W; Deurloo, Koen L; van Hannen, Erik J; Thijsen, Steven F T

2017-06-01

Mycoplasma genitalium (MG) and Trichomonas vaginalis (TV) are common sexual transmitted infections (STI). However, most STI screening programmes do not include routinely detection of these pathogens. Consequently, epidemiological data about MG and TV in the general population is lacking. The current study aims to give insight into the prevalence of both infections, thereby guiding decisions whether testing for these pathogens should be included routinely. Between February 2013 and August 2015, all samples sent to the laboratory of Diakonessenhuis Utrecht for STI testing (i.e. testing for Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG)) were additionally examined for the presence of MG and TV by means of a laboratory-developed RT-PCR. Samples were collected by our hospital or by regional general practitioners. A total of 5628 PCR's were evaluated. In 7.5%, one or more STI were detected. CT was found in 5% and MG was positive in 1.9%. NG was detected in 0.5% and TV was detected in 0.6% of the samples. CT was found more often in primary care than in hospital setting (9.7% vs. 3.0%, p < .05). The same was shown for NG (1.1% vs. 0.2%, p < .05). More men than women were positive for CT (11.2% vs. 3.8%, p < .05) and NG (1.4% vs. 0.3%, p < .05). MG is more prevalent than NG and TV in a regional Dutch population. Furthermore, TV is equally common as NG. Based on our prevalence data, including MG and TV in STI testing protocols should be considered in the future.

Prevalence and risk factors for patent Toxocara infections in cats and cat owners' attitude towards deworming.

PubMed

Nijsse, R; Ploeger, H W; Wagenaar, J A; Mughini-Gras, L

2016-12-01

The prevalence of and risk factors for shedding Toxocara eggs in cats older than 6 months were determined by examining 670 faecal samples collected in 4 cross-sectional studies in the Netherlands. Additionally, cat owners provided information on their attitude towards routine deworming. Samples were examined using the centrifugal sedimentation flotation method. Overall Toxocara prevalence was 7.2 %. Multivariable logistic regression analysis revealed that young age and living in rural areas were significant risk factors for shedding Toxocara eggs. Moreover, the more time a cat was allowed to roam outdoors, the higher was its risk to shed Toxocara as compared to cats with no outdoor access at all. For 199 cats (81.6 % of cats subjected to a deworming regimen) owners provided the reason for treatment. The main reason for routine deworming (80.4 %) concerned the cat's health and only 10.6 % of the cats were treated for public health reasons. Moreover, the generally advocated four-times-a-year deworming advice was applied on only 24.5 % of cats. We concluded that free roaming is a key factor in the acquisition of patent Toxocara infections leading to the environmental contamination with Toxocara eggs. Additionally, the knowledge of cat owners is still insufficient to expect them to make sound decisions on routine deworming.

Significance of biological resource collection and tumor tissue bank creation.

PubMed

Yu, Ying-Yan; Zhu, Zheng-Gang

2010-01-15

Progress in the molecular oncology of gastrointestinal carcinomas depends on high quality cancer tissues for research. Recent acceleration on new technological platforms as well as the "omics" revolution increases the demands on tissues and peripheral blood for research at the DNA, mRNA and protein levels. Tissue bank creation emerges as a priority. Tumor tissue banks are facilities that are organized to collect, store and distribute samples of tumor and normal tissue for further use in basic and translational cancer research. The samples are generally obtained immediately after excision, prior to fixation, to ensure optimal preservation of proteins and nucleic acids. It is possible for surgeons or pathologists to collect fresh tissue prospectively during their routine dissection procedures. Most tissue banks are "project-driven" tumor banks, which are specialized collections of tumor samples on which their research is based. Systematic collection of all available tumor tissue is much rarer. High quality tissue banks need the collaboration of clinicians and basic scientists, but also the informed consent of patients and ethical approval. Through the standard operation procedure, snap frozen fresh tissue collection, storage and quality control for cryopreserved tissues are the pivotal factors on tissue bank construction and maintaining. The purpose of the tissue bank creation is enhancing the quality and speed on both the basic and translational research on gastrointestinal cancer. The quality assurance and quality control are handled based on reviewing HE staining slides or touch imprint cytology by pathologists.

Evacuated blood-collection tubes for haematological tests - a quality evaluation prior to their intended use for specimen collection.

PubMed

Gros, Nataša

2013-05-01

An inappropriate anticoagulant concentration in a blood sample can cause cell shrinkage and affect the haematocrit and mean corpuscular volume (MCV). In evacuated blood-collection tubes there are two parameters affecting the quality of the product: the anticoagulant amount introduced into the tube during its production and the internal under-pressure at the instant of the blood-specimen collection affecting the draw-volume. No testing procedures that would give an insight into the anticoagulant concentration that can be expected for blood samples after specimen collection have been available up until now. The methodology suggested here combines the draw-volume test performed with deionised water using a laboratory made measuring device, and a conductivity measurement. The corrections taking into account the air pressure and ambient temperature provide an insight into the anticoagulant concentration that can be expected for blood samples. Results presented in the form of a nomogram facilitate the routine use of the suggested methodology. Our 338-day study confirmed significant differences and variations in the quality and the anticoagulant concentrations of the K₃EDTA and K2EDTA tubes of different producers and identified different examples of non-compliance with the norms during the shelf life of the tubes. The quality evaluation of the evacuated blood-collection tubes prior to their intended use as suggested here can, in everyday laboratory practice, ensure that the tubes are used only if, and only until, their quality is adequate.

Advanced flight design systems subsystem performance models. Sample model: Environmental analysis routine library

NASA Technical Reports Server (NTRS)

Parker, K. C.; Torian, J. G.

1980-01-01

A sample environmental control and life support model performance analysis using the environmental analysis routines library is presented. An example of a complete model set up and execution is provided. The particular model was synthesized to utilize all of the component performance routines and most of the program options.

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

PubMed Central

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

2016-01-01

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

Inferring microevolution from museum collections and resampling: lessons learned from Cepaea.

PubMed

Ożgo, Małgorzata; Liew, Thor-Seng; Webster, Nicole B; Schilthuizen, Menno

2017-01-01

Natural history collections are an important and largely untapped source of long-term data on evolutionary changes in wild populations. Here, we utilize three large geo-referenced sets of samples of the common European land-snail Cepaea nemoralis stored in the collection of Naturalis Biodiversity Center in Leiden, the Netherlands. Resampling of these populations allowed us to gain insight into changes occurring over 95, 69, and 50 years. Cepaea nemoralis is polymorphic for the colour and banding of the shell; the mode of inheritance of these patterns is known, and the polymorphism is under both thermal and predatory selection. At two sites the general direction of changes was towards lighter shells (yellow and less heavily banded), which is consistent with predictions based on on-going climatic change. At one site no directional changes were detected. At all sites there were significant shifts in morph frequencies between years, and our study contributes to the recognition that short-term changes in the states of populations often exceed long-term trends. Our interpretation was limited by the few time points available in the studied collections. We therefore stress the need for natural history collections to routinely collect large samples of common species, to allow much more reliable hind-casting of evolutionary responses to environmental change.

Collection of biological samples in forensic toxicology.

PubMed

Dinis-Oliveira, R J; Carvalho, F; Duarte, J A; Remião, F; Marques, A; Santos, A; Magalhães, T

2010-09-01

Forensic toxicology is the study and practice of the application of toxicology to the purposes of the law. The relevance of any finding is determined, in the first instance, by the nature and integrity of the specimen(s) submitted for analysis. This means that there are several specific challenges to select and collect specimens for ante-mortem and post-mortem toxicology investigation. Post-mortem specimens may be numerous and can endow some special difficulties compared to clinical specimens, namely those resulting from autolytic and putrefactive changes. Storage stability is also an important issue to be considered during the pre-analytic phase, since its consideration should facilitate the assessment of sample quality and the analytical result obtained from that sample. The knowledge on degradation mechanisms and methods to increase storage stability may enable the forensic toxicologist to circumvent possible difficulties. Therefore, advantages and limitations of specimen preservation procedures are thoroughfully discussed in this review. Presently, harmonized protocols for sampling in suspected intoxications would have obvious utility. In the present article an overview is given on sampling procedures for routinely collected specimens as well as on alternative specimens that may provide additional information on the route and timing of exposure to a specific xenobiotic. Last, but not least, a discussion on possible bias that can influence the interpretation of toxicological results is provided. This comprehensive review article is intented as a significant help for forensic toxicologists to accomplish their frequently overwhelming mission.

Comparison of a novel passive sampler to standard water-column sampling for organic contaminants associated with wastewater effluents entering a New Jersey stream

USGS Publications Warehouse

Alvarez, D.A.; Stackelberg, P.E.; Petty, J.D.; Huckins, J.N.; Furlong, E.T.; Zaugg, S.D.; Meyer, M.T.

2005-01-01

Four water samples collected using standard depth and width water-column sampling methodology were compared to an innovative passive, in situ, sampler (the polar organic chemical integrative sampler or POCIS) for the detection of 96 organic wastewater-related contaminants (OWCs) in a stream that receives agricultural, municipal, and industrial wastewaters. Thirty-two OWCs were identified in POCIS extracts whereas 9-24 were identified in individual water-column samples demonstrating the utility of POCIS for identifying contaminants whose occurrence are transient or whose concentrations are below routine analytical detection limits. Overall, 10 OWCs were identified exclusively in the POCIS extracts and only six solely identified in the water-column samples, however, repetitive water samples taken using the standard method during the POCIS deployment period required multiple trips to the sampling site and an increased number of samples to store, process, and analyze. Due to the greater number of OWCs detected in the POCIS extracts as compared to individual water-column samples, the ease of performing a single deployment as compared to collecting and processing multiple water samples, the greater mass of chemical residues sequestered, and the ability to detect chemicals which dissipate quickly, the passive sampling technique offers an efficient and effective alternative for detecting OWCs in our waterways for wastewater contaminants.

Cell-block procedure in endoscopic ultrasound-guided-fine-needle-aspiration of gastrointestinal solid neoplastic lesions

PubMed Central

Ieni, Antonio; Barresi, Valeria; Todaro, Paolo; Caruso, Rosario Alberto; Tuccari, Giovanni

2015-01-01

In the present review we have analyzed the clinical applications of endoscopic ultrasound-guided-fine-needle-aspiration (EUS-FNA) and the methodological aspects obtained by cell-block procedure (CBP) in the diagnostic approach to the gastrointestinal neoplastic pathology. CBP showed numerous advantages in comparison to the cytologic routine smears; in particular, better preservation of cell architecture, achievement of routine haematoxylin-eosin staining equivalent to histological slides and possibility to perform immunohistochemistry or molecular analyses represented the most evident reasons to choose this method. Moreover, by this approach, the differential diagnosis of solid gastrointestinal neoplasias may be more easily achieved and the background of contaminant non-neoplastic gastrointestinal avoided. Finally, biological samples collected by EUS-FNA CBP-assisted should be investigated in order to identify and quantify further potential molecular markers. PMID:26322154

Influence of different anaesthetic protocols over the sperm quality on the fresh, chilled (4°C) and frozen-thawed epididymal sperm samples in domestic dogs.

PubMed

Batista, M; Vilar, J; Rosario, I; Terradas, E

2016-10-01

This study assessed the influence of three different anaesthetic protocols on semen quality obtained from the epididymis. Sixty male dogs undergoing to routine sterilization were assigned to three anaesthetic protocols: thiopental group (TG, n = 20), propofol group (PG, n = 20) and ketamine-dexmedetomidine group (KDG, n = 20). Immediately after orchidectomy, the cauda epididymides and vas deferent ducts were isolated and then a retrograde flushing was performed to collect spermatozoa. In experiment 1, after the initial evaluation of the semen (sperm concentration, sperm motility and the percentages of live spermatozoa, abnormal spermatozoa and acrosome membrane integrity), semen samples were diluted in Tris-glucose-egg yolk extender and chilled for 48 hr, and the sperm motility was assessed at 6, 24 and 48 hr. In experiment 2, semen samples were diluted in Tris-glucose-egg yolk extender and chilled for 24 hr, and then samples were frozen in two extenders with different glycerol concentrations, to reach a final concentration of 50-100 × 10(6) spermatozoa ml(-1) , 20% egg yolk, 0.5% Equex and 4% and 5% glycerol, respectively. Mean values of total sperm concentration, sperm viability and the percentages of intact acrosome and abnormal spermatozoa were not significantly different between experimental groups, and therefore, the anaesthetic protocols assessed did not affect sperm parameters mentioned above. However, our study confirmed a detrimental effect of the use of thiopental (TG) over the total sperm motility (p < 0.05) and progressive sperm motility (p < 0.05) of the fresh and chilled epididymal sperm samples. The anaesthetic protocols including the application of propofol or ketamine-dexmedetomidine can be used to recover sperm in domestic canids without significant changes in sperm quality compared when semen is collected routinely and these techniques could be applicable to endangered wild canids. © 2016 Blackwell Verlag GmbH.

Diagnostic utility and cost-effectiveness of reflex bacterial culture for the detection of urinary tract infection in dogs with low urine specific gravity.

PubMed

Tivapasi, Musavenga T; Hodges, Joanne; Byrne, Barbara A; Christopher, Mary M

2009-09-01

Urinary tract infections (UTIs) may be subclinical or difficult to detect in dilute urine as sediment abnormalities may not be observed. In our laboratory, bacterial culture is automatically performed (reflex culture) on samples with urine specific gravity (USG)< or =1.013 to increase the likelihood of detecting infection. The value of routine culture of dilute urine, however, has not been fully assessed. The purpose of this retrospective study was to evaluate the frequency of positive bacterial cultures and analyze the diagnostic utility and cost-effectiveness of culture compared with routine sediment examination for detecting UTI in dilute urine specimens from dogs. Urinalysis and concurrent aerobic bacterial culture results were obtained from the electronic medical record system at the University of California-Davis Veterinary Medical Teaching Hospital for samples with USG< or =1.013 analyzed from July 1998 through January 2005. Urine collection method, presence of leukocytes and bacteria, bacterial culture results, and clinical diagnosis were recorded. Cost-effectiveness of reflex culture, based on low USG as the sole criterion, was evaluated. Of 1264 urine specimens, 106 (8.4%) had positive bacterial cultures. Using culture as the gold standard, sediment evaluation had a diagnostic sensitivity of 58.5% and specificity of 98.3% (diagnostic accuracy 94.9%). An additional cost of $60 per patient was incurred, leading to average annual costs of $11,668 for reflex bacterial cultures of all samples with low USG, regardless of collection method. Within our study population, 10 urine samples needed to be cultured for each true positive result. The sensitivity of urine sediment evaluation is low for UTI in dilute urine samples; however, reflex bacterial culture does not appear to be cost-effective in dogs with USG< or =1.013 in the absence of active urine sediment or high clinical suspicion for UTI.

Evaluation of a sticky trap for collecting Aedes (Stegomyia) adults in a dengue-endemic area in Thailand.

PubMed

Facchinelli, Luca; Koenraadt, Constantianus J M; Fanello, Caterina; Kijchalao, Udom; Valerio, Laura; Jones, James W; Scott, Thomas W; della Torre, Alessandra

2008-06-01

Development of new operational techniques for collection and monitoring of adult Stegomyia mosquitoes is considered a pressing need for surveillance and prevention of arboviruses. Here we report the results from a trial carried out in 2 dengue-endemic villages in Thailand to compare the ability to collect Aedes adults of a sticky trap versus a CDC backpack aspirator, which has been used routinely at the study area for entomological/epidemiological surveys. Our comparison was based on a comparable sampling effort required to carry out collections with 2 approaches. Over 19,000 specimens were collected, approximately 90% of which were Culex spp. Sticky traps collected significantly more Aedes aegypti and Aedes albopictus females than did backpack aspirators when located outdoors. The percentage of positive sticky-trap catches was double for Ae. aegypti and almost 20 times higher for Ae. albopictus. Operational benefits of the sticky trap are discussed within the context of the results obtained.

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

Not Available

An Apple IIe microcomputer is being used to collect data and to control a pyrolysis system. Pyrolysis data for bitumen and kerogen are widely used to estimate source rock maturity. For a detailed analysis of kinetic parameters, however, data must be obtained more precisely than for routine pyrolysis. The authors discuss the program which controls the temperature ramp of the furnace that heats the sample, and collects data from a thermocouple in the furnace and from the flame ionization detector measuring evolved hydrocarbons. These data are stored on disk for later use by programs that display the results of themore » experiment or calculate kinetic parameters. The program is written in Applesoft BASIC with subroutines in Apple assembler for speed and efficiency.« less

The nature of air pollution and the methods available for measuring it

PubMed Central

Ellison, J. McK.

1965-01-01

At present the principal sources of energy in Europe are coal and oil and fuels derived from them, and in European towns air pollution consists mainly of their combustion products. These combustion products naturally divide into two categories, gaseous and particulate, which are very different chemically and which behave very differently when they are near collecting surfaces; they therefore require very different techniques both for collecting and for estimating samples. Some methods of measurement, suitable for everyday routine use in Europe, are described; these offer a compromise between completeness and economy, and can help to give a general outline of the air pollution situation without undue complexity or prohibitive cost. PMID:14315712

Native SAD is maturing

PubMed Central

Rose, John P.; Wang, Bi-Cheng; Weiss, Manfred S.

2015-01-01

Native SAD phasing uses the anomalous scattering signal of light atoms in the crystalline, native samples of macromolecules collected from single-wavelength X-ray diffraction experiments. These atoms include sodium, magnesium, phosphorus, sulfur, chlorine, potassium and calcium. Native SAD phasing is challenging and is critically dependent on the collection of accurate data. Over the past five years, advances in diffraction hardware, crystallographic software, data-collection methods and strategies, and the use of data statistics have been witnessed which allow ‘highly accurate data’ to be routinely collected. Today, native SAD sits on the verge of becoming a ‘first-choice’ method for both de novo and molecular-replacement structure determination. This article will focus on advances that have caught the attention of the community over the past five years. It will also highlight both de novo native SAD structures and recent structures that were key to methods development. PMID:26175902

Subrandom methods for multidimensional nonuniform sampling.

PubMed

Worley, Bradley

2016-08-01

Methods of nonuniform sampling that utilize pseudorandom number sequences to select points from a weighted Nyquist grid are commonplace in biomolecular NMR studies, due to the beneficial incoherence introduced by pseudorandom sampling. However, these methods require the specification of a non-arbitrary seed number in order to initialize a pseudorandom number generator. Because the performance of pseudorandom sampling schedules can substantially vary based on seed number, this can complicate the task of routine data collection. Approaches such as jittered sampling and stochastic gap sampling are effective at reducing random seed dependence of nonuniform sampling schedules, but still require the specification of a seed number. This work formalizes the use of subrandom number sequences in nonuniform sampling as a means of seed-independent sampling, and compares the performance of three subrandom methods to their pseudorandom counterparts using commonly applied schedule performance metrics. Reconstruction results using experimental datasets are also provided to validate claims made using these performance metrics. Copyright © 2016 Elsevier Inc. All rights reserved.

Widely applicable MATLAB routines for automated analysis of saccadic reaction times.

PubMed

Leppänen, Jukka M; Forssman, Linda; Kaatiala, Jussi; Yrttiaho, Santeri; Wass, Sam

2015-06-01

Saccadic reaction time (SRT) is a widely used dependent variable in eye-tracking studies of human cognition and its disorders. SRTs are also frequently measured in studies with special populations, such as infants and young children, who are limited in their ability to follow verbal instructions and remain in a stable position over time. In this article, we describe a library of MATLAB routines (Mathworks, Natick, MA) that are designed to (1) enable completely automated implementation of SRT analysis for multiple data sets and (2) cope with the unique challenges of analyzing SRTs from eye-tracking data collected from poorly cooperating participants. The library includes preprocessing and SRT analysis routines. The preprocessing routines (i.e., moving median filter and interpolation) are designed to remove technical artifacts and missing samples from raw eye-tracking data. The SRTs are detected by a simple algorithm that identifies the last point of gaze in the area of interest, but, critically, the extracted SRTs are further subjected to a number of postanalysis verification checks to exclude values contaminated by artifacts. Example analyses of data from 5- to 11-month-old infants demonstrated that SRTs extracted with the proposed routines were in high agreement with SRTs obtained manually from video records, robust against potential sources of artifact, and exhibited moderate to high test-retest stability. We propose that the present library has wide utility in standardizing and automating SRT-based cognitive testing in various populations. The MATLAB routines are open source and can be downloaded from http://www.uta.fi/med/icl/methods.html .

Determinants of routine immunization costing in Benin and Ghana in 2011.

PubMed

Ahanhanzo, Césaire Damien; Huang, Xiao Xian; Le Gargasson, Jean-Bernard; Sossou, Justin; Nyonator, Frank; Colombini, Anais; Gessner, Bradford D

2015-05-07

Existing tools to evaluate costs do not always capture the heterogeneity of costs at the facility level. This study seeks to address this issue through an analysis of determinants of health facility immunization costs. A statistical analysis on facility routine delivery and vaccine costs was conducted using ordinary least squares regression. Explanatory variables included the number of doses administered; proportion of time spent by facility staff on immunization; average staff wage; whether the health facility had enough staff; presence of cold chain equipment; distance to a vaccine collection point; and, facility ownership. Data were drawn from representative samples of primary care facilities in Benin and Ghana (46 and 50 facilities, respectively) collected as part of the EPIC studies. Weighted average RI immunization facility cost was US$ 16,459 in Ghana and US$ 14,994 in Benin. The regression found total doses administered to be positively and significantly associated with facility cost in both countries. A 10% increase in doses resulted in a 4% increase in cost in Ghana, and a 7.5% increase in Benin. In Ghana, the proportion of immunization time, presence of cold chain, and sufficiency of staff were positively and significantly associated with total cost. In Benin, facility cost was negatively and significantly related to distance to the vaccine collection point. In the pooled sample, facilities in capital cities were associated with significantly higher costs. This study provides evidence on the importance of the level of scale in determining facility immunization cost, as well as the role of availability of health workers and time they spend on immunization in Ghana and Benin. This type of analysis can provide insights into the costs of scaling up immunization services, and can assist with development of more efficient immunization strategies. Copyright © 2015 Elsevier Ltd. All rights reserved.

Costs and financing of routine immunization: Approach and selected findings of a multi-country study (EPIC).

PubMed

Brenzel, Logan; Young, Darwin; Walker, Damian G

2015-05-07

Few detailed facility-based costing studies of routine immunization (RI) programs have been conducted in recent years, with planners, managers and donors relying on older information or data from planning tools. To fill gaps and improve quality of information, a multi-country study on costing and financing of routine immunization and new vaccines (EPIC) was conducted in Benin, Ghana, Honduras, Moldova, Uganda and Zambia. This paper provides the rationale for the launch of the EPIC study, as well as outlines methods used in a Common Approach on facility sampling, data collection, cost and financial flow estimation for both the routine program and new vaccine introduction. Costing relied on an ingredients-based approach from a government perspective. Estimating incremental economic costs of new vaccine introduction in contexts with excess capacity are highlighted. The use of more disaggregated System of Health Accounts (SHA) coding to evaluate financial flows is presented. The EPIC studies resulted in a sample of 319 primary health care facilities, with 65% of facilities in rural areas. The EPIC studies found wide variation in total and unit costs within each country, as well as between countries. Costs increased with level of scale and socio-economic status of the country. Governments are financing an increasing share of total RI financing. This study provides a wealth of high quality information on total and unit costs and financing for RI, and demonstrates the value of in-depth facility approaches. The paper discusses the lessons learned from using a standardized approach, as well as proposes further areas of methodology development. The paper discusses how results can be used for resource mobilization and allocation, improved efficiency of services at the country level, and to inform policies at the global level. Efforts at routinizing cost analysis to support sustainability efforts would be beneficial. Copyright © 2015 Elsevier Ltd. All rights reserved.

Water Quality of the Snake River and Five Eastern Tributaries in the Upper Snake River Basin, Grand Teton National Park, Wyoming, 1998-2002

USGS Publications Warehouse

Clark, Melanie L.; Sadler, Wilfrid J.; O'Ney, Susan E.

2004-01-01

To address water-resource management objectives of the National Park Service in Grand Teton National Park, the U.S. Geological Survey in cooperation with the National Park Service has conducted water-quality sampling in the upper Snake River Basin. Routine sampling of the Snake River was conducted during water years 1998-2002 to monitor the water quality of the Snake River through time. A synoptic study during 2002 was conducted to supplement the routine Snake River sampling and establish baseline water-quality conditions of five of its eastern tributaries?Pilgrim Creek, Pacific Creek, Buffalo Fork, Spread Creek, and Ditch Creek. Samples from the Snake River and the five tributaries were collected at 12 sites and analyzed for field measurements, major ions and dissolved solids, nutrients, selected trace metals, pesticides, and suspended sediment. In addition, the eastern tributaries were sampled for fecal-indicator bacteria by the National Park Service during the synoptic study. Major-ion chemistry of the Snake River varies between an upstream site above Jackson Lake near the northern boundary of Grand Teton National Park and a downstream site near the southern boundary of the Park, in part owing to the inputs from the eastern tributaries. Water type of the Snake River changes from sodium bicarbonate at the upstream site to calcium bicarbonate at the downstream site. The water type of the five eastern tributaries is calcium bicarbonate. Dissolved solids in samples collected from the Snake River were significantly higher at the upstream site (p-value<0.001), where concentrations in 43 samples ranged from 62 to 240 milligrams per liter, compared to the downstream site where concentrations in 33 samples ranged from 77 to 141 milligrams per liter. Major-ion chemistry of Pilgrim Creek, Pacific Creek, Buffalo Fork, Spread Creek, and Ditch Creek generally did not change substantially between the upstream sites near the National Park Service boundary with the National Forest and the downstream sites near the Snake River; however, variations in the major ions and dissolved solids existed between basins. Variations probably result from differences in geology between the tributary basins. Concentrations of dissolved ammonia, nitrite, and nitrate in all samples collected from the Snake River and the five eastern tributaries were less than water-quality criteria for surface waters in Wyoming. Concentrations of total nitrogen and total phosphorus in samples from the Snake River and the tributaries generally were less than median concentrations determined for undeveloped streams in the United States; however, concentrations in some samples did exceed ambient total-nitrogen and total-phosphorus criteria for forested mountain streams in the Middle Rockies ecoregion recommended by the U.S. Environmental Protection Agency to address cultural eutrophication. Sources for the excess nitrogen and phosphorus probably are natural because these basins have little development and cultivation. Concentrations of trace metals and pesticides were low and less than water-quality criteria for surface waters in Wyoming in samples collected from the Snake River and the five eastern tributaries. Atrazine, dieldrin, EPTC, or tebuthiuron were detected in estimated concentrations of 0.003 microgram per liter or less in 5 of 27 samples collected from the Snake River. An estimated concentration of 0.008 microgram per liter of metolachlor was detected in one sample from the Buffalo Fork. The estimated concentrations were less than the reporting levels for the pesticide analytical method. Suspended-sediment concentrations in 43 samples from the upstream site on the Snake River ranged from 1 to 604 milligrams per liter and were similar to suspended-sediment concentrations in 33 samples from the downstream site, which ranged from 1 to 648 milligrams per liter. Suspended-sediment concentrations in 38 samples collected from the tributary streams ranged from 1 t

Nurse staffing levels and outcomes - mining the UK national data sets for insight.

PubMed

Leary, Alison; Tomai, Barbara; Swift, Adrian; Woodward, Andrew; Hurst, Keith

2017-04-18

Purpose Despite the generation of mass data by the nursing workforce, determining the impact of the contribution to patient safety remains challenging. Several cross-sectional studies have indicated a relationship between staffing and safety. The purpose of this paper is to uncover possible associations and explore if a deeper understanding of relationships between staffing and other factors such as safety could be revealed within routinely collected national data sets. Design/methodology/approach Two longitudinal routinely collected data sets consisting of 30 years of UK nurse staffing data and seven years of National Health Service (NHS) benchmark data such as survey results, safety and other indicators were used. A correlation matrix was built and a linear correlation operation was applied (Pearson product-moment correlation coefficient). Findings A number of associations were revealed within both the UK staffing data set and the NHS benchmarking data set. However, the challenges of using these data sets soon became apparent. Practical implications Staff time and effort are required to collect these data. The limitations of these data sets include inconsistent data collection and quality. The mode of data collection and the itemset collected should be reviewed to generate a data set with robust clinical application. Originality/value This paper revealed that relationships are likely to be complex and non-linear; however, the main contribution of the paper is the identification of the limitations of routinely collected data. Much time and effort is expended in collecting this data; however, its validity, usefulness and method of routine national data collection appear to require re-examination.

Detection of Poliovirus Circulation by Environmental Surveillance in the Absence of Clinical Cases in Israel and the Palestinian Authority

PubMed Central

Manor, Y.; Handsher, R.; Halmut, T.; Neuman, M.; Bobrov, A.; Rudich, H.; Vonsover, A.; Shulman, L.; Kew, O.; Mendelson, E.

1999-01-01

The global eradication of poliomyelitis, believed to be achievable around the year 2000, relies on strategies which include high routine immunization coverage and mass vaccination campaigns, along with continuous monitoring of wild-type virus circulation by using the laboratory-based acute flaccid paralysis (AFP) surveillance. Israel and the Palestinian Authority are located in a geographical region in which poliovirus is still endemic but have been free of poliomyelitis since 1988 as a result of intensive immunization programs and mass vaccination campaigns. To monitor the wild-type virus circulation, environmental surveillance of sewage samples collected monthly from 25 to 30 sites across the country was implemented in 1989 and AFP surveillance began in 1994. The sewage samples were processed in the laboratory with a double-selective tissue culture system, which enabled economical processing of large number of samples. Between 1989 and 1997, 2,294 samples were processed, and wild-type poliovirus was isolated from 17 of them in four clusters, termed “silent outbreaks,” in September 1990 (type 3), between May and September 1991 (type 1), between October 1994 and June 1995 (type 1), and in December 1996 (type 1). Fifteen of the 17 positive samples were collected in the Gaza Strip, 1 was collected in the West Bank, and 1 was collected in the Israeli city of Ashdod, located close to the Gaza Strip. The AFP surveillance system failed to detect the circulating wild-type viruses. These findings further emphasize the important role that environmental surveillance can play in monitoring the eradication of polioviruses. PMID:10325305

Prednisolone and prednisone neo-formation in bovine urine after sampling.

PubMed

Arioli, F; Casati, A; Fidani, M; Silvestri, M; Pompa, G

2012-06-01

The rise in the frequency of detecting prednisolone in bovine urine from northern Italy has come into focus of attention in recent years. The possibility that neo-formation of prednisolone or that prednisone may occur in urine after collection of samples was therefore investigated. Cow urine collected for official routine controls in Lombardy containing more than 80 ng/ml cortisol, and prednisolone and prednisone below the decision limit (CCα) of the method (0.4 and 0.5 ng/ml, respectively) was used. The C1-2 dehydrogenation of naturally present cortisol and cortisone was checked by incubating urine, both contaminated and uncontaminated with faeces, at 37°C and by collecting samples at 0, 1, 2, 4, 6 and 24 h. The influence of Helix pomatia juice was also investigated in order to determine whether deconjugation could influence the reliability of the results. All samples were analysed by HPLC-MS3 for the presence of cortisol, cortisone, prednisolone and prednisone in negative electrospray ionisation mode, utilising the consecutive reaction monitoring of product ions derived from the formate molecular adduct ([M+HCOO]-). The observed neo-formation of prednisolone shows that inappropriate temperatures in sample storage and processing can result in an incorrect accusation of non-compliance. The faecal contamination of urine, performed with the aim to mimic a collection conducted without the necessary care, moreover, evoked a high increase in prednisolone concentration in two out of seven animals. Moreover, H. pomatia juice had no significant effect on the prednisolone concentration, indicating that this corticosteroid is present in its free form in cow urine.

A Nursing Intelligence System to Support Secondary Use of Nursing Routine Data

PubMed Central

Rauchegger, F.; Ammenwerth, E.

2015-01-01

Summary Background Nursing care is facing exponential growth of information from nursing documentation. This amount of electronically available data collected routinely opens up new opportunities for secondary use. Objectives To present a case study of a nursing intelligence system for reusing routinely collected nursing documentation data for multiple purposes, including quality management of nursing care. Methods The SPIRIT framework for systematically planning the reuse of clinical routine data was leveraged to design a nursing intelligence system which then was implemented using open source tools in a large university hospital group following the spiral model of software engineering. Results The nursing intelligence system is in routine use now and updated regularly, and includes over 40 million data sets. It allows the outcome and quality analysis of data related to the nursing process. Conclusions Following a systematic approach for planning and designing a solution for reusing routine care data appeared to be successful. The resulting nursing intelligence system is useful in practice now, but remains malleable for future changes. PMID:26171085

Detection of significant variation in acoustic output of an electromagnetic lithotriptor.

PubMed

Pishchalnikov, Yuri A; McAteer, James A; Vonderhaar, R Jason; Pishchalnikova, Irina V; Williams, James C; Evan, Andrew P

2006-11-01

We describe the observation of significant instability in the output of an electromagnetic lithotriptor. This instability had a form that was not detected by routine assessment, but rather was observed only by collecting many consecutive shock waves in nonstop regimen. A Dornier DoLi-50 lithotriptor used exclusively for basic research was tested and approved by the regional technician. This assessment included hydrophone measures at select power levels with the collection of about 25 shock waves per setting. Subsequent laboratory characterization used a fiberoptic hydrophone and storage oscilloscope for data acquisition. Waveforms were collected nonstop for hundreds of pulses. Output was typically stable for greater than 1,000 shock waves but substantial fluctuations in acoustic pressures were also observed. For example, output at power level 3 (mean peak positive acoustic pressure +/- SD normally 44 +/- 2 MPa) increased dramatically to greater than 50 MPa or decreased significantly to approximately 30 MPa for hundreds of shock waves. The cause of instability was eventually traced to a faulty lithotriptor power supply. Instability in lithotriptor acoustic output can occur and it may not be detected by routine assessment. Collecting waveforms in a nonstop regimen dramatically increases sampling size, improving the detection of instability. Had the instability that we observed occurred during patient treatment, the energy delivered may well have exceeded the planned dose. Since the potential for adverse effects in lithotripsy increases as the dose is increased, it would be valuable to develop ways to better monitor the acoustic output of lithotriptors.

Lot quality assurance sampling for monitoring coverage and quality of a targeted condom social marketing programme in traditional and non-traditional outlets in India

PubMed Central

Piot, Bram; Navin, Deepa; Krishnan, Nattu; Bhardwaj, Ashish; Sharma, Vivek; Marjara, Pritpal

2010-01-01

Objectives This study reports on the results of a large-scale targeted condom social marketing campaign in and around areas where female sex workers are present. The paper also describes the method that was used for the routine monitoring of condom availability in these sites. Methods The lot quality assurance sampling (LQAS) method was used for the assessment of the geographical coverage and quality of coverage of condoms in target areas in four states and along selected national highways in India, as part of Avahan, the India AIDS initiative. Results A significant general increase in condom availability was observed in the intervention area between 2005 and 2008. High coverage rates were gradually achieved through an extensive network of pharmacies and particularly of non-traditional outlets, whereas traditional outlets were instrumental in providing large volumes of condoms. Conclusion LQAS is seen as a valuable tool for the routine monitoring of the geographical coverage and of the quality of delivery systems of condoms and of health products and services in general. With a relatively small sample size, easy data collection procedures and simple analytical methods, it was possible to inform decision-makers regularly on progress towards coverage targets. PMID:20167732

C-reactive protein and high mobility group box 1 in dogs with gastric dilatation and volvulus.

PubMed

Uhrikova, Ivana; Rauserova-Lexmaulova, Leona; Rehakova, Kristina; Scheer, Peter; Doubek, Jaroslav

2015-01-01

To (1) measure C-reactive protein (CRP) and high mobility group box 1 (HMGB1) and (2) evaluate their prognostic value and relationship to severity of systemic inflammatory response syndrome, routine hematological and acid-base parameters in dogs with gastric dilatation volvulus (GDV). Prospective observational study from September 2010 to June 2012. Veterinary teaching hospital. Forty-one client-owned dogs with GDV. None. Blood was collected before surgery (baseline), postsurgery, 6-10 hours postsurgery, and 18-22 hours postsurgery. CRP and HMGB1 were measured in all samples, and routine hematological, biochemical, and acid-base analyses were performed. Only baseline and postsurgery samples were used from nonsurvivors (n = 10). CRP increased significantly from postsurgery sampling to 18-22 hours postsurgery, while HMGB1 did not change over time. There was a significant difference in HMGB1 between survivors and nonsurvivors over time. Both proteins correlated with systemic inflammatory response syndrome severity, total leukocyte, segmented neutrophils, and band counts. HMGB1 correlated also with acid-base parameters (pH, bicarbonate, base excess). HMGB1 and CRP behaved differently in regards to their kinetic patterns, with HMGB1 appearing to better reflect the severity of tissue injury in dogs with GDV than CRP. © Veterinary Emergency and Critical Care Society 2015.

Prevalence of Staphylococcus, including Methicillin-Resistant Staphylococcus aureus, in a Physical Therapy Education Facility.

PubMed

Dhagat, Priya V; Gibbs, Karen A; Rohde, Rodney E

2015-01-01

The purpose of this study was to assess the prevalence of Staphylococcus species, including methicillin-resistant Staphylococcus aureus (MRSA), in a physical therapy (PT) education facility. The PT laboratory classrooms were routinely used by graduate PT students and faculty, undergraduate anatomy students, and licensed practitioners for continuing education purposes. A total of 88 swab samples were collected from plinths and other equipment and plated onto mannitol salt agar (MSA). Suspected S. aureus colonies were confirmed by Staphyloslide latex testing. S. aureus isolates were plated to HardyCHROM agar to identify MRSA. VITEK antibiotic susceptibility testing confirmed MRSA isolates. Forty-seven samples showed growth (47/88, 53%), and 7 tested positive for S. aureus (7/47, 15%). Of those 7, one demonstrated oxacillin resistance and was confirmed as MRSA (1/7, 2%). Remaining samples grew other species of Staphylococcus and gram-negative bacilli. Given high classroom utilization, staphylococci environmental prevalence would be expected. However, the presence of MRSA was unexpected. Results demonstrate the potential for easily transmissible and potentially harmful organisms to be present in multi-use classrooms utilized by health professions students where frequent skin-to-skin contact occurs. Strict, routine cleaning of plinths and other equipment is imperative in reducing exposure risk.

Lot quality assurance sampling for monitoring coverage and quality of a targeted condom social marketing programme in traditional and non-traditional outlets in India.

PubMed

Piot, Bram; Mukherjee, Amajit; Navin, Deepa; Krishnan, Nattu; Bhardwaj, Ashish; Sharma, Vivek; Marjara, Pritpal

2010-02-01

This study reports on the results of a large-scale targeted condom social marketing campaign in and around areas where female sex workers are present. The paper also describes the method that was used for the routine monitoring of condom availability in these sites. The lot quality assurance sampling (LQAS) method was used for the assessment of the geographical coverage and quality of coverage of condoms in target areas in four states and along selected national highways in India, as part of Avahan, the India AIDS initiative. A significant general increase in condom availability was observed in the intervention area between 2005 and 2008. High coverage rates were gradually achieved through an extensive network of pharmacies and particularly of non-traditional outlets, whereas traditional outlets were instrumental in providing large volumes of condoms. LQAS is seen as a valuable tool for the routine monitoring of the geographical coverage and of the quality of delivery systems of condoms and of health products and services in general. With a relatively small sample size, easy data collection procedures and simple analytical methods, it was possible to inform decision-makers regularly on progress towards coverage targets.

Ethnographic study of ICT-supported collaborative work routines in general practice.

PubMed

Swinglehurst, Deborah; Greenhalgh, Trisha; Myall, Michelle; Russell, Jill

2010-12-29

Health informatics research has traditionally been dominated by experimental and quasi-experimental designs. An emerging area of study in organisational sociology is routinisation (how collaborative work practices become business-as-usual). There is growing interest in the use of ethnography and other in-depth qualitative approaches to explore how collaborative work routines are enacted and develop over time, and how electronic patient records (EPRs) are used to support collaborative work practices within organisations. Following Feldman and Pentland, we will use 'the organisational routine' as our unit of analysis. In a sample of four UK general practices, we will collect narratives, ethnographic observations, multi-modal (video and screen capture) data, documents and other artefacts, and analyse these to map and compare the different understandings and enactments of three common routines (repeat prescribing, coding and summarising, and chronic disease surveillance) which span clinical and administrative spaces and which, though 'mundane', have an important bearing on quality and safety of care. In a detailed qualitative analysis informed by sociological theory, we aim to generate insights about how complex collaborative work is achieved through the process of routinisation in healthcare organisations. Our study offers the potential not only to identify potential quality failures (poor performance, errors, failures of coordination) in collaborative work routines but also to reveal the hidden work and workarounds by front-line staff which bridge the model-reality gap in EPR technologies and via which "automated" safety features have an impact in practice.

Ethnographic study of ICT-supported collaborative work routines in general practice

PubMed Central

2010-01-01

Background Health informatics research has traditionally been dominated by experimental and quasi-experimental designs. An emerging area of study in organisational sociology is routinisation (how collaborative work practices become business-as-usual). There is growing interest in the use of ethnography and other in-depth qualitative approaches to explore how collaborative work routines are enacted and develop over time, and how electronic patient records (EPRs) are used to support collaborative work practices within organisations. Methods/design Following Feldman and Pentland, we will use 'the organisational routine' as our unit of analysis. In a sample of four UK general practices, we will collect narratives, ethnographic observations, multi-modal (video and screen capture) data, documents and other artefacts, and analyse these to map and compare the different understandings and enactments of three common routines (repeat prescribing, coding and summarising, and chronic disease surveillance) which span clinical and administrative spaces and which, though 'mundane', have an important bearing on quality and safety of care. In a detailed qualitative analysis informed by sociological theory, we aim to generate insights about how complex collaborative work is achieved through the process of routinisation in healthcare organisations. Discussion Our study offers the potential not only to identify potential quality failures (poor performance, errors, failures of coordination) in collaborative work routines but also to reveal the hidden work and workarounds by front-line staff which bridge the model-reality gap in EPR technologies and via which "automated" safety features have an impact in practice. PMID:21190583

Water quality of the tidal Potomac River and Estuary; hydrologic data report, 1981 water year, with a section on collection and analysis of chlorophyll-a

USGS Publications Warehouse

Blanchard, Stephen F.; Coupe, Richard H.; Woodward, Joan C.

1982-01-01

This report contains data on the physical and chemical properties measured in the Tidal Potomac River and Estuary during the 1981 water year. Data were collected at least weekly at five stations, and periodically at 15 stations and at two other stations near the mouth of the Potomac River in Chesapeake Bay. Each of the five stations represent a cross section at which the transport of selected dissolved and suspended materials can be computed. The remaining 17 stations are locations at which data were collected for special studies of selected phenomena, such as salt water migration and dissolved oxygen dynamics. Samples were routinely analyzed for chlorophyll-a, nitrogen, pheophytin, phosphorus, silica and suspended sediment. Additional samples were analyzed for adenosine triphosphate, algal growth potential, alkalinity, calcium, chloride, dissolved-solids residue, fluoride, iron, manganese, magnesium, nitrifying bacteria, organic carbon, potassium, seston, sodium, and sulfate. In addition, in-situ measurements of dissolved oxygen, specific conductance, pH, temperature, solar radiation, and secchi disk transparency were made. (USGS)

Consistently Low Prevalence of Syphilis among Female Sex Workers in Jinan, China: Findings from Two Consecutive Respondent Driven Sampling Surveys

PubMed Central

Liao, Meizhen; Nie, Xijuan; Pan, Rongjian; Wang, Chuangxin; Ruan, Shiman; Zhang, Changqing; Kang, Dianming; Fu, Jihua; Qian, Yuesheng; Tao, Xiaorun; Zhao, Jinkou

2012-01-01

Background Routine surveillance using convenient sampling found low prevalence of HIV and syphilis among female sex workers in China. Two consecutive surveys using respondent driven sampling were conducted in 2008 and 2009 to examine the prevalence of HIV and syphilis among female sex workers in Jinan, China. Methods A face-to-face interview was conducted to collect demographic, behavioral and service utilization information using a structured questionnaire. Blood samples were drawn for serological tests of HIV-1 antibody and syphilis antibody. Respondent Driven Sampling Analysis Tool was used to generate population level estimates. Results In 2008 and in 2009, 363 and 432 subjects were recruited and surveyed respectively. Prevalence of syphilis was 2.8% in 2008 and 2.2% in 2009, while no HIV case was found in both years. Results are comparable to those from routine sentinel surveillance system in the city. Only 60.8% subjects in 2008 and 48.3% in 2009 reported a consistent condom use with clients during the past month. Over 50% subjects had not been covered by any HIV-related services in the past year, with only 15.6% subjects in 2008 and 13.1% in 2009 ever tested for HIV. Conclusions Despite the low prevalence of syphilis and HIV, risk behaviors are common. Targeted interventions to promote the safe sex and utilization of existing intervention services are still needed to keep the epidemic from growing. PMID:22539944

Surveillance, epidemiological, and virological detection of highly pathogenic H5N1 avian influenza viruses in duck and poultry from Bangladesh.

PubMed

Ansari, Wahedul Karim; Parvej, Md Shafiullah; El Zowalaty, Mohamed E; Jackson, Sally; Bustin, Stephen A; Ibrahim, Adel K; El Zowalaty, Ahmed E; Rahman, Md Tanvir; Zhang, Han; Khan, Mohammad Ferdousur Rahman; Ahamed, Md Mostakin; Rahman, Md Fasiur; Rahman, Marzia; Nazir, K H M Nazmul Hussain; Ahmed, Sultan; Hossen, Md Liakot; Kafi, Md Abdul; Yamage, Mat; Debnath, Nitish C; Ahmed, Graba; Ashour, Hossam M; Masudur Rahman, Md; Noreddin, Ayman; Rahman, Md Bahanur

2016-09-25

Avian influenza viruses (AIVs) continue to pose a global threat. Waterfowl are the main reservoir and are responsible for the spillover of AIVs to other hosts. This study was conducted as part of routine surveillance activities in Bangladesh and it reports on the serological and molecular detection of H5N1 AIV subtype. A total of 2169 cloacal and 2191 oropharyngeal swabs as well as 1725 sera samples were collected from live birds including duck and chicken in different locations in Bangladesh between the years of 2013 and 2014. Samples were tested using virus isolation, serological tests and molecular methods of RT-PCR. Influenza A viruses were detected using reverse transcription PCR targeting the virus matrix (M) gene in 41/4360 (0.94%) samples including both cloacal and oropharyngeal swab samples, 31 of which were subtyped as H5N1 using subtype-specific primers. Twenty-one live H5N1 virus isolates were recovered from those 31 samples. Screening of 1,868 blood samples collected from the same birds using H5-specific ELISA identified 545/1603 (34%) positive samples. Disconcertingly, an analysis of 221 serum samples collected from vaccinated layer chicken in four districts revealed that only 18 samples (8.1%) were seropositive for anti H5 antibodies, compared to unvaccinated birds (n=105), where 8 samples (7.6%) were seropositive. Our result indicates that the vaccination program as currently implemented should be reviewed and updated. In addition, surveillance programs are crucial for monitoring the efficacy of the current poultry vaccinations programs, and to monitor the circulating AIV strains and emergence of AIV subtypes in Bangladesh. Copyright © 2016. Published by Elsevier B.V.

Acid-etching technique of non-decalcified bone samples for visualizing osteocyte-lacuno-canalicular network using scanning electron microscope.

PubMed

Lampi, Tiina; Dekker, Hannah; Ten Bruggenkate, Chris M; Schulten, Engelbert A J M; Mikkonen, Jopi J W; Koistinen, Arto; Kullaa, Arja M

2018-01-01

The aim of this study was to define the acid-etching technique for bone samples embedded in polymethyl metacrylate (PMMA) in order to visualize the osteocyte lacuno-canalicular network (LCN) for scanning electron microscopy (SEM). Human jaw bone tissue samples (N = 18) were collected from the study population consisting of patients having received dental implant surgery. After collection, the bone samples were fixed in 70% ethanol and non-decalcified samples embedded routinely into polymethyl metacrylate (PMMA). The PMMA embedded specimens were acid-etched in either 9 or 37% phosphoric acid (PA) and prepared for SEM for further analysis. PMMA embedded bone specimens acid-etched by 9% PA concentration accomplishes the most informative and favorable visualization of the LCN to be observed by SEM. Etching of PMMA embedded specimens is recommendable to start with 30 s or 40 s etching duration in order to find the proper etching duration for the samples examined. Visualizing osteocytes and LCN provides a tool to study bone structure that reflects changes in bone metabolism and diseases related to bone tissue. By proper etching protocol of non-decalcified and using scanning electron microscope it is possible to visualize the morphology of osteocytes and the network supporting vitality of bone tissue.

Application of high-performance anion-exchange chromatography-pulsed amperometric detection for measuring carbohydrates in routine daily filter samples collected by a national network: 2. Examination of sugar alcohols/polyols, sugars, and anhydrosugars in the upper Midwest

NASA Astrophysics Data System (ADS)

Sullivan, A. P.; Frank, N.; Kenski, D. M.; Collett, J. L., Jr.

2011-04-01

Carbohydrate measurements of ambient samples can provide insights into the biogenic fraction of the organic carbon (OC) aerosol. However, lack of measurement on a routine basis limits data analysis. In a companion paper, 1 year of archived 1-in-6 day FRM (Federal Reference Monitor) filter samples from the PM2.5 NAAQS compliance monitoring network collected at 10 sites in the upper Midwest were analyzed using high-performance anion-exchange chromatography with pulsed amperometric detection to determine the regional impact of biomass burning. Along with levoglucosan, 13 other carbohydrates were simultaneously measured, including two more anhydrosugars (mannosan and galactosan), five sugars (arabinose, galactose, glucose, mannose, xylose), and six sugar alcohols/polyols (glycerol, methyltetrols, threitol/erythritol, xylitol, sorbitol, mannitol). This paper focuses on the results from these carbohydrates in order to investigate their sources and trends both spatially and temporally. Mannosan, galactosan, arabinose, xylose, and threitol/erythritol all correlated with levoglucosan (R2 from 0.43 to 0.97), suggesting biomass burning as their main source. Glucose and mannitol exhibited higher concentrations in summer and at more southern sites, likely due to vegetation differences at the sites. Using mannitol, the contribution of spores to OC was found to be <1%. Methyltetrols were highly correlated with water-soluble OC (R2 from 0.63 to 0.95) and in higher concentrations at more eastern sites. This spatial pattern is possibly due to these sites being downwind of the high isoprene emission zones that occur in the western part of the Midwest from oak forests in the Ozarks and spruce forests in the northern lake states.

77 FR 69506 - Agency Information Collection Activities: Submission for the Office of Management and Budget (OMB...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-11-19

... conduct or sponsor, and that a person is not required to respond to, a collection of information unless it... Non-Routine Emergency Generic Problems. 3. Current OMB approval number: 3150-0012. 4. The form number... possible non-routine generic problems which would require prompt action from the NRC to preclude potential...

The drivers of facility-based immunization performance and costs. An application to Moldova.

PubMed

Maceira, Daniel; Goguadze, Ketevan; Gotsadze, George

2015-05-07

This paper identifies factors that affect the cost and performance of the routine immunization program in Moldova through an analysis of facility-based data collected as part of a multi-country costing and financing study of routine immunization (EPIC). A nationally representative sample of health care facilities (50) was selected through multi-stage, stratified random sampling. Data on inputs, unit prices and facility outputs were collected during October 3rd 2012-January 14th 2013 using a pre-tested structured questionnaire. Ordinary least square (OLS) regression analysis was performed to determine factors affecting facility outputs (number of doses administered and fully immunized children) and explaining variation in total facility costs. The study found that the number of working hours, vaccine wastage rates, and whether or not a doctor worked at a facility (among other factors) were positively and significantly associated with output levels. In addition, the level of output, price of inputs and share of the population with university education were significantly associated with higher facility costs. A 1% increase in fully immunized child would increase total cost by 0.7%. Few costing studies of primary health care services in developing countries evaluate the drivers of performance and cost. This exercise attempted to fill this knowledge gap and helped to identify organizational and managerial factors at a primary care district and national level that could be addressed by improved program management aimed at improved performance. Copyright © 2015 Elsevier Ltd. All rights reserved.

The consequence of delayed fixation on subsequent preservation of urine cells.

PubMed

Ahmed, Hussain G; Tom, Murtada Am

2011-01-01

Degenerative changes caused by delays in urine preservation contribute to false-negative and false-positive interpretation of urothelial disease in cytology. The aim of this study is to assess whether the delay of fixation of urine samples makes any significant difference to urine cytology and morphology, and the limit of acceptability of delay for routine use in the hospital laboratory. Three cell collection fluids were evaluated by analyzing the preservation and degeneration of cells in urine samples. In this study, 50 voided urine specimens were taken at random from females complaining of vaginal discharge. Each specimen was divided into three sterile containers. The first was immediately centrifugated and the deposit was smeared onto a cleaned micro slide and immediately fixed into 95% ethyl alcohol for 15 minutes. The remaining two were prepared in the same manner, however, the second after two hours of collection and the third after four hours of collection. The degree of degeneration and thus the preservation were assessed by a table of chosen criteria, then ranked and analyzed using Friedman's nonparametric test, at p=0.05. The results showed a significant difference between the preservation and the delay in urine fixation, p<0.0001. Any delay in fixation of urine specimen for cytology affects the preservation of cells, which may result in miss diagnosis. It is recommended that urine samples for cytology should be fixed immediately after collection.

Empiric antibiotic treatment for urinary tract infection in preschool children: susceptibilities of urine sample isolates.

PubMed

Butler, Christopher C; O'Brien, Kathryn; Wootton, Mandy; Pickles, Timothy; Hood, Kerenza; Howe, Robin; Waldron, Cherry-Ann; Thomas-Jones, Emma; Dudley, Jan; Van Der Voort, Judith; Rumsby, Kate; Little, Paul; Downing, Harriet; Harman, Kim; Hay, Alastair D

2016-04-01

Antibiotic treatment recommendations based on susceptibility data from routinely submitted urine samples may be biased because of variation in sampling, laboratory procedures and inclusion of repeat samples, leading to uncertainty about empirical treatment. To describe and compare susceptibilities of Escherichia coli cultured from routinely submitted samples, with E. coli causing urinary tract infection (UTI) from a cohort of systematically sampled, acutely unwell children. Susceptibilities of 1458 E. coli isolates submitted during the course of routine primary care for children <5 years (routine care samples), compared to susceptibilities of 79 E. coli isolates causing UTI from 5107 children <5 years presenting to primary care with an acute illness [systematic sampling: the Diagnosis of Urinary Tract infection in Young children (DUTY) cohort]. The percentage of E. coli sensitive to antibiotics cultured from routinely submitted samples were as follows: amoxicillin 45.1% (95% confidence interval: 42.5-47.7%); co-amoxiclav using the lower systemic break point (BP) 86.6% (84.7-88.3%); cephalexin 95.1% (93.9-96.1%); trimethoprim 74.0% (71.7-76.2%) and nitrofurantoin 98.2% (97.4-98.8%). The percentage of E. coli sensitive to antibiotics cultured from systematically sampled DUTY urines considered to be positive for UTI were as follows: amoxicillin 50.6% (39.8-61.4%); co-amoxiclav using the systemic BP 83.5% (73.9-90.1%); co-amoxiclav using the urinary BP 94.9% (87.7-98.4%); cephalexin 98.7% (93.2-99.8%); trimethoprim 70.9% (60.1-80.0%); nitrofurantoin 100% (95.3-100.0%) and ciprofloxacin 96.2% (89.4-98.7%). Escherichia coli susceptibilities from routine and systematically obtained samples were similar. Most UTIs in preschool children remain susceptible to nitrofurantoin, co-amoxiclav and cephalexin. © The Author 2016. Published by Oxford University Press. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

Using patient-reported outcomes in schizophrenia: the Scottish Schizophrenia Outcomes Study.

PubMed

Hunter, Robert; Cameron, Rosie; Norrie, John

2009-02-01

The primary aim of the Scottish Schizophrenia Outcomes Study (SSOS) was to assess the feasibility and utility of routinely collecting outcome data in everyday clinical settings. Data were collected over three years in the Scottish National Health Service (NHS). There were two secondary aims of SSOS: first, to compare data from patient-rated, objective, and clinician-rated outcomes, and second, to describe trends in outcome data and service use across Scotland over the three years of the study (2002-2005). This study used a naturalistic, longitudinal, observational cohort design. A representative sample of 1,015 persons with ICD-10 F20-F29 diagnoses (schizophrenia, schizotypal disorders, or delusional disorders) was assessed annually using the clinician-rated measure, the Health of the Nation Outcome Scale (HoNOS), and the patient-reported assessment, the Avon Mental Health Measure (Avon). Objective outcomes data and information on services and interventions were collected. Data were analyzed with regression modeling. Of the 1,015 persons recruited, 78% of the cohort (N=789) completed the study. Over the study period, significant decreases were seen in the number of hospitalizations, incidence of attempted suicide and self-harm, and civil detentions. Avon scores indicated significant improvement on all subscales (behavior, social, access, and mental health) and on the total score. However, HoNOS scores on the behavior and symptom subscales did not change, scores on the impairment subscale increased significantly (indicating increased levels of impairment), and scores on the social subscale decreased significantly (indicating improved social functioning). This study has demonstrated that it is feasible within the Scottish NHS to routinely collect meaningful outcomes data in schizophrenia. Patient-reported assessments were also successfully collected and used in care plans. This model shows that it is possible to incorporate patient-reported assessments into routine care for schizophrenia. Such assessments may provide useful data for clinicians and may improve treatment adherence. The pattern of outcomes and interventions confirms that despite the introduction of guidelines, new treatments, and new services, people with schizophrenia continue to have high levels of chronic disability.

Contamination of the cold water distribution system of health care facilities by Legionella pneumophila: do we know the true dimension?

PubMed

Arvand, M; Jungkind, K; Hack, A

2011-04-21

German water guidelines do not recommend routine assessment of cold water for Legionella in healthcare facilities, except if the water temperature at distal sites exceeds 25°C. This study evaluates Legionella contamination in cold and warm water supplies of healthcare facilities in Hesse, Germany, and analyses the relationship between cold water temperature and Legionella contamination. Samples were collected from four facilities, with cases of healthcare-associated Legionnaires' disease or notable contamination of their water supply. Fifty-nine samples were from central lines and 625 from distal sites, comprising 316 cold and 309 warm water samples. Legionella was isolated from central lines in two facilities and from distal sites in four facilities. 17% of all central and 32% of all distal samples were contaminated. At distal sites, cold water samples were more frequently contaminated with Legionella (40% vs 23%, p <0.001) and with higher concentrations of Legionella (≥1,000 colony-forming unit/100 ml) (16% vs 6%, p<0.001) than warm water samples. There was no clear correlation between the cold water temperature at sampling time and the contamination rate. 35% of cold water samples under 20 °C at collection were contaminated. Our data highlight the importance of assessing the cold water supply of healthcare facilities for Legionella in the context of an intensified analysis.

Discovering time-trends of the German populations exposure to contaminants by analysis of human samples of the German Environmental Specimen Bank (ESB).

PubMed

Göen, Thomas; Lermen, Dominik; Hildebrand, Jörg; Bartel-Steinbach, Martina; Weber, Till; Kolossa-Gehring, Marike

2018-06-12

The German Environmental Specimen Bank (ESB) is a monitoring instrument of the German Federal Ministry for the Environment, Nature Conservationand Nuclear Safety. The permanent biobank facility is run since 1981 containing environmental and human samples from Germany. All samples are collected according to standard operating procedures (SOP). An annually standardized collection of human samples at four different regional sites of the country has been established since 1997. Routine sampling is done once a year, recruiting healthy non occupationally exposed students aged 20-29 years, in an equal gender distribution. The number of participants recruited is approximately 120 students per site and year. Directly after the annual sampling process, the human samples are analyzed for selected environmental chemicals. The time-trends of lead in blood, mercury and pentachlorophenol in 24 h-urine and polychlorinated biphenyls in plasma demonstrated a decrease of exposure during the last two decades by about 40 - 90 percent. In parallel retrospective studies using cryo-archived samples revealed increasing time trends of emerging chemicals used as substitutes for regulated toxicants. The data demonstrates the great relevance of the ESB for the health related environmental monitoring and shows the importance of human biomonitoring as a tool in information based policy making. Copyright © 2018 Elsevier B.V. All rights reserved.

Radium-226 body burden in U miners by measurement of Rn in exhaled breath.

PubMed

Srivastava, G K; Raghavayya, M; Kotrappa, P; Somasundaram, S

1986-02-01

Uranium miners were made to inhale Rn-free medical O2 and exhale through a 5.2-1 A1 chamber before reporting to work. The chamber was sealed and isolated from the sampling circuit. An electrostatic plate collected the freshly formed Rn-decay products. The subsequent programmed alpha counting of the plate yielded a Rn concentration in the exhaled breath. Assuming that the exhaled breath represents a certain fraction of the Rn produced inside the body, the body burden of 226Ra was calculated. Standardisation of this procedure and the data collected on 310 miners are discussed. The procedure is simple and applicable for routine measurements. The miner needs to be in the laboratory for only 10 min. The system is also portable for field application. For routine use, the minimum detectable concentration is 3.87 Bq X m-3 which corresponds to a body burden of 0.26 kBq in a typical miner, if one assumes the Rn release fraction from the body as 84%. The system offers a more convenient and sensitive alternative to whole-body counting of workers for 226Ra.

Sodium citrate vacuum tubes validation: preventing preanalytical variability in routine coagulation testing.

PubMed

Lima-Oliveira, Gabriel; Lippi, Giuseppe; Salvagno, Gian Luca; Montagnana, Martina; Picheth, Geraldo; Guidi, Gian Cesare

2013-04-01

Sometimes in-vitro diagnostic devices (e.g. blood collection tubes) are not validated before use or when the producer's brand is changed. The aim of this study was to validate five brands of sodium citrate vacuum tubes. Blood specimens from 50 volunteers were collected in five different tube brands (I: Venosafe, II: VACUETTE, III: BD Vacutainer, IV: LABOR IMPORT and V: S-Monovette). Routine coagulation tests [activated partial thromboplastin time (aPTT), prothrombin time (PT), and fibrinogen (FIB)] were performed on ACL TOP instrument using HemosIL reagents. The significance of the differences between samples was assessed by paired Student's t-test, set at P < 0.005. Significant differences were observed for: PT when comparing I vs. II, I vs. III, I vs. V, II vs. III, II vs. IV, II vs. V, III vs. IV, III vs. V and IV vs. V; aPTT when comparing I vs. II, I vs. III, I vs. IV, II vs. IV, III vs. IV and IV vs. V. No differences were observed among brands for FIB determination. We suggest that every laboratory management should both standardize the procedures and frequently evaluate the quality of in-vitro diagnostic devices.

Single crystal to polycrystal neutron transmission simulation

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

Dessieux, Luc Lucius; Stoica, Alexandru Dan; Bingham, Philip R.

A collection of routines for calculation of the total cross section that determines the attenuation of neutrons by crystalline solids is presented. The total cross section is calculated semi-empirically as a function of crystal structure, neutron energy, temperature, and crystal orientation. The semi-empirical formula includes the contribution of parasitic Bragg scattering to the total cross section using both the crystal’s mosaic spread value and its orientation with respect to the neutron beam direction as parameters. These routines allow users to enter a distribution of crystal orientations for calculation of total cross sections of user defined powder or pseudo powder distributions,more » which enables simulation of non-uniformities such as texture and strain. In conclusion, the spectra for neutron transmission simulations in the neutron thermal energy range (2 meV–100 meV) are presented for single crystal and polycrystal samples and compared to measurements.« less

Breath analysis using external cavity diode lasers: a review

NASA Astrophysics Data System (ADS)

Bayrakli, Ismail

2017-04-01

Most techniques that are used for diagnosis and therapy of diseases are invasive. Reliable noninvasive methods are always needed for the comfort of patients. Owing to its noninvasiveness, ease of use, and easy repeatability, exhaled breath analysis is a very good candidate for this purpose. Breath analysis can be performed using different techniques, such as gas chromatography mass spectrometry (MS), proton transfer reaction-MS, and selected ion flow tube-MS. However, these devices are bulky and require complicated procedures for sample collection and preconcentration. Therefore, these are not practical for routine applications in hospitals. Laser-based techniques with small size, robustness, low cost, low response time, accuracy, precision, high sensitivity, selectivity, low detection limit, real-time, and point-of-care detection have a great potential for routine use in hospitals. In this review paper, the recent advances in the fields of external cavity lasers and breath analysis for detection of diseases are presented.

Single crystal to polycrystal neutron transmission simulation

DOE PAGES

Dessieux, Luc Lucius; Stoica, Alexandru Dan; Bingham, Philip R.

2018-02-02

A collection of routines for calculation of the total cross section that determines the attenuation of neutrons by crystalline solids is presented. The total cross section is calculated semi-empirically as a function of crystal structure, neutron energy, temperature, and crystal orientation. The semi-empirical formula includes the contribution of parasitic Bragg scattering to the total cross section using both the crystal’s mosaic spread value and its orientation with respect to the neutron beam direction as parameters. These routines allow users to enter a distribution of crystal orientations for calculation of total cross sections of user defined powder or pseudo powder distributions,more » which enables simulation of non-uniformities such as texture and strain. In conclusion, the spectra for neutron transmission simulations in the neutron thermal energy range (2 meV–100 meV) are presented for single crystal and polycrystal samples and compared to measurements.« less

Amendment to examination and investigation sample requirements--FDA. Direct final rule.

PubMed

1998-09-25

The Food and Drug Administration (FDA) is amending its regulations regarding the collection of twice the quantity of food, drug, or cosmetic estimated to be sufficient for analysis. This action increases the dollar amount that FDA will consider to determine whether to routinely collect a reserve sample of a food, drug, or cosmetic product in addition to the quantity sufficient for analysis. Experience has demonstrated that the current dollar amount does not adequately cover the cost of most quantities sufficient for analysis plus reserve samples. This direct final rule is part of FDA's continuing effort to achieve the objectives of the President's "Reinventing Government" initiative, and is intended to reduce the burden of unnecessary regulations on food, drugs, and cosmetics without diminishing the protection of the public health. Elsewhere in this issue of the Federal Register, FDA is publishing a companion proposed rule under FDA's usual procedures for notice and comment to provide a procedural framework to finalize the rule in the event the agency receives any significant adverse comment and withdraws this direct final rule.

Pushpoint sampling for defining spatial and temporal variations in contaminant concentrations in sediment pore water near the ground-water / surface-water interface

USGS Publications Warehouse

Zimmerman, Marc J.; Massey, Andrew J.; Campo, Kimberly W.

2005-01-01

During four periods from April 2002 to June 2003, pore-water samples were taken from river sediment within a gaining reach (Mill Pond) of the Sudbury River in Ashland, Massachusetts, with a temporary pushpoint sampler to determine whether this device is an effective tool for measuring small-scale spatial variations in concentrations of volatile organic compounds and selected field parameters (specific conductance and dissolved oxygen concentration). The pore waters sampled were within a subsurface plume of volatile organic compounds extending from the nearby Nyanza Chemical Waste Dump Superfund site to the river. Samples were collected from depths of 10, 30, and 60 centimeters below the sediment surface along two 10-meter-long, parallel transects extending into the river. Twenty-five volatile organic compounds were detected at concentrations ranging from less than 1 microgram per liter to hundreds of micrograms per liter (for example, 1,2-dichlorobenzene, 490 micrograms per liter; cis-1,2-dichloroethene, 290 micrograms per liter). The most frequently detected compounds were either chlorobenzenes or chlorinated ethenes. Many of the compounds were detected only infrequently. Quality-control sampling indicated a low incidence of trace concentrations of contaminants. Additional samples collected with passive-water-diffusion-bag samplers yielded results comparable to those collected with the pushpoint sampler and to samples collected in previous studies at the site. The results demonstrate that the pushpoint sampler can yield distinct samples from sites in close proximity; in this case, sampling sites were 1 meter apart horizontally and 20 or 30 centimeters apart vertically. Moreover, the pushpoint sampler was able to draw pore water when inserted to depths as shallow as 10 centimeters below the sediment surface without entraining surface water. The simplicity of collecting numerous samples in a short time period (routinely, 20 to 30 per day) validates the use of a pushpoint sampler as a highly effective tool for mapping the extent of contaminated subsurface plumes, determining their constituents and loadings, and performing technical studies that may be relevant to bioremediation and other activities.

Which family physicians work routinely with nurse practitioners, physician assistants or certified nurse midwives.

PubMed

Peterson, Lars E; Blackburn, Brenna; Petterson, Stephen; Puffer, James C; Bazemore, Andrew; Phillips, Robert L

2014-01-01

Facing rising numbers of insured with implementation of the Affordable Care Act, policy makers are interested in building teams of providers that can accommodate a growing demand for primary care services. Nurse Practitioners (NPs), Physician Assistants (PAs), and Certified Nurse Midwives (CNMs) already augment the physician workforce, particularly in rural areas. Our objective was to determine what physician and areal-level characteristics were associated with working with NPs, PAs or CNMs. The sample consisted of a convenience sample of physicians through the American Board of Family Medicine (ABFM) website in the fall of 2011. We linked these data to demographic and practice information collected by the ABFM and with provider information supplied from the National Provider Identifier file aggregated at the Primary Care Service Area level. Hierarchical logistic regression models were used to determine variables associated with working with NPs, PAs, or CNMs. Of the 3,855 family physicians in our sample, 60% reported routinely working with NPs, PAs, or CNMs. In regression analysis, characteristics positively associated with working with NPs, PAs, or CNMs were providing gynecological care (Odds Ratio = 1.23 [95% confidence interval, 1.06-1.42]), multispecialty group practice (OR = 1.72 [1.36-2.18]), any rural setting, and higher availability of PAs (OR = 1.40 [1.10-1.79]). Restrictive NP scope of practice laws failed to reach significance (OR = 0.86 [0.71-1.05]). This study suggests that the number of family physicians routinely working with NPs, PAs, and CNMs continues to increase, which may allow for improved access to health care, particularly in rural areas. © 2013 National Rural Health Association.

[Saarland Growth Study: sampling design].

PubMed

Danker-Hopfe, H; Zabransky, S

2000-01-01

The use of reference data to evaluate the physical development of children and adolescents is part of the daily routine in the paediatric ambulance. The construction of such reference data is based on the collection of extensive reference data. There are different kinds of reference data: cross sectional references, which are based on data collected from a big representative cross-sectional sample of the population, longitudinal references, which are based on follow-up surveys of usually smaller samples of individuals from birth to maturity, and mixed longitudinal references, which are a combination of longitudinal and cross-sectional reference data. The advantages and disadvantages of the different methods of data collection and the resulting reference data are discussed. The Saarland Growth Study was conducted for several reasons: growth processes are subject to secular changes, there are no specific reference data for children and adolescents from this part of the country and the growth charts in use in the paediatric praxis are possibly not appropriate any more. Therefore, the Saarland Growth Study served two purposes a) to create actual regional reference data and b) to create a database for future studies on secular trends in growth processes of children and adolescents from Saarland. The present contribution focusses on general remarks on the sampling design of (cross-sectional) growth surveys and its inferences for the design of the present study.

The case of biobank with the law: between a legal and scientific fiction.

PubMed

Sándor, Judit; Bárd, Petra; Tamburrini, Claudio; Tännsjö, Torbjörn

2012-06-01

According to estimates more than 400 biobanks currently operate across Europe. The term 'biobank' indicates a specific field of genetic study that has quietly developed without any significant critical reflection across European societies. Although scientists now routinely use this phrase, the wider public is still confused when the word 'bank' is being connected with the collection of their biological samples. There is a striking lack of knowledge of this field. In the recent Eurobarometer survey it was demonstrated that even in 2010 two-thirds of the respondents had never even heard about biobanks. The term gives the impression that a systematic collection of biological samples can constitute a 'bank' of considerable financial worth, where the biological samples, which are insignificant in isolation but are valuable as a collection, can be preserved, analysed and put to 'profitable use'. By studying the practices of the numerous already existing biobanks, the authors address the following questions: to what extent does the term 'biobank' reflect the normative concept of using biological samples for the purposes of biomedical research? Furthermore, is it in harmony with the so far agreed legal-ethical consensus in Europe or does it deliberately pull science to the territory of a new, ambiguous commercial field? In other words, do biobanks constitute a medico-legal fiction or are they substantively different from other biomedical research protocols on human tissues?

An analysis of workplace exposures to benzene over four decades at a petrochemical processing and manufacturing facility (1962-1999).

PubMed

Sahmel, J; Devlin, K; Burns, A; Ferracini, T; Ground, M; Paustenbach, D

2013-01-01

Benzene, a known carcinogen, can be generated as a by-product during the use of petroleum-based raw materials in chemical manufacturing. The aim of this study was to analyze a large data set of benzene air concentration measurements collected over nearly 40 years during routine employee exposure monitoring at a petrochemical manufacturing facility. The facility used ethane, propane, and natural gas as raw materials in the production of common commercial materials such as polyethylene, polypropylene, waxes, adhesives, alcohols, and aldehydes. In total, 3607 benzene air samples were collected at the facility from 1962 to 1999. Of these, in total 2359 long-term (>1 h) personal exposure samples for benzene were collected during routine operations at the facility between 1974 and 1999. These samples were analyzed by division, department, and job title to establish employee benzene exposures in different areas of the facility over time. Sampling data were also analyzed by key events over time, including changes in the occupational exposure limits (OELs) for benzene and key equipment process changes at the facility. Although mean benzene concentrations varied according to operation, in nearly all cases measured benzene quantities were below the OEL in place at the time for benzene (10 ppm for 1974-1986 and 1 ppm for 1987-1999). Decreases in mean benzene air concentrations were also found when data were evaluated according to 7- to 10-yr periods following key equipment process changes. Further, an evaluation of mortality rates for a retrospective employee cohort (n = 3938) demonstrated that the average personal benzene exposures at this facility (0.89 ppm for the period 1974-1986 and 0.125 ppm for the period 1987-1999) did not result in increased standardized mortality ratio (SMRs) for diseases or malignancies of the lymphatic system. The robust nature of this data set provides comprehensive exposure information that may be useful for assessing human benzene exposures at similar facilities. The data also provide a basis for comparable measured exposure levels and the potential for adverse health effects. These data may also prove beneficial for comparing relative exposure potential for production versus nonproduction operations and the relationship between area and personal breathing zone samples.

Validation of adipose lipid content as a body condition index for polar bears

USGS Publications Warehouse

McKinney, Melissa A.; Atwood, Todd C.; Dietz, Rune; Sonne, Christian; Iverson, Sara J.; Peacock, Elizabeth

2014-01-01

Body condition is a key indicator of individual and population health. Yet, there is little consensus as to the most appropriate condition index (CI), and most of the currently used CIs have not been thoroughly validated and are logistically challenging. Adipose samples from large datasets of capture biopsied, remote biopsied, and harvested polar bears were used to validate adipose lipid content as a CI via tests of accuracy, precision, sensitivity, biopsy depth, and storage conditions and comparisons to established CIs, to measures of health and to demographic and ecological parameters. The lipid content analyses of even very small biopsy samples were highly accurate and precise, but results were influenced by tissue depth at which the sample was taken. Lipid content of capture biopsies and samples from harvested adult females was correlated with established CIs and/or conformed to expected biological variation and ecological changes. However, lipid content of remote biopsies was lower than capture biopsies and harvested samples, possibly due to lipid loss during dart retrieval. Lipid content CI is a biologically relevant, relatively inexpensive and rapidly assessed CI and can be determined routinely for individuals and populations in order to infer large-scale spatial and long-term temporal trends. As it is possible to collect samples during routine harvesting or remotely using biopsy darts, monitoring and assessment of body condition can be accomplished without capture and handling procedures or noninvasively, which are methods that are preferred by local communities. However, further work is needed to apply the method to remote biopsies.

Validation of adipose lipid content as a body condition index for polar bears

PubMed Central

McKinney, Melissa A; Atwood, Todd; Dietz, Rune; Sonne, Christian; Iverson, Sara J; Peacock, Elizabeth

2014-01-01

Body condition is a key indicator of individual and population health. Yet, there is little consensus as to the most appropriate condition index (CI), and most of the currently used CIs have not been thoroughly validated and are logistically challenging. Adipose samples from large datasets of capture biopsied, remote biopsied, and harvested polar bears were used to validate adipose lipid content as a CI via tests of accuracy, precision, sensitivity, biopsy depth, and storage conditions and comparisons to established CIs, to measures of health and to demographic and ecological parameters. The lipid content analyses of even very small biopsy samples were highly accurate and precise, but results were influenced by tissue depth at which the sample was taken. Lipid content of capture biopsies and samples from harvested adult females was correlated with established CIs and/or conformed to expected biological variation and ecological changes. However, lipid content of remote biopsies was lower than capture biopsies and harvested samples, possibly due to lipid loss during dart retrieval. Lipid content CI is a biologically relevant, relatively inexpensive and rapidly assessed CI and can be determined routinely for individuals and populations in order to infer large-scale spatial and long-term temporal trends. As it is possible to collect samples during routine harvesting or remotely using biopsy darts, monitoring and assessment of body condition can be accomplished without capture and handling procedures or noninvasively, which are methods that are preferred by local communities. However, further work is needed to apply the method to remote biopsies. PMID:24634735

Detection of the diuretic hydrochlorothiazide in a doping control urine sample as the result of a non-steroidal anti-inflammatory drug (NSAID) tablet contamination.

PubMed

Helmlin, Hans-Jörg; Mürner, André; Steiner, Samuel; Kamber, Matthias; Weber, Christina; Geyer, Hans; Guddat, Sven; Schänzer, Wilhelm; Thevis, Mario

2016-10-01

Hydrochlorothiazide (HCTZ, 6-chloro-3,4-dihydro-2H-1,2,4-benzothiadiazine-7-sulfonamide-1,1-dioxide) belongs to the class of diuretic agents that represent one of today's cornerstones of the treatment of hypertensive patients. In addition to its clinical relevance, HCTZ is prohibited in sports according to the regulations of the World Anti-Doping Agency (WADA) at all times and has frequently been detected in sports drug testing urine samples worldwide since its ban was introduced in 1988. Despite these facts, the adverse analytical finding concerning HCTZ in an in-competition routine doping control sample collected in December 2014 was further investigated, particularly motivated by the comparably low urinary concentration of the drug accounting for approximately 5ng/mL. The athlete in question did not declare the use of any nutritional supplement or medication other than the ingestion of a non-steroidal anti-inflammatory drug (NSAID) prior to competition. Hence, the drug (formulated as coated tablet) provided by the athlete as well as the corresponding retention sample of the manufacturer were analyzed. Noteworthy, both samples confirmed the presence of about 2μg of HCTZ per tablet. In order to further probe for the plausibility of the observed urinary HCTZ concentrations with the scenario of drug ingestion and subsequent doping control sample collection, administration studies with produced HCTZ-spiked placebo-tablets (2.5μg of HCTZ/tablet) were conducted. Urine specimens were collected prior to and after ingestion of the drug and subjected to routine doping control analytical procedures employing liquid chromatography/tandem mass spectrometry. While blank urine samples returned negative test results, post-administration specimens were found to contain HCTZ at concentrations of approximately 1-16ng/mL, which supported the athlete's inadvertent intake of HCTZ via contaminated NSAID tablets. Due to the substantial sensitivity of test methods employed today by doping control laboratories, even drug contaminations ranging within the good manufacturing practice (GMP) limit of 10ppm overall carry-over can evidently lead to adverse analytical findings. This calls into question whether selected (classes of) substances such as diuretics should be reported only when exceeding a defined reporting level and/or whether adverse analytical findings of non-threshold substances should be reported with an estimated semi-quantitative concentration of the identified substance to facilitate the result management by anti-doping organizations. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

The Cost-Effectiveness of Cervical Self-Sampling to Improve Routine Cervical Cancer Screening: The Importance of Respondent Screening History and Compliance.

PubMed

Burger, Emily A; Sy, Stephen; Nygård, Mari; Kim, Jane J

2017-01-01

Human papillomavirus (HPV) testing allows women to self-collect cervico-vaginal cells at home (i.e., self-sampling). Using primary data from a randomized pilot study, we evaluated the long-term consequences and cost-effectiveness of using self-sampling to improve participation to routine cervical cancer screening in Norway. We compared a strategy reflecting screening participation (using reminder letters) to strategies that involved mailing self-sampling device kits to women noncompliant to screening within a 5- or 10-year period under two scenarios: (A) self-sampling respondents had moderate under-screening histories, or (B) respondents to self-sampling had moderate and severe under-screening histories. Model outcomes included quality-adjusted life-years (QALY) and lifetime costs. The "most cost-effective" strategy was identified as the strategy just below $100,000 per QALY gained. Mailing self-sampling device kits to all women noncompliant to screening within a 5- or 10-year period can be more effective and less costly than the current reminder letter policy; however, the optimal self-sampling strategy was dependent on the profile of self-sampling respondents. For example, "10-yearly self-sampling" is preferred ($95,500 per QALY gained) if "5-yearly self-sampling" could only attract moderate under-screeners; however, "5-yearly self-sampling" is preferred if this strategy could additionally attract severe under-screeners. Targeted self-sampling of noncompliers likely represents good value-for-money; however, the preferred strategy is contingent on the screening histories and compliance of respondents. The magnitude of the health benefit and optimal self-sampling strategy is dependent on the profile and behavior of respondents. Health authorities should understand these factors prior to selecting and implementing a self-sampling policy. Cancer Epidemiol Biomarkers Prev; 26(1); 95-103. ©2016 AACR. ©2016 American Association for Cancer Research.

An Optimized Set of Fluorescence In Situ Hybridization Probes for Detection of Pancreatobiliary Tract Cancer in Cytology Brush Samples.

PubMed

Barr Fritcher, Emily G; Voss, Jesse S; Brankley, Shannon M; Campion, Michael B; Jenkins, Sarah M; Keeney, Matthew E; Henry, Michael R; Kerr, Sarah M; Chaiteerakij, Roongruedee; Pestova, Ekaterina V; Clayton, Amy C; Zhang, Jun; Roberts, Lewis R; Gores, Gregory J; Halling, Kevin C; Kipp, Benjamin R

2015-12-01

Pancreatobiliary cancer is detected by fluorescence in situ hybridization (FISH) of pancreatobiliary brush samples with UroVysion probes, originally designed to detect bladder cancer. We designed a set of new probes to detect pancreatobiliary cancer and compared its performance with that of UroVysion and routine cytology analysis. We tested a set of FISH probes on tumor tissues (cholangiocarcinoma or pancreatic carcinoma) and non-tumor tissues from 29 patients. We identified 4 probes that had high specificity for tumor vs non-tumor tissues; we called this set of probes pancreatobiliary FISH. We performed a retrospective analysis of brush samples from 272 patients who underwent endoscopic retrograde cholangiopancreatography for evaluation of malignancy at the Mayo Clinic; results were available from routine cytology and FISH with UroVysion probes. Archived residual specimens were retrieved and used to evaluate the pancreatobiliary FISH probes. Cutoff values for FISH with the pancreatobiliary probes were determined using 89 samples and validated in the remaining 183 samples. Clinical and pathologic evidence of malignancy in the pancreatobiliary tract within 2 years of brush sample collection was used as the standard; samples from patients without malignancies were used as negative controls. The validation cohort included 85 patients with malignancies (46.4%) and 114 patients with primary sclerosing cholangitis (62.3%). Samples containing cells above the cutoff for polysomy (copy number gain of ≥2 probes) were classified as positive in FISH with the UroVysion and pancreatobiliary probes. Multivariable logistic regression was used to estimate associations between clinical and pathology findings and results from FISH. The combination of FISH probes 1q21, 7p12, 8q24, and 9p21 identified cancer cells with 93% sensitivity and 100% specificity in pancreatobiliary tissue samples and were therefore included in the pancreatobiliary probe set. In the validation cohort of brush samples, pancreatobiliary FISH identified samples from patients with malignancy with a significantly higher level of sensitivity (64.7%) than the UroVysion probes (45.9%) (P < .001) or routine cytology analysis (18.8%) (P < .001), but similar specificity (92.9%, 90.8%, and 100.0% respectively). Factors significantly associated with detection of carcinoma, in adjusted analyses, included detection of polysomy by pancreatobiliary FISH (P < .001), a mass by cross-sectional imaging (P < .001), cancer cells by routine cytology (overall P = .003), as well as absence of primary sclerosing cholangitis (P = .011). We identified a set of FISH probes that detects cancer cells in pancreatobiliary brush samples from patients with and without primary sclerosing cholangitis with higher levels of sensitivity than UroVysion probes. Cytologic brushing test results and clinical features were independently associated with detection of cancer and might be used to identify patients with pancreatobiliary cancers. Copyright © 2015 AGA Institute. Published by Elsevier Inc. All rights reserved.

Measuring the Impact of Enterprise Education and Entrepreneurship Support in Higher Education: Can Routinely Collected Data Be of Use?

ERIC Educational Resources Information Center

Smith, Kelly

2015-01-01

Policy makers and others charged with driving economic growth often assume a link between entrepreneurship education and business start-up. However, there is little by way of supporting literature in this regard, with few studies exploring impact measures that relate to actual venture creation. This paper considers two routinely collected data…

The REporting of studies Conducted using Observational Routinely-collected health Data (RECORD) Statement

PubMed Central

Benchimol, Eric I.; Smeeth, Liam; Guttmann, Astrid; Harron, Katie; Moher, David; Petersen, Irene; Sørensen, Henrik T.; von Elm, Erik; Langan, Sinéad M.

2015-01-01

Routinely collected health data, obtained for administrative and clinical purposes without specific a priori research goals, are increasingly used for research. The rapid evolution and availability of these data have revealed issues not addressed by existing reporting guidelines, such as Strengthening the Reporting of Observational Studies in Epidemiology (STROBE). The REporting of studies Conducted using Observational Routinely collected health Data (RECORD) statement was created to fill these gaps. RECORD was created as an extension to the STROBE statement to address reporting items specific to observational studies using routinely collected health data. RECORD consists of a checklist of 13 items related to the title, abstract, introduction, methods, results, and discussion section of articles, and other information required for inclusion in such research reports. This document contains the checklist and explanatory and elaboration information to enhance the use of the checklist. Examples of good reporting for each RECORD checklist item are also included herein. This document, as well as the accompanying website and message board (http://www.record-statement.org), will enhance the implementation and understanding of RECORD. Through implementation of RECORD, authors, journals editors, and peer reviewers can encourage transparency of research reporting. PMID:26440803

The REporting of studies Conducted using Observational Routinely-collected health Data (RECORD) statement.

PubMed

Benchimol, Eric I; Smeeth, Liam; Guttmann, Astrid; Harron, Katie; Moher, David; Petersen, Irene; Sørensen, Henrik T; von Elm, Erik; Langan, Sinéad M

2015-10-01

Routinely collected health data, obtained for administrative and clinical purposes without specific a priori research goals, are increasingly used for research. The rapid evolution and availability of these data have revealed issues not addressed by existing reporting guidelines, such as Strengthening the Reporting of Observational Studies in Epidemiology (STROBE). The REporting of studies Conducted using Observational Routinely collected health Data (RECORD) statement was created to fill these gaps. RECORD was created as an extension to the STROBE statement to address reporting items specific to observational studies using routinely collected health data. RECORD consists of a checklist of 13 items related to the title, abstract, introduction, methods, results, and discussion section of articles, and other information required for inclusion in such research reports. This document contains the checklist and explanatory and elaboration information to enhance the use of the checklist. Examples of good reporting for each RECORD checklist item are also included herein. This document, as well as the accompanying website and message board (http://www.record-statement.org), will enhance the implementation and understanding of RECORD. Through implementation of RECORD, authors, journals editors, and peer reviewers can encourage transparency of research reporting.

[The REporting of studies Conducted using Observational Routinely-collected health Data (RECORD) statement].

PubMed

Benchimol, Eric I; Smeeth, Liam; Guttmann, Astrid; Harron, Katie; Hemkens, Lars G; Moher, David; Petersen, Irene; Sørensen, Henrik T; von Elm, Erik; Langan, Sinéad M

2016-10-01

Routinely collected health data, obtained for administrative and clinical purposes without specific a priori research goals, are increasingly used for research. The rapid evolution and availability of these data have revealed issues not addressed by existing reporting guidelines, such as Strengthening the Reporting of Observational Studies in Epidemiology (STROBE). The REporting of studies Conducted using Observational Routinely collected health Data (RECORD) statement was created to fill these gaps. RECORD was created as an extension to the STROBE statement to address reporting items specific to observational studies using routinely collected health data. RECORD consists of a checklist of 13 items related to the title, abstract, introduction, methods, results, and discussion section of articles, and other information required for inclusion in such research reports. This document contains the checklist as well as explanatory and elaboration information to enhance the use of the checklist. Examples of good reporting for each RECORD checklist item are also included. This document, as well as the accompanying website and message board (http://www.record-statement.org), will improve the implementation and understanding of RECORD. By implementing RECORD, authors, journals editors, and peer reviewers can enhance transparency of research reporting. Copyright © 2016. Published by Elsevier GmbH.

GC-C-IRMS in routine doping control practice: 3 years of drug testing data, quality control and evolution of the method.

PubMed

Polet, Michael; Van Eenoo, Peter

2015-06-01

In order to detect the misuse of endogenous anabolic steroids, doping control laboratories require methods that allow differentiation between endogenous steroids and their synthetic copies. Gas chromatography combustion isotope ratio mass spectrometry (GC-C-IRMS) is capable of measuring the carbon isotope ratio of urinary steroids and this allows differentiation between both. GC-C-IRMS and its application to doping control has evolved a lot during the last decade and so have the World Anti-Doping Agency (WADA) technical documents that describe how GC-C-IRMS should be applied. Especially the WADA technical document of 2014 introduced a number of obligatory quality controls and a fixed methodology that should be used by all the doping control laboratories. This document imposed more uniform methods between the laboratories in order to decrease the interlaboratory standard deviation and acquire similar results for the analysis of the same urine samples. In this paper, 3 years of drug testing data of our GC-C-IRMS method in routine doping control practice is described, with an emphasis on the new WADA technical document and its implementation. Useful data for other doping control laboratories is presented focussing on general method setup, quality control and data collected from routine samples. The paper concentrates on how IRMS results shift or remain similar by switching to the 2014 WADA technical document and gives insight in a straightforward approach to calculate the measurement uncertainty.

Prospective surveillance for influenza. virus in Chinese swine farms.

PubMed

Anderson, Benjamin D; Ma, Mai-Juan; Wang, Guo-Lin; Bi, Zhen-Qiang; Lu, Bing; Wang, Xian-Jun; Wang, Chuang-Xin; Chen, Shan-Hui; Qian, Yan-Hua; Song, Shao-Xia; Li, Min; Zhao, Teng; Wu, Meng-Na; Borkenhagen, Laura K; Cao, Wu-Chun; Gray, Gregory C

2018-05-16

Pork production in China is rapidly increasing and swine production operations are expanding in size and number. However, the biosecurity measures necessary to prevent swine disease transmission, particularly influenza. viruses (IAV) that can be zoonotic, are often inadequate. Despite this risk, few studies have attempted to comprehensively study IAV ecology in swine production settings. Here, we present environmental and animal sampling data collected in the first year of an ongoing five-year prospective epidemiological study to assess IAV ecology as it relates to swine workers, their pigs, and the farm environment. From March 2015 to February 2016, we collected 396 each of environmental swab, water, bioaerosol, and fecal/slurry samples, as well as 3300 pig oral secretion samples from six farms in China. The specimens were tested with molecular assays for IAV. Of these, 46 (11.6%) environmental swab, 235 (7.1%) pig oral secretion, 23 (5.8%) water, 20 (5.1%) bioaerosol, and 19 (4.8%) fecal/slurry specimens were positive for influenza. by qRT-PCR. Risk factors for IAV detection among collected samples were identified using bivariate logistic regression. Overall, these first year data suggest that IAV is quite ubiquitous in the swine production environment and demonstrate an association between the different types of environmental sampling used. Given the mounting evidence that some of these viruses freely move between pigs and swine workers, and that mixing of these viruses can yield progeny viruses with pandemic potential, it seems imperative that routine surveillance for novel IAVs be conducted in commercial swine farms.

Cross-sectional study of the sperm quality in semen samples from spinal cord injured men after long-term cryopreservation.

PubMed

Krebs, J; Göcking, K; Kissling-Niggli, M; Pannek, J

2015-03-01

The deterioration of semen quality occurs very early after spinal cord injury (SCI). Thus, routine cryopreservation of semen early after injury has been recommended. However, there is currently a lack of data concerning the effects of long-term cryopreservation on the quality of spermatozoa from SCI men. We have therefore investigated the quality of spermatozoa from SCI men before and after long-term cryopreservation. The semen cryobank of a SCI rehabilitation center was screened for samples with a storage duration of more than 3 years, to carry out a cross-sectional study regarding the sperm quality of semen samples from SCI men. Semen quality analysis was carried out according to the WHO-Guidelines. The quality of 28 semen samples from 16 SCI men was investigated prior to and a median 11 years (95% CI 7-13 years) after cryopreservation. Prior to cryopreservation, ejaculate volume (median = 1.7 mL, 95% CI 1-3 mL) and sperm concentration (median = 106 × 10(6) /mL, 95% CI 82-132 × 10(6) /mL) were within normal limits, but total sperm motility (median = 19%, 95% CI 13-22%) and viability (median = 27%, 95% CI 19-45%) were reduced. Cryopreservation resulted in a significant (p < 0.0001) decrease in total sperm motility (median = 2.5%, 95% CI 0-4%) and viability (median = 7%, 95% CI 6-13%). There were no significant (p = 0.75) differences between the semen parameters of samples collected early (up to 3 weeks) after SCI and those collected later. Complete SCI had a significantly (p < 0.0001) negative effect on the sperm viability of the fresh semen samples, and tetraplegia had a significantly (p < 0.035) negative effect on both pre-cryopreservation sperm viability and post-cryopreservation motility. The assisted ejaculation technique had no significant (p > 0.053) effect on semen quality. Long-term cryopreservation of semen from SCI men results in essentially immotile sperm with minimal viability. Thus, routine long-term cryobanking of semen harvested early after SCI cannot be recommended. © 2015 American Society of Andrology and European Academy of Andrology.

Activity spaces of men who have sex with men: An initial exploration of geographic variation in locations of routine, potential sexual risk, and prevention behaviors.

PubMed

Vaughan, Adam S; Kramer, Michael R; Cooper, Hannah L F; Rosenberg, Eli S; Sullivan, Patrick S

2017-02-01

Theory and research on HIV and among men who have sex with men (MSM) have long suggested the importance of non-residential locations in defining structural exposures. Despite this, most studies within these fields define place as a residential context, neglecting the potential influence of non-residential locations on HIV-related outcomes. The concept of activity spaces, defined as a set of locations to which an individual is routinely exposed, represents one theoretical basis for addressing this potential imbalance. Using a one-time online survey to collect demographic, behavioral, and spatial data from MSM, this paper describes activity spaces and examines correlates of this spatial variation. We used latent class analysis to identify categories of activity spaces using spatial data on home, routine, potential sexual risk, and HIV prevention locations. We then assessed individual and area-level covariates for their associations with these categories. Classes were distinguished by the degree of spatial variation in routine and prevention behaviors (which were the same within each class) and in sexual risk behaviors (i.e., sex locations and locations of meeting sex partners). Partner type (e.g. casual or main) represented a key correlate of the activity space. In this early examination of activity spaces in an online sample of MSM, patterns of spatial behavior represent further evidence of significant spatial variation in locations of routine, potential HIV sexual risk, and HIV prevention behaviors among MSM. Although prevention behaviors tend to have similar geographic variation as routine behaviors, locations where men engage in potentially high-risk behaviors may be more spatially focused for some MSM than for others. Copyright © 2016 Elsevier Ltd. All rights reserved.

Factors Related to Women's Childbirth Satisfaction in Physiologic and Routine Childbirth Groups

PubMed Central

Jafari, Elham; Mohebbi, Parvin; Mazloomzadeh, Saeideh

2017-01-01

Background: Women's satisfaction with childbirth is an important measure of the quality of maternity care services. This study aims to address factors related to women's childbirth satisfaction in physiological and routine childbirth groups. Materials and Methods: This descriptive-analytical study was conducted among 340 women in physiological and routine childbirth groups in 2012. Women were selected through convenience sampling method in the routine group and by census in the physiological group. Data were collected using a 5-part questionnaire composed of demographic and obstetrics details, Mackey's Childbirth Satisfaction Rating Scale (CSRS), satisfied with birth setting, Labor Agentry Scale (LAS), and Visual Analogue Scale (VAS), which was completed by interview 24 hours after childbirth. Data were analyzed using the Statistical Package for the Social Sciences version 18 software using Pearson correlation test, independent t-test, analysis of variance, and linear, multivariate regression model at the significant level of P < 0.05. Results: In both the physiological and routine childbirth groups, satisfaction was found related to the severity of pain (P < 0.05), self-control (P < 0.0001), and birth setting satisfaction (P < 0.0001). In the physiological group, satisfaction was significantly related to previous knowledge of childbirth (P = 0.024), attitude toward the recent pregnancy (P = 0.007), and perceived severity of pain (P = 0.016). However, in the routine group, satisfaction was related only to intentional pregnancy (P = 0.002). In neither group, satisfaction was related to demographic characteristics, maternal parity, and participation in pregnancy and childbirth classes or maternal feelings toward the onset of childbirth (P > 0.05). Conclusions: Improved physical structure and setting of birth room, nonmedical pain relief, mothers' involvement in the process of labor, and sense of being in control are associated with mothers' satisfaction. PMID:28706547

Factors Related to Women's Childbirth Satisfaction in Physiologic and Routine Childbirth Groups.

PubMed

Jafari, Elham; Mohebbi, Parvin; Mazloomzadeh, Saeideh

2017-01-01

Women's satisfaction with childbirth is an important measure of the quality of maternity care services. This study aims to address factors related to women's childbirth satisfaction in physiological and routine childbirth groups. This descriptive-analytical study was conducted among 340 women in physiological and routine childbirth groups in 2012. Women were selected through convenience sampling method in the routine group and by census in the physiological group. Data were collected using a 5-part questionnaire composed of demographic and obstetrics details, Mackey's Childbirth Satisfaction Rating Scale (CSRS), satisfied with birth setting, Labor Agentry Scale (LAS), and Visual Analogue Scale (VAS), which was completed by interview 24 hours after childbirth. Data were analyzed using the Statistical Package for the Social Sciences version 18 software using Pearson correlation test, independent t -test, analysis of variance, and linear, multivariate regression model at the significant level of P < 0.05. In both the physiological and routine childbirth groups, satisfaction was found related to the severity of pain ( P < 0.05), self-control ( P < 0.0001), and birth setting satisfaction ( P < 0.0001). In the physiological group, satisfaction was significantly related to previous knowledge of childbirth ( P = 0.024), attitude toward the recent pregnancy ( P = 0.007), and perceived severity of pain ( P = 0.016). However, in the routine group, satisfaction was related only to intentional pregnancy ( P = 0.002). In neither group, satisfaction was related to demographic characteristics, maternal parity, and participation in pregnancy and childbirth classes or maternal feelings toward the onset of childbirth ( P > 0.05). Improved physical structure and setting of birth room, nonmedical pain relief, mothers' involvement in the process of labor, and sense of being in control are associated with mothers' satisfaction.

Comparison of routine urinalysis and urine Gram stain for detection of bacteriuria in dogs.

PubMed

Way, Leilani Ireland; Sullivan, Lauren A; Johnson, Valerie; Morley, Paul S

2013-01-01

To determine the utility of performing urine Gram stain for detection of bacteriuria compared to routine urine sediment examination and bacterial aerobic urine culture. Prospective, observational study. University teaching hospital. Urine samples acquired via cystocentesis through convenience sampling from 103 dogs presenting to a tertiary referral institution. All samples underwent routine urinalysis, including sediment examination, as well as urine Gram stain and quantitative bacterial aerobic urine culture. The urine Gram stain demonstrated improved sensitivity (96% versus 76%), specificity (100% versus 77%), positive predictive value (100% versus 83%), and negative predictive value (93% versus 69%) when identifying bacteriuria, compared to routine urine sediment examination. The urine Gram stain is highly sensitive and specific when detecting the presence of bacteria in canine urine samples. Gram staining should be considered when bacteriuria is highly suspected and requires rapid identification while bacterial culture is pending. © Veterinary Emergency and Critical Care Society 2013.

A new laboratory-based surveillance system (Respiratory DataMart System) for influenza and other respiratory viruses in England: results and experience from 2009 to 2012.

PubMed

Zhao, H; Green, H; Lackenby, A; Donati, M; Ellis, J; Thompson, C; Bermingham, A; Field, J; Sebastianpillai, P; Zambon, M; Watson, Jm; Pebody, R

2014-01-23

During the 2009 influenza A(H1N1) pandemic, a new laboratory-based virological sentinel surveillance system, the Respiratory DataMart System (RDMS), was established in a network of 14 Health Protection Agency (now Public Health England (PHE)) and National Health Service (NHS) laboratories in England. Laboratory results (both positive and negative) were systematically collected from all routinely tested clinical respiratory samples for a range of respiratory viruses including influenza, respiratory syncytial virus (RSV), rhinovirus, parainfluenza virus, adenovirus and human metapneumovirus (hMPV). The RDMS also monitored the occurrence of antiviral resistance of influenza viruses. Data from the RDMS for the 2009–2012 period showed that the 2009 pandemic influenza virus caused three waves of activity with different intensities during the pandemic and post pandemic periods. Peaks in influenza A(H1N1)pdm09 positivity (defined as number of positive samples per total number of samples tested) were seen in summer and autumn in 2009, with slightly higher peak positivity observed in the first post-pandemic season in 2010/2011. The influenza A(H1N1)pdm09 virus strain almost completely disappeared in the second postpandemic season in 2011/2012. The RDMS findings are consistent with other existing community-based virological and clinical surveillance systems. With a large sample size, this new system provides a robust supplementary mechanism, through the collection of routinely available laboratory data at minimum extra cost, to monitor influenza as well as other respiratory virus activity. A near real-time, daily reporting mechanism in the RDMS was established during the London 2012 Olympic and Paralympic Games. Furthermore, this system can be quickly adapted and used to monitor future influenza pandemics and other major outbreaks of respiratory infectious disease, including novel pathogens.

A recurrent, multistate outbreak of salmonella serotype agona infections associated with dry, unsweetened cereal consumption, United States, 2008.

PubMed

Russo, Elizabeth T; Biggerstaff, Gwen; Hoekstra, R Michael; Meyer, Stephanie; Patel, Nehal; Miller, Benjamin; Quick, Rob

2013-02-01

An outbreak of Salmonella enterica serotype Agona infections associated with nationwide distribution of cereal from Company X was identified in April 2008. This outbreak was detected using PulseNet, the national molecular subtyping network for foodborne disease surveillance, which coincided with Company X's voluntary recall of unsweetened puffed rice and wheat cereals after routine product sampling yielded Salmonella Agona. A case patient was defined as being infected with the outbreak strain of Salmonella Agona, with illness onset from 1 January through 1 July 2008. Case patients were interviewed using a standard questionnaire, and the proportion of ill persons who reported eating Company X puffed rice cereal was compared with Company X's market share data using binomial testing. The Minnesota Department of Agriculture inspected the cereal production facility and collected both product and environmental swab samples. Routine surveillance identified 33 case patients in 17 states. Of 32 patients interviewed, 24 (83%) reported eating Company X puffed rice cereal. Company X puffed rice cereal represented 0.063% of the total ready-to-eat dry cereal market share in the United States at the time of the investigation. Binomial testing suggested that the proportion of exposed case patients would not likely occur by chance (P < 0.0001). Of 17 cereal samples collected from case patient homes for laboratory testing, 2 (12%) yielded Salmonella Agona indistinguishable from the outbreak strain. Twelve environmental swabs and nine product samples from the cereal plant yielded the outbreak strain of Salmonella Agona. Company X cereal was implicated in a similar outbreak of Salmonella Agona infection in 1998 with the same outbreak strain linked to the same production facility. We hypothesize that a recent construction project at this facility created an open wall near the cereal production area allowing reintroduction of Salmonella Agona into the product, highlighting the resilience of Salmonella in dry food production environments.

Surface-Water Quality and Nutrient Loads in the Nepaug Reservoir Watershed, Northwestern Connecticut, 1999-2001

USGS Publications Warehouse

Morrison, Jonathan; Colombo, Michael J.

2006-01-01

Water quality was characterized at three tributary watersheds to the Nepaug Reservoir-Nepaug River, Phelps Brook, and Clear Brook-from October 1998 through September 2001 to document existing water-quality conditions and evaluate potential future effects of the removal of sand and gravel from areas of the watershed. Some removal operations may include removal of vegetation and top soil and steepening of slopes. Routine water samples collected monthly in all three watersheds were analyzed for nutrients, organic carbon, major ions, and fecal indicator bacteria. Results of the analyses indicate that, in general, the water quality in all three tributary watersheds is good and meets standards established for drinking-water supplies for nitrate, but does not always meet contact-recreation standards for bacteria. Median concentrations of total nitrogen, total phosphorus, and total organic carbon were highest in the routine monthly samples from Phelps Brook and lowest from Clear Brook. Samples also were collected during selected storms to examine changes in concentrations of nutrients during periods of high streamflow. The maximum values measured for total nitrogen, total phosphorus, and total organic carbon were in storm samples from Clear Brook. The Nepaug River watershed delivered the largest loads of total nitrogen, total phosphorus, and total organic carbon to the reservoir. Yields of nutrients and organic carbon differed significantly from year to year and among the three watersheds. Yields of total nitrogen and total organic carbon were largest from Phelps Brook and smallest from Clear Brook. The yields of total phosphorus were largest from Nepaug River and smallest from Phelps Brook. In comparison to other watersheds in Connecticut, annual loads and yields from the three streams were lower than those of developed urban areas and comparable to those of other rural and forested basins. Delivery of nutrients and organic carbon to the reservoir took place mostly during the spring with the exception of those constituents delivered during Tropical Storm Floyd, a large fall storm.

The Savannah River Site`s Groundwater Monitoring Program, first quarter 1989

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

Not Available

The Environmental Monitoring Section of the Environmental and Health Protection (EHP) Department administers the Savannah River Site`s Groundwater Monitoring Program. During first quarter 1989 (January--March), EHP conducted routine sampling of monitoring wells and drinking water locations. EHP collected the drinking water samples from Savannah River Site (SRS) drinking water systems supplied by wells. EHP established two sets of flagging criteria in 1986 to assist in the management of sample results. The flagging criteria aid personnel in sample scheduling, interpretation of data, and trend identification. The flagging criteria are based on detection limits, background levels in SRS groundwater, and drinking watermore » standards. An explanation of flagging criteria for the first quarter is presented in the Flagging Criteria section of this document. All analytical results from first quarter 1989 are listed in this report, which is distributed to all waste-site custodians.« less

The Savannah River Site`s Groundwater Monitoring Program, third quarter 1989

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

Not Available

The Environmental Monitoring Section of the Environmental and Health Protection (EHP) Department administers the Savannah River Site`s Groundwater Monitoring Program. During third quarter 1989 (July--September), EHP conducted routine sampling of monitoring wells and drinking water locations. EHP collected the drinking water samples from Savannah River Site (SRS) drinking water systems supplied by wells. EHP established two sets of flagging criteria in 1986 to assist in the management of sample results. The flagging criteria do not define contamination levels; instead they aid personnel in sample scheduling, interpretation of data, and trend identification. The flagging criteria are based on detection limits, backgroundmore » levels in SRS groundwater, and drinking water standards. An explanation of flagging criteria for the third quarter is presented in the Flagging Criteria section of this document. All analytical results from third quarter 1989 are listed in this report, which is distributed to all waste-site custodians.« less

The Savannah River Site's Groundwater Monitoring Program, third quarter 1989

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

Not Available

The Environmental Monitoring Section of the Environmental and Health Protection (EHP) Department administers the Savannah River Site's Groundwater Monitoring Program. During third quarter 1989 (July--September), EHP conducted routine sampling of monitoring wells and drinking water locations. EHP collected the drinking water samples from Savannah River Site (SRS) drinking water systems supplied by wells. EHP established two sets of flagging criteria in 1986 to assist in the management of sample results. The flagging criteria do not define contamination levels; instead they aid personnel in sample scheduling, interpretation of data, and trend identification. The flagging criteria are based on detection limits, backgroundmore » levels in SRS groundwater, and drinking water standards. An explanation of flagging criteria for the third quarter is presented in the Flagging Criteria section of this document. All analytical results from third quarter 1989 are listed in this report, which is distributed to all waste-site custodians.« less

The Savannah River Site's Groundwater Monitoring Program, first quarter 1989

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

Not Available

The Environmental Monitoring Section of the Environmental and Health Protection (EHP) Department administers the Savannah River Site's Groundwater Monitoring Program. During first quarter 1989 (January--March), EHP conducted routine sampling of monitoring wells and drinking water locations. EHP collected the drinking water samples from Savannah River Site (SRS) drinking water systems supplied by wells. EHP established two sets of flagging criteria in 1986 to assist in the management of sample results. The flagging criteria aid personnel in sample scheduling, interpretation of data, and trend identification. The flagging criteria are based on detection limits, background levels in SRS groundwater, and drinking watermore » standards. An explanation of flagging criteria for the first quarter is presented in the Flagging Criteria section of this document. All analytical results from first quarter 1989 are listed in this report, which is distributed to all waste-site custodians.« less

Case-finding for common mental disorders of anxiety and depression in primary care: an external validation of routinely collected data.

PubMed

John, Ann; McGregor, Joanne; Fone, David; Dunstan, Frank; Cornish, Rosie; Lyons, Ronan A; Lloyd, Keith R

2016-03-15

The robustness of epidemiological research using routinely collected primary care electronic data to support policy and practice for common mental disorders (CMD) anxiety and depression would be greatly enhanced by appropriate validation of diagnostic codes and algorithms for data extraction. We aimed to create a robust research platform for CMD using population-based, routinely collected primary care electronic data. We developed a set of Read code lists (diagnosis, symptoms, treatments) for the identification of anxiety and depression in the General Practice Database (GPD) within the Secure Anonymised Information Linkage Databank at Swansea University, and assessed 12 algorithms for Read codes to define cases according to various criteria. Annual incidence rates were calculated per 1000 person years at risk (PYAR) to assess recording practice for these CMD between January 1(st) 2000 and December 31(st) 2009. We anonymously linked the 2799 MHI-5 Caerphilly Health and Social Needs Survey (CHSNS) respondents aged 18 to 74 years to their routinely collected GP data in SAIL. We estimated the sensitivity, specificity and positive predictive value of the various algorithms using the MHI-5 as the gold standard. The incidence of combined depression/anxiety diagnoses remained stable over the ten-year period in a population of over 500,000 but symptoms increased from 6.5 to 20.7 per 1000 PYAR. A 'historical' GP diagnosis for depression/anxiety currently treated plus a current diagnosis (treated or untreated) resulted in a specificity of 0.96, sensitivity 0.29 and PPV 0.76. Adding current symptom codes improved sensitivity (0.32) with a marginal effect on specificity (0.95) and PPV (0.74). We have developed an algorithm with a high specificity and PPV of detecting cases of anxiety and depression from routine GP data that incorporates symptom codes to reflect GP coding behaviour. We have demonstrated that using diagnosis and current treatment alone to identify cases for depression and anxiety using routinely collected primary care data will miss a number of true cases given changes in GP recording behaviour. The Read code lists plus the developed algorithms will be applicable to other routinely collected primary care datasets, creating a platform for future e-cohort research into these conditions.

Routine data for disease surveillance in the undeveloped region of the OR Tambo district of the Eastern Cape Province.

PubMed

Kabuya, Chrispin; Wright, Graham; Odama, Anthony; O'Mahoney, Don

2014-01-01

The research team needed to upsize the solution previously tested so that it could expand the routine data collected via tablet computers. The research team identified the general flow of data within clinics. Data was mainly collected from registers, which were later converted to electronic form and checked for duplication. A database was designed for the collection of demographic data (Patient Master Index), which was aimed at eliminating duplication of patients' data in several registers. Open Data Kit (ODK) Collect was setup on Android tablets for collecting disease related routine data, while ODK Aggregate as the storage and aggregates of data captured by ODK Collect and the Patient Master Index for demographic data, were setup on an Apple Mini Mac server. Data collection is in progress. The expected results include improved data quality, reliability and quick access to summary data. Secondly, instant retrieval of patient demographic details and clinic numbers are included. Thirdly, ability to form standard reporting from the SQL database and lastly exporting data into the TIER.net and DHIS systems via CVS files thus eliminating the need for data capturers are shown.

Methods to improve routine bioassay monitoring for freshly separated, poorly transported plutonium

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

Bihl, D.E.; Lynch, T.P.; Carbaugh, E.H.

1988-09-01

Several human cases involving inhalation of plutonium oxide at Hanford have shown clearance half-times from the lung that are much longer than the 500-day half-time recommended for class Y plutonium in Publication 30 of the International Commission on Radiological Protection(ICRP). The more tenaciously retained material is referred to as super class Y plutonium. The ability to detect super class Y plutonium by current routine bioassay measurements is shown to be poor. Pacific Northwest Laboratory staff involved in the Hanford Internal Dosimetry Program investigated four methods to se if improvements in routine monitoring of workers for fresh super class Y plutoniummore » are feasible. The methods were lung counting, urine sampling, fecal sampling, and use of diethylenetriaminepentaacetate (DTPA) to enhance urinary excretion. Use of DTPA was determined to be not feasible. Routine fecal sampling was found to be feasible but not recommended. Recommendations were made to improve the detection level for routine annual urinalysis and routine annual lung counting. 12 refs., 9 figs., 7 tabs.« less

Sampling and analysis method for measuring airborne coal dust mass in mixtures with limestone (rock) dust.

PubMed

Barone, T L; Patts, J R; Janisko, S J; Colinet, J F; Patts, L D; Beck, T W; Mischler, S E

2016-01-01

Airborne coal dust mass measurements in underground bituminous coal mines can be challenged by the presence of airborne limestone dust, which is an incombustible dust applied to prevent the propagation of dust explosions. To accurately measure the coal portion of this mixed airborne dust, the National Institute for Occupational Safety and Health (NIOSH) developed a sampling and analysis protocol that used a stainless steel cassette adapted with an isokinetic inlet and the low temperature ashing (LTA) analytical method. The Mine Safety and Health Administration (MSHA) routinely utilizes this LTA method to quantify the incombustible content of bulk dust samples collected from the roof, floor, and ribs of mining entries. The use of the stainless steel cassette with isokinetic inlet allowed NIOSH to adopt the LTA method for the analysis of airborne dust samples. Mixtures of known coal and limestone dust masses were prepared in the laboratory, loaded into the stainless steel cassettes, and analyzed to assess the accuracy of this method. Coal dust mass measurements differed from predicted values by an average of 0.5%, 0.2%, and 0.1% for samples containing 20%, 91%, and 95% limestone dust, respectively. The ability of this method to accurately quantify the laboratory samples confirmed the validity of this method and allowed NIOSH to successfully measure the coal fraction of airborne dust samples collected in an underground coal mine.

Sampling and analysis method for measuring airborne coal dust mass in mixtures with limestone (rock) dust

PubMed Central

Barone, T. L.; Patts, J. R.; Janisko, S. J.; Colinet, J. F.; Patts, L. D.; Beck, T. W.; Mischler, S. E.

2016-01-01

Airborne coal dust mass measurements in underground bituminous coal mines can be challenged by the presence of airborne limestone dust, which is an incombustible dust applied to prevent the propagation of dust explosions. To accurately measure the coal portion of this mixed airborne dust, the National Institute for Occupational Safety and Health (NIOSH) developed a sampling and analysis protocol that used a stainless steel cassette adapted with an isokinetic inlet and the low temperature ashing (LTA) analytical method. The Mine Safety and Health Administration (MSHA) routinely utilizes this LTA method to quantify the incombustible content of bulk dust samples collected from the roof, floor, and ribs of mining entries. The use of the stainless steel cassette with isokinetic inlet allowed NIOSH to adopt the LTA method for the analysis of airborne dust samples. Mixtures of known coal and limestone dust masses were prepared in the laboratory, loaded into the stainless steel cassettes, and analyzed to assess the accuracy of this method. Coal dust mass measurements differed from predicted values by an average of 0.5%, 0.2%, and 0.1% for samples containing 20%, 91%, and 95% limestone dust, respectively. The ability of this method to accurately quantify the laboratory samples confirmed the validity of this method and allowed NIOSH to successfully measure the coal fraction of airborne dust samples collected in an underground coal mine. PMID:26618374

COMPARISON OF A GENUS-SPECIFIC CONVENTIONAL PCR AND A SPECIES-SPECIFIC NESTED-PCR FOR MALARIA DIAGNOSIS USING FTA COLLECTED SAMPLES FROM KINGDOM OF SAUDI ARABIA.

PubMed

Al-Harthi, Saeed A

2015-12-01

Molecular tools are increasingly accepted as the most sensitive and reliable techniques for malaria diagnosis and epidemiological surveys. Also, collection of finger prick blood spots onto filter papers is the most simple and affordable method for samples preservation and posterior molecular analysis, especially in rural endemic regions where malaria remains a major health problem. Two malaria molecular diagnostic tests, a Plasmodium genus-specific conventional PCR and a Plasmodium species-specific Nested PCR, were evaluated using DNA templates prepared from Whatman-FTA cards' dry blood spots using both, Methanol-fixation/Heat-extraction and FTA commercial purification kit. A total of 121 blood samples were collected from six Saudi south-western endemic districts both, as thick and thin films for routine microscopic screening and onto FTA cards for molecular studies. Out of the 121 samples, 75 were P. falciparum positive by at least one technique. No other species of Plasmodium were detected. P. falciparum parasites were identified in 69/75 (92%) samples by microscopic screening in health care centers. P. genus-specific PCR was able to amplify P. falciparum DNA in 41/75 (55%) and 59/75 (79%) samples using Methanol-fixation/Heat-extraction and FTA purification kit, respectively. P. species-specific Nested PCR revealed 68/75 (91%) and 75/75 (100%) positive samples using DNA templates were isolated by Methanol-fixation/Heat- extraction and FTA purification methods, respectively. The species-specific Nested PCR applied to Whatman-FTA preserved and processed blood samples represents the best alternative to classical microscopy for malaria diagnosis, particularly in epidemiological screening.

Biomonitoring of 37 trace elements in blood samples from inhabitants of northern Germany by ICP-MS.

PubMed

Heitland, Peter; Köster, Helmut D

2006-01-01

The trace elements Ag, As, Au, B, Ba, Be, Bi, Cd, Ce, Co, Cs, Cu, Ga, Hf, Hg, In, La, Mn, Mo, Ni, Pb, Pd, Rb, Rh, Ru, Sb, Se, Sn, Sr, Te, Th, Tl, U, V, W, Y and Zr were determined in 130 human blood samples from occupationally non-exposed volunteers living in the greater area of Bremen in northern Germany. The blood samples were collected in lithium heparin monovettes developed for trace metal determination and were analysed by inductively coupled plasma mass spectrometry (ICP-MS) with an octopole-based collision/reaction cell. For sample introduction into the ICP, the blood samples were diluted 1/10 (V/V) with a 0.1% Triton-X-100 and 0.5% (V/V) ammonia solution. The method validation of our developed routine method is described for all 37 elements and results about internal and external quality assurance are discussed. Information on exposure conditions of all human subjects were collected by questionnaire-based interviews, including smoking habits, seafood consumption and the type of dental alloys in the teeth. Mean values, geometric mean values, ranges and selected percentiles of all elemental concentrations in human blood are presented, which helps toxicologists and clinical chemists planning research about exposition to metals and health effects caused by exposition to metals.

[Using routine data for quality of care assessments: a critical review, taking quality indicators for the "National Disease Management Guideline for Chronic Heart Failure" as an example].

PubMed

Laux, Gunter; Nothacker, Monika; Weinbrenner, Susanne; Störk, Stefan; Blozik, Eva; Peters-Klimm, Frank; Szecsenyi, Jürgen; Scherer, Martin

2011-01-01

In December 2009, the first version of the German Disease Management Guideline (DM-CPG) for chronic heart failure was completed, including a set of proposed quality indicators for heart failure. This article explores whether proposed indicators can be derived from data collected routinely in general practices. For this purpose, previous experiences and data from the research project CONTENT (CONTinuous morbidity registration Epidemiologic NeTwork) conducted under guidance of the Department of General Medicine and Health Services Research at the University of Heidelberg, Germany, were applied. The availability of numerators and denominators needed for calculating the four quality indicators for diagnosis and pharmacotherapy proposed in the DM-CPG was checked within so-called "routine data" from the existing dataset of the CONTENT project. Within the given context, routine data are defined as data that are periodically transmitted from health care providers to cost units within the health care system. A thorough assessment has revealed that within the given context only one indicator could be deduced from routine data collection. This was the indicator measuring the proportion of patients receiving beta receptor antagonists, compared to all patients with heart failure NYHA class II to IV. Indeed, this single indicator will only be computable if the NYHA grade of heart failure severity and the presence or absence of contraindications to beta receptor antagonist therapy are routinely collected and the data merged into a central database. Against the background of these results it is obvious that a fully developed, transsectoral concept for data collection and data transfer needs to be implemented.

Formal behavioral evaluation of enrichment programs on a zookeeper's schedule: a case study with a polar bear (Ursus Maritimus) at the Bronx Zoo.

PubMed

Canino, Wendy; Powell, David

2010-01-01

We conducted a brief study of the effectiveness of environmental enrichment for a polar bear at the Bronx Zoo with two objectives in mind. First we wanted to determine if a novel method of collecting data that easily fits into a zookeeper's work routine would produce usable data and if so, we wanted to evaluate the effectiveness of some new items that had been purchased for enriching the polar bear in reducing his pacing behavior. Observations were recorded for 119 days over a period of 5 months from April 2007 through August 2007. Five new items and eight previously used items were rotated and presented to the polar bear in the morning and afternoon. We recorded the bear's behavior five times per day as we passed by his exhibit during our regular work routine. Predictably, we found that the newer enrichment items were more effective at increasing play and decreasing pacing, as well as other more subtle effects on his behavior that helped us to design a better enrichment routine. More importantly, we found that this method of "multi-point scan sampling" was effective at producing ample and reliable data that could be used to analyze the bear's behavior without adding significant work to the keepers' daily routine. (c) 2009 Wiley-Liss, Inc.

Sexual networks: the integration of social and genetic data.

PubMed

Day, S; Ward, H; Ison, C; Bell, G; Weber, J

1998-12-01

New methods for studying sexual networks are presented, drawing upon routine procedures followed in genitourinary medicine clinics in the UK for tracing partners and identifying strains of infection. The routine social procedures were developed to incorporate a structured interview. The routine microbiological diagnosis of gonorrhoea was augmented by phenotyping and the development of new genetic techniques for the fine discrimination of gonococcal strains (opa-typing). Selected results from a study in Sheffield, UK show that each method has limitations, when conducted separately, but these are minimised when the methods are combined. Moreover, the use of simple and routine methods of data collection resolve issues of scale and sample that have beset other network studies, as they provide a means of covering a larger and defined population. Popular concepts about these methods are discussed in the conclusion. The integrated approach employed in our research raises questions both about social methods, 'of people who lie, particularly when they talk about sex', and about microbiological methods, 'of genes that tell the truth' and bypass what people say and think altogether. We argue that these stereotypes are misleading insofar as they suggest that genetic techniques can substitute for the social, and we suggest that even the finest discrimination of organisms at the genetic level will never obviate the need for their interpretation in the light of social data.

Influence of centrifuge brake on residual platelet count and routine coagulation tests in citrated plasma.

PubMed

Daves, Massimo; Giacomuzzi, Katia; Tagnin, Enrico; Jani, Erika; Adcock Funk, Dorothy M; Favaloro, Emmanuel J; Lippi, Giuseppe

2014-04-01

Sample centrifugation is an essential step in the coagulation laboratory, as clotting tests are typically performed on citrated platelet (PLT) poor plasma (PPP). Nevertheless, no clear indication has been provided as to whether centrifugation of specimens should be performed with the centrifuge brake set to on or off. Fifty consecutive sodium citrate anticoagulated samples were collected and divided into two aliquots. The former was centrifuged as for Clinical Laboratory Standards Institute (CLSI) guidelines with the centrifuge brake set to on, whereas the latter was centrifuged again as for CLSI guidelines, but with the brake set to off. In the PPP of all samples, a PLT count was performed, followed by the analysis of activated partial thromboplastin time (APTT), prothrombin time (PT) and fibrinogen (FBG). The PLT count after samples centrifugation was substantially reduced, either with centrifuge brake set to on or off (5 ± 1 versus 3 ± 1 × 10/l; P = 0.009). The frequency of samples exceeding a PLT count less than 10 × 10/l was nearly double in samples centrifuged with the brake on than in those with the brake off (14 versus 8%; P < 0.01). Although no significant difference was found for APTT values, PT was slightly prolonged using the centrifuge brake set to on (mean bias 0.2 s; P < 0.001). FBG values were also significantly higher using the centrifuge brake set to on (mean bias 0.29 g/l; P < 0.001). The results of this study indicate that sample centrifugation for routine coagulation testing should be preferably performed with the centrifuge brake set to off for providing a better quality specimen.

Identification of Lactobacillus from the Saliva of Adult Patients with Caries Using Matrix-Assisted Laser Desorption/Ionization Time-Of-Flight Mass Spectrometry

PubMed Central

Ma, Qingwei; Song, Yeqing; Zhang, Qian; Wang, Xiaoyan; Chen, Feng

2014-01-01

Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) mass spectrometry (MS) has been presented as a superior method for the detection of microorganisms in body fluid samples (e.g., blood, saliva, pus, etc.) However, the performance of MALDI-TOF MS in routine identification of caries-related Lactobacillus isolates from saliva of adult patients with caries has not been determined. In the present study, we introduced a new MALDI-TOF MS system for identification of lactobacilli. Saliva samples were collected from 120 subjects with caries. Bacteria were isolated and cultured, and each isolate was identified by both 16S rRNA sequencing and MALDI-TOF MS. The identification results obtained by MALDI-TOF MS were concordant at the genus level with those of conventional 16S rRNA-based sequencing for 88.6% of lactobacilli (62/70) and 95.5% of non-lactobacilli (21/22). Up to 96 results could be obtained in parallel on a single MALDI target, suggesting that this is a reliable high-throughput approach for routine identification of lactobacilli. However, additional reference strains are necessary to increase the sensitivity and specificity of species-level identification. PMID:25166027

Suicide Information Database-Cymru: a protocol for a population-based, routinely collected data linkage study to explore risks and patterns of healthcare contact prior to suicide to identify opportunities for intervention

PubMed Central

John, Ann; Dennis, M; Kosnes, L; Gunnell, D; Scourfield, J; Ford, D V; Lloyd, K

2014-01-01

Introduction Prevention of suicide is a global public health challenge extending beyond mental health services. Linking routinely collected health and social care system data records for the same individual across different services and over time has enormous potential in suicide research. Most previous research linking suicide mortality data with routinely collected electronic health records involves only one or two domains of healthcare provision such as psychiatric inpatient care. This protocol paper describes the development of a population-based, routinely collected data linkage study: the Suicide Information Database Cymru (SID-Cymru). SID-Cymru aims to contribute to the information available on people who complete suicide. Methods and analysis SID-Cymru will facilitate a series of electronic case–control studies based in the Secure Anonymised Information Linkage (SAIL) Databank. We have identified 2664 cases of suicide in Wales between 2003 and 2011 from routinely collected mortality data using International Classification of Diseases, Tenth Revision, codes X60–X84 (intentional self-harm) and Y10–Y34 (undetermined intent). Each case will be matched by age and sex to at least five controls. Records will be collated and linked from routinely collected health and social data in Wales for each individual. Conditional logistic regression will be applied to produce crude and confounder (including general practice, socioeconomic status) adjusted ORs. Ethics and dissemination The SAIL Databank has the required ethical permissions in place to analyse anonymised data. Ethical approval has been granted by the Information Governance Review Panel (IGRP). Findings will be disseminated through peer-reviewed publications, consultations with stakeholders and national/international conference presentations. The improved understanding of the prior health, nature of previous contacts with services and wider social circumstances of those who complete suicide will assist in prevention policy, service organisation and delivery. SID-Cymru is funded through the National Institute for Social Care and Health Research, Welsh Government (RFS-12-25). PMID:25424996

Emergency Department Query for Patient-Centered Approaches to Sexual Orientation and Gender Identity

PubMed Central

Schneider, Eric B.; Kodadek, Lisa M.; Adler, Rachel R.; Ranjit, Anju; Torain, Maya; Shields, Ryan Y.; Snyder, Claire; Schuur, Jeremiah D.; Vail, Laura; German, Danielle; Peterson, Susan; Lau, Brandyn D.

2017-01-01

Importance The Institute of Medicine and The Joint Commission recommend routine documentation of patients’ sexual orientation in health care settings. Currently, very few health care systems collect these data since patient preferences and health care professionals’ support regarding collection of data about patient sexual orientation are unknown. Objective To identify the optimal patient-centered approach to collect sexual orientation data in the emergency department (ED) in the Emergency Department Query for Patient-Centered Approaches to Sexual Orientation and Gender Identity study. Design, Setting, and Participants An exploratory, sequential, mixed-methods design was used first to evaluate qualitative interviews conducted in the Baltimore, Maryland, and Washington, DC, areas. Fifty-three patients and 26 health care professionals participated in the qualitative interviews. Interviews were followed by a national online survey, in which 1516 (potential) patients (244 lesbian, 289 gay, 179 bisexual, and 804 straight) and 429 ED health care professionals (209 physicians and 220 nurses) participated. Survey participants were recruited using random digit dialing and address-based sampling techniques. Main Outcomes and Measures Qualitative interviews were used to obtain the perspectives of patients and health care professionals on sexual orientation data collection, and a quantitative survey was used to gauge patients' and health care professionals' willingness to provide or obtain sexual orientation information. Results Mean (SD) age of patient and clinician participants was 49 (16.4) and 51 (9.4) years, respectively. Qualitative interviews suggested that patients were less likely to refuse to provide sexual orientation than providers expected. Nationally, 154 patients (10.3%) reported that they would refuse to provide sexual orientation; however, 333 (77.8%) of all clinicians thought patients would refuse to provide sexual orientation. After adjustment for demographic characteristics, only bisexual patients had increased odds of refusing to provide sexual orientation compared with heterosexual patients (odds ratio, 2.40; 95% CI, 1.26-4.56). Conclusions and Relevance Patients and health care professionals have discordant views on routine collection of data on sexual orientation. A minority of patients would refuse to provide sexual orientation. Implementation of a standardized, patient-centered approach for routine collection of sexual orientation data is required on a national scale to help to identify and address health disparities among lesbian, gay, and bisexual populations. PMID:28437523

How iSamples (Internet of Samples in the Earth Sciences) Improves Sample and Data Stewardship in the Next Generation of Geoscientists

NASA Astrophysics Data System (ADS)

Hallett, B. W.; Dere, A. L. D.; Lehnert, K.; Carter, M.

2016-12-01

Vast numbers of physical samples are routinely collected by geoscientists to probe key scientific questions related to global climate change, biogeochemical cycles, magmatic processes, mantle dynamics, etc. Despite their value as irreplaceable records of nature the majority of these samples remain undiscoverable by the broader scientific community because they lack a digital presence or are not well-documented enough to facilitate their discovery and reuse for future scientific and educational use. The NSF EarthCube iSamples Research Coordination Network seeks to develop a unified approach across all Earth Science disciplines for the registration, description, identification, and citation of physical specimens in order to take advantage of the new opportunities that cyberinfrastructure offers. Even as consensus around best practices begins to emerge, such as the use of the International Geo Sample Number (IGSN), more work is needed to communicate these practices to investigators to encourage widespread adoption. Recognizing the importance of students and early career scientists in particular to transforming data and sample management practices, the iSamples Education and Training Working Group is developing training modules for sample collection, documentation, and management workflows. These training materials are made available to educators/research supervisors online at http://earthcube.org/group/isamples and can be modularized for supervisors to create a customized research workflow. This study details the design and development of several sample management tutorials, created by early career scientists and documented in collaboration with undergraduate research students in field and lab settings. Modules under development focus on rock outcrops, rock cores, soil cores, and coral samples, with an emphasis on sample management throughout the collection, analysis and archiving process. We invite others to share their sample management/registration workflows and to develop training modules. This educational approach, with evolving digital materials, can help prepare future scientists to perform research in a way that will contribute to EarthCube data integration and discovery.

Histopathologic study of eosinophilic bronchointerstitial pneumonia caused by Crenosoma striatum in the hedgehog.

PubMed

Hoseini, Seyed Mohammad; Youssefi, Mohammad Reza; Mousapour, Aliasghar; Dozouri, Rohollah; Eshkevari, Shahab Ramezanpour; Nikzad, Mohammad; Nikzad, Reza; Omidzahir, Shila

2014-06-01

Crenosoma striatum is a species of parasitic nematodes from the family Crenosomatidae responsible for pathologic lung lesions in the hedgehog (Erinaceus europaeus). Infection with C. striatum can cause weight loss, dry cough, and bronchitis. In the present study, hedgehogs killed by road accidents, or trapped and found dead on farms in different parts of Mazandaran province (Iran), were transferred to the laboratory. After dissection, parasite samples collected from the lung were placed into 70% alcohol. After clarification with lactophenol and subsequent staining, the nematodes were identified as C. striatum according to previously published guidelines. For histopathologic examination, lung samples were collected. The tissues were fixed and following routine processing, sections were stained with hematoxylin and eosin. Microscopic diagnoses included hyperemia, eosinophilic bronchointerstitial pneumonia, thickening of the interstitium, and eosinophilic microabscesses in bronchial airways. Eosinophilic pneumonia was characterized by eosinophil and other mononuclear leukocyte infiltration within the lung interstitium. Crenosoma striatum can lead to mortality in hedgehogs.

A minimally invasive method for extraction of sturgeon oocytes

USGS Publications Warehouse

Candrl, James S.; Papoulias, Diana M.; Tillitt, Donald E.

2010-01-01

Fishery biologists, hatchery personnel, and caviar fishers routinely extract oocytes from sturgeon (Acipenseridae) to determine the stage of maturation by checking egg quality. Typically, oocytes are removed either by inserting a catheter into the oviduct or by making an incision in the body cavity. Both methods can be time-consuming and stressful to the fish. We describe a device to collect mature oocytes from sturgeons quickly and effectively with minimal stress on the fish. The device is made by creating a needle from stainless steel tubing and connecting it to a syringe with polyvinyl chloride tubing. The device is filled with saline solution or water, the needle is inserted into the abdominal wall, and eggs are extracted from the fish. Using this device, an oocyte sample can be collected in less than 30 s. Such sampling leaves a minute wound that heals quickly and does not require suturing. The extractor device can easily be used in the field or hatchery, reduces fish handling time, and minimizes stress.

Prevalence and associated risk factors for syphilis in women with recurrent miscarriages.

PubMed

Hussain Laghari, Arshad; Sultana, Viqar; Hussain Samoo, Akhtar; Makhija, Pirbhomal; Ara, Jehan; Hira

2014-03-01

A Cross Sectional population based serological studies was conducted to determine the prevalence and associated risk factors for syphilis women with recurrent miscarriages. Patient's 5ml whole blood was collected through venepuncture technique. Data were collected by all women answered a questionnaire and by investigating blood sample VDRL test and FTA-ABS test. The study was conducted in a confidential manner and numbers were used to identify the participant. Total 256 women were included in the present study. Mean age of women was 29.4 years while range was 21 to 38 years (206/256). Out of the 256 samples, 05 (1.9%) were positive for active syphilis. Majority belonged to low socioeconomic group, uneducated and had previous congenital anomaly. Active infection with Treponema pallidum (T.P) in women belonging to low socioeconomic level were disquieting. This is probably due to illiteracy and high proportion of unsafe sexual behavior. It is also suggestive that seropositive status is often discovered in routine serological studies during pregnancy.

Routine health information system utilization and factors associated thereof among health workers at government health institutions in East Gojjam Zone, Northwest Ethiopia.

PubMed

Shiferaw, Atsede Mazengia; Zegeye, Dessalegn Tegabu; Assefa, Solomon; Yenit, Melaku Kindie

2017-08-07

Using reliable information from routine health information systems over time is an important aid to improving health outcomes, tackling disparities, enhancing efficiency, and encouraging innovation. In Ethiopia, routine health information utilization for enhancing performance is poor among health workers, especially at the peripheral levels of health facilities. Therefore, this study aimed to assess routine health information system utilization and associated factors among health workers at government health institutions in East Gojjam Zone, Northwest Ethiopia. An institution based cross-sectional study was conducted at government health institutions of East Gojjam Zone, Northwest Ethiopia from April to May, 2013. A total of 668 health workers were selected from government health institutions, using the cluster sampling technique. Data collected using a standard structured and self-administered questionnaire and an observational checklist were cleaned, coded, and entered into Epi-info version 3.5.3, and transferred into SPSS version 20 for further statistical analysis. Variables with a p-value of less than 0.05 at multiple logistic regression analysis were considered statistically significant factors for the utilization of routine health information systems. The study revealed that 45.8% of the health workers had a good level of routine health information utilization. HMIS training [AOR = 2.72, 95% CI: 1.60, 4.62], good data analysis skills [AOR = 6.40, 95%CI: 3.93, 10.37], supervision [AOR = 2.60, 95% CI: 1.42, 4.75], regular feedback [AOR = 2.20, 95% CI: 1.38, 3.51], and favorable attitude towards health information utilization [AOR = 2.85, 95% CI: 1.78, 4.54] were found significantly associated with a good level of routine health information utilization. More than half of the health workers working at government health institutions of East Gojjam were poor health information users compared with the findings of others studies. HMIS training, data analysis skills, supervision, regular feedback, and favorable attitude were factors related to routine health information system utilization. Therefore, a comprehensive training, supportive supervision, and regular feedback are highly recommended for improving routine health information utilization among health workers at government health facilities.

The cost-effectiveness of cervical self-sampling to improve routine cervical cancer screening: The importance of respondent screening history and compliance

PubMed Central

Burger, Emily A; Sy, Stephen; Nygård, Mari; Kim, Jane J

2016-01-01

Background Human papillomavirus (HPV) testing allows women to self-collect cervico-vaginal cells at home (i.e., self-sampling). Using primary data from a randomized pilot study, we evaluated the long-term consequences and cost-effectiveness of using self-sampling to improve participation to routine cervical cancer screening in Norway. Methods We compared a strategy reflecting screening participation (using reminder letters) to strategies that involved mailing self-sampling device kits to women non-compliant to screening within a 5-year or 10-year period under two scenarios: A) self-sampling respondents had moderate under-screening histories, or B) respondents to self-sampling had moderate and severe under-screening histories. Model outcomes included quality-adjusted life-years (QALY) and lifetime costs. The ‘most cost-effective’ strategy was identified as the strategy just below $100,000 per QALY gained. Results Mailing self-sampling device kits to all women non-compliant to screening within a 5-year or 10-year period can be more effective and less costly than the current reminder letter policy; however, the optimal self-sampling strategy was dependent on the profile of self-sampling respondents. For example, ‘10-yearly self-sampling’ is preferred ($95,500 per QALY gained) if ‘5-yearly self-sampling’ could only attract moderate under-screeners; however, ‘5-yearly self-sampling’ is preferred if this strategy could additionally attract severe under-screeners. Conclusions Targeted self-sampling of non-compliers likely represents good value-for-money; however, the preferred strategy is contingent on the screening histories and compliance of respondents. Impact The magnitude of the health benefit and optimal self-sampling strategy is dependent on the profile and behavior of respondents. Health authorities should understand these factors prior to selecting and implementing a self-sampling policy. PMID:27624639

Wautersia: The Contingency Water Container Bacterial Contamination Investigation

NASA Technical Reports Server (NTRS)

Shkedi, Brienne; Labuda, Laura; Bruce, Rebekah

2009-01-01

The Orbiter delivers water to the International Space Station (ISS) in Contingency Water Containers (CWCs) on each flight to the ISS. These CWCs are routinely sampled during each mission to verify the quality of the delivered water. Of the 5 samples returned on STS118/ 13A.1 in August 2007, two exhibited microbial growth exceeding potable water acceptability limits and historical data by orders of magnitude . The microbe was identified as Wautersia species and an investigation was launched to find the source of the contamination. Since then, samples collected on subsequent flights indicated additional CWCs had the same bacteria, as well as several on-orbit systems. An investigation was launched to try to find and address the source of the bacterial contamination. This paper will discuss how Wautersia was found, what Wautersia is, the investigation, and resolution.

Application of adaptive cluster sampling to low-density populations of freshwater mussels

USGS Publications Warehouse

Smith, D.R.; Villella, R.F.; Lemarie, D.P.

2003-01-01

Freshwater mussels appear to be promising candidates for adaptive cluster sampling because they are benthic macroinvertebrates that cluster spatially and are frequently found at low densities. We applied adaptive cluster sampling to estimate density of freshwater mussels at 24 sites along the Cacapon River, WV, where a preliminary timed search indicated that mussels were present at low density. Adaptive cluster sampling increased yield of individual mussels and detection of uncommon species; however, it did not improve precision of density estimates. Because finding uncommon species, collecting individuals of those species, and estimating their densities are important conservation activities, additional research is warranted on application of adaptive cluster sampling to freshwater mussels. However, at this time we do not recommend routine application of adaptive cluster sampling to freshwater mussel populations. The ultimate, and currently unanswered, question is how to tell when adaptive cluster sampling should be used, i.e., when is a population sufficiently rare and clustered for adaptive cluster sampling to be efficient and practical? A cost-effective procedure needs to be developed to identify biological populations for which adaptive cluster sampling is appropriate.

Comparison of hematologic values in blood samples with lithium heparin or dipotassium ethylenediaminetetraacetic acid anticoagulants in Hispaniolan Amazon parrots (Amazona ventralis).

PubMed

Guzman, David Sanchez-Migallon; Mitchell, Mark A; Gaunt, Stephen D; Beaufrère, Hugues; Tully, Thomas N

2008-06-01

Blood samples were collected from 20 Hispaniolan Amazon parrots (Amazona ventralis) and were divided into tubes that contained dipotassium ethylenediaminetetraacetic acid (K2EDTA) and lithium heparin. Complete blood cell counts were determined in each sample within 2 hours of collection. The level of agreement in results was moderate for plasma protein, packed cell volume (PCV), and leukocyte, monocyte, and lymphocyte counts between the anticoagulants. Plasma protein and PCV values were significantly lower in samples with lithium heparin than in those with K2EDTA, whereas lymphocyte numbers were significantly higher in lithium heparin samples than in K2EDTA samples. The level of agreement was good for the other cell types (heterophils, eosinophils, and basophils) when comparing the different anticoagulants. The poor level of agreement between anticoagulants with the increase in thrombocyte clumping in lithium heparin samples indicates that the use of lithium heparin as anticoagulant may affect thrombocyte count. No negative effects on morphology and staining of blood cells were apparent in smears from heparin samples compared with K2EDTA samples. Within the different values compared, the limits of agreement are small enough to be confident that lithium heparin can be used for routine CBC counts in a clinical setting. The use of the same anticoagulant should be recommended to follow trends within the same patient, especially when considering plasma protein concentration, PCV, and lymphocyte count.

Curating NASA's Past, Present, and Future Astromaterial Sample Collections

NASA Technical Reports Server (NTRS)

Zeigler, R. A.; Allton, J. H.; Evans, C. A.; Fries, M. D.; McCubbin, F. M.; Nakamura-Messenger, K.; Righter, K.; Zolensky, M.; Stansbery, E. K.

2016-01-01

The Astromaterials Acquisition and Curation Office at NASA Johnson Space Center (hereafter JSC curation) is responsible for curating all of NASA's extraterrestrial samples. JSC presently curates 9 different astromaterials collections in seven different clean-room suites: (1) Apollo Samples (ISO (International Standards Organization) class 6 + 7); (2) Antarctic Meteorites (ISO 6 + 7); (3) Cosmic Dust Particles (ISO 5); (4) Microparticle Impact Collection (ISO 7; formerly called Space-Exposed Hardware); (5) Genesis Solar Wind Atoms (ISO 4); (6) Stardust Comet Particles (ISO 5); (7) Stardust Interstellar Particles (ISO 5); (8) Hayabusa Asteroid Particles (ISO 5); (9) OSIRIS-REx Spacecraft Coupons and Witness Plates (ISO 7). Additional cleanrooms are currently being planned to house samples from two new collections, Hayabusa 2 (2021) and OSIRIS-REx (2023). In addition to the labs that house the samples, we maintain a wide variety of infra-structure facilities required to support the clean rooms: HEPA-filtered air-handling systems, ultrapure dry gaseous nitrogen systems, an ultrapure water system, and cleaning facilities to provide clean tools and equipment for the labs. We also have sample preparation facilities for making thin sections, microtome sections, and even focused ion-beam sections. We routinely monitor the cleanliness of our clean rooms and infrastructure systems, including measurements of inorganic or organic contamination, weekly airborne particle counts, compositional and isotopic monitoring of liquid N2 deliveries, and daily UPW system monitoring. In addition to the physical maintenance of the samples, we track within our databases the current and ever changing characteristics (weight, location, etc.) of more than 250,000 individually numbered samples across our various collections, as well as more than 100,000 images, and countless "analog" records that record the sample processing records of each individual sample. JSC Curation is co-located with JSC's Astromaterials Research Office, which houses a world-class suite of analytical instrumentation and scientists. We leverage these labs and personnel to better curate the samples. Part of the cu-ration process is planning for the future, and we refer to these planning efforts as "advanced curation". Advanced Curation is tasked with developing procedures, technology, and data sets necessary for curating new types of collections as envi-sioned by NASA exploration goals. We are (and have been) planning for future cu-ration, including cold curation, extended curation of ices and volatiles, curation of samples with special chemical considerations such as perchlorate-rich samples, and curation of organically- and biologically-sensitive samples.

Capture and surveillance of quad-bike (ATV)-related injuries in administrative data collections.

PubMed

Mitchell, Rebecca J; Grzebieta, Raphael; Rechnitzer, George

2016-09-01

Identifying quad-bike-related injuries in administrative data collections can be problematic. This study sought to determine whether quad-bike-related injuries could be identified in routinely collected administrative data collections in New South Wales (NSW), Australia, and to determine the information recorded according to World Health Organization (WHO) injury surveillance guidelines that could assist injury prevention efforts. Five routinely collected administrative data collections in NSW in the period 2000-2012 were reviewed. The WHO core minimum data items recorded in each of the five data collections ranged from 37.5% to 75.0%. Age and sex of the injured individual were the only data items that were recorded in all data collections. The data collections did not contain detailed information on the circumstances of quad bike incidents. Major improvements are needed in the information collected in these data-sets, if their value is to be increased and used for injury prevention purposes.

Cross-neutralization between three mumps viruses & mapping of haemagglutinin-neuraminidase (HN) epitopes.

PubMed

Vaidya, Sunil R; Dvivedi, Garima M; Jadhav, Santoshkumar M

2016-01-01

The reports from the countries where mumps vaccine is given as routine immunization suggest differences in mumps virus neutralizing antibody titres when tested with vaccine and wild type viruses. Such reports are unavailable from countries like India where mumps vaccine is not included in routine immunization. We, therefore, undertook this study to understand the cross-neutralization activity of Indian mumps viruses. By using commercial mumps IgG enzyme immunoassay (EIA) and a rapid focus reduction neutralization test (FRNT), a panel of serum samples was tested. The panel consisted of 14 acute and 14 convalescent serum samples collected during a mumps outbreak and 18 archived serum samples. Two wild types (genotypes C and G) and Leningrad-Zagreb vaccine strain (genotype N) were used for the challenge experiments and FRNT titres were determined and further compared. The HN protein sequence of three mumps viruses was analyzed for the presence of key epitopes. All serum samples effectively neutralized mumps virus wild types and a vaccine strain. However, significantly lower FRNT titres were noted to wild types than to vaccine strain (P<0.05). The comparison between EIA and FRNT results revealed 95.6 per cent agreement. No amino acid changes were seen in the epitopes in the Indian wild type strains. All potential N-linked glycosylation sites were observed in Indian strains. Good cross-neutralization activity was observed for three mumps virus strains, however, higher level of FRNT titres was detected for mumps virus vaccine strain compared to Indian wild type isolates.

Prevalence of human herpes virus types 1-7 in the semen of men attending an infertility clinic and correlation with semen parameters.

PubMed

Neofytou, Eirini; Sourvinos, George; Asmarianaki, Maria; Spandidos, Demetrios A; Makrigiannakis, Antonios

2009-06-01

To determine the prevalence of herpes viruses in the semen of an asymptomatic male cohort with and without infertility problems and its association with altered semen parameters. A prospective randomized study. Medical school and IVF clinic. One hundred seventy-two male patients undergoing routine semen analysis: 80 with normal semen parameters (control group) and 92 with abnormal semen parameters. Semen samples were collected by masturbation. The DNA from the Herpesviridae family (herpes simplex virus 1 [HSV-1], herpes simplex virus 2 [HSV-2], Varicella zoster virus [VZV], Epstein-Barr virus [EBV], cytomegalovirus [CMV], human herpes virus type 6 [HHV-6], human herpes virus type 7 [HHV-7]) and routine semen parameters. Viral DNA was detected in 143/172 (83.1%) of the total samples for at least one herpes virus: HSV-1, 2.5%; VZV, 1.2%; EBV, 45%; CMV, 62.5%; HHV-6, 70%; HHV-7, 0% in the normal semen samples and HSV-1, 2.1%; VZV, 3.2%; EBV, 39.1%; CMV, 56.5%; HHV-6, 66.3%; HHV-7, 0% in the abnormal semen samples. No association was found between the presence of viral DNA and semen parameters. Interestingly, a statistical significance between leukocytospermia and the presence of EBV DNA was observed. The DNA of herpes viruses is frequently detected in the semen of asymptomatic fertile and infertile male patients. Further studies are required to investigate the role of herpes viruses in male factor infertility.

Culture-independent Analysis of Pediatric Broncho-alveolar Lavage (BAL) Specimens.

PubMed

Zachariah, Philip; Ryan, Chanelle; Nadimpalli, Sruti; Coscia, Gina; Kolb, Michelle; Smith, Hannah; Foca, Marc; Saiman, Lisa; Planet, Paul J

2018-06-07

The clinical utility of culture-independent testing of pediatric bronchoalveolar lavage (BAL) specimens is unknown. Additionally, the variability of the pediatric pulmonary microbiome with patient characteristics is not well understood. Study subjects were ≤22 years old and underwent BAL from May 2013 - July 2015 as part of clinical care. DNA extracted from BAL specimens was used for 16S rRNA gene-based (16S-based) microbiome analysis, and results compared to routine cultures from the same samples. Indices of microbial diversity and relative taxon abundances were compared based on subject characteristics. From 81 participants (51% male, median age 9 years), 89 samples were collected and the 16S rRNA genes of 77 (86.5%) samples were successfully analyzed. Subjects included 23 cystic fibrosis (CF), 19 immunocompromised (IC), and 28 non-immunocompromised (nIC) patients. Of 68 organisms identified in culture, 16S-based analyses were concordant with culture results in 66 (97.1%), and also identified potentially clinically significant taxa missed by cultures (e.g. Staphylococcus, Legionella, Pseudomonas). Significant differences in abundance were noted mostly for non-cultured taxa with diagnosis and antibiotic use (Veillonella, Corynebacterium, Haemophilus). The microbiota of CF samples was less diverse and a "core" group of fifteen taxa shared across samples was identified. 16S-based culture independent analysis was concordant with routine cultures and showed potential to detect non-cultured pathogens. While 16S- based testing identified relative changes in organism abundance associated with clinical characteristics, distinct microbiome profiles associated with disease states were not identified.

Informed decision-making before changing to RDT: a comparison of microscopy, rapid diagnostic test and molecular techniques for the diagnosis and identification of malaria parasites in Kassala, eastern Sudan.

PubMed

Osman, Mamoun M M; Nour, Bakri Y M; Sedig, Mohamed F; De Bes, Laura; Babikir, Adil M; Mohamedani, Ahmed A; Mens, Petra F

2010-12-01

Rapid diagnostic tests (RDTs) are promoted for the diagnosis of malaria in many countries. The question arises whether laboratories where the current method of diagnosis is microscopy should also switch to RDT. This problem was studied in Kassala, Sudan where the issue of switching to RDT is under discussion. Two hundred and three blood samples were collected from febrile patients suspected of having malaria. These were subsequently analysed with microscopy, RDT (SD Bioline P.f/P.v) and PCR for the detection and identification of Plasmodium parasites. Malaria parasites were detected in 36 blood samples when examined microscopically, 54 (26.6%) samples were found positive for malaria parasites by RDT, and 44 samples were positive by PCR. Further analysis showed that the RDT used in our study resulted in a relatively high number of false positive samples. When microscopy was compared with PCR, an agreement of 96.1% and k = 0.88 (sensitivity 85.7% and specificity 100%) was found. However, when RDT was compared with PCR, an agreement of only 81.2 and k = 0.48 (sensitivity 69% and specificity 84%) was found. PCR has proven to be one of the most specific and sensitive diagnostic methods, particularly for malaria cases with low parasitaemia. However, this technique has limitations in its routine use under resource-limited conditions, such as our study location. At present, based on these results, microscopy remains the best option for routine diagnosis of malaria in Kassala, eastern Sudan. © 2010 Blackwell Publishing Ltd.

Multisite tumor sampling enhances the detection of intratumor heterogeneity at all different temporal stages of tumor evolution.

PubMed

Erramuzpe, Asier; Cortés, Jesús M; López, José I

2018-02-01

Intratumor heterogeneity (ITH) is an inherent process of tumor development that has received much attention in previous years, as it has become a major obstacle for the success of targeted therapies. ITH is also temporally unpredictable across tumor evolution, which makes its precise characterization even more problematic since detection success depends on the precise temporal snapshot at which ITH is analyzed. New and more efficient strategies for tumor sampling are needed to overcome these difficulties which currently rely entirely on the pathologist's interpretation. Recently, we showed that a new strategy, the multisite tumor sampling, works better than the routine sampling protocol for the ITH detection when the tumor time evolution was not taken into consideration. Here, we extend this work and compare the ITH detections of multisite tumor sampling and routine sampling protocols across tumor time evolution, and in particular, we provide in silico analyses of both strategies at early and late temporal stages for four different models of tumor evolution (linear, branched, neutral, and punctuated). Our results indicate that multisite tumor sampling outperforms routine protocols in detecting ITH at all different temporal stages of tumor evolution. We conclude that multisite tumor sampling is more advantageous than routine protocols in detecting intratumor heterogeneity.

Ascent/descent ancillary data production user's guide

NASA Technical Reports Server (NTRS)

Brans, H. R.; Seacord, A. W., II; Ulmer, J. W.

1986-01-01

The Ascent/Descent Ancillary Data Product, also called the A/D BET because it contains a Best Estimate of the Trajectory (BET), is a collection of trajectory, attitude, and atmospheric related parameters computed for the ascent and descent phases of each Shuttle Mission. These computations are executed shortly after the event in a post-flight environment. A collection of several routines including some stand-alone routines constitute what is called the Ascent/Descent Ancillary Data Production Program. A User's Guide for that program is given. It is intended to provide the reader with all the information necessary to generate an Ascent or a Descent Ancillary Data Product. It includes descriptions of the input data and output data for each routine, and contains explicit instructions on how to run each routine. A description of the final output product is given.

Cytogenetic study is not essential in patients with aplastic anemia

PubMed Central

Dutta, Atreyee; De, Rajib; Dolai, Tuphan K; Mitra, Pradip K; Halder, Ajanta

2017-01-01

Depending on contemporary treatment approach of aggressive immunosuppression, Aplastic Anemia (AA) is caused by immunological destruction of otherwise normal hematopoietic stem cells. The aim was to summarize the cytogenetic abnormalities in AA patients and the frequency of Fanconi Anemia (FA) in morphologically normal AA patients in eastern India. Ethical clearances were obtained from both institutions involved in this study. Out of 72800 patients attending the outpatient department, 520 pancytopenia patients were screened for AA after Bone marrow (BM) aspiration and biopsy. Samples were collected from 117 cases in 3 phases. 51 peripheral venous blood (PVB) samples in the first phase, 19 BM & PVB paired samples in the second phase and 47 BM samples in third phase were collected followed by leukocyte and/or BM stem cell culture. Next GTG banding and karyotyping were performed. PVB was collected from 63 (< 50 years) AA patients and stress cytogenetics was done to diagnose FA. In the first phase of the study, out of 51 PVB samples, 1 (1.96%) showed a unique chromosomal abnormality, i.e. 45,XY,rob(14:21)(p10:q10)[20]. In the second phase of study, among 19 BM & PVB paired samples, 1 (5.26%) showed abnormal karyotype i.e. 45,X,-Y[3]/46,XY[47]. In the third phase of the study, 47 BM samples showed normal karyotype. Only 6 (9.52%) cases were found positive for stress cytogenetics. A negligible percentage showing cytogenetic abnormality in such a considerable number of AA cases indicates that routine cytogenetic analysis of AA patient is not essential. A significant percentage was positive for stress cytogenetics; suggestive for FA, even the patients were morphologically normal. PMID:29181263

Effectiveness of Current Practices for Disinfecting Medical Equipment in a Radiology Department.

PubMed

Hubble, William L; Turner, James Austin; Heuertz, Rita

2016-01-01

To evaluate the effectiveness of routine, daily disinfection practices on the control of microorganisms on nuclear medicine equipment in a radiology department. During phase 1, surface samples were collected from various sites in the nuclear medicine division of a radiology department at a single institution. These samples were transferred onto growth plates for evaluation and speciation by a clinical microbiologist. Collection sites that yielded potentially pathogenic bacteria or high numbers (> 100) of colonies of likely nonpathogenic bacteria were identified for resampling. During phase 2, secondary samples were taken at the resampling sites after disinfection. These secondary samples also were evaluated to determine the efficacy of the departmental disinfection practices on surface cleanliness. Phase 1 sampling identified 10 sites that harbored either potentially pathogenic bacteria or high numbers of likely nonpathogenic bacteria. Evaluation of postdisinfection samples indicated elimination of potentially pathogenic bacteria and reduction of likely nonpathogenic colonies. The variety of surfaces and equipment found in radiology departments can present unique challenges for effective disinfection. Porous materials and intricate imaging and peripheral devices require special consideration when designing and maintaining department cleaning policies. The disinfection practices in place at the institution were effective in reducing or eliminating bacteria; however, recolonization after cleaning was recognized as a possibility. Educating staff about the value of disinfecting contact surfaces between patients is necessary to achieve optimum sanitization in the radiology department. © 2016 American Society of Radiologic Technologists.

Upfront dilution of ferritin samples to reduce hook effect, improve turnaround time and reduce costs.

PubMed

Wu, Shu Juan; Hayden, Joshua A

2018-02-15

Sandwich immunoassays offer advantages in the clinical laboratory but can yield erroneously low results due to hook (prozone) effect, especially with analytes whose concentrations span several orders of magnitude such as ferritin. This study investigated a new approach to reduce the likelihood of hook effect in ferritin immunoassays by performing upfront, five-fold dilutions of all samples for ferritin analysis. The impact of this change on turnaround time and costs were also investigated. Ferritin concentrations were analysed in routine clinical practice with and without upfront dilutions on Siemens Centaur® XP (Siemens Healthineers, Erlang, Germany) immunoanalysers. In addition, one month of baseline data (1026 results) were collected prior to implementing upfront dilutions and one month of data (1033 results) were collected after implementation. Without upfront dilutions, hook effect was observed in samples with ferritin concentrations as low as 86,028 µg/L. With upfront dilutions, samples with ferritin concentrations as high as 126,050 µg/L yielded values greater than the measurement interval and would have been diluted until an accurate value was obtained. The implementation of upfront dilution of ferritin samples led to a decrease in turnaround time from a median of 2 hours and 3 minutes to 1 hour and 18 minutes (P = 0.002). Implementation of upfront dilutions of all ferritin samples reduced the possibility of hook effect, improved turnaround time and saved the cost of performing additional dilutions.

Can technical, functional and structural characteristics of dental units predict Legionella pneumophila and Pseudomonas aeruginosa contamination?

PubMed

Aprea, Luigi; Cannova, Lucia; Firenze, Alberto; Bivona, Maria S; Amodio, Emanuele; Romano, Nino

2010-12-01

Legionella pneumophila and Pseudomonas aeruginosa are common colonizers of water environments, particularly dental unit waterlines. The aim of this study was to assess whether the technical, functional and structural characteristics of dental units can influence the presence and the levels of opportunistic pathogens. Overall, 42 water samples were collected from dental units in a teaching hospital in Palermo, Italy, including 21 samples from the 21 taps supplied by the municipal water distribution system and 21 samples from oral rinsing cups at 21 dental units. L. pneumophila was present in 16 out of 21 water samples (76.2%) from dental units, and the median concentration was higher in samples from oral rinsing cups than in those from taps (P < 0.001). P. aeruginosa was equally distributed in water samples collected from oral rinsing cups and from taps. Some characteristics of dental units (age, number of chairs per room, number of patients per day and water temperature) were slightly associated with the presence of P. aeruginosa, but not with contamination by L. pneumophila. Our experience suggests that L. pneumophila is frequently detected in dental units, as reported in previous studies, whereas P. aeruginosa is not a frequent contaminant. As a consequence, microbiological control of water quality should be routinely performed, and should include the detection of opportunistic pathogens when bacterial contamination is expected.

Diagnosis of Bubonic Plague by PCR in Madagascar under Field Conditions

PubMed Central

Rahalison, L.; Vololonirina, E.; Ratsitorahina, M.; Chanteau, S.

2000-01-01

The diagnostic value of a PCR assay that amplifies a 501-bp fragment of the Yersinia pestis caf1 gene has been determined in a reference laboratory with 218 bubo aspirates collected from patients with clinically suspected plague managed in a regional hospital in Madagascar. The culture of Y. pestis and the detection of the F1 antigen (Ag) by enzyme-linked immunosorbent assay (ELISA) were used as reference diagnostic methods. The sensitivity of PCR was 89% (57 of 64) for the Y. pestis-positive patients, and 80.7% (63 of 78) for the F1 Ag-positive patients. The specificity of PCR for the culture-, F1 Ag-, and antibody-negative patients (n = 105) was 100%. Because in Madagascar most patients with plague are managed and their clinical samples are collected in remote villages, the usefulness of PCR was evaluated for routine diagnostic use in the operational conditions of the control program. The sensitivity of PCR was 50% (25 of 50) relative to the results of culture and 35.2% (19 of 54) relative to the results of the F1 Ag immunocapture ELISA. The specificity of PCR under these conditions was 96%. In conclusion, the PCR method was found to be very specific but not as sensitive as culture or the F1 Ag detection method. The limitation in sensitivity may have been due to suboptimal field conditions and the small volumes of samples used for DNA extraction. This technique is not recommended as a routine diagnostic test for plague in Madagascar. PMID:10618097

Automated saliva processing for LC-MS/MS: Improving laboratory efficiency in cortisol and cortisone testing.

PubMed

Antonelli, Giorgia; Padoan, Andrea; Artusi, Carlo; Marinova, Mariela; Zaninotto, Martina; Plebani, Mario

2016-04-01

The aim of this study was to implement in our routine practice an automated saliva preparation protocol for quantification of cortisol (F) and cortisone (E) by LC-MS/MS using a liquid handling platform, maintaining the previously defined reference intervals with the manual preparation. Addition of internal standard solution to saliva samples and calibrators and SPE on μ-elution 96-well plate were performed by liquid handling platform. After extraction, the eluates were submitted to LC-MS/MS analysis. The manual steps within the entire process were to transfer saliva samples in suitable tubes, to put the cap mat and transfer of the collection plate to the LC auto sampler. Transference of the reference intervals from the manual to the automated procedure was established by Passing Bablok regression on 120 saliva samples analyzed simultaneously with the two procedures. Calibration curves were linear throughout the selected ranges. The imprecision ranged from 2 to 10%, with recoveries from 95 to 116%. Passing Bablok regression demonstrated no significant bias. The liquid handling platform translates the manual steps into automated operations allowing for saving hands-on time, while maintaining assay reproducibility and ensuring reliability of results, making it implementable in our routine with the previous established reference intervals. Copyright © 2015 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

An operational method for the real-time monitoring of E. coli numbers in bathing waters.

PubMed

Lebaron, Philippe; Henry, A; Lepeuple, A-S; Pena, G; Servais, P

2005-06-01

The aim of this study was to investigate the potential application of the beta-d-glucuronidase (GLUase) activity measurement for the routine detection and quantification of E. coli in marine bathing waters. GLUase activity was measured as the rate of hydrolysis of 4-methylumbelliferyl-beta-d-glucuronide. Culturable E. coli were quantified by the most probable number (MPN) microplate method. Both methods were applied to a large set of seawater samples. Significant correlation was found between the log of GLUase activity and the log of culturable E. coli. The mean coefficient of variation (CV) of the GLUase activity was less than 15% at concentrations around the current standards of International regulations whereas the CV of the microplate method was around 30%. When samples were stored at 4 degrees C and 20 degrees C, the mean CV of the GLUase activity remained below 15% up to 6 hours after sample collection whereas the range of variation of the microplate method varied between 10 and 50%. We concluded that the GLUase activity is an operational, reproducible, simple, very rapid and low cost method for the real-time enumeration of E. coli in bathing waters and should be preferred to the microplate method. The GLUase activity method should be routinely applied to the rapid enumeration of E. coli in recreational waters and recommendations for its application were suggested to water quality managers.

Possible Rickettsia massiliae Infection in Greece: an Imported Case.

PubMed

Chochlakis, Dimosthenis; Bongiorni, Christine; Partalis, Nikolaos; Tselentis, Yannis; Psaroulaki, Anna

2016-07-22

Tick-borne rickettsioses are endemic in Greece; however, until recently, only Rickettsia typhi and R. conorii were tested routinely in human samples arriving at the National Reference Center. During the last few years, the identification of different rickettsia species in ticks led to the introduction of other spotted fever group rickettsiae in routine analysis. Under the new scheme, R. massiliae is now tested routinely in human samples; herein, we describe a human case of this infection.

A proposed method to minimize waste from institutional radiation safety surveillance programs through the application of expected value statistics.

PubMed

Emery, R J

1997-03-01

Institutional radiation safety programs routinely use wipe test sampling and liquid scintillation counting analysis to indicate the presence of removable radioactive contamination. Significant volumes of liquid waste can be generated by such surveillance activities, and the subsequent disposal of these materials can sometimes be difficult and costly. In settings where large numbers of negative results are regularly obtained, the limited grouping of samples for analysis based on expected value statistical techniques is possible. To demonstrate the plausibility of the approach, single wipe samples exposed to varying amounts of contamination were analyzed concurrently with nine non-contaminated samples. Although the sample grouping inevitably leads to increased quenching with liquid scintillation counting systems, the effect did not impact the ability to detect removable contamination in amounts well below recommended action levels. Opportunities to further improve this cost effective semi-quantitative screening procedure are described, including improvements in sample collection procedures, enhancing sample-counting media contact through mixing and extending elution periods, increasing sample counting times, and adjusting institutional action levels.

Selected water-quality data from the Cedar River and Cedar Rapids well fields, Cedar Rapids, Iowa, 2006-10

USGS Publications Warehouse

Littin, Gregory R.

2012-01-01

The Cedar River alluvial aquifer is the primary source of municipal water in the Cedar Rapids, Iowa area. Municipal wells are completed in the alluvial aquifer approximately 40 to 80 feet below land surface. The City of Cedar Rapids and the U.S. Geological Survey have been conducting a cooperative study of the groundwater-flow system and water quality of the aquifer since 1992. Cooperative reports between the City of Cedar Rapids and the U.S. Geological Survey have documented hydrologic and water-quality data, geochemistry, and groundwater models. Water-quality samples were collected for studies involving well field monitoring, trends, source-water protection, groundwater geochemistry, surface-water-groundwater interaction, and pesticides in groundwater and surface water. Water-quality analyses were conducted for major ions (boron, bromide, calcium, chloride, fluoride, iron, magnesium, manganese, potassium, silica, sodium, and sulfate), nutrients (ammonia as nitrogen, nitrite as nitrogen, nitrite plus nitrate as nitrogen, and orthophosphate as phosphorus), dissolved organic carbon, and selected pesticides including two degradates of the herbicide atrazine. Physical characteristics (alkalinity, dissolved oxygen, pH, specific conductance and water temperature) were measured in the field and recorded for each water sample collected. This report presents the results of routine water-quality data-collection activities from January 2006 through December 2010. Methods of data collection, quality-assurance, and water-quality analyses are presented. Data include the results of water-quality analyses from quarterly sampling from monitoring wells, municipal wells, and the Cedar River.

Improving care coordination using organisational routines.

PubMed

Prætorius, Thim

2016-01-01

The purpose of this paper is to systematically apply theory of organisational routines to standardised care pathways. The explanatory power of routines is used to address open questions in the care pathway literature about their coordinating and organising role, the way they change and can be replicated, the way they are influenced by the organisation and the way they influence health care professionals. Theory of routines is systematically applied to care pathways in order to develop theoretically derived propositions. Care pathways mirror routines by being recurrent, collective and embedded and specific to an organisation. In particular, care pathways resemble standard operating procedures that can give rise to recurrent collective action patterns. In all, 11 propositions related to five categories are proposed by building on these insights: care pathways and coordination, change, replication, the organisation and health care professionals. Research limitations/implications - The paper is conceptual and uses care pathways as illustrative instances of hospital routines. The propositions provide a starting point for empirical research. The analysis highlights implications that health care professionals and managers have to consider in relation to coordination, change, replication, the way the organisation influences care pathways and the way care pathways influence health care professionals. Originality/value - Theory on organisational routines offers fundamental, yet unexplored, insights into hospital processes, including in particular care coordination.

[Application of laboratory information system in the management of the key indicators of quality inspection].

PubMed

Guo, Ye; Chen, Qian; Wu, Wei; Cui, Wei

2015-03-31

To establish a system of monitoring the key indicator of quality for inspection (KIQI) on a laboratory information system (LIS), and to have a better management of KIQI. Clinical sample made in PUMCH were collected during the whole of 2014. Next, interactive input program were designed to accomplish data collecting of the disqualification rate of samples, the mistake rate of samples and the occasions of losing samples, etc. Then, a series moment of sample collection, laboratory sample arrived, sample test, sample check, response to critical value, namely, trajectory information left on LIS were recorded and the qualification rate of TAT, the notification rate of endangering result were calculated. Finally, the information about quality control were collected to build an internal quality control database and the KIQI, such as the out-of-control rate of quality control and the total error of test items were monitored. The inspection of the sample management shows the disqualification rates in 2014 were all below the target, but the rates in January and February were a little high and the rates of four wards were above 2%. The mistake rates of samples was 0.47 cases/10 000 cases, attaining the target (< 2 cases/10 000 cases). Also, there was no occasion of losing samples in 2014, attaining the target too. The inspection of laboratory reports shows the qualification rates of TAT was within the acceptable range (> 95%), however the rates of blood routine in November (94.75%) was out of range. We have solved the problem by optimizing the processes. The notification rate of endangering result attained the target (≥ 98%), while the rate of timely notification is needed to improve. Quality inspection shows the CV of APTT in August (5.02%) was rising significantly, beyond the accepted CV (5.0%). We have solved the problem by changing the reagent. The CV of TT in 2014 were all below the allowable CV, thus the allowable CV of the next year lower to 10%. It is an objective and effective method to manage KIQI with the powerful management mode of database and information process capability on LIS.

The Savannah River Site`s groundwater monitoring program. Third quarter 1990

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

Not Available

1991-05-06

The Environmental Protection Department/Environmental Monitoring Section (EPD/EMS) administers the Savannah River Site`s (SRS) Groundwater Monitoring Program. During third quarter 1990 (July through September) EPD/EMS conducted routine sampling of monitoring wells and drinking water locations. EPD/EMS established two sets of flagging criteria in 1986 to assist in the management of sample results. The flagging criteria do not define contamination levels; instead they aid personnel in sample scheduling, interpretation of data, and trend identification. The flagging criteria are based on detection limits, background levels in SRS groundwater, and drinking water standards. All analytical results from third quarter 1990 are listed in thismore » report, which is distributed to all site custodians. One or more analytes exceeded Flag 2 in 87 monitoring well series. Analytes exceeded Flat 2 for the first since 1984 in 14 monitoring well series. In addition to groundwater monitoring, EPD/EMS collected drinking water samples from SRS drinking water systems supplied by wells. The drinking water samples were analyzed for radioactive constituents.« less

The Savannah River Site's groundwater monitoring program

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

Not Available

1991-05-06

The Environmental Protection Department/Environmental Monitoring Section (EPD/EMS) administers the Savannah River Site's (SRS) Groundwater Monitoring Program. During third quarter 1990 (July through September) EPD/EMS conducted routine sampling of monitoring wells and drinking water locations. EPD/EMS established two sets of flagging criteria in 1986 to assist in the management of sample results. The flagging criteria do not define contamination levels; instead they aid personnel in sample scheduling, interpretation of data, and trend identification. The flagging criteria are based on detection limits, background levels in SRS groundwater, and drinking water standards. All analytical results from third quarter 1990 are listed in thismore » report, which is distributed to all site custodians. One or more analytes exceeded Flag 2 in 87 monitoring well series. Analytes exceeded Flat 2 for the first since 1984 in 14 monitoring well series. In addition to groundwater monitoring, EPD/EMS collected drinking water samples from SRS drinking water systems supplied by wells. The drinking water samples were analyzed for radioactive constituents.« less

Polio and Measles Down the Drain: Environmental Enterovirus Surveillance in the Netherlands, 2005 to 2015.

PubMed

Benschop, Kimberley S M; van der Avoort, Harrie G; Jusic, Edin; Vennema, Harry; van Binnendijk, Rob; Duizer, Erwin

2017-07-01

Polioviruses (PVs) are members of the genus Enterovirus In the Netherlands, the exclusion of PV circulation is based on clinical enterovirus (EV) surveillance (CEVS) of EV-positive cases and routine environmental EV surveillance (EEVS) conducted on sewage samples collected in the region of the Netherlands where vaccination coverage is low due to religious reasons. We compared the EEVS data to those of the CEVS to gain insight into the relevance of EEVS for poliovirus and nonpolio enterovirus surveillance. Following the polio outbreak in Syria, EEVS was performed at the primary refugee center in Ter Apel in the Netherlands, and data were compared to those of CEVS and EEVS. Furthermore, we assessed the feasibility of poliovirus detection by EEVS using measles virus detection in sewage during a measles outbreak as a proxy. Two Sabin-like PVs were found in routine EEVS, 11 Sabin-like PVs were detected in the CEVS, and one Sabin-like PV was found in the Ter Apel sewage. We observed significant differences between the three programs regarding which EVs were found. In 6 sewage samples collected during the measles outbreak in 2013, measles virus RNA was detected in regions where measles cases were identified. In conclusion, we detected PVs, nonpolio EVs, and measles virus in sewage and showed that environmental surveillance is useful for poliovirus detection in the Netherlands, where live oral poliovirus vaccine is not used and communities with lower vaccination coverage exist. EEVS led to the detection of EV types not seen in the CEVS, showing that EEVS is complementary to CEVS. IMPORTANCE We show that environmental enterovirus surveillance complements clinical enterovirus surveillance for poliovirus detection, or exclusion, and for nonpolio enterovirus surveillance. Even in the presence of adequate surveillance, only a very limited number of Sabin-like poliovirus strains were detected in a 10-year period, and no signs of transmission of oral polio vaccine (OPV) strains were found in a country using exclusively inactivated polio vaccine (IPV). Measles viruses can be detected during an outbreak in sewage samples collected and concentrated following procedures used for environmental enterovirus surveillance. Copyright © 2017 American Society for Microbiology.

Polio and Measles Down the Drain: Environmental Enterovirus Surveillance in the Netherlands, 2005 to 2015

PubMed Central

Benschop, Kimberley S. M.; van der Avoort, Harrie G.; Jusic, Edin; Vennema, Harry; van Binnendijk, Rob

2017-01-01

ABSTRACT Polioviruses (PVs) are members of the genus Enterovirus. In the Netherlands, the exclusion of PV circulation is based on clinical enterovirus (EV) surveillance (CEVS) of EV-positive cases and routine environmental EV surveillance (EEVS) conducted on sewage samples collected in the region of the Netherlands where vaccination coverage is low due to religious reasons. We compared the EEVS data to those of the CEVS to gain insight into the relevance of EEVS for poliovirus and nonpolio enterovirus surveillance. Following the polio outbreak in Syria, EEVS was performed at the primary refugee center in Ter Apel in the Netherlands, and data were compared to those of CEVS and EEVS. Furthermore, we assessed the feasibility of poliovirus detection by EEVS using measles virus detection in sewage during a measles outbreak as a proxy. Two Sabin-like PVs were found in routine EEVS, 11 Sabin-like PVs were detected in the CEVS, and one Sabin-like PV was found in the Ter Apel sewage. We observed significant differences between the three programs regarding which EVs were found. In 6 sewage samples collected during the measles outbreak in 2013, measles virus RNA was detected in regions where measles cases were identified. In conclusion, we detected PVs, nonpolio EVs, and measles virus in sewage and showed that environmental surveillance is useful for poliovirus detection in the Netherlands, where live oral poliovirus vaccine is not used and communities with lower vaccination coverage exist. EEVS led to the detection of EV types not seen in the CEVS, showing that EEVS is complementary to CEVS. IMPORTANCE We show that environmental enterovirus surveillance complements clinical enterovirus surveillance for poliovirus detection, or exclusion, and for nonpolio enterovirus surveillance. Even in the presence of adequate surveillance, only a very limited number of Sabin-like poliovirus strains were detected in a 10-year period, and no signs of transmission of oral polio vaccine (OPV) strains were found in a country using exclusively inactivated polio vaccine (IPV). Measles viruses can be detected during an outbreak in sewage samples collected and concentrated following procedures used for environmental enterovirus surveillance. PMID:28432101

UMTRA Project water sampling and analysis plan, Durango, Colorado. Revision 1

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

NONE

1995-09-01

Planned, routine ground water sampling activities at the US Department of Energy (DOE) Uranium Mill Tailings Remedial Action (UMTRA) Project site in Durango, Colorado, are described in this water sampling and analysis plan. The plan identifies and justifies the sampling locations, analytical parameters, detection limits, and sampling frequency for the routine monitoring stations at the site. The ground water data are used to characterize the site ground water compliance strategies and to monitor contaminants of potential concern identified in the baseline risk assessment (DOE, 1995a). Regulatory basis for routine ground water monitoring at UMTRA Project sites is derived from themore » US EPA regulations in 40 CFR Part 192 (1994) and EPA standards of 1995 (60 FR 2854). Sampling procedures are guided by the UMTRA Project standard operating procedures (SOP) (JEG, n.d.), the Technical Approach Document (TAD) (DOE, 1989), and the most effective technical approach for the site.« less

A formative evaluation of the implementation of a medication safety data collection tool in English healthcare settings: A qualitative interview study using normalisation process theory.

PubMed

Rostami, Paryaneh; Ashcroft, Darren M; Tully, Mary P

2018-01-01

Reducing medication-related harm is a global priority; however, impetus for improvement is impeded as routine medication safety data are seldom available. Therefore, the Medication Safety Thermometer was developed within England's National Health Service. This study aimed to explore the implementation of the tool into routine practice from users' perspectives. Fifteen semi-structured interviews were conducted with purposely sampled National Health Service staff from primary and secondary care settings. Interview data were analysed using an initial thematic analysis, and subsequent analysis using Normalisation Process Theory. Secondary care staff understood that the Medication Safety Thermometer's purpose was to measure medication safety and improvement. However, other uses were reported, such as pinpointing poor practice. Confusion about its purpose existed in primary care, despite further training, suggesting unsuitability of the tool. Decreased engagement was displayed by staff less involved with medication use, who displayed less ownership. Nonetheless, these advocates often lacked support from management and frontline levels, leading to an overall lack of engagement. Many participants reported efforts to drive scale-up of the use of the tool, for example, by securing funding, despite uncertainty around how to use data. Successful improvement was often at ward-level and went unrecognised within the wider organisation. There was mixed feedback regarding the value of the tool, often due to a perceived lack of "capacity". However, participants demonstrated interest in learning how to use their data and unexpected applications of data were reported. Routine medication safety data collection is complex, but achievable and facilitates improvements. However, collected data must be analysed, understood and used for further work to achieve improvement, which often does not happen. The national roll-out of the tool has accelerated shared learning; however, a number of difficulties still exist, particularly in primary care settings, where a different approach is likely to be required.

A formative evaluation of the implementation of a medication safety data collection tool in English healthcare settings: A qualitative interview study using normalisation process theory

PubMed Central

Ashcroft, Darren M.; Tully, Mary P.

2018-01-01

Background Reducing medication-related harm is a global priority; however, impetus for improvement is impeded as routine medication safety data are seldom available. Therefore, the Medication Safety Thermometer was developed within England’s National Health Service. This study aimed to explore the implementation of the tool into routine practice from users’ perspectives. Method Fifteen semi-structured interviews were conducted with purposely sampled National Health Service staff from primary and secondary care settings. Interview data were analysed using an initial thematic analysis, and subsequent analysis using Normalisation Process Theory. Results Secondary care staff understood that the Medication Safety Thermometer’s purpose was to measure medication safety and improvement. However, other uses were reported, such as pinpointing poor practice. Confusion about its purpose existed in primary care, despite further training, suggesting unsuitability of the tool. Decreased engagement was displayed by staff less involved with medication use, who displayed less ownership. Nonetheless, these advocates often lacked support from management and frontline levels, leading to an overall lack of engagement. Many participants reported efforts to drive scale-up of the use of the tool, for example, by securing funding, despite uncertainty around how to use data. Successful improvement was often at ward-level and went unrecognised within the wider organisation. There was mixed feedback regarding the value of the tool, often due to a perceived lack of “capacity”. However, participants demonstrated interest in learning how to use their data and unexpected applications of data were reported. Conclusion Routine medication safety data collection is complex, but achievable and facilitates improvements. However, collected data must be analysed, understood and used for further work to achieve improvement, which often does not happen. The national roll-out of the tool has accelerated shared learning; however, a number of difficulties still exist, particularly in primary care settings, where a different approach is likely to be required. PMID:29489842

Geosamples.org: Shared Cyberinfrastructure for Geoscience Samples

NASA Astrophysics Data System (ADS)

Lehnert, Kerstin; Allison, Lee; Arctur, David; Klump, Jens; Lenhardt, Christopher

2014-05-01

Many scientific domains, specifically in the geosciences, rely on physical samples as basic elements for study and experimentation. Samples are collected to analyze properties of natural materials and features that are key to our knowledge of Earth's dynamical systems and evolution, and to preserve a record of our environment over time. Huge volumes of samples have been acquired over decades or even centuries and stored in a large number and variety of institutions including museums, universities and colleges, state geological surveys, federal agencies, and industry. All of these collections represent highly valuable, often irreplaceable records of nature that need to be accessible so that they can be re-used in future research and for educational purposes. Many sample repositories are keen to use cyberinfrastructure capabilities to enhance access to their collections on the internet and to support and streamline collection management (accessioning of new samples, labeling, handling sample requests, etc.), but encounter substantial challenges and barriers to integrate digital sample management into their daily routine. They lack the resources (staff, funding) and infrastructure (hardware, software, IT support) to develop and operate web-enabled databases, to migrate analog sample records into digital data management systems, and to transfer paper- or spreadsheet-based workflows to electronic systems. Use of commercial software is often not an option as it incurs high costs for licenses, requires IT expertise for installation and maintenance, and often does not match the needs of the smaller repositories, being designed for large museums or different types of collections (art, archeological, biological). Geosamples.org is an alliance of sample repositories (academic, US federal and state surveys, industry) and data facilities that aims to develop a cyberinfrastructure that will dramatically advance access to physical samples for the research community, government agencies, students, educators, and the general public, while supporting, simplifying, and standardizing the work of curators in repositories, museums, and universities, and even for individual investigators who manage personal or project-based sample collections in their lab. Geosamples.org builds upon best practices and cyberinfrastructure for sample identification, registration, and documentation developed by the IGSN e.V., an international organization that governs the International Geosample Number, a persistent unique identifier for physical samples. Geosamples.org will develop a Digital Environment for Sample Curation (DESC) that will facilitate the creation, identification, and registration of 'virtual samples' and network them into an 'Internet of Samples' that will allow to discover, access, and track online physical samples, the data derived by their study, and the publications that contain these data. DESC will provide easy-to-use software tools for curators to maintain digital catalogs of their collections, to provide online access to the catalog to search for and request samples, manage sample requests and users, track collection usage and impact. Geosamples.org will also work toward joint practices for the recognition of intellectual property, build mechanisms to create sustainable business models for continuing maintenance and evolution of managing sample resources, and integrate the sample management life-cycle into professional and cultural practice of science.

PCR-based analysis of microbial communities during the EuroGeoMars campaign at Mars Desert Research Station, Utah

NASA Astrophysics Data System (ADS)

Thiel, Cora S.; Ehrenfreund, Pascale; Foing, Bernard; Pletser, Vladimir; Ullrich, Oliver

2011-07-01

The search for evidence of past or present life on Mars will require the detection of markers that indicate the presence of life. Because deoxyribonucleic acid (DNA) is found in all known living organisms, it is considered to be a ‘biosignature’ of life. The main function of DNA is the long-term storage of genetic information, which is passed on from generation to generation as hereditary material. The Polymerase Chain Reaction (PCR) is a revolutionary technique which allows a single fragment or a small number of fragments of a DNA molecule to be amplified millions of times, making it possible to detect minimal traces of DNA. The compactness of the contemporary PCR instruments makes routine sample analysis possible with a minimum amount of laboratory space. Furthermore the technique is effective, robust and straightforward. Our goal was to establish a routine for the detection of DNA from micro-organisms using the PCR technique during the EuroGeoMars simulation campaign. This took place at the Mars Society's Mars Desert Research Station (MDRS) in Utah in February 2009 (organized with the support of the International Lunar Exploration Working Group (ILEWG), NASA Ames and the European Space Research and Technology Centre (ESTEC)). During the MDRS simulation, we showed that it is possible to establish a minimal molecular biology lab in the habitat for the immediate on-site analysis of samples by PCR after sample collection. Soil and water samples were taken at different locations and soil depths. The sample analysis was started immediately after the crew returned to the habitat laboratory. DNA was isolated from micro-organisms and used as a template for PCR analysis of the highly conserved ribosomal DNA to identify representatives of the different groups of micro-organisms (bacteria, archaea and eukarya). The PCR products were visualized by agarose gel electrophoresis and documented by transillumination and digital imaging. The microbial diversity in the collected samples was analysed with respect to sampling depth and the presence or absence of vegetation. For the first time, we have demonstrated that it is possible to perform direct on-site DNA analysis by PCR at MDRS, a simulated planetary habitat in an extreme environment that serves as a model for preparation and optimization of techniques to be used for future Mars exploration.

Soil examination for a forensic trace evidence laboratory-Part 3: A proposed protocol for the effective triage and management of soil examinations.

PubMed

Woods, Brenda; Lennard, Chris; Kirkbride, K Paul; Robertson, James

2016-05-01

In the past, forensic soil examination was a routine aspect of forensic trace evidence examinations. The apparent need for soil examinations then went through a period of decline and with it the capability of many forensic laboratories to carry out soil examinations. In more recent years, interest in soil examinations has been renewed due-at least in part-to soil examinations contributing to some high profile investigations. However, much of this renewed interest has been in organisations with a primary interest in soil and geology rather than forensic science. We argue the need to reinstate soil examinations as a trace evidence sub-discipline within forensic science laboratories and present a pathway to support this aim. An examination procedure is proposed that includes: (i) appropriate sample collection and storage by qualified crime scene examiners; (ii) exclusionary soil examinations by trace evidence scientists within a forensic science laboratory; (iii) inclusionary soil examinations by trace evidence scientists within a forensic science laboratory; and (iv) higher-level examination of soils by specialist soil scientists and palynologists. Soil examinations conducted by trace evidence scientists will be facilitated if the examinations are conducted using the instrumentation routinely used by these examiners. Hence, the proposed examination protocol incorporates instrumentation in routine use in a forensic trace evidence laboratory. Finally, we report on an Australian soil scene variability study and a blind trial that demonstrate the utility of the proposed protocol for the effective triage and management of soil samples by forensic laboratories. Crown Copyright © 2016. Published by Elsevier Ireland Ltd. All rights reserved.

Developing a weather observation routine during ICARUS

NASA Astrophysics Data System (ADS)

Mei, F.; Hubbe, J. M.; de Boer, G.; Lawrence, D.; Shupe, M.; Ivey, M.; Dexheimer, D.; Schmid, B.

2016-12-01

Starting in 2014, the Atmospheric Radiation Measurement (ARM) program began a major reconfiguration to more tightly link measurements and atmospheric models. As part of this the reconfiguration, ARM's North Slope of Alaska (NSA) site is being upgraded to include additional observations to support modeling and process studies. The Inaugural Campaigns for ARM Research using Unmanned Systems (ICARUS) have been launched in 2016. This internal initiative at Oliktok Point, Alaska focus on developing routine operations of Unmanned Aerial Systems (UAS) and Tethered Balloon Systems (TBS). The main purpose of ICARUS is to collect spatial data about surface radiation, heat fluxes, and vertical profiles of the basic atmospheric state (temperature, humidity, and horizontal wind). Based on the data collected during ICARUS, we will develop the operation routines for each atmospheric state measurement, and then optimize the operation schedule to maximize the data collection capacity. The statistical representation of important atmospheric state parameters will be discussed.

Image-analysis library

NASA Technical Reports Server (NTRS)

1980-01-01

MATHPAC image-analysis library is collection of general-purpose mathematical and statistical routines and special-purpose data-analysis and pattern-recognition routines for image analysis. MATHPAC library consists of Linear Algebra, Optimization, Statistical-Summary, Densities and Distribution, Regression, and Statistical-Test packages.

Sodium citrate blood contamination by K2 -ethylenediaminetetraacetic acid (EDTA): impact on routine coagulation testing.

PubMed

Lima-Oliveira, G; Salvagno, G L; Danese, E; Favaloro, E J; Guidi, G C; Lippi, G

2015-06-01

The potential cross-contamination of additives between primary blood tubes is a well-known problem during sample collection. The aim of this study was to assess the impact of citrated blood contamination with different amounts of dipotassium ethylenediaminetetraacetic (K2 EDTA blood) on activated partial thromboplastin time (APTT), prothrombin time (PT), and fibrinogen. Blood was collected from 15 ostensibly healthy volunteers into four 0.109 m citrate blood tubes followed by one K2 EDTA blood tube. The citrate tubes of each subject were pooled and divided in five aliquots. The whole blood of the K2 EDTA tube was then added in scalar amounts to autologous citrated blood aliquots, to obtain K2 EDTA contamination ranging from 0% to 43%, and thus mimic potential pre-analytical contamination. A statistically and clinically significant prolongation was observed for both APTT and PT between 29% and 43% K2 EDTA contamination, whereas the decrease of fibrinogen values became statistically and clinically significant at 43% K2 EDTA contamination. The results of this investigation show that contamination of citrated blood with as much as 29% of K2 EDTA blood generates a significant bias in results of routine clotting assays. This has serious implications for patient safety and management. © 2014 John Wiley & Sons Ltd.

Monitoring the use and outcomes of new devices and procedures: how does coding affect what Hospital Episode Statistics contribute? Lessons from 12 emerging procedures 2006-10.

PubMed

Patrick, Hannah; Sims, Andrew; Burn, Julie; Bousfield, Derek; Colechin, Elaine; Reay, Christopher; Alderson, Neil; Goode, Stephen; Cunningham, David; Campbell, Bruce

2013-03-01

New devices and procedures are often introduced into health services when the evidence base for their efficacy and safety is limited. The authors sought to assess the availability and accuracy of routinely collected Hospital Episodes Statistics (HES) data in the UK and their potential contribution to the monitoring of new procedures. Four years of HES data (April 2006-March 2010) were analysed to identify episodes of hospital care involving a sample of 12 new interventional procedures. HES data were cross checked against other relevant sources including national or local registers and manufacturers' information. HES records were available for all 12 procedures during the entire study period. Comparative data sources were available from national (5), local (2) and manufacturer (2) registers. Factors found to affect comparisons were miscoding, alternative coding and inconsistent use of subsidiary codes. The analysis of provider coverage showed that HES is sensitive at detecting centres which carry out procedures, but specificity is poor in some cases. Routinely collected HES data have the potential to support quality improvements and evidence-based commissioning of devices and procedures in health services but achievement of this potential depends upon the accurate coding of procedures.

Predicting polycyclic aromatic hydrocarbons using a mass fraction approach in a geostatistical framework across North Carolina.

PubMed

Reyes, Jeanette M; Hubbard, Heidi F; Stiegel, Matthew A; Pleil, Joachim D; Serre, Marc L

2018-01-09

Currently in the United States there are no regulatory standards for ambient concentrations of polycyclic aromatic hydrocarbons (PAHs), a class of organic compounds with known carcinogenic species. As such, monitoring data are not routinely collected resulting in limited exposure mapping and epidemiologic studies. This work develops the log-mass fraction (LMF) Bayesian maximum entropy (BME) geostatistical prediction method used to predict the concentration of nine particle-bound PAHs across the US state of North Carolina. The LMF method develops a relationship between a relatively small number of collocated PAH and fine Particulate Matter (PM2.5) samples collected in 2005 and applies that relationship to a larger number of locations where PM2.5 is routinely monitored to more broadly estimate PAH concentrations across the state. Cross validation and mapping results indicate that by incorporating both PAH and PM2.5 data, the LMF BME method reduces mean squared error by 28.4% and produces more realistic spatial gradients compared to the traditional kriging approach based solely on observed PAH data. The LMF BME method efficiently creates PAH predictions in a PAH data sparse and PM2.5 data rich setting, opening the door for more expansive epidemiologic exposure assessments of ambient PAH.

Identification of novel serum peptide biomarkers for high-altitude adaptation: a comparative approach

NASA Astrophysics Data System (ADS)

Yang, Juan; Li, Wenhua; Liu, Siyuan; Yuan, Dongya; Guo, Yijiao; Jia, Cheng; Song, Tusheng; Huang, Chen

2016-05-01

We aimed to identify serum biomarkers for screening individuals who could adapt to high-altitude hypoxia at sea level. HHA (high-altitude hypoxia acclimated; n = 48) and HHI (high-altitude hypoxia illness; n = 48) groups were distinguished at high altitude, routine blood tests were performed for both groups at high altitude and at sea level. Serum biomarkers were identified by comparing serum peptidome profiling between HHI and HHA groups collected at sea level. Routine blood tests revealed the concentration of hemoglobin and red blood cells were significantly higher in HHI than in HHA at high altitude. Serum peptidome profiling showed that ten significantly differentially expressed peaks between HHA and HHI at sea level. Three potential serum peptide peaks (m/z values: 1061.91, 1088.33, 4057.63) were further sequence identified as regions of the inter-α trypsin inhibitor heavy chain H4 fragment (ITIH4 347-356), regions of the inter-α trypsin inhibitor heavy chain H1 fragment (ITIH1 205-214), and isoform 1 of fibrinogen α chain precursor (FGA 588-624). Expression of their full proteins was also tested by ELISA in HHA and HHI samples collected at sea level. Our study provided a novel approach for identifying potential biomarkers for screening people at sea level who can adapt to high altitudes.

Rapid determination of actinides in asphalt samples

DOE PAGES

Maxwell, Sherrod L.; Culligan, Brian K.; Hutchison, Jay B.

2014-01-12

A new rapid method for the determination of actinides in asphalt samples has been developed that can be used in emergency response situations or for routine analysis If a radiological dispersive device (RDD), Improvised Nuclear Device (IND) or a nuclear accident such as the accident at the Fukushima Nuclear Power Plant in March, 2011 occurs, there will be an urgent need for rapid analyses of many different environmental matrices, including asphalt materials, to support dose mitigation and environmental clean up. The new method for the determination of actinides in asphalt utilizes a rapid furnace step to destroy bitumen and organicsmore » present in the asphalt and sodium hydroxide fusion to digest the remaining sample. Sample preconcentration steps are used to collect the actinides and a new stacked TRU Resin + DGA Resin column method is employed to separate the actinide isotopes in the asphalt samples. The TRU Resin plus DGA Resin separation approach, which allows sequential separation of plutonium, uranium, americium and curium isotopes in asphalt samples, can be applied to soil samples as well.« less

Androgens and innate immunity in rehabilitated semi-captive orangutans (Pongo pygmaeus morio) from Malaysian Borneo.

PubMed

Prall, Sean P; Ambu, Laurentius; Nathan, Senthilvel; Alsisto, Sylvia; Ramirez, Diana; Muehlenbein, Michael P

2015-06-01

Despite the implications for the development of life-history traits, endocrine-immune trade-offs in apes are not well studied. This is due, in part, to difficulty in sampling wild primates, and lack of methods available for immune measures using samples collected noninvasively. Evidence for androgen-mediated immune trade-offs in orangutans is virtually absent, and very little is known regarding their pattern of adrenal development and production of adrenal androgens. To remedy both of these deficiencies, sera were collected from orangutans (Pongo pygmaeus morio) (N = 38) at the Sepilok Orangutan Rehabilitation Centre, Sabah, Malaysia, during routine health screenings. Testosterone, dehydroepiandrosterone (DHEA), and dehydroepiandrosterone-sulfate (DHEA-S) were assayed, along with two measures of functional innate immunity. DHEA-S concentrations, but not DHEA, increased with age in this sample of 1-18 year old animals. DHEA concentrations were higher in animals with higher levels of serum bacteria killing ability, while DHEA-S and testosterone concentrations were higher in animals with reduced complement protein activity. Patterns of DHEA-S concentration in this sample are consistent with patterns of adrenarche observed in other apes. Results from this study suggest that in addition to testosterone, DHEA and DHEA-S may have potent effects on immunological activity in this species. © 2015 Wiley Periodicals, Inc.

Integrated field lysimetry and porewater sampling for evaluation of chemical mobility in soils and established vegetation.

PubMed

Matteson, Audrey R; Mahoney, Denis J; Gannon, Travis W; Polizzotto, Matthew L

2014-07-04

Potentially toxic chemicals are routinely applied to land to meet growing demands on waste management and food production, but the fate of these chemicals is often not well understood. Here we demonstrate an integrated field lysimetry and porewater sampling method for evaluating the mobility of chemicals applied to soils and established vegetation. Lysimeters, open columns made of metal or plastic, are driven into bareground or vegetated soils. Porewater samplers, which are commercially available and use vacuum to collect percolating soil water, are installed at predetermined depths within the lysimeters. At prearranged times following chemical application to experimental plots, porewater is collected, and lysimeters, containing soil and vegetation, are exhumed. By analyzing chemical concentrations in the lysimeter soil, vegetation, and porewater, downward leaching rates, soil retention capacities, and plant uptake for the chemical of interest may be quantified. Because field lysimetry and porewater sampling are conducted under natural environmental conditions and with minimal soil disturbance, derived results project real-case scenarios and provide valuable information for chemical management. As chemicals are increasingly applied to land worldwide, the described techniques may be utilized to determine whether applied chemicals pose adverse effects to human health or the environment.

Integrated Field Lysimetry and Porewater Sampling for Evaluation of Chemical Mobility in Soils and Established Vegetation

PubMed Central

Gannon, Travis W.; Polizzotto, Matthew L.

2014-01-01

Potentially toxic chemicals are routinely applied to land to meet growing demands on waste management and food production, but the fate of these chemicals is often not well understood. Here we demonstrate an integrated field lysimetry and porewater sampling method for evaluating the mobility of chemicals applied to soils and established vegetation. Lysimeters, open columns made of metal or plastic, are driven into bareground or vegetated soils. Porewater samplers, which are commercially available and use vacuum to collect percolating soil water, are installed at predetermined depths within the lysimeters. At prearranged times following chemical application to experimental plots, porewater is collected, and lysimeters, containing soil and vegetation, are exhumed. By analyzing chemical concentrations in the lysimeter soil, vegetation, and porewater, downward leaching rates, soil retention capacities, and plant uptake for the chemical of interest may be quantified. Because field lysimetry and porewater sampling are conducted under natural environmental conditions and with minimal soil disturbance, derived results project real-case scenarios and provide valuable information for chemical management. As chemicals are increasingly applied to land worldwide, the described techniques may be utilized to determine whether applied chemicals pose adverse effects to human health or the environment. PMID:25045915

Longitudinal Urinary Protein Variability in Participants of the Space Flight Simulation Program.

PubMed

Khristenko, Nina A; Larina, Irina M; Domon, Bruno

2016-01-04

Urine is a valuable material for the diagnosis of renal pathologies and to investigate the effects of their treatment. However, the variability in protein abundance in the context of normal homeostasis remains a major challenge in urinary proteomics. In this study, the analysis of urine samples collected from healthy individuals, rigorously selected to take part in the MARS-500 spaceflight simulation program, provided a unique opportunity to estimate normal concentration ranges for an extended set of urinary proteins. In order to systematically identify and reliably quantify peptides/proteins across a large sample cohort, a targeted mass spectrometry method was developed. The performance of parallel reaction monitoring (PRM) analyses was improved by implementing tight control of the monitoring windows during LC-MS/MS runs, using an on-the-fly correction routine. Matching the experimentally obtained MS/MS spectra with reference fragmentation patterns allowed dependable peptide identifications to be made. Following optimization and evaluation, the targeted method was applied to investigate protein abundance variability in 56 urine samples, collected from six volunteers participating in the MARS-500 program. The intrapersonal protein concentration ranges were determined for each individual and showed unexpectedly high abundance variation, with an average difference of 1 order of magnitude.

Rapid Bedside Inactivation of Ebola Virus for Safe Nucleic Acid Tests.

PubMed

Rosenstierne, Maiken Worsøe; Karlberg, Helen; Bragstad, Karoline; Lindegren, Gunnel; Stoltz, Malin Lundahl; Salata, Cristiano; Kran, Anne-Marte Bakken; Dudman, Susanne Gjeruldsen; Mirazimi, Ali; Fomsgaard, Anders

2016-10-01

Rapid bedside inactivation of Ebola virus would be a solution for the safety of medical and technical staff, risk containment, sample transport, and high-throughput or rapid diagnostic testing during an outbreak. We show that the commercially available Magna Pure lysis/binding buffer used for nucleic acid extraction inactivates Ebola virus. A rapid bedside inactivation method for nucleic acid tests is obtained by simply adding Magna Pure lysis/binding buffer directly into vacuum blood collection EDTA tubes using a thin needle and syringe prior to sampling. The ready-to-use inactivation vacuum tubes are stable for more than 4 months, and Ebola virus RNA is preserved in the Magna Pure lysis/binding buffer for at least 5 weeks independent of the storage temperature. We also show that Ebola virus RNA can be manually extracted from Magna Pure lysis/binding buffer-inactivated samples using the QIAamp viral RNA minikit. We present an easy and convenient method for bedside inactivation using available blood collection vacuum tubes and reagents. We propose to use this simple method for fast, safe, and easy bedside inactivation of Ebola virus for safe transport and routine nucleic acid detection. Copyright © 2016, American Society for Microbiology. All Rights Reserved.

Development and evaluation of a multiple-plate fraction collector for sample processing: application to radioprofiling in drug metabolism studies.

PubMed

Barros, Anthony; Ly, Van T; Chando, Theodore J; Ruan, Qian; Donenfeld, Scott L; Holub, David P; Christopher, Lisa J

2011-04-05

Microplate scintillation counters are utilized routinely in drug metabolism laboratories for the off-line radioanalysis of fractions collected during HPLC radioprofiling. In this process, the current fraction collection technology is limited by the number of plates that can be used per injection as well as the potential for sample loss due to dripping or spraying as the fraction collector head moves from well to well or between plates. More importantly, sample throughput is limited in the conventional process, since the collection plates must be manually exchanged after each injection. The Collect PAL, an innovative multiple-plate fraction collector, was developed to address these deficiencies and improve overall sample throughput. It employs a zero-loss design and has sub-ambient temperature control. Operation of the system is completely controlled with software and up to 24 (96- or 384-well) fraction collection plates can be loaded in a completely automated run. The system may also be configured for collection into various-sized tubes or vials. At flow rates of 0.5 or 1.0 mL/min and at collection times of 10 or 15s, the system precisely delivered 83-μL fractions (within 4.1% CV) and 250-μL fractions (within 1.4% CV), respectively, of three different mobile phases into 12 mm × 32 mm vials. Similarly, at a flow rate of 1 mL/min and 10s collection times, the system precisely dispensed mobile phase containing a [(14)C]-radiolabeled compound across an entire 96-well plate (% CV was within 5.3%). Triplicate analyses of metabolism test samples containing [(14)C]buspirone and its metabolites, derived from three different matrices (plasma, urine and bile), indicated that the Collect PAL produced radioprofiles that were reproducible and comparable to the current technology; the % CV for 9 selected peaks in the radioprofiles generated with the Collect PAL were within 9.3%. Radioprofiles generated by collecting into 96- and 384-well plates were qualitatively comparable; however, the peak resolution was greater in the profiles that were collected in 384-well plates due to the collection of a larger number of fractions per minute. In conclusion, this new and innovative fraction collector generated radioprofile results that were comparable to current technology and should provide a major improvement in capacity and throughput for radioprofiling studies. Copyright © 2010 Elsevier B.V. All rights reserved.

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

EPA Science Inventory

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

Argon Collection And Purification For Proliferation Detection

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

Achey, R.; Hunter, D.

2015-10-09

In order to determine whether a seismic event was a declared/undeclared underground nuclear weapon test, environmental samples must be taken and analyzed for signatures that are unique to a nuclear explosion. These signatures are either particles or gases. Particle samples are routinely taken and analyzed under the Comprehensive Nuclear-Test-Ban Treaty Organization (CTBTO) verification regime as well as by individual countries. Gas samples are analyzed for signature gases, especially radioactive xenon. Underground nuclear tests also produce radioactive argon, but that signature is not well monitored. A radioactive argon signature, along with other signatures, can more conclusively determine whether an event wasmore » a nuclear test. This project has developed capabilities for collecting and purifying argon samples for ultra-low-background proportional counting. SRNL has developed a continuous gas enrichment system that produces an output stream containing 97% argon from whole air using adsorbent separation technology (the flow diagram for the system is shown in the figure). The vacuum swing adsorption (VSA) enrichment system is easily scalable to produce ten liters or more of 97% argon within twelve hours. A gas chromatographic separation using a column of modified hydrogen mordenite molecular sieve has been developed that can further purify the sample to better than 99% purity after separation from the helium carrier gas. The combination of these concentration and purification systems has the capability of being used for a field-deployable system for collecting argon samples suitable for ultra-low-background proportional counting for detecting nuclear detonations under the On-Site Inspection program of the CTBTO verification regime. The technology also has applications for the bulk argon separation from air for industrial purposes such as the semi-conductor industry.« less

[Comparison of the performance of the ECLusys anti-HCV reagent with the Lumipulse f and HISCL 2000-i HCVAb assays].

PubMed

Sugiura, Aya; Iwahara, Kunihiro; Suga, Yasuyuki; Uchiyama, Sachinori; Maekawa, Masato

2012-09-01

We compared the ECLusys Anti-HCV (ECL) reagent to the Lumipulse f (LPf) and HISCL (HIS) HCV assays. In a correlation test using 210 routine clinical specimens measured using the Lumipulse method (96 positive and 114 negative), most of the results were consistent for all specimens. In a dilution sensitivity test using three different routine positive specimens, the ECL assay enabled detection at higher levels of sensitivity than either the LPf or the HIS assay. Moreover, when the distribution of the cut-off index (C.O.I.) values of the routine LPf negative specimens were compared to those on the ECL and HIS assays, it was found that on the ECL assay, most of the specimens had cut-off index values < 0.1, indicating a more clear-cut distribution. In a specificity test using high RF positive specimens(n = 33), pregnancy specimens (n = 35), cytomegalovirus (CMV) antibody positive specimens (n = 36), and high M protein positive specimens (n = 21), the ECL assay yielded positive results for a CMV antibody positive specimen and three high M protein positive specimens. Further testing using samples from the same patients collected on different days than these four samples resulted in a second positive result for the CMV positive specimen, and single antigen measurement yielded a Core/NS3 positive result, as well, suggesting past infection. However, since negative results were obtained for the three M protein positive specimens, the possibility of this being a ECLusys non-specific reaction could not be ruled out. The above results confirmed that the ECL assay provides superior fundamental performance, and possesses test performance nearly identical to that of the existing measurement methods that are widely used at a large number of facilities, and would therefore be a suitable assay for use in routine HCV antibody screening.

Sources and preparation of data for assessing trends in concentrations of pesticides in streams of the United States, 1992–2010

USGS Publications Warehouse

Martin, Jeffrey D.; Eberle, Michael; Nakagaki, Naomi

2011-01-01

This report updates a previously published water-quality dataset of 44 commonly used pesticides and 8 pesticide degradates suitable for a national assessment of trends in pesticide concentrations in streams of the United States. Water-quality samples collected from January 1992 through September 2010 at stream-water sites of the U.S. Geological Survey (USGS) National Water-Quality Assessment (NAWQA) Program and the National Stream Quality Accounting Network (NASQAN) were compiled, reviewed, selected, and prepared for trend analysis. The principal steps in data review for trend analysis were to (1) identify analytical schedule, (2) verify sample-level coding, (3) exclude inappropriate samples or results, (4) review pesticide detections per sample, (5) review high pesticide concentrations, and (6) review the spatial and temporal extent of NAWQA pesticide data and selection of analytical methods for trend analysis. The principal steps in data preparation for trend analysis were to (1) select stream-water sites for trend analysis, (2) round concentrations to a consistent level of precision for the concentration range, (3) identify routine reporting levels used to report nondetections unaffected by matrix interference, (4) reassign the concentration value for routine nondetections to the maximum value of the long-term method detection level (maxLT-MDL), (5) adjust concentrations to compensate for temporal changes in bias of recovery of the gas chromatography/mass spectrometry (GCMS) analytical method, and (6) identify samples considered inappropriate for trend analysis. Samples analyzed at the USGS National Water Quality Laboratory (NWQL) by the GCMS analytical method were the most extensive in time and space and, consequently, were selected for trend analysis. Stream-water sites with 3 or more water years of data with six or more samples per year were selected for pesticide trend analysis. The selection criteria described in the report produced a dataset of 21,988 pesticide samples at 212 stream-water sites. Only 21,144 pesticide samples, however, are considered appropriate for trend analysis.

Adoption of routine telemedicine in Norway: the current picture

PubMed Central

Zanaboni, Paolo; Knarvik, Undine; Wootton, Richard

2014-01-01

Background Telemedicine appears to be ready for wider adoption. Although existing research evidence is useful, the adoption of routine telemedicine in healthcare systems has been slow. Objective We conducted a study to explore the current use of routine telemedicine in Norway, at national, regional, and local levels, to provide objective and up-to-date information and to estimate the potential for wider adoption of telemedicine. Design A top-down approach was used to collect official data on the national use of telemedicine from the Norwegian Patient Register. A bottom-up approach was used to collect complementary information on the routine use of telemedicine through a survey conducted at the five largest publicly funded hospitals. Results Results show that routine telemedicine has been adopted in all health regions in Norway and in 68% of hospitals. Despite being widely adopted, the current level of use of telemedicine is low compared to the number of face-to-face visits. Examples of routine telemedicine can be found in several clinical specialties. Most services connect different hospitals in secondary care, and they are mostly delivered as teleconsultations via videoconference. Conclusions Routine telemedicine in Norway has been widely adopted, probably for geographical reasons, as in other settings. However, the level of use of telemedicine in Norway is rather low, and it has significant potential for further development as an alternative to face-to-face outpatient visits. This study is a first attempt to map routine telemedicine at regional, institutional, and clinical levels, and it provides useful information to understand the adoption of telemedicine in routine healthcare and to measure change in future updates. PMID:24433942

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

Saccomanno, G.

This work, supported by the United States Department of Energy, continues to add data on the health effects of cigarette smoking and radon exposure. Since the beginning of this contract, 473 sputum samples have been collected from 286 uranium workers who are routinely screened in an effort to identify cell changes that could signal possible progression to lung cancer; seven new lung cancer cases have been identified during this period. At this time, there are 426 lung cancer cases in the uranium miner tumor registry with diagnostic slides from surgery and/or autopsy; an additional 40 cases have been diagnosed withmore » sputum cytology only.« less

Prevalence of Toxocara canis in Dogs, North West Bank of Palestine

PubMed Central

2011-01-01

This study was performed to investigate the prevalence of Toxocara canis in local districts in North West Bank of Palestine. Fecal samples from 132 dogs were collected in Nablus, Tulkarm, and Jenin cities from September 2008 to April 2009 and examined for T. canis eggs with the floating technique. The overall infection rate of toxocariasis in dogs was 36.4%. The dogs less than 6 months old showed higher infection rates than those older than 12 months (P=0.04). Vigorous interventions are necessary, such as routine coprological examinations of dogs and prescription of anthelmintics to infected dogs. PMID:21738276

Antimicrobial-resistant Klebsiella species isolated from free-range chicken samples in an informal settlement.

PubMed

Fielding, Burtram C; Mnabisa, Amanda; Gouws, Pieter A; Morris, Thureyah

2012-02-29

Sub-therapeutic doses of antimicrobial agents are administered routinely to poultry to aid growth and to prevent disease, with prolonged exposure often resulting in bacterial resistance. Crossover of antibiotic resistant bacteria from poultry to humans poses a risk to human health. In this study, 17 chicken samples collected from a vendor operating in an informal settlement in the Cape Town Metropolitan area, South Africa were screened for antimicrobial-resistant Gram-negative bacilli using the Kirby Bauer disk diffusion assay. IN TOTAL, SIX ANTIBIOTICS WERE SCREENED: ampicillin, ciprofloxacin, gentamicin, nalidixic acid, tetracycline and trimethoprim. Surprisingly, Klebsiella ozaenae was identified in 96 and K. rhinoscleromatis in 6 (n=102) of the samples tested. Interestingly, ∼40% of the isolated Klebsiella spp. showed multiple resistance to at least three of the six antibiotics tested. Klebsiella ozaenae and K. rhinoscleromatis cause clinical chronic rhinitis and are almost exclusively associated with people living in areas of poor hygiene.

Routine sampling and the control of Legionella spp. in cooling tower water systems.

PubMed

Bentham, R H

2000-10-01

Cooling water samples from 31 cooling tower systems were cultured for Legionella over a 16-week summer period. The selected systems were known to be colonized by Legionella. Mean Legionella counts and standard deviations were calculated and time series correlograms prepared for each system. The standard deviations of Legionella counts in all the systems were very large, indicating great variability in the systems over the time period. Time series analyses demonstrated that in the majority of cases there was no significant relationship between the Legionella counts in the cooling tower at time of collection and the culture result once it was available. In the majority of systems (25/28), culture results from Legionella samples taken from the same systems 2 weeks apart were not statistically related. The data suggest that determinations of health risks from cooling towers cannot be reliably based upon single or infrequent Legionella tests.

Investigation of Tank 241-AN-101 Floating Solids

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

Kraft, Douglas P.; Meznarich, H. K.

Tank 241-AN-101 is the receiver tank for retrieval of several C-Farms waste tanks, including Tanks 241-C-102 and 241-C-111. Tank 241 C 111 received first-cycle decontamination waste from the bismuth phosphate process and Plutonium and Uranium Extraction cladding waste, as well as hydraulic fluid. Three grab samples, 1AN-16-01, 1AN-16-01A, and 1AN-16-01B, were collected at the surface of Tank 241-AN-101 on April 25, 2016, after Tank 241-C-111 retrieval was completed. Floating solids were observed in the three grab samples in the 11A hot cell after the samples were received at the 222-S Laboratory. Routine chemical analyses, solid phase characterization on the floatingmore » and settled solids, semivolatile organic analysis mainly on the aqueous phase for identification of degradation products of hydraulic fluids were performed. Investigation of the floating solids is reported.« less

Simultaneous measurements of carbon monoxide and ozone in the NASA Global Atmospheric Sampling Program (GASP)

NASA Astrophysics Data System (ADS)

Newell, R. E.; Wu, M.-F.

It is noted that the Global Atmospheric Sampling Program (GASP) was intended to establish global baseline values of selected atmospheric constituents that could be used for studies of the dynamics of the sampled region as well as for modeling purposes. Instrument packages were carried on four Boeing 747 aircraft in routine commercial service. Carbon monoxide and ozone data were collected simultaneously from early 1977 to early 1979 when GASP terminated. CO was measured with an infrared absorption analyzer using dual isotope fluorescence. Ozone was measured via absorption of UV light. Correlations between the CO and the O3 are tabulated; they are clearly negative for both troposphere and stratosphere in middle latitudes, indicating that transport processes between the stratosphere and troposphere (discussed) dominate. But in the low latitude troposphere the correlations are positive, indicating the possible influence of photochemical effects.

Human leukocyte antigen typing using buccal swabs as accurate and non-invasive substitute for venipuncture in children at risk for celiac disease.

PubMed

Adriaanse, Marlou P M; Vreugdenhil, Anita C E; Vastmans, Véronique; Groeneveld, Lisette; Molenbroeck, Stefan; Schott, Dina A; Voorter, Christina E M; Tilanus, Marcel G J

2016-10-01

Human leukocyte antigen (HLA) typing is an important step in the diagnostic algorithm for celiac disease (CD) and is also used for screening purposes. Collection of blood is invasive and accompanied with emotional impact especially in children. Genetic technological progress now enables HLA typing from buccal cell samples. This study evaluated the reliability and feasibility of HLA typing for CD-associated HLA polymorphisms using buccal swabs as routine test in high-risk individuals. Blood and buccal swabs of 77 children and adolescents with high risk for CD were prospectively collected in this cohort study. Buccal swab collection was performed either by the investigator at the outpatient clinic or by the patient or its parents at home. To evaluate the possibility of self-administration, three families performed the test at home. DNA was extracted using an adapted QIAamp method. Quantity, quality, and purity of DNA were recorded. HLA-DRB1, HLA-DQA1, and HLA-DQB1 typing was examined on buccal cell-derived and blood-derived DNA at low and, if necessary, high resolution level, using sequence-specific oligonucleotide and sequence-based typing, respectively. DNA isolation using buccal swabs yielded a good quality and sufficient quantity of DNA to perform HLA-DQ typing in all individuals. HLA typing results on buccal cell-derived DNA were identical to typing on blood-derived DNA, also for the self-administered samples. Introduction of the buccal swab test for HLA typing of CD risk in routine diagnostics can omit the current venipuncture and enables self-administration at home. Therefore, the buccal swab test is beneficial for individuals with a clinical suspicion for CD, as well as for screening purposes in high-risk populations. © 2016 Journal of Gastroenterology and Hepatology Foundation and John Wiley & Sons Australia, Ltd.

Gingival crevicular blood for screening of blood glucose level in patients with & without diabetes: a chair-side test.

PubMed

Bhavsar, M V; Brahmbhatt, N A; Sahayata, V; Bhavsar, N V

2016-05-01

Diabetes is a pandemic disease with increasing prevalence and serious complications. Periodontitis being one of its presentation and is its sixth recognized complication. This study compares blood glucose levels in gingival crevicular blood of patients with and without diabetes elicited during routine periodontal probing and venous blood sample. Seventy patients with moderate gingivitis and periodontitis positive for bleeding on probing were chosen. All the subjects were divided in two groups, group I consisted of 35 diabetic and group II of 35 non-diabetic subjects. Blood from the gingiva of the most inflamed site was collected with the test strip of a glucose self-monitoring device, and the blood glucose levels were measured. At the same time, intravenous blood was collected for measurement in a laboratory glucose analyzer. Gingival index and probing pocket depth were evaluated for each subject at same time. The mean GCB levels and VB derived from all samples were 156.07 ± 49.23 mg dl(-1) and 156 ± 49.89 mg dl(-1) , respectively, for diabetic group and 90.80 ± 11.07 and 93.41 ± 9.30 for non-diabetic group. In both the groups, the difference between GCB and VB glucose levels was non-significant (P > 0.005). Highly significant correlation between GCB and VB (r = 0.972 for diabetic and r = 0.721 for non-diabetic) in both the groups was found. The data from this study show that GCB collected during diagnostic periodontal examination can be an excellent source for estimation of blood sugar or glucometric analysis. This technique is also suitable for routine screening of diabetic and early diagnosis of unknown diabetic cases. © 2015 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Chapter IX. Bedtime Routines in Toddlerhood: Prevalence, Consistency, and Associations with Nighttime Sleep

PubMed Central

Staples, Angela D.; Bates, John E.; Petersen, Isaac T.

2016-01-01

The ability to transition from wakefulness to sleep is one of the most important tasks in the development of sleep during early childhood. Although establishing regular bedtime routines for children with sleep problems can be clinically effective in reducing the number of signaled night awakenings and increasing amounts of sleep, it is unclear whether a regular bedtime routine would be associated with either the frequency of signaled night awakenings or nightly sleep minutes in a non-clinical sample of children. This study examined the role of a regular bedtime routine on the development of sleep regulation and consolidation in a community sample of young children. Adherence to a bedtime routine was concurrently associated with a greater amount of nightly sleep at 36 and 42 months. In addition, adherence to a bedtime routine predicted an increase in nightly sleep minutes over a six-month period. Finally, this study demonstrated that adherence to a bedtime routine was particularly supportive of developmental gains for children of mothers who used consistent parenting practices during the day. PMID:25704740

Stability of Proteins in Dried Blood Spot Biobanks*

PubMed Central

Björkesten, Johan; Enroth, Stefan; Shen, Qiujin; Wik, Lotta; Hougaard, David M.; Cohen, Arieh S.; Sörensen, Lene; Giedraitis, Vilmantas; Ingelsson, Martin; Larsson, Anders; Kamali-Moghaddam, Masood; Landegren, Ulf

2017-01-01

An important motivation for the construction of biobanks is to discover biomarkers that identify diseases at early, potentially curable stages. This will require biobanks from large numbers of individuals, preferably sampled repeatedly, where the samples are collected and stored under conditions that preserve potential biomarkers. Dried blood samples are attractive for biobanking because of the ease and low cost of collection and storage. Here we have investigated their suitability for protein measurements. Ninety-two proteins with relevance for oncology were analyzed using multiplex proximity extension assays (PEA) in dried blood spots collected on paper and stored for up to 30 years at either +4 °C or −24 °C. Our main findings were that (1) the act of drying only slightly influenced detection of blood proteins (average correlation of 0.970), and in a reproducible manner (correlation of 0.999), (2) detection of some proteins was not significantly affected by storage over the full range of three decades (34 and 76% of the analyzed proteins at +4 °C and −24 °C, respectively), whereas levels of others decreased slowly during storage with half-lives in the range of 10 to 50 years, and (3) detectability of proteins was less affected in dried samples stored at −24 °C compared with at +4 °C, as the median protein abundance had decreased to 80 and 93% of starting levels after 10 years of storage at +4 °C or −24 °C, respectively. The results of our study are encouraging as they suggest an inexpensive means to collect large numbers of blood samples, even by the donors themselves, and to transport, and store biobanked samples as spots of whole blood dried on paper. Combined with emerging means to measure hundreds or thousands of protein, such biobanks could prove of great medical value by greatly enhancing discovery as well as routine analysis of blood biomarkers. PMID:28501802

Determination of Water Soluble Organic Carbon Collected ~1 km above the Earth's Surface during a Mid-Atlantic Air Quality Episode and Comparison to Aerosol Optical Properties

NASA Astrophysics Data System (ADS)

Brent, L. C.; He, H.; Arkinson, H. L.; Stehr, J. W.; Ring, A.; Marufu, L.; Reiner, J.; Sander, L. C.; Dickerson, R. R.

2014-12-01

Routine, light aircraft air-monitoring conducted in MD provides insight into atmospheric photochemical processing as a function of altitude in the boundary layer and lower free troposphere. We present correlations between the optical properties and chemical composition of aerosols at ~1 km altitude over Maryland. Data were collected during the peak smog day and a dissipation day during an air quality episode studied in DISCOVER-AQ, July 2011. Post flight filter sample analysis shows a positive trend between measurable carboxylate concentrations and particle size with a recirculating, aged, urban air mass influenced with southeasterly marine winds (peak day). A westerly influx of air from the Ohio River Valley on the dissipation day was depleted in carboxylates compared with samples collected over the same location two days prior. These samples contained quantifiable concentrations of cis-pinonic acid, a reaction product of pinene after ozonation and photochemical oxidation. New techniques were developed to improve airborne data collection and analysis of water soluble organic acids (WSOA), a frequently dominant fraction of particulate matter (PM). An ion chromatographic mass spectrometric method was developed using NIST Standard Referencing Material 1649b, Urban Dust, as a surrogate material to achieve separation and resolution of at least 34 organic acids. Analysis of aircraft filter samples resulted in detection of 16 organic acids of which 12 were quantified. Eight inorganic species were also quantified. Aged, re-circulated metropolitan air showed a greater number of dicarboxylic acids than new transport air from the west and may provide a useful test of SOA formation theory.

Evidence of possible vertical transmission of Tembusu virus in ducks.

PubMed

Zhang, Ying; Li, Xiuli; Chen, Hao; Ti, Jinfeng; Yang, Guoping; Zhang, Lu; Lu, Yunjian; Diao, Youxiang

2015-09-30

In 2013, Tembusu virus (TMUV) infection was successively observed on several breeding duck farms in Shandong province, China. Affected ducks showed consistently acute anorexia, diarrhea and egg production drop. 125 hatching eggs produced by TMUV infected breeding ducks from four duck farms were collected. Among them, 35 hatching eggs were selected randomly from all before incubation for vitelline membrane samples collection. The rest of 90 hatching eggs were incubated routinely. As a result, 16 hatching eggs were found non-embryonated, 28 duck embryos died during incubation and 46 newly hatched ducklings were obtained. Vitelline membranes of non-embryonated hatching eggs, vitelline membrane, brain or liver samples of dead embryos and brain samples of newly hatched ducklings were collected for virus detection. Samples collected from one egg, embryo or duckling were treated as one. Consequently, 18 of 35 (51.43%) hatching eggs, 2 of 16 (12.50%) non-embryonated duck eggs, 17 of 28 (60.71%) dead duck embryos and 5 of 46 (10.87%) newly hatched ducklings were detected positive for TMUV using NS3-based RT-PCR. Overall, 42 of 125 (33.6%) eggs were positive for TMUV. A virus strain, designated as TMUV-SDDE, was isolated from one of these dead duck embryos which were detected TMUV positive. The results of phylogenetic analysis showed that E gene of TMUV-SDDE virus was closely related to other TMUV strains isolated in China during 2010-2013. Pathogenicity studies showed that TMUV-SDDE strain was virulent to ducklings. This is the first report that TMUV is isolated from duck embryos. The findings provide evidence of possible vertical transmission of TMUV from breeding ducks to ducklings. Copyright © 2015 Elsevier B.V. All rights reserved.

Isothermal multiple displacement amplification: a methodical approach enhancing molecular routine diagnostics of microcarcinomas and small biopsies.

PubMed

Mairinger, Fabian D; Walter, Robert Fh; Vollbrecht, Claudia; Hager, Thomas; Worm, Karl; Ting, Saskia; Wohlschläger, Jeremias; Zarogoulidis, Paul; Zarogoulidis, Konstantinos; Schmid, Kurt W

2014-01-01

Isothermal multiple displacement amplification (IMDA) can be a powerful tool in molecular routine diagnostics for homogeneous and sequence-independent whole-genome amplification of notably small tumor samples, eg, microcarcinomas and biopsies containing a small amount of tumor. Currently, this method is not well established in pathology laboratories. We designed a study to confirm the feasibility and convenience of this method for routine diagnostics with formalin-fixed, paraffin-embedded samples prepared by laser-capture microdissection. A total of 250 μg DNA (concentration 5 μg/μL) was generated by amplification over a period of 8 hours with a material input of approximately 25 cells, approximately equivalent to 175 pg of genomic DNA. In the generated DNA, a representation of all chromosomes could be shown and the presence of elected genes relevant for diagnosis in clinical samples could be proven. Mutational analysis of clinical samples could be performed without any difficulty and showed concordance with earlier diagnostic findings. We established the feasibility and convenience of IMDA for routine diagnostics. We also showed that small amounts of DNA, which were not analyzable with current molecular methods, could be sufficient for a wide field of applications in molecular routine diagnostics when they are preamplified with IMDA.

Microbial quality of water in dental unit waterlines.

PubMed

Nikaeen, Mahnaz; Hatamzadeh, Maryam; Sabzevari, Zohre; Zareh, Omolbanin

2009-09-01

Dental unit waterlines (DUWLs) are ideal environment for development of microbial biofilms. Microbial contamination of water in DUWLs is thought to be the result of biofilm formation as it could serves as a haven for pathogens. The aim of this study was to assess microbial quality of water in dental unit waterlines of dental units located at the dental school of Isfahan University of Medical Sciences. Water samples were collected from air/water syringe and high-speed handpiece. Generally, 100-200 ml water samples were collected aseptically in sterile containers with sodium thiosulfate at the beginning of the day after a 2 minute purge. Samples were transferred to the laboratory in insulated box with cooling packs and examined for total viable heterotrophic bacteria and fungi. The heterotrophic plate count levels were significantly exceeded the American Dental Association recommendations for DUWL water quality (< 200 CFU/ml), in both air/water syringe (84%, CFU/ml: 500-20000) and high-speed handpiece (96%, CFU/ml: 710-36800) samples. However, there was no significant difference between the level of contamination in the air/water syringe and high-speed handpiece. Fungi were found in 28% and 36% of air/water syringe and high-speed handpiece samples, respectively; and filamentous fungi were the most frequently isolated fungi. DUWLs should be subjected to routine microbial monitoring and to a decontamination protocol in order to minimize the risk of exposure to potential pathogens from dental units.

Residence-Based Fear of Crime: A Routine Activities Approach.

PubMed

Lai, Yung-Lien; Ren, Ling; Greenleaf, Richard

2017-07-01

Most fear-of-crime research uses resident's neighborhood as a key reference location to measure fear, yet the location effects of one's own dwelling unit on crime-specific fear has not been explicitly studied theoretically in the literature. Drawing upon routine activities theory, this study undertakes an investigation into the levels and determinants of residence-based fear of crime across three racial/ethnic groups-Whites, African Americans, and non-White Hispanics. Data used in the analyses were collected from a random-sample telephone survey of 1,239 respondents in Houston, Texas. The results derived from factor analyses revealed that residents do distinguish between fear in the neighborhood and fear at home. Proximity to motivated offenders measured by perception of crime was found to be the most salient predictor of fear, followed by the measures of target vulnerability and capable guardianship. In addition, residence-based fear varies significantly across racial/ethnic groups. The significance of these findings and the policy implications are highlighted.

EVALUATION OF REGISTRATION, COMPRESSION AND CLASSIFICATION ALGORITHMS

NASA Technical Reports Server (NTRS)

Jayroe, R. R.

1994-01-01

Several types of algorithms are generally used to process digital imagery such as Landsat data. The most commonly used algorithms perform the task of registration, compression, and classification. Because there are different techniques available for performing registration, compression, and classification, imagery data users need a rationale for selecting a particular approach to meet their particular needs. This collection of registration, compression, and classification algorithms was developed so that different approaches could be evaluated and the best approach for a particular application determined. Routines are included for six registration algorithms, six compression algorithms, and two classification algorithms. The package also includes routines for evaluating the effects of processing on the image data. This collection of routines should be useful to anyone using or developing image processing software. Registration of image data involves the geometrical alteration of the imagery. Registration routines available in the evaluation package include image magnification, mapping functions, partitioning, map overlay, and data interpolation. The compression of image data involves reducing the volume of data needed for a given image. Compression routines available in the package include adaptive differential pulse code modulation, two-dimensional transforms, clustering, vector reduction, and picture segmentation. Classification of image data involves analyzing the uncompressed or compressed image data to produce inventories and maps of areas of similar spectral properties within a scene. The classification routines available include a sequential linear technique and a maximum likelihood technique. The choice of the appropriate evaluation criteria is quite important in evaluating the image processing functions. The user is therefore given a choice of evaluation criteria with which to investigate the available image processing functions. All of the available evaluation criteria basically compare the observed results with the expected results. For the image reconstruction processes of registration and compression, the expected results are usually the original data or some selected characteristics of the original data. For classification processes the expected result is the ground truth of the scene. Thus, the comparison process consists of determining what changes occur in processing, where the changes occur, how much change occurs, and the amplitude of the change. The package includes evaluation routines for performing such comparisons as average uncertainty, average information transfer, chi-square statistics, multidimensional histograms, and computation of contingency matrices. This collection of routines is written in FORTRAN IV for batch execution and has been implemented on an IBM 360 computer with a central memory requirement of approximately 662K of 8 bit bytes. This collection of image processing and evaluation routines was developed in 1979.

[Quality of birth care in maternity hospitals of Rio de Janeiro, Brazil].

PubMed

d'Orsi, Eleonora; Chor, Dóra; Giffin, Karen; Angulo-Tuesta, Antonia; Barbosa, Gisele Peixoto; Gama, Andrea de Souza; Reis, Ana Cristina; Hartz, Zulmira

2005-08-01

To evaluate the quality of birth care based on the World Health Organization guidelines. A case-control study was carried out in a public and a private maternity hospitals contracted by the Brazilian Health System in the city of Rio de Janeiro, Brazil, from October 1998 to March 1999. The sample comprised 461 women in the public maternity hospital (230 vaginal deliveries and 231 Cesarean sections) and 448 women in the private one (224 vaginal deliveries and 224 Cesarean sections). Data was collected through interviews with puerperal women and review of medical records. A summarization score of quality of delivery care was constructed. There was low frequency of practices that should be encouraged, such as having an accompanying person (1% in the private hospital for both vaginal delivery and C-sections), freedom of movements throughout labor (9.6% of C-sections in the public hospital and 9.9% of vaginal deliveries in the private hospital) and breastfeeding in the delivery room (6.9% of C-sections in the public hospital and 8.0% of C-sections in the private hospital). There was a high frequency of known harmful practices such as enema administration (38.4%); routine pubic shaving; routine intravenous infusion (88.8%); routine use of oxytocin (64.4%), strict bed rest throughout labor (90.1%) and routine supine position in labor (98.7%) in vaginal deliveries. The best summarizing scores were seen in the public maternity hospital. The two maternity hospitals have a high frequency of interventions during birth care. In spite of providing care to higher risk pregnant women, the public maternity hospital has a less interventionist profile than the private one. Procedures carried out on a routine basis should be pondered based on evidence of their benefits.

Analytical evaluation of the automated galectin-3 assay on the Abbott ARCHITECT immunoassay instruments.

PubMed

Gaze, David C; Prante, Christian; Dreier, Jens; Knabbe, Cornelius; Collet, Corinne; Launay, Jean-Marie; Franekova, Janka; Jabor, Antonin; Lennartz, Lieselotte; Shih, Jessie; del Rey, Jose Manuel; Zaninotto, Martina; Plebani, Mario; Collinson, Paul O

2014-06-01

Galectin-3 is secreted from macrophages and binds and activates fibroblasts forming collagen. Tissue fibrosis is central to the progression of chronic heart failure (CHF). We performed a European multicentered evaluation of the analytical performance of the two-step routine and Short Turn-Around-Time (STAT) galectin-3 immunoassay on the ARCHITECT i1000SR, i2000SR, and i4000SR (Abbott Laboratories). We evaluated the assay precision and dilution linearity for both routine and STAT assays and compared serum and plasma, and fresh vs. frozen samples. The reference interval and biological variability were also assessed. Measurable samples were compared between ARCHITECT instruments and between the routine and STAT assays and also to a galectin-3 ELISA (BG Medicine). The total assay coefficient of variation (CV%) was 2.3%-6.2% and 1.7%-7.4% for the routine and STAT assays, respectively. Both assays demonstrated linearity up to 120 ng/mL. Galectin-3 concentrations were higher in plasma samples than in serum samples and correlated well between fresh and frozen samples (R=0.997), between the routine and STAT assays, between the ARCHITECT i1000 and i2000 instruments and with the galectin-3 ELISA. The reference interval on 627 apparently healthy individuals (53% male) yielded upper 95th and 97.5th percentiles of 25.2 and 28.4 ng/mL, respectively. Values were significantly lower in subjects younger than 50 years. The galectin-3 routine and STAT assays on the Abbott ARCHITECT instruments demonstrated good analytical performance. Further clinical studies are required to demonstrate the diagnostic and prognostic potential of this novel marker in patients with CHF.

Continuous blood pressure monitoring via non-invasive radial artery applanation tonometry and invasive arterial catheter demonstrates good agreement in patients undergoing colon carcinoma surgery.

PubMed

Sun, Jing; Chen, Hanjian; Zheng, Jun; Mao, Bin; Zhu, Shengmei; Feng, Jingyi

2017-12-01

Radial artery applanation tonometry (RAAT) has been developed and utilized for continuous arterial pressure monitoring. However, evidence is lacking to clinically verify the RAAT technology and identify appropriate patient groups before routine clinical use. This study aims to evaluate the RAAT technology by comparing systolic blood pressure (SBP), mean blood pressure (MBP) and diastolic blood pressure (DBP) values in patients undergoing colon carcinoma surgery. Blood Pressure (BP) values obtained via RAAT (TL-300, Tensys Medical Inc., San Diego, CA, USA) and conventional arterial catheterization from 30 colon carcinoma surgical patients were collected and compared via Bland-Atman method, linear regression and 4-quadrant plot concordance analysis. For SBPs, MBPs and DBPs, means of the differences (±standard deviation; 95% limits of agreement) were -0.9 (±7.6; -15.7 to 13.9) mmHg, 3.1 (±6.5; -9.6 to 15.8) mmHg and 4.3 (±7.4; -10.3 to 18.8) mmHg, respectively. Linear regression coefficients of determination were 0.8706 for SBPs, 0.8353 for MBPs and 0.6858 for DBPs. Four-quadrant concordance correlation coefficients were 0.8740, 0.8522 and 0.7108 for SBPs, MBPs and DBPs, respectively. A highly selected patient collective undergoing colon carcinoma surgery was studied. BP measurements obtained via the TL-300 had clinically acceptable agreement with that acquired invasively using an arterial catheter. For use in clinical routine, it is necessary to take measures for improvement regarding movement artifacts and dilution of noise. A large sample size of patients under various conditions is also needed to further evaluate the RAAT technology before clinically routine use.

Research Vessel Meteorological and Oceanographic Systems Support Satellite and Model Validation Studies

NASA Astrophysics Data System (ADS)

Smith, S. R.; Lopez, N.; Bourassa, M. A.; Rolph, J.; Briggs, K.

2012-12-01

The research vessel data center at the Florida State University routinely acquires, quality controls, and distributes underway surface meteorological and oceanographic observations from vessels. The activities of the center are coordinated by the Shipboard Automated Meteorological and Oceanographic System (SAMOS) initiative in partnership with the Rolling Deck to Repository (R2R) project. The data center evaluates the quality of the observations, collects essential metadata, provides data quality feedback to vessel operators, and ensures the long-term data preservation at the National Oceanographic Data Center. A description of the SAMOS data stewardship protocols will be provided, including dynamic web tools that ensure users can select the highest quality observations from over 30 vessels presently recruited to the SAMOS initiative. Research vessels provide underway observations at high-temporal frequency (1 min. sampling interval) that include navigational (position, course, heading, and speed), meteorological (air temperature, humidity, wind, surface pressure, radiation, rainfall), and oceanographic (surface sea temperature and salinity) samples. Recruited vessels collect a high concentration of data within the U.S. continental shelf and also frequently operate well outside routine shipping lanes, capturing observations in extreme ocean environments (Southern Ocean, Arctic, South Atlantic and Pacific). The unique quality and sampling locations of research vessel observations and there independence from many models and products (RV data are rarely distributed via normal marine weather reports) makes them ideal for validation studies. We will present comparisons between research vessel observations and model estimates of the sea surface temperature and salinity in the Gulf of Mexico. The analysis reveals an underestimation of the freshwater input to the Gulf from rivers, resulting in an overestimation of near coastal salinity in the model. Additional comparisons between surface atmospheric products derived from satellite observations and the underway research vessel observations will be shown. The strengths and limitations of research observations for validation studies will be highlighted through these case studies.

Development and evaluation of a nested-PCR assay for Senecavirus A diagnosis.

PubMed

Feronato, Cesar; Leme, Raquel A; Diniz, Jaqueline A; Agnol, Alais Maria Dall; Alfieri, Alice F; Alfieri, Amauri A

2018-02-01

Senecavirus A (SVA) has been associated with vesicular disease in weaned and adult pigs and with high mortality of newborn piglets. This study aimed to establish a nested-PCR assay for the routine diagnosis of SVA infection. Tissue samples (n = 177) were collected from 37 piglets of 18 pig farms located in four different Brazilian states. For the nested-PCR, a primer set was defined to amplify an internal VP1 fragment of 316 bp of SVA genome. Of the 37 piglets, 15 (40.5%) and 23 (62.2%) were positive for the SVA in the RT-PCR and nested-PCR assays, respectively. The SVA RNA was detected in 61/177 (34.5%) samples with the RT-PCR, while the nested-PCR assay showed 84/177 (47.5%) samples with the virus (p < 0.05). According to the herds, 11 (61.1%) and 16 (88.9%) of the 18 pig herds were positive for the SVA in the RT-PCR and nested-PCR assays, respectively. Nucleotide sequencing analysis revealed similarities of 98.7-100% among SVA Brazilian strains and of 86.6-98% with SVA strains from other countries. The nested-PCR assay in this study was suitable to recover the SVA RNA in biological specimens, piglets, and/or herds that were considered as negative in the RT-PCR assay, and is proposed for the routine investigation of the SVA infection in piglets, especially when other techniques are not available or when a great number of samples has to be examined.

Cross-neutralization between three mumps viruses & mapping of haemagglutinin-neuraminidase (HN) epitopes

PubMed Central

Vaidya, Sunil R.; Dvivedi, Garima M.; Jadhav, Santoshkumar M.

2016-01-01

Background & objectives: The reports from the countries where mumps vaccine is given as routine immunization suggest differences in mumps virus neutralizing antibody titres when tested with vaccine and wild type viruses. Such reports are unavailable from countries like India where mumps vaccine is not included in routine immunization. We, therefore, undertook this study to understand the cross-neutralization activity of Indian mumps viruses. Methods: By using commercial mumps IgG enzyme immunoassay (EIA) and a rapid focus reduction neutralization test (FRNT), a panel of serum samples was tested. The panel consisted of 14 acute and 14 convalescent serum samples collected during a mumps outbreak and 18 archived serum samples. Two wild types (genotypes C and G) and Leningrad-Zagreb vaccine strain (genotype N) were used for the challenge experiments and FRNT titres were determined and further compared. The HN protein sequence of three mumps viruses was analyzed for the presence of key epitopes. Results: All serum samples effectively neutralized mumps virus wild types and a vaccine strain. However, significantly lower FRNT titres were noted to wild types than to vaccine strain (P<0.05). The comparison between EIA and FRNT results revealed 95.6 per cent agreement. No amino acid changes were seen in the epitopes in the Indian wild type strains. All potential N-linked glycosylation sites were observed in Indian strains. Interpretation & conclusions: Good cross-neutralization activity was observed for three mumps virus strains, however, higher level of FRNT titres was detected for mumps virus vaccine strain compared to Indian wild type isolates. PMID:26997012

Development of a specific immunomagnetic capture-PCR for rapid detection of viable Mycoplasma agalactiae in sheep milk samples.

PubMed

Sanna, G; Lecca, V; Foddai, A; Tola, S

2014-12-01

To develop an immunomagnetic capture (IMC) to detect viable Mycoplasma agalactiae in routine ovine milk samples. Polyclonal antibodies against two M. agalactiae membrane surface proteins (P80 and P55) were covalently conjugated to magnetic beads (MBs) to form MB-Ab80 and MB-Ab55. Mycoplasma agalactiae cells were captured by a specific antigen-antibody reaction and magnetic separation. Immunomagnetic capture (IMC) was used to isolate and concentrate M. agalactiae in serial decimal dilutions and in artificially contaminated milk to facilitate subsequent detection by PCR. A 375-bp fragment of M. agalactiae was amplified using a pair of M. agalactiae-specific primers in PCR. The limit of detection of IMC-PCR method ranged from 10 to 10(2)  CCU ml(-1) when mycoplasmas were resuspended in PBS and from 10(2) to 10(3)  CCU ml(-1) when mycoplasmas were resuspended in uncontaminated ovine milk. This study also describes the application of IMC-PCR method to test for M. agalactiae in 516 milk samples collected from sheep with suspected contagious agalactia. Its performance was evaluated relative to culture. This report has demonstrated for the first time, the effective use of rapid and reliable IMC combined with PCR assay for the detection of viable M. agalactiae. The method IMC-PCR provides an alternative to conventional microbiological detection, method and it could be applied to quick detection of M. agalactiae in routine sheep milk samples. © 2014 The Authors published by John Wiley & Sons Ltd on behalf of Society for Applied Microbiology.

Novel and classical human astroviruses in stool and cerebrospinal fluid: comprehensive screening in a tertiary care hospital, Switzerland.

PubMed

Cordey, Samuel; Vu, Diem-Lan; Zanella, Marie-Celine; Turin, Lara; Mamin, Aline; Kaiser, Laurent

2017-09-20

Classical human astroviruses (HAstV) are the third most common cause of non-bacterial acute gastroenteritis. Due to the lack of routine molecular assays, novel HAstV are underdiagnosed and the magnitude of their contribution to clinical disease remains unknown. To better understand their prevalence and the susceptible patient profile, we conducted a comprehensive screening of novel and classical HAstV in stool and cerebrospinal fluid (CSF) samples collected for clinical care in a tertiary care hospital using a specially designed rRT-PCR panel for the detection of novel (MLB1-3 and VA1-4) and classical HAstV. Of the 654 stool samples, 20 were positive for HAstV, and the novel (n=10; 3 MLB1, 4 MLB2; 3 VA2) and classical (n=10) serotypes were equally prevalent. None of the 105 CSF samples were positive. Investigating the patient profile, we found a higher prevalence (P=0.0002) of both novel and classical HAstV in pediatric stool samples (3.4% and 3%, respectively) compared with adult stool samples (0.5% and 0.7%, respectively). Furthermore, all novel and classical HAstV-positive pediatric subjects were ≤four years old, demonstrating similar susceptible populations. Forty-five percent of positive patients were immunocompromised (novel: 40%, classical: 50%). A comparison of novel and classical HAstV-positive cases showed a lower viral load for novel HAstV (P=0.0007) with significantly more upper respiratory symptoms (70% of subjects; P=0.02); this observation may suggest a unique pathogenic pathway. This study confirms the clinical and epidemiological relevance of novel HAstV and identifies a target population in which routine screening may yield clinically valuable information.

Comparison of microbiological diagnosis of urinary tract infection in young children by routine health service laboratories and a research laboratory: Diagnostic cohort study.

PubMed

Birnie, Kate; Hay, Alastair D; Wootton, Mandy; Howe, Robin; MacGowan, Alasdair; Whiting, Penny; Lawton, Michael; Delaney, Brendan; Downing, Harriet; Dudley, Jan; Hollingworth, William; Lisles, Catherine; Little, Paul; O'Brien, Kathryn; Pickles, Timothy; Rumsby, Kate; Thomas-Jones, Emma; Van der Voort, Judith; Waldron, Cherry-Ann; Harman, Kim; Hood, Kerenza; Butler, Christopher C; Sterne, Jonathan A C

2017-01-01

To compare the validity of diagnosis of urinary tract infection (UTI) through urine culture between samples processed in routine health service laboratories and those processed in a research laboratory. We conducted a prospective diagnostic cohort study in 4808 acutely ill children aged <5 years attending UK primary health care. UTI, defined as pure/predominant growth ≥105 CFU/mL of a uropathogen (the reference standard), was diagnosed at routine health service laboratories and a central research laboratory by culture of urine samples. We calculated areas under the receiver-operator curve (AUC) for UTI predicted by pre-specified symptoms, signs and dipstick test results (the "index test"), separately according to whether samples were obtained by clean catch or nappy (diaper) pads. 251 (5.2%) and 88 (1.8%) children were classified as UTI positive by health service and research laboratories respectively. Agreement between laboratories was moderate (kappa = 0.36; 95% confidence interval [CI] 0.29, 0.43), and better for clean catch (0.54; 0.45, 0.63) than nappy pad samples (0.20; 0.12, 0.28). In clean catch samples, the AUC was lower for health service laboratories (AUC = 0.75; 95% CI 0.69, 0.80) than the research laboratory (0.86; 0.79, 0.92). Values of AUC were lower in nappy pad samples (0.65 [0.61, 0.70] and 0.79 [0.70, 0.88] for health service and research laboratory positivity, respectively) than clean catch samples. The agreement of microbiological diagnosis of UTI comparing routine health service laboratories with a research laboratory was moderate for clean catch samples and poor for nappy pad samples and reliability is lower for nappy pad than for clean catch samples. Positive results from the research laboratory appear more likely to reflect real UTIs than those from routine health service laboratories, many of which (particularly from nappy pad samples) could be due to contamination. Health service laboratories should consider adopting procedures used in the research laboratory for paediatric urine samples. Primary care clinicians should try to obtain clean catch samples, even in very young children.

Order in the Home: Family Routines Moderate the Impact of Financial Hardship

ERIC Educational Resources Information Center

Budescu, Mia; Taylor, Ronald D.

2013-01-01

The study examined whether frequency of adolescent reported family routines moderated the relation between caregivers' perceptions of financial resources and adolescents' behavioral and academic outcomes among a sample of inner-city African American families. The sample consisted of 115 adolescents (average age = 15.95) and their female caregivers…

Feasibility of Xpert Ebola Assay in Médecins Sans Frontières Ebola Program, Guinea

PubMed Central

Chaillet, Pascale; Sow, Mamadou Saliou; Amand, Mathieu; van Vyve, Charlotte; Jonckheere, Sylvie; Crestani, Rosa; Sprecher, Armand; Van Herp, Michel; Chua, Arlene; Piriou, Erwan; Koivogui, Lamine; Antierens, Annick

2016-01-01

Rapid diagnostic methods are essential in control of Ebola outbreaks and lead to timely isolation of cases and improved epidemiologic surveillance. Diagnosis during Ebola outbreaks in West Africa has relied on PCR performed in laboratories outside this region. Because time between sampling and PCR results can be considerable, we assessed the feasibility and added value of using the Xpert Ebola Assay in an Ebola control program in Guinea. A total of 218 samples were collected during diagnosis, treatment, and convalescence of patients. Median time for obtaining results was reduced from 334 min to 165 min. Twenty-six samples were positive for Ebola virus. Xpert cycle thresholds were consistently lower, and 8 (31%) samples were negative by routine PCR. Several logistic and safety issues were identified. We suggest that implementation of the Xpert Ebola Assay under programmatic conditions is feasible and represents a major advance in diagnosis of Ebola virus disease without apparent loss of assay sensitivity. PMID:26812466

Feasibility of Xpert Ebola Assay in Médecins Sans Frontières Ebola Program, Guinea.

PubMed

Van den Bergh, Rafael; Chaillet, Pascale; Sow, Mamadou Saliou; Amand, Mathieu; van Vyve, Charlotte; Jonckheere, Sylvie; Crestani, Rosa; Sprecher, Armand; Van Herp, Michel; Chua, Arlene; Piriou, Erwan; Koivogui, Lamine; Antierens, Annick

2016-02-01

Rapid diagnostic methods are essential in control of Ebola outbreaks and lead to timely isolation of cases and improved epidemiologic surveillance. Diagnosis during Ebola outbreaks in West Africa has relied on PCR performed in laboratories outside this region. Because time between sampling and PCR results can be considerable, we assessed the feasibility and added value of using the Xpert Ebola Assay in an Ebola control program in Guinea. A total of 218 samples were collected during diagnosis, treatment, and convalescence of patients. Median time for obtaining results was reduced from 334 min to 165 min. Twenty-six samples were positive for Ebola virus. Xpert cycle thresholds were consistently lower, and 8 (31%) samples were negative by routine PCR. Several logistic and safety issues were identified. We suggest that implementation of the Xpert Ebola Assay under programmatic conditions is feasible and represents a major advance in diagnosis of Ebola virus disease without apparent loss of assay sensitivity.

Integrated Blood Barcode Chips

PubMed Central

Fan, Rong; Vermesh, Ophir; Srivastava, Alok; Yen, Brian K.H.; Qin, Lidong; Ahmad, Habib; Kwong, Gabriel A.; Liu, Chao-Chao; Gould, Juliane; Hood, Leroy; Heath, James R.

2008-01-01

Blood comprises the largest version of the human proteome1. Changes of plasma protein profiles can reflect physiological or pathological conditions associated with many human diseases, making blood the most important fluid for clinical diagnostics2-4. Nevertheless, only a handful of plasma proteins are utilized in routine clinical tests. This is due to a host of reasons, including the intrinsic complexity of the plasma proteome1, the heterogeneity of human diseases and the fast kinetics associated with protein degradation in sampled blood5. Simple technologies that can sensitively sample large numbers of proteins over broad concentration ranges, from small amounts of blood, and within minutes of sample collection, would assist in solving these problems. Herein, we report on an integrated microfluidic system, called the Integrated Blood Barcode Chip (IBBC). It enables on-chip blood separation and the rapid measurement of a panel of plasma proteins from small quantities of blood samples including a fingerprick of whole blood. This platform holds potential for inexpensive, non-invasive, and informative clinical diagnoses, particularly, for point-of-care. PMID:19029914

Direct analysis of organic priority pollutants by IMS

NASA Technical Reports Server (NTRS)

Giam, C. S.; Reed, G. E.; Holliday, T. L.; Chang, L.; Rhodes, B. J.

1995-01-01

Many routine methods for monitoring of trace amounts of atmospheric organic pollutants consist of several steps. Typical steps are: (1) collection of the air sample; (2) trapping of organics from the sample; (3) extraction of the trapped organics; and (4) identification of the organics in the extract by GC (gas chromatography), HPLC (High Performance Liquid Chromatography), or MS (Mass Spectrometry). These methods are often cumbersome and time consuming. A simple and fast method for monitoring atmospheric organics using an IMS (Ion Mobility Spectrometer) is proposed. This method has a short sampling time and does not require extraction of the organics since the sample is placed directly in the IMS. The purpose of this study was to determine the responses in the IMS to organic 'priority pollutants'. Priority pollutants including representative polycyclic aromatic hydrocarbons (PAHs), phthalates, phenols, chlorinated pesticides, and polychlorinated biphenyls (PCB's) were analyzed in both the positive and negative detection mode at ambient atmospheric pressure. Detection mode and amount detected are presented.

Antibiotic Residues in Milk from Three Popular Kenyan Milk Vending Machines.

PubMed

Kosgey, Amos; Shitandi, Anakalo; Marion, Jason W

2018-05-01

Milk vending machines (MVMs) are growing in popularity in Kenya and worldwide. Milk vending machines dispense varying quantities of locally sourced, pasteurized milk. The Kenya Dairy Board has a regulatory framework, but surveillance is weak because of several factors. Milk vending machines' milk is not routinely screened for antibiotics, thereby increasing potential for antibiotic misuse. To investigate, a total of 80 milk samples from four commercial providers ( N = 25), street vendors ( N = 21), and three MVMs ( N = 34) were collected and screened in Eldoret, Kenya. Antibiotic residue surveillance occurred during December 2016 and January 2017 using Idexx SNAP ® tests for tetracyclines, sulfamethazine, beta-lactams, and gentamicin. Overall, 24% of MVM samples and 24% of street vendor samples were presumably positive for at least one antibiotic. No commercial samples were positive. Research into cost-effective screening methods and increased monitoring by food safety agencies are needed to uphold hazard analysis and critical control point for improving antibiotic stewardship throughout the Kenyan private dairy industry.

Driving under the influence of cannabis: pitfalls, validation, and quality control of a UPLC-MS/MS method for the quantification of tetrahydrocannabinol in oral fluid collected with StatSure, Quantisal, or Certus collector.

PubMed

Wille, Sarah M R; Di Fazio, Vincent; Ramírez-Fernandez, Maria del Mar; Kummer, Natalie; Samyn, Nele

2013-02-01

"Driving under the influence of drugs" (DUID) has a large impact on the worldwide mortality risk. Therefore, DUID legislations based on impairment or analytical limits are adopted. Drug detection in oral fluid is of interest due to the ease of sampling during roadside controls. The prevalence of Δ9-tetrahydrocannabinol (THC) in seriously injured drivers ranges from 0.5% to 7.6% in Europe. For these reasons, the quantification of THC in oral fluid collected with 3 alternative on-site collectors is presented and discussed in this publication. An ultra-performance liquid chromatography-mass spectrometric quantification method for THC in oral fluid samples collected with the StatSure (Diagnostic Systems), Quantisal (Immunalysis), and Certus (Concateno) devices was validated according to the international guidelines. Small sample volumes of 100-200 μL were extracted using hexane. Special attention was paid to factors such as matrix effects, THC adsorption onto the collector, and stability in the collection fluid. A relatively high-throughput analysis was developed and validated according to ISO 17025 requirements. Although the effects of the matrix on the quantification could be minimized using a deuterated internal standard, and stability was acceptable according the validation data, adsorption of THC onto the collectors was a problem. For the StatSure device, THC was totally recovered from the collector pad after storage for 24 hours at room temperature or 7 days at 4°C. A loss of 15%-25% was observed for the Quantisal collector, whereas the recovery from the Certus device was irreproducible (relative standard deviation, 44%-85%) and low (29%-80%). During the roadside setting, a practical problem arose: small volumes of oral fluid (eg, 300 μL) were collected. However, THC was easily detected and concentrations ranged from 8 to 922 ng/mL in neat oral fluid. A relatively high-throughput analysis (40 samples in 4 hours) adapted for routine DUID analysis was developed and validated for THC quantification in oral fluid samples collected from drivers under the influence of cannabis.

Phylogenetic Analysis of Rubella Viruses Identified in Uganda, 2003–2012

PubMed Central

Namuwulya, Prossy; Abernathy, Emily; Bukenya, Henry; Bwogi, Josephine; Tushabe, Phionah; Birungi, Molly; Seguya, Ronald; Kabaliisa, Theopista; Alibu, Vincent P.; Kayondo, Jonathan K.; Rivailler, Pierre; Icenogle, Joseph; Bakamutumaho, Barnabas

2014-01-01

Molecular data on rubella viruses are limited in Uganda despite the importance of congenital rubella syndrome (CRS). Routine rubella vaccination, while not administered currently in Uganda, is expected to begin by 2015. The World Health Organization recommends that countries without rubella vaccination programs assess the burden of rubella and CRS before starting a routine vaccination program. Uganda is already involved in integrated case-based surveillance, including laboratory testing to confirm measles and rubella, but molecular epidemiologic aspects of rubella circulation have so far not been documented in Uganda. Twenty throat swab or oral fluid samples collected from 12 districts during routine rash and fever surveillance between 2003 and 2012 were identified as rubella virus RNA positive and PCR products encompassing the region used for genotyping were sequenced. Phylogenetic analysis of the 20 sequences identified 19 genotype 1G viruses and 1 genotype 1E virus. Genotype-specific trees showed that the Uganda viruses belonged to specific clusters for both genotypes 1G and 1E and grouped with similar sequences from neighboring countries. Genotype 1G was predominant in Uganda. More epidemiological and molecular epidemiological data are required to determine if genotype 1E is also endemic in Uganda. The information obtained in this study will assist the immunization program in monitoring changes in circulating genotypes. PMID:24700073

Phylogenetic analysis of rubella viruses identified in Uganda, 2003-2012.

PubMed

Namuwulya, Prossy; Abernathy, Emily; Bukenya, Henry; Bwogi, Josephine; Tushabe, Phionah; Birungi, Molly; Seguya, Ronald; Kabaliisa, Theopista; Alibu, Vincent P; Kayondo, Jonathan K; Rivailler, Pierre; Icenogle, Joseph; Bakamutumaho, Barnabas

2014-12-01

Molecular data on rubella viruses are limited in Uganda despite the importance of congenital rubella syndrome (CRS). Routine rubella vaccination, while not administered currently in Uganda, is expected to begin by 2015. The World Health Organization recommends that countries without rubella vaccination programs assess the burden of rubella and CRS before starting a routine vaccination program. Uganda is already involved in integrated case-based surveillance, including laboratory testing to confirm measles and rubella, but molecular epidemiologic aspects of rubella circulation have so far not been documented in Uganda. Twenty throat swab or oral fluid samples collected from 12 districts during routine rash and fever surveillance between 2003 and 2012 were identified as rubella virus RNA positive and PCR products encompassing the region used for genotyping were sequenced. Phylogenetic analysis of the 20 sequences identified 19 genotype 1G viruses and 1 genotype 1E virus. Genotype-specific trees showed that the Uganda viruses belonged to specific clusters for both genotypes 1G and 1E and grouped with similar sequences from neighboring countries. Genotype 1G was predominant in Uganda. More epidemiological and molecular epidemiological data are required to determine if genotype 1E is also endemic in Uganda. The information obtained in this study will assist the immunization program in monitoring changes in circulating genotypes. © 2014 Wiley Periodicals, Inc.

MATHEMATICAL ROUTINES FOR ENGINEERS AND SCIENTISTS

NASA Technical Reports Server (NTRS)

Kantak, A. V.

1994-01-01

The purpose of this package is to provide the scientific and engineering community with a library of programs useful for performing routine mathematical manipulations. This collection of programs will enable scientists to concentrate on their work without having to write their own routines for solving common problems, thus saving considerable amounts of time. This package contains sixteen subroutines. Each is separately documented with descriptions of the invoking subroutine call, its required parameters, and a sample test program. The functions available include: maxima, minima, and sort of vectors; factorials; random number generator (uniform or Gaussian distribution); complimentary error function; fast Fourier Transformation; Simpson's Rule integration; matrix determinate and inversion; Bessel function (J Bessel function for any order, and modified Bessel function for zero order); roots of a polynomial; roots of non-linear equation; and the solution of first order ordinary differential equations using Hamming's predictor-corrector method. There is also a subroutine for using a dot matrix printer to plot a given set of y values for a uniformly increasing x value. This package is written in FORTRAN 77 (Super Soft Small System FORTRAN compiler) for batch execution and has been implemented on the IBM PC computer series under MS-DOS with a central memory requirement of approximately 28K of 8 bit bytes for all subroutines. This program was developed in 1986.

Rapid MALDI-TOF mass spectrometry strain typing during a large outbreak of Shiga-Toxigenic Escherichia coli.

PubMed

Christner, Martin; Trusch, Maria; Rohde, Holger; Kwiatkowski, Marcel; Schlüter, Hartmut; Wolters, Manuel; Aepfelbacher, Martin; Hentschke, Moritz

2014-01-01

In 2011 northern Germany experienced a large outbreak of Shiga-Toxigenic Escherichia coli O104:H4. The large amount of samples sent to microbiology laboratories for epidemiological assessment highlighted the importance of fast and inexpensive typing procedures. We have therefore evaluated the applicability of a MALDI-TOF mass spectrometry based strategy for outbreak strain identification. Specific peaks in the outbreak strain's spectrum were identified by comparative analysis of archived pre-outbreak spectra that had been acquired for routine species-level identification. Proteins underlying these discriminatory peaks were identified by liquid chromatography tandem mass spectrometry and validated against publicly available databases. The resulting typing scheme was evaluated against PCR genotyping with 294 E. coli isolates from clinical samples collected during the outbreak. Comparative spectrum analysis revealed two characteristic peaks at m/z 6711 and m/z 10883. The underlying proteins were found to be of low prevalence among genome sequenced E. coli strains. Marker peak detection correctly classified 292 of 293 study isolates, including all 104 outbreak isolates. MALDI-TOF mass spectrometry allowed for reliable outbreak strain identification during a large outbreak of Shiga-Toxigenic E. coli. The applied typing strategy could probably be adapted to other typing tasks and might facilitate epidemiological surveys as part of the routine pathogen identification workflow.

Acute Toxoplasma gondii infection in children with reactive hyperplasia of the cervical lymph nodes.

PubMed

Bilal, Jalal A; Alsammani, Mohamed A; Ahmed, Mohamed I

2014-07-01

To determine the seroprevalence of Toxoplasma gondii (T. gondii) in children with reactive hyperplasia of the cervical lymph nodes. This cross-sectional prospective study was conducted in Khartoum Children Emergency Hospital, Khartoum, Sudan between January 2010 and April 2011. Eighty children with cervical lymphadenopathy were selected using random sampling. Their lymph nodes were aspirated for cytology, and a blood sample was collected from all patients for routine laboratory analysis and T. gondii IgG and IgM antibodies. Among 80 children with cervical lymphadenopathy, 60 (75%) had non-specific reactive hyperplasia. The seroprevalence of T. gondii among children with cervical lymphadenopathy was 27.5% (n=22), and the seropositivity of acute T. gondii among those with reactive hyperplasia was 36.7% (n=22/60). Lymph nodes in the T. gondii positive group were mobile and warm (p<0.05). The clinical features and laboratory tests were insignificant predictors of acute T. gondii infection with reactive hyperplasia of the cervical lymph nodes. The prevalence of acute T. gondii infection is high among children with non-specific reactive hyperplasia of the cervical lymph nodes. Routine laboratory studies are not helpful in the diagnosis of T. gondii infection with reactive hyperplasia of the lymph nodes however, serological studies may be requested prior to invasive procedures.

An Integrated Framework Advancing Membrane Protein Modeling and Design

PubMed Central

Weitzner, Brian D.; Duran, Amanda M.; Tilley, Drew C.; Elazar, Assaf; Gray, Jeffrey J.

2015-01-01

Membrane proteins are critical functional molecules in the human body, constituting more than 30% of open reading frames in the human genome. Unfortunately, a myriad of difficulties in overexpression and reconstitution into membrane mimetics severely limit our ability to determine their structures. Computational tools are therefore instrumental to membrane protein structure prediction, consequently increasing our understanding of membrane protein function and their role in disease. Here, we describe a general framework facilitating membrane protein modeling and design that combines the scientific principles for membrane protein modeling with the flexible software architecture of Rosetta3. This new framework, called RosettaMP, provides a general membrane representation that interfaces with scoring, conformational sampling, and mutation routines that can be easily combined to create new protocols. To demonstrate the capabilities of this implementation, we developed four proof-of-concept applications for (1) prediction of free energy changes upon mutation; (2) high-resolution structural refinement; (3) protein-protein docking; and (4) assembly of symmetric protein complexes, all in the membrane environment. Preliminary data show that these algorithms can produce meaningful scores and structures. The data also suggest needed improvements to both sampling routines and score functions. Importantly, the applications collectively demonstrate the potential of combining the flexible nature of RosettaMP with the power of Rosetta algorithms to facilitate membrane protein modeling and design. PMID:26325167

High diagnostic yield by CSF-PCR for entero- and herpes simplex viruses and TBEV serology in adults with acute aseptic meningitis in Stockholm.

PubMed

Franzen-Rohl, Elisabeth; Larsson, Kenny; Skoog, Eva; Tiveljung-Lindell, Annika; Grillner, Lena; Aurelius, Elisabeth; Glimåker, Martin

2008-01-01

Acute aseptic meningitis (AAM) affects 10-20/100,000 inhabitants per years in Sweden. Up to the beginning of the 1980s the diagnoses were made by virus isolation and/or determination of viral antibodies in serum. The development of PCR for detection of viruses in CSF samples has increased the sensitivity and diagnostic efficiency considerably. We investigated the aetiology of AAM and the diagnostic efficiency in an adult population in Stockholm, using a limited first-line combination of microbiological assays. CSF and serum samples, consecutively collected in 419 patients with clinical symptoms of AAM in northern Stockholm during 1999-2004, were included. PCR assays for herpes simplex virus (HSV) DNA and enterovirus (EV) RNA in the CSF as well as ELISA for IgM in serum to tick-borne encephalitis virus (TBEV) were performed routinely. A viral diagnosis was obtained in 255 of the 419 cases (62%) with these routinely performed assays. Clinical findings in combination with additional diagnostic tests resulted in an overall aetiological yield of 72%. EV was the major causative agent (27%) followed by TBEV (21%) and HSV-2 (19%). We conclude that consistent use of CSF-PCR for EV and HSV and TBEV serology established a diagnosis in the majority of AAM patients.

A methodological protocol for selecting and quantifying low-value prescribing practices in routinely collected data: an Australian case study.

PubMed

Brett, Jonathan; Elshaug, Adam G; Bhatia, R Sacha; Chalmers, Kelsey; Badgery-Parker, Tim; Pearson, Sallie-Anne

2017-05-03

Growing imperatives for safety, quality and responsible resource allocation have prompted renewed efforts to identify and quantify harmful or wasteful (low-value) medical practices such as test ordering, procedures and prescribing. Quantifying these practices at a population level using routinely collected health data allows us to understand the scale of low-value medical practices, measure practice change following specific interventions and prioritise policy decisions. To date, almost all research examining health care through the low-value lens has focused on medical services (tests and procedures) rather than on prescribing. The protocol described herein outlines a program of research funded by Australia's National Health and Medical Research Council to select and quantify low-value prescribing practices within Australian routinely collected health data. We start by describing our process for identifying and cataloguing international low-value prescribing practices. We then outline our approach to translate these prescribing practices into indicators that can be applied to Australian routinely collected health data. Next, we detail methods of using Australian health data to quantify these prescribing practices (e.g. prevalence of low-value prescribing and related costs) and their downstream health consequences. We have approval from the necessary Australian state and commonwealth human research ethics and data access committees to undertake this work. The lack of systematic and transparent approaches to quantification of low-value practices in routinely collected data has been noted in recent reviews. Here, we present a methodology applied in the Australian context with the aim of demonstrating principles that can be applied across jurisdictions in order to harmonise international efforts to measure low-value prescribing. The outcomes of this research will be submitted to international peer-reviewed journals. Results will also be presented at national and international pharmacoepidemiology and health policy forums such that other jurisdictions have guidance to adapt this methodology.

Correlation of PROMIS Physical Function and Pain CAT Instruments With Oswestry Disability Index and Neck Disability Index in Spine Patients.

PubMed

Papuga, Mark O; Mesfin, Addisu; Molinari, Robert; Rubery, Paul T

2016-07-15

A prospective and retrospective cross-sectional cohort analysis. The aim of this study was to show that Patient-Reported Outcomes Measurement Information System (PROMIS) computer adaptive testing (CAT) assessments for physical function and pain interference can be efficiently collected in a standard office visit and to evaluate these scores with scores from previously validated Oswestry Disability Index (ODI) and Neck Disability Index (NDI) providing evidence of convergent validity for use in patients with spine pathology. Spinal surgery outcomes are highly variable, and substantial debate continues regarding the role and value of spine surgery. The routine collection of patient-based outcomes instruments in spine surgery patients may inform this debate. Traditionally, the inefficiency associated with collecting standard validated instruments has been a barrier to routine use in outpatient clinics. We utilized several CAT instruments available through PROMIS and correlated these with the results obtained using "gold standard" legacy outcomes measurement instruments. All measurements were collected at a routine clinical visit. The ODI and the NDI assessments were used as "gold standard" comparisons for patient-reported outcomes. PROMIS CAT instruments required 4.5 ± 1.8 questions and took 35 ± 16 seconds to complete, compared with ODI/NDI requiring 10 questions and taking 188 ± 85 seconds when administered electronically. Linear regression analysis of retrospective scores involving a primary back complaint revealed moderate to strong correlations between ODI and PROMIS physical function with r values ranging from 0.5846 to 0.8907 depending on the specific assessment and patient subsets examined. Routine collection of physical function outcome measures in clinical practice offers the ability to inform and improve patient care. We have shown that several PROMIS CAT instruments can be efficiently administered during routine clinical visits. The moderate to strong correlations found validate the utility of computer adaptive testing when compared with the gold standard "static" legacy assessments. 4.

Examining the cost of delivering routine immunization in Honduras.

PubMed

Janusz, Cara Bess; Castañeda-Orjuela, Carlos; Molina Aguilera, Ida Berenice; Felix Garcia, Ana Gabriela; Mendoza, Lourdes; Díaz, Iris Yolanda; Resch, Stephen C

2015-05-07

Many countries have introduced new vaccines and expanded their immunization programs to protect additional risk groups, thus raising the cost of routine immunization delivery. Honduras recently adopted two new vaccines, and the country continues to broaden the reach of its program to adolescents and adults. In this article, we estimate and examine the economic cost of the Honduran routine immunization program for the year 2011. The data were gathered from a probability sample of 71 health facilities delivering routine immunization, as well as 8 regional and 1 central office of the national immunization program. Data were collected on vaccinations delivered, staff time dedicated to the program, cold chain equipment and upkeep, vehicle use, infrastructure, and other recurrent and capital costs at each health facility and administrative office. Annualized economic costs were estimated from a modified societal perspective and reported in 2011 US dollars. With the addition of rotavirus and pneumococcal conjugate vaccines, the total cost for routine immunization delivery in Honduras for 2011 was US$ 32.5 million. Vaccines and related supplies accounted for 23% of the costs. Labor, cold chain, and vehicles represented 54%, 4%, and 1%, respectively. At the facility level, the non-vaccine system costs per dose ranged widely, from US$ 25.55 in facilities delivering fewer than 500 doses per year to US$ 2.84 in facilities with volume exceeding 10,000 doses per year. Cost per dose was higher in rural facilities despite somewhat lower wage rates for health workers in these settings; this appears to be driven by lower demand for services per health worker in sparsely populated areas, rather than increased cost of outreach. These more-precise estimates of the operational costs to deliver routine immunizations provide program managers with important information for mobilizing resources to help sustain the program and for improving annual planning and budgeting as well as longer-term resource allocation decisions. Copyright © 2015. Published by Elsevier Ltd.

Collecting urban health indicators from routinely available sources: development and piloting of a tool for the collection of existing data for EURO-URHIS 2.

PubMed

Higgerson, James; Pope, Dan; Birt, Christopher A; van Ameijden, Erik; Verma, Arpana

2017-05-01

EURO-URHIS 2 aimed to collect comparable health indicators across a large number of urban areas (UAs) across Europe and Vietnam using four data collection tools. This paper outlines the process for the selection of indicators to be collected from routinely available sources, and the piloting of the data collection tool. A long-list of indicators potentially collectable from routinely available sources was generated by the EURO-URHIS 2 consortium. Key contacts from each UA completed an e-mail survey reporting for each indicator whether it could be collected using the given definition, an alternative definition or not at all. Additionally participants listed the 20 leading causes of death for their UAs from the Eurostat 65. Results were compiled to inform indicator selection for the main data collection phase. Responses were received for 25 of 28 eligible UAs. Of the 29 proposed indicators, 55.1% ( n = 16) were accepted without change, 24.1% ( n = 7) were re-allocated to other data collection tools and 17.2% ( n = 5) were accepted after a modification of the EURO-URHIS 2 definition. This scoping exercise and piloting phase for the 'existing data tool' for the project was useful and informative. It provided detailed information on what could be collected, and an opportunity to modify indicator definitions to maximize response rates. These results are only applicable to those UAs returning results and cannot be generalized. Detailed interrogation of definitions is essential to this sort of data collection, and the process described was designed with cross-national comparability in mind. © The Author 2015. Published by Oxford University Press on behalf of the European Public Health Association. All rights reserved.

Improving data collection processes for routine evaluation of treatment cost-effectiveness.

PubMed

Monto, Sari; Penttilä, Riku; Kärri, Timo; Puolakka, Kari; Valpas, Antti; Talonpoika, Anna-Maria

2016-04-01

The healthcare system in Finland has begun routine collection of health-related quality of life (HRQoL) information for patients in hospitals to support more systematic cost-effectiveness analysis (CEA). This article describes the systematic collection of HRQoL survey data, and addresses challenges in the implementation of patient surveys and acquisition of cost data in the case hospital. Challenges include problems with incomplete data and undefined management processes. In order to support CEA of hospital treatments, improvements are sought from the process management literature and in the observation of healthcare professionals. The article has been written from an information system and process management perspective, concluding that process ownership, automation of data collection and better staff training are keys to generating more reliable data.

Automated Broad-Range Molecular Detection of Bacteria in Clinical Samples

PubMed Central

Hoogewerf, Martine; Vandenbroucke-Grauls, Christina M. J. E.; Savelkoul, Paul H. M.

2016-01-01

Molecular detection methods, such as quantitative PCR (qPCR), have found their way into clinical microbiology laboratories for the detection of an array of pathogens. Most routinely used methods, however, are directed at specific species. Thus, anything that is not explicitly searched for will be missed. This greatly limits the flexibility and universal application of these techniques. We investigated the application of a rapid universal bacterial molecular identification method, IS-pro, to routine patient samples received in a clinical microbiology laboratory. IS-pro is a eubacterial technique based on the detection and categorization of 16S-23S rRNA gene interspace regions with lengths that are specific for each microbial species. As this is an open technique, clinicians do not need to decide in advance what to look for. We compared routine culture to IS-pro using 66 samples sent in for routine bacterial diagnostic testing. The samples were obtained from patients with infections in normally sterile sites (without a resident microbiota). The results were identical in 20 (30%) samples, IS-pro detected more bacterial species than culture in 31 (47%) samples, and five of the 10 culture-negative samples were positive with IS-pro. The case histories of the five patients from whom these culture-negative/IS-pro-positive samples were obtained suggest that the IS-pro findings are highly clinically relevant. Our findings indicate that an open molecular approach, such as IS-pro, may have a high added value for clinical practice. PMID:26763956

Comparison of sodium, potassium, calcium, magnesium, zinc, copper and iron concentrations of elements in 24-h urine and spot urine in hypertensive patients with healthy renal function.

PubMed

Zhang, Tianjing; Chang, Xiaoyu; Liu, Wanlu; Li, Xiaoxia; Wang, Faxuan; Huang, Liping; Liao, Sha; Liu, Xiuying; Zhang, Yuhong; Zhao, Yi

2017-12-01

Sodium, potassium, calcium, magnesium, zinc, copper and iron are associated with the sequela of hypertension. The most reliable method for testing those elements is by collecting 24-h urine samples. However, this is cumbersome and collection of spot urine is more convenient in some circumstance. The aim of this study was to compare the concentrations of different elements in 24-h urine and spot urine. Data was collected from a sub-study of China Salt Substitute and Stroke Study. 240 participants were recruited randomly from 12 villages in two counties in Ningxia, China. Both spot and 24-h urine specimens were collected from each patient. Routine urine test was conducted, and concentration of elements was measured using microwave digestion and Inductively Coupled Plasma-Optical Emission Spectrometry. Partial correlation analysis and Spearman correlation analysis were used to investigate the concentration of different elements and the relationship between 24- h urine and spot urine. A partial correlation in sodium, potassium, calcium, magnesium and iron was found between paired 24-h urine and spot urine samples except copper and zinc: 0.430, 0.426, 0.550, 0.221 and 0.191 respectively. Spot urine can replace 24-h urine for estimating some of the elements in hypertensive patients with normal renal function. Copyright © 2017 Elsevier GmbH. All rights reserved.

A healthy volunteer study to investigate trace element contamination of blood samples by stainless steel venepuncture needles.

PubMed

Hodnett, Darragh; Wood, David M; Raja, Kishor; Dargan, Paul I; Shah, Anoop D

2012-02-01

The trace elements cobalt (Co), chromium (Cr), manganese (Mn) and nickel (Ni) are normally present at low concentrations in blood. There has been a concern that stainless steel venepuncture needles typically used for collection of blood samples may contaminate these samples, leading to the masking of deficiency states or causing potential clinical confusion as to whether an individual has a "toxic" concentration. To determine whether there is any difference between the concentrations of the trace elements obtained by different methods of blood sampling. We took blood samples using a standard venepuncture needle, a "butterfly" winged infusion needle (three consecutive samples) and a plastic intravenous cannula (three consecutive samples) from 10 healthy volunteers. We measured the concentrations of Co, Cr, Mn and Ni in the samples using Inductively Coupled Plasma Mass Spectrometry, and used analysis of variance (ANOVA) to investigate if there was any difference between the methods of blood sampling. The mean ± standard deviation blood metal concentrations were: Co 0.33 ± 0.2 μg/l, Cr 2.43 ± 1.55 μg/l, Mn 8.07 ± 7.74 μg/l and Ni 10.4 ± 4.69 μg/l. There was considerable variation between blood metal concentrations of individual subjects and a few sporadic high values. By ANOVA, there was no significant difference between the metal concentrations measured using different methods of blood collection. It is not necessary to routinely use a plastic cannula for blood sampling for trace element analysis. However, it is possible that sporadic contamination due to stainless steel needles may occur, so we would recommend that unexpected high concentrations are verified by taking a second sample taken through a plastic cannula.

Removal of bacteria from boar ejaculates by Single Layer Centrifugation can reduce the use of antibiotics in semen extenders.

PubMed

Morrell, J M; Wallgren, M

2011-01-01

There is considerable interest world-wide in reducing the use of antibiotics to stem the development of antibiotic-resistant strains of bacteria. An alternative to the routine addition of antibiotics to semen extenders in livestock breeding would be to separate the spermatozoa from bacterial contaminants in the semen immediately after collection. The present study was designed to determine whether such separation was possible by Single Layer Centrifugation (SLC) using the colloid Androcoll™-P. The results showed that complete removal (6 out of 10 samples), or considerable reduction of bacterial contaminants (4 out of 10 samples) was possible with this method. The type of bacteria and/or the length of time between collection and SLC-processing affected the removal of bacteria, with motile flagellated bacteria being more likely to be present after SLC than non-flagellated bacteria. Although further studies are necessary, these preliminary results suggest that the use of SLC when processing boar semen for AI doses might enable antibiotic usage in semen extenders to be reduced. Copyright © 2010 Elsevier B.V. All rights reserved.

Mass Spectrometric Imaging Using Laser Ablation and Solvent Capture by Aspiration (LASCA)

NASA Astrophysics Data System (ADS)

Brauer, Jonathan I.; Beech, Iwona B.; Sunner, Jan

2015-09-01

A novel interface for ambient, laser ablation-based mass spectrometric imaging (MSI) referred to as laser ablation and solvent capture by aspiration (LASCA) is presented and its performance demonstrated using selected, unaltered biological materials. LASCA employs a pulsed 2.94 μm laser beam for specimen ablation. Ablated materials in the laser plumes are collected on a hanging solvent droplet with electric field-enhanced trapping, followed by aspiration of droplets and remaining plume material in the form of a coarse aerosol into a collection capillary. The gas and liquid phases are subsequently separated in a 10 μL-volume separatory funnel, and the solution is analyzed with electrospray ionization in a high mass resolution Q-ToF mass spectrometer. The LASCA system separates the sampling and ionization steps in MSI and combines high efficiencies of laser plume sampling and of electrospray ionization (ESI) with high mass resolution MS. Up to 2000 different compounds are detected from a single ablation spot (pixel). Using the LASCA platform, rapid (6 s per pixel), high sensitivity, high mass-resolution ambient imaging of "as-received" biological material is achieved routinely and reproducibly.

Evidence of a sewer vapor transport pathway at the USEPA ...

EPA Pesticide Factsheets

The role of sewer lines as preferential pathways for vapor intrusion is poorly understood. Although the importance of sewer lines for volatile organic compound (VOC) transport has been documented at a small number of sites with vapor intrusion, sewer lines are not routinely sampled during most vapor intrusion investigations. We have used a tracer study and VOC concentration measurements to evaluate the role of the combined sanitary/storm sewer line in VOC transport at the USEPA vapor intrusion research duplex in Indianapolis, Indiana. The results from the tracer study demonstrated gas migration from the sewer main line into the duplex. The migration pathway appears to be complex and may include leakage from the sewer lateral at a location below the building foundation. Vapor samples collected from the sewer line demonstrated the presence of tetrachloroethene (PCE) and chloroform in the sewer main in front of the duplex and at multiple sample locations within the sewer line upstream of the duplex. These test results combined with results from the prior multi-year study of the duplex indicate that the sewer line plays an important role in transport of VOCs from the subsurface source to the immediate vicinity of the duplex building envelope. Highlights • The sewer line is an important pathway for VOC transport at the USEPA duplex. • The importance of this pathway was not identified during prior study of the duplex. • Sewer lines should be routinely evaluated

Pharmaceuticals and Personal Care Products in Archived U.S. Biosolids from the 2001 EPA National Sewage Sludge Survey

PubMed Central

McClellan, Kristin; Halden, Rolf U.

2010-01-01

In response to the U.S. National Academies’ call for a better assessment of chemical pollutants contained in the approximately 6.9 million dry tons of digested municipal sludge produced annually in the United States, the mean concentration of 72 pharmaceuticals and personal care products (PPCP) were determined in 110 biosolids samples collected by the U.S. Environmental Protection Agency (EPA) in its 2001 National Sewage Sludge Survey. Composite samples of archived biosolids, collected at 94 U.S. wastewater treatment plants from 32 states and the District of Columbia, were analyzed by liquid chromatography tandem mass spectrometry using EPA Method 1694. Thirty-eight (54%) of the 72 analytes were detected in at least one composite sample at concentrations ranging from 0.002 to 48 mg kg−1 dry weight. Triclocarban and triclosan were the most abundant analytes with mean concentrations of 36 ± 8 and 12.6 ± 3.8 mg kg−1 (n = 5), respectively, accounting for 65% of the total PPCP mass found. The loading to U.S. soils from nationwide biosolids recycling was estimated at 210–250 metric tons per year for the sum of the 72 PPCPs investigated. The results of this nationwide reconnaissance of PPCPs in archived U.S. biosolids mirror in contaminant occurrences, frequencies and concentrations, those reported by the U.S. EPA for samples collected in 2006/07. This demonstrates that PPCP releases in U.S. biosolids have been ongoing for many years and the most abundant PPCPs appear to show limited fluctuations in mass over time when assessed on a nationwide basis. The here demonstrated use of five mega composite samples holds promise for conducting cost-effective, routine monitoring on a regional basis. PMID:20106500

The NOSAMS sample preparation laboratory in the next millenium: Progress after the WOCE program

NASA Astrophysics Data System (ADS)

Gagnon, Alan R.; McNichol, Ann P.; Donoghue, Joanne C.; Stuart, Dana R.; von Reden, Karl; Nosams

2000-10-01

Since 1991, the primary charge of the National Ocean Sciences AMS (NOSAMS) facility at the Woods Hole Oceanographic Institution has been to supply high throughput, high precision AMS 14C analyses for seawater samples collected as part of the World Ocean Circulation Experiment (WOCE). Approximately 13,000 samples taken as part of WOCE should be fully analyzed by the end of Y2K. Additional sample sources and techniques must be identified and incorporated if NOSAMS is to continue in its present operation mode. A trend in AMS today is the ability to routinely process and analyze radiocarbon samples that contain tiny amounts (<100 μg) of carbon. The capability to mass-produce small samples for 14C analysis has been recognized as a major facility goal. The installation of a new 134-position MC-SNICS ion source, which utilizes a smaller graphite target cartridge than presently used, is one step towards realizing this goal. New preparation systems constructed in the sample preparation laboratory (SPL) include an automated bank of 10 small-volume graphite reactors, an automated system to process organic carbon samples, and a multi-dimensional preparative capillary gas chromatograph (PCGC).

SAMOS Surface Fluxes

NASA Astrophysics Data System (ADS)

Smith, Shawn; Bourassa, Mark

2014-05-01

The development of a new surface flux dataset based on underway meteorological observations from research vessels will be presented. The research vessel data center at the Florida State University routinely acquires, quality controls, and distributes underway surface meteorological and oceanographic observations from over 30 oceanographic vessels. These activities are coordinated by the Shipboard Automated Meteorological and Oceanographic System (SAMOS) initiative in partnership with the Rolling Deck to Repository (R2R) project. Recently, the SAMOS data center has used these underway observations to produce bulk flux estimates for each vessel along individual cruise tracks. A description of this new flux product, along with the underlying data quality control procedures applied to SAMOS observations, will be provided. Research vessels provide underway observations at high-temporal frequency (1 min. sampling interval) that include navigational (position, course, heading, and speed), meteorological (air temperature, humidity, wind, surface pressure, radiation, rainfall), and oceanographic (surface sea temperature and salinity) samples. Vessels recruited to the SAMOS initiative collect a high concentration of data within the U.S. continental shelf and also frequently operate well outside routine shipping lanes, capturing observations in extreme ocean environments (Southern, Arctic, South Atlantic, and South Pacific oceans). These observations are atypical for their spatial and temporal sampling, making them very useful for many applications including validation of numerical models and satellite retrievals, as well as local assessments of natural variability. Individual SAMOS observations undergo routine automated quality control and select vessels receive detailed visual data quality inspection. The result is a quality-flagged data set that is ideal for calculating turbulent flux estimates. We will describe the bulk flux algorithms that have been applied to the observations and the choices of constants that are used. Analysis of the preliminary SAMOS flux products will be presented, including spatial and temporal coverage for each derived parameter. The unique quality and sampling locations of research vessel observations and their independence from many models and products makes them ideal for validation studies. The strengths and limitations of research observations for flux validation studies will be discussed. The authors welcome a discussion with the flux community regarding expansion of the SAMOS program to include additional international vessels, thus facilitating and expansion of this research vessel-based flux product.

Short communication prevalence of susceptibility to etravirine by genotype and phenotype in samples received for routine HIV type 1 resistance testing in the United States.

PubMed

Picchio, Gaston; Vingerhoets, Johan; Tambuyzer, Lotke; Coakley, Eoin; Haddad, Mojgan; Witek, James

2011-12-01

Abstract The prevalence of susceptibility to etravirine was investigated among clinical samples submitted for routine clinical testing in the United States using two separate weighted genotypic scoring systems. The presence of etravirine mutations and susceptibility to etravirine by phenotype of clinical samples from HIV-1-infected patients, submitted to Monogram Biosciences for routine resistance testing between June 2008 and June 2009, were analyzed. Susceptibility by genotype was determined using the Monogram and Tibotec etravirine-weighted genotypic scoring systems, with scores of ≤3 and ≤2, respectively, indicating full susceptibility. Susceptibility by phenotype was determined using the PhenoSense HIV assay, with lower and higher clinical cut-offs of 2.9 and 10, respectively. The frequency of individual etravirine mutations and the impact of the K103N mutation on susceptibility to etravirine by genotype were also determined. Among the 5482 samples with ≥1 defined nonnucleoside reverse transcriptase inhibitor (NNRTI) mutations associated with resistance, 67% were classed as susceptible to etravirine by genotype by both scoring systems. Susceptibility to etravirine by phenotype was higher (76%). The proportion of first-generation NNRTI-resistant samples with (n=3598) and without (n=1884) K103N with susceptibility to etravirine by genotype was 77% and 49%, respectively. Among samples susceptible to first-generation NNRTIs (n=9458), >99% of samples were susceptible to etravirine by phenotype (FC <2.9); the remaining samples had FC ≥2.9-10. In summary, among samples submitted for routine clinical testing in the United States, a high proportion of samples with first-generation NNRTI resistance was susceptible to etravirine by genotype and phenotype. A higher proportion of NNRTI-resistant samples with K103N than without was susceptible to etravirine.

Neighborhoods and Adolescent Health-Risk Behavior: An Ecological Network Approach1

PubMed Central

Browning, Christopher R.; Soller, Brian; Jackson, Aubrey L.

2014-01-01

This study integrates insights from social network analysis, activity space perspectives, and theories of urban and spatial processes to present an innovative approach to neighborhood effects on health-risk behavior among youth. We suggest spatial patterns of neighborhood residents’ non-home routine activities may be conceptualized as ecological, or “eco”-networks, which are two-mode networks that indirectly link residents through socio-spatial overlap in routine activities. We further argue structural configurations of eco-networks are consequential for youth’s behavioral health. In this study we focus on a key structural feature of eco-networks—the neighborhood-level extent to which households share two or more activity locations, or eco-network reinforcement—and its association with two dimensions of health-risk behavior, substance use and delinquency/sexual activity. Using geographic data on non-home routine activity locations among respondents from the Los Angeles Family and Neighborhood Survey (L.A.FANS), we constructed neighborhood-specific eco-networks by connecting sampled households to “activity clusters,” which are sets of spatially-proximate activity locations. We then measured eco-network reinforcement and examined its association with adolescent dimensions of health risk behavior employing a sample of 830 youth ages 12-17 nested in 65 census tracts. We also examined whether neighborhood-level social processes (collective efficacy and intergenerational closure) mediate the association between eco-network reinforcement and the outcomes considered. Results indicated eco-network reinforcement exhibits robust negative associations with both substance use and delinquency/sexual activity scales. Eco-network reinforcement effects were not explained by potential mediating variables. In addition to introducing a novel theoretical and empirical approach to neighborhood effects on youth, our findings highlight the importance of eco-network reinforcement for adolescent behavioral health. PMID:25011958

Significance of headwater streams and perennial springs in ecological monitoring in Shenandoah National Park

USGS Publications Warehouse

Snyder, Craig D.; Webb, James R.; Young, John A.; Johnson, Zane B.

2013-01-01

Shenandoah National Park has been monitoring water chemistry and benthic macroinvertebrates in stream ecosystems since 1979. These monitoring efforts were designed to assess the status and trends in stream condition associated with atmospheric deposition (acid rain) and changes in forest health due to gypsy moth infestations. The primary objective of the present research was to determine whether the current long-term macroinvertebrate and water-quality monitoring program in Shenandoah National Park was failing to capture important information on the status and trends in stream condition by not sufficiently representing smaller, headwater streams. The current benthic-macroinvertebrate and water-chemistry sampling designs do not include routine collection of data from streams with contributing watershed areas smaller than 100 hectares, even though these small streams represent the overwhelming proportion of total stream length in the park. In this study, we sampled headwater sites, including headwater stream reaches (contributing watershed area approximately 100 hectares (ha) and perennial springs, in the park for aquatic macroinvertebrates and water chemistry and compared the results with current and historical data collected at long-term ecological monitoring (LTEM) sites on larger streams routinely sampled as part of ongoing monitoring efforts. The larger purpose of the study was to inform ongoing efforts by park managers to evaluate the effectiveness and efficiency of the current aquatic monitoring program in light of other potential stressors (for example, climate change) and limited resources. Our results revealed several important findings that could influence management decisions regarding long-term monitoring of park streams. First, we found that biological indicators of stream condition at headwater sites and perennial springs generally were more indicative of lower habitat quality and were more spatially variable than those observed at sites on routinely monitored larger streams. We hypothesized that poorer stream condition observed in smaller streams was due to stream drying that occurs more frequently in headwater areas. We also found that biological and water-chemistry measures responded differently to landscape drivers. Variation in most biological endpoints was driven primarily by stream size and was only secondarily associated with bedrock geology. In contrast, water chemistry showed essentially the opposite pattern, with underlying geology explaining much of the variation and stream size being of secondary importance. Therefore, expanding the LTEM program to include headwater areas would yield substantially different biological information, whereas broad inferences regarding spatial patterns in water chemistry would probably not change. Although significant differences in community composition were observed among streams of different sizes, no taxa were unique to headwater sites. All taxa collected at the 45 headwater sites also had been collected at one or more LTEM sites during one or more years. This observation indicates that headwater sites in the park may be structured by biotic nestedness; consequently, focusing management efforts on preserving the species pool at the larger LTEM sites would likely result in the protection of most taxa parkwide. Finally, linkages (correlations) between water chemistry and biological measures of stream condition were signficantly stronger when assessed at the LTEM sites than when assessed at the springs or headwater sites, indicating that conditions at downstream sites may be better indicators of water-quality trends.

Integration of Multiplex Bead Assays for Parasitic Diseases into a National, Population-Based Serosurvey of Women 15-39 Years of Age in Cambodia

PubMed Central

Priest, Jeffrey W.; Jenks, M. Harley; Moss, Delynn M.; Mao, Bunsoth; Buth, Sokhal; Wannemuehler, Kathleen; Soeung, Sann Chan; Lucchi, Naomi W.; Udhayakumar, Venkatachalam; Gregory, Christopher J.; Huy, Rekol; Muth, Sinuon; Lammie, Patrick J.

2016-01-01

Collection of surveillance data is essential for monitoring and evaluation of public health programs. Integrated collection of household-based health data, now routinely carried out in many countries through demographic health surveys and multiple indicator surveys, provides critical measures of progress in health delivery. In contrast, biomarker surveys typically focus on single or related measures of malaria infection, HIV status, vaccination coverage, or immunity status for vaccine-preventable diseases (VPD). Here we describe an integrated biomarker survey based on use of a multiplex bead assay (MBA) to simultaneously measure antibody responses to multiple parasitic diseases of public health importance as part of a VPD serological survey in Cambodia. A nationally-representative cluster-based survey was used to collect serum samples from women of child-bearing age. Samples were tested by MBA for immunoglobulin G antibodies recognizing recombinant antigens from Plasmodium falciparum and P. vivax, Wuchereria bancrofti, Toxoplasma gondii, Taenia solium, and Strongyloides stercoralis. Serologic IgG antibody results were useful both for generating national prevalence estimates for the parasitic diseases of interest and for confirming the highly focal distributions of some of these infections. Integrated surveys offer an opportunity to systematically assess the status of multiple public health programs and measure progress toward Millennium Development Goals. PMID:27136913

Analysis of biofluids in aqueous environment based on mid-infrared spectroscopy.

PubMed

Fabian, Heinz; Lasch, Peter; Naumann, Dieter

2005-01-01

In this study we describe a semiautomatic Fourier transform infrared spectroscopic methodology for the analysis of liquid serum samples, which combines simple sample introduction with high sample throughput. The applicability of this new infrared technology to the analysis of liquid serum samples from a cohort of cattle naturally infected with bovine spongiform encephalopathy and from controls was explored in comparison to the conventional approach based on transmission infrared spectroscopy of dried serum films. Artifical neural network analysis of the infrared data was performed to differentiate between bovine spongiform encephalopathy-negative controls and animals in the late stage of the disease. After training of artifical neural network classifiers, infrared spectra of sera from an independent external validation data set were analyzed. In this way, sensitivities between 90 and 96% and specificities between 84 and 92% were achieved, respectively, depending upon the strategy of data collection and data analysis. Based on these results, the advantages and limitations of the liquid sample technique and the dried film approach for routine analysis of biofluids are discussed. 2005 Society of Photo-Optical Instrumentation Engineers.

Presence of Toxoplasma gondii in Drinking Water from an Endemic Region in Southern Mexico.

PubMed

Hernandez-Cortazar, Ivonne B; Acosta-Viana, Karla Y; Guzman-Marin, Eugenia; Ortega-Pacheco, Antonio; Segura-Correa, Jose C; Jimenez-Coello, Matilde

2017-05-01

Toxoplasmosis can be acquired through the ingestion of contaminated drinking water with oocysts of Toxoplasma gondii, highly resistant to the routinely disinfection processes; based on chlorination commonly used in the water supply industry. The aim of this study was to determine the presence of T. gondii DNA in samples of public drinking water from an endemic region of southern Mexico. In total 74 samples of water (5 L each) were collected from the three well fields (I, II, and III) and 71 independent wells, distributing public drinking water to the city of Merida Yucatan, after passing through the chlorination process. Water samples were filtered and concentrated by a sucrose solution, then DNA was extracted and evaluated through a nested-PCR (nPCR) specific for T. gondii. Positive samples were detected in 5.4% (4/74) of the water samples. This is the first report of the presence of T. gondii DNA in public drinking water from a large city in southern Mexico, where their consumption without any postpurification treatment could pose a risk for acquiring the infection in the urban population.

Medical Findings and Toxicological Analysis in Infant Death by Balloon Gas Asphyxia: A Case Report.

PubMed

Cuypers, Eva; Rosier, Elien; Loix, Sara; Develter, Wim; Van Den Bogaert, Wouter; Wuestenbergs, Joke; Van de Voorde, Wim; Tytgat, Jan

2017-05-01

In recent years, the increasing number of asphyxiation cases due to helium inhalation is remarkable. All described cases in the literature where diagnosed as suicide. In this article, however, we describe a triple infant homicide in which helium, as balloon gas, was administered to three young children after sedation causing asphyxiation and death through the medical findings and toxicological analysis. During autopsy, in addition to standard toxicological samples, gas samples from lungs as well as lung tissue itself were directly collected into headspace vials. Besides routine toxicological analysis, which revealed toxic levels of doxylamine, qualitative analysis on gas and lung samples was performed using headspace gas chromatography-mass spectrometry. As carrier gas, the commonly used helium was replaced by nitrogen. In gas samples from lungs of all three children, no helium was found. Nevertheless, lung tissue samples were found positive on helium. Therefore, sedation followed by asphyxia due to helium inhalation can strongly be assumed as the cause of death of all three children. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Comparison of pneumatic tube system with manual transport for routine chemistry, hematology, coagulation and blood gas tests.

PubMed

Pupek, Alex; Matthewson, Beverly; Whitman, Erin; Fullarton, Rachel; Chen, Yu

2017-08-28

The pneumatic tube system (PTS) is commonly used in modern clinical laboratories to provide quick specimen delivery. However, its impact on sample integrity and laboratory testing results are still debatable. In addition, each PTS installation and configuration is unique to its institution. We sought to validate our Swisslog PTS by comparing routine chemistry, hematology, coagulation and blood gas test results and sample integrity indices between duplicate samples transported either manually or by PTS. Duplicate samples were delivered to the core laboratory manually by human courier or via the Swisslog PTS. Head-to-head comparisons of 48 routine chemistry, hematology, coagulation and blood gas laboratory tests, and three sample integrity indices were conducted on 41 healthy volunteers and 61 adult patients. The PTS showed no impact on sample hemolysis, lipemia, or icterus indices (all p<0.05). Although alkaline phosphatase, total bilirubin and hemoglobin reached statistical significance (p=0.009, 0.027 and 0.012, respectively), all had very low average bias which ranged from 0.01% to 2%. Potassium, total hemoglobin and percent deoxyhemoglobin were statistically significant for the neonatal capillary tube study (p=0.011, 0.033 and 0.041, respectively) but no biases greater than ±4% were identified for these parameters. All observed differences of these 48 laboratory tests were not clinically significant. The modern PTS investigated in this study is acceptable for reliable sample delivery for routine chemistry, hematology, coagulation and blood gas (in syringe and capillary tube) laboratory tests.

Helminth Fauna in Captive European Gray Wolves (Canis lupus lupus) in Germany.

PubMed

Bindke, Johanna Daniela; Springer, Andrea; Böer, Michael; Strube, Christina

2017-01-01

Captive as well as free-ranging wolves, which are currently recolonizing Germany, may harbor a variety of gastrointestinal parasites. This study investigated endoparasites in captive European gray wolves ( Canis lupus lupus ) using coproscopical methods. Fecal samples were collected monthly between October 2012 and November 2013 from 18 wolf enclosures in 14 German zoological gardens, representing 72 individual wolves. In total, 1,041 fecal samples including 26 bulk samples were analyzed by the sedimentation and flotation method. The most frequently detected egg morphotypes included five nematodes [Ancylostomatidae ( Ancylostoma or Uncinaria spp.), Toxocara canis, Toxascaris leonina, Trichuris vulpis , and Capillaria / Eucoleus spp.], one cestode (Taeniidae) and one trematode ( Alaria alata ). 44.76% of all samples were positive for at least one of these egg morphotypes. Overall, Ancylostomatidae showed the highest frequency (30.84% of all samples), followed by Capillaria/Eucoleus spp. (19.88%), Toxocara canis (5.19%), taeniids (3.75%), Trichuris vulpis and Alaria alata (3.65% each), and Toxascaris leonina (1.25%). As fecal samples were collected from the environment and could not be assigned to individual wolves, sample results were combined per zoo and month. General linear mixed models were employed to analyze the effect of season and management factors on the occurrence of Ancylostomatidae, Capillaria/Eucoleus spp., Toxocara canis and taeniids. No statistically significant effect of season was found, whereas anthelmintic treatment negatively affected Ancylostomatidae egg excretion. Detected parasites and their prevalences are comparable to previous studies on wolf parasitism conducted elsewhere in Europe. As many of the most prevalent helminths are of zoonotic importance, routine anthelmintic treatment of captive wolves should be recommended.

Assessing the Risk Factors of Cyber and Mobile Phone Bullying Victimization in a Nationally Representative Sample of Singapore Youth.

PubMed

Holt, Thomas J; Fitzgerald, Sarah; Bossler, Adam M; Chee, Grace; Ng, Esther

2016-04-01

This study utilized routine activity theory to examine the relationships between online behaviors, target suitability, and cyber and mobile phone-based bullying victimization in a nationally representative sample of youth from nine schools across Singapore. Key measures in all three categories-access to technology, online routine behaviors, and target suitability-were significant predictors of both forms of bullying victimization. In particular, females and victims of physical bullying were more likely to experience both forms of victimization. Access to technology and online routine behaviors predicted cyber and mobile phone-based bullying victimization differently. These findings demonstrate that routine activity theory is a viable framework to understand online bullying in non-Western nations, consistent with the existing literature on Western nations. © The Author(s) 2014.

Measuring routine nursing service efficiency: a comparison of cost per patient day and data envelopment analysis models.

PubMed Central

Nunamaker, T R

1983-01-01

This article provides an illustrative application of Data Envelopment Analysis (DEA) methodology to the measurement of routine nursing service efficiency at a group of Wisconsin hospitals. The DEA efficiency ratings and cost savings estimates are then compared to those resulting from application of Medicare's routine cost limitation to the sample data. DEA is also used to determine if any changes in the potential for efficient operations occurred during the 1978-1979 period. Empirical results were representative of the fundamental differences existing between the DEA and cost per patient day approaches. No evidence was found to support the notion that the overall potential for efficient delivery of routine services by the sample institutions was greater in one year than another. PMID:6874357

Quality in practice: integrating routine collection of patient language data into hospital practice.

PubMed

Hudelson, Patricia; Dominicé Dao, Melissa; Durieux-Paillard, Sophie

2013-09-01

Timely identification of patients' language needs can facilitate the provision of language-appropriate services and contribute to quality of care, clinical outcomes and patient satisfaction. At the University Hospitals of Geneva, Switzerland, timely organization of interpreter services was hindered by the lack of systematic patient language data collection. We explored the feasibility and acceptability of a procedure for collecting patient language data at the first point of contact, prior to its hospital-wide implementation. During a one-week period, receptionists and triage nurses in eight clinical services tested a new procedure for collecting patient language data. Patients were asked to identify their primary language and other languages they would be comfortable speaking with their doctor. Staff noted patients' answers on a paper form and provided informal feedback on their experience with the procedure. Registration staff encountered few difficulties collecting patient language data and thought that the two questions could easily be incorporated into existing administrative routines. Following the pilot test, two language fields with scroll-down language menus were added to the electronic patient file, and the subsequent filling-in of these fields has been rapid and hospital wide. Our experience suggests that routine collection of patient language data at first point of contact is both feasible and acceptable and that involving staff in a pilot project may facilitate hospital-wide implementation. Future efforts should focus on exploring the sensitivity and specificity of the proposed questions, as well as the impact of data collection on interpreter use.

Safety of a quadrivalent meningococcal serogroups A, C, W and Y conjugate vaccine (MenACWY-CRM) administered with routine infant vaccinations: results of an open-label, randomized, phase 3b controlled study in healthy infants.

PubMed

Abdelnour, Arturo; Silas, Peter E; Lamas, Marta Raquel Valdés; Aragón, Carlos Fernándo Grazioso; Chiu, Nan-Chang; Chiu, Cheng-Hsun; Acuña, Teobaldo Herrera; Castrejón, Tirza De León; Izu, Allen; Odrljin, Tatjana; Smolenov, Igor; Hohenboken, Matthew; Dull, Peter M

2014-02-12

The highest risk for invasive meningococcal disease (IMD) is in infants aged <1 year. Quadrivalent meningococcal conjugate vaccination has the potential to prevent IMD caused by serogroups A, C, W and Y. This phase 3b, multinational, open-label, randomized, parallel-group, multicenter study evaluated the safety of a 4-dose series of MenACWY-CRM, a quadrivalent meningococcal conjugate vaccine, concomitantly administered with routine vaccinations to healthy infants. Two-month-old infants were randomized 3:1 to receive MenACWY-CRM with routine vaccines or routine vaccines alone at ages 2, 4, 6 and 12 months. Adverse events (AEs) that were medically attended and serious adverse events (SAEs) were collected from all subjects from enrollment through 18 months of age. In a subset, detailed safety data (local and systemic solicited reactions and all AEs) were collected for 7 days post vaccination. The primary objective was a non-inferiority comparison of the percentages of subjects with ≥1 severe systemic reaction during Days 1-7 after any vaccination of MenACWY-CRM plus routine vaccinations versus routine vaccinations alone (criterion: upper limit of 95% confidence interval [CI] of group difference <6%). A total of 7744 subjects were randomized with 1898 in the detailed safety arm. The percentage of subjects with severe systemic reactions was 16% after MenACWY-CRM plus routine vaccines and 13% after routine vaccines alone (group difference 3.0% (95% CI -0.8, 6.4%). Although the non-inferiority criterion was not met, post hoc analysis controlling for significant center and group-by-center differences revealed that MenACWY-CRM plus routine vaccinations was non-inferior to routine vaccinations alone (group difference -0.1% [95% CI -4.9%, 4.7%]). Rates of solicited AEs, medically attended AEs, and SAEs were similar across groups. In a large multinational safety study, a 4-dose series of MenACWY-CRM concomitantly administered with routine vaccines was clinically acceptable with a similar safety profile to routine vaccines given alone. Copyright © 2013 Elsevier Ltd. All rights reserved.

Quantification of Protozoa and Viruses from Small Water Volumes

PubMed Central

Bonilla, J. Alfredo; Bonilla, Tonya D.; Abdelzaher, Amir M.; Scott, Troy M.; Lukasik, Jerzy; Solo-Gabriele, Helena M.; Palmer, Carol J.

2015-01-01

Large sample volumes are traditionally required for the analysis of waterborne pathogens. The need for large volumes greatly limits the number of samples that can be processed. The goals of this study were to compare extraction and detection procedures for quantifying protozoan parasites and viruses from small volumes of marine water. The intent was to evaluate a logistically simpler method of sample collection and processing that would facilitate direct pathogen measures as part of routine monitoring programs. Samples were collected simultaneously using a bilayer device with protozoa capture by size (top filter) and viruses capture by charge (bottom filter). Protozoan detection technologies utilized for recovery of Cryptosporidium spp. and Giardia spp. were qPCR and the more traditional immunomagnetic separation—IFA-microscopy, while virus (poliovirus) detection was based upon qPCR versus plaque assay. Filters were eluted using reagents consistent with the downstream detection technologies. Results showed higher mean recoveries using traditional detection methods over qPCR for Cryptosporidium (91% vs. 45%) and poliovirus (67% vs. 55%) whereas for Giardia the qPCR-based methods were characterized by higher mean recoveries (41% vs. 28%). Overall mean recoveries are considered high for all detection technologies. Results suggest that simultaneous filtration may be suitable for isolating different classes of pathogens from small marine water volumes. More research is needed to evaluate the suitability of this method for detecting pathogens at low ambient concentration levels. PMID:26114244

Quantification of Protozoa and Viruses from Small Water Volumes.

PubMed

Bonilla, J Alfredo; Bonilla, Tonya D; Abdelzaher, Amir M; Scott, Troy M; Lukasik, Jerzy; Solo-Gabriele, Helena M; Palmer, Carol J

2015-06-24

Large sample volumes are traditionally required for the analysis of waterborne pathogens. The need for large volumes greatly limits the number of samples that can be processed. The aims of this study were to compare extraction and detection procedures for quantifying protozoan parasites and viruses from small volumes of marine water. The intent was to evaluate a logistically simpler method of sample collection and processing that would facilitate direct pathogen measures as part of routine monitoring programs. Samples were collected simultaneously using a bilayer device with protozoa capture by size (top filter) and viruses capture by charge (bottom filter). Protozoan detection technologies utilized for recovery of Cryptosporidium spp. and Giardia spp. were qPCR and the more traditional immunomagnetic separation-IFA-microscopy, while virus (poliovirus) detection was based upon qPCR versus plaque assay. Filters were eluted using reagents consistent with the downstream detection technologies. Results showed higher mean recoveries using traditional detection methods over qPCR for Cryptosporidium (91% vs. 45%) and poliovirus (67% vs. 55%) whereas for Giardia the qPCR-based methods were characterized by higher mean recoveries (41% vs. 28%). Overall mean recoveries are considered high for all detection technologies. Results suggest that simultaneous filtration may be suitable for isolating different classes of pathogens from small marine water volumes. More research is needed to evaluate the suitability of this method for detecting pathogens at low ambient concentration levels.

Mars Sample Return mission: Two alternate scenarios

NASA Technical Reports Server (NTRS)

1991-01-01

Two scenarios for accomplishing a Mars Sample Return mission are presented herein. Mission A is a low cost, low mass scenario, while Mission B is a high technology, high science alternative. Mission A begins with the launch of one Titan IV rocket with a Centaur G' upper stage. The Centaur performs the trans-Mars injection burn and is then released. The payload consists of two lander packages and the Orbital Transfer Vehicle, which is responsible for supporting the landers during launch and interplanetary cruise. After descending to the surface, the landers deploy small, local rovers to collect samples. Mission B starts with 4 Titan IV launches, used to place the parts of the Planetary Transfer Vehicle (PTV) into orbit. The fourth launch payload is able to move to assemble the entire vehicle by simple docking routines. Once complete, the PTV begins a low thrust trajectory out from low Earth orbit, through interplanetary space, and into low Martian orbit. It deploys a communication satellite into a 1/2 sol orbit and then releases the lander package at 500 km altitude. The lander package contains the lander, the Mars Ascent Vehicle (MAV), two lighter than air rovers (called Aereons), and one conventional land rover. The entire package is contained with a biconic aeroshell. After release from the PTV, the lander package descends to the surface, where all three rovers are released to collect samples and map the terrain.

Surge Block Method for Controlling Well Clogging and Sampling Sediment during Bioremediation

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

Wu, Wei-min; Watson, David B; Luo, Jian

2013-01-01

A surge block treatment method (i.e. inserting a solid rod plunger with a flat seal that closely fits the casing interior into a well and stocking it up and down) was performed for the rehabilitation of wells clogged with biomass and for the collection of time series sediment samples during in situ bioremediation tests for U(VI) immobilization at a the U.S. Department of Energy site in Oak Ridge, TN. The clogging caused by biomass growth had been controlled by using routine surge block treatment for18 times over a nearly four year test period. The treatment frequency was dependent of themore » dosage of electron donor injection and microbial community developed in the subsurface. Hydraulic tests showed that the apparent aquifer transmissivity at a clogged well with an inner diameter (ID) of 10.16 cm was increased by 8 13 times after the rehabilitation, indicating the effectiveness of the rehabilitation. Simultaneously with the rehabilitation, the surge block method was successfully used for collecting time series sediment samples composed of fine particles (clay and silt) from wells with ID 1.9 10.16 cm for the analysis of mineralogical and geochemical composition and microbial community during the same period. Our results demonstrated that the surge block method provided a cost-effective approach for both well rehabilitation and frequent solid sampling at the same location.« less

A plasma arc reactor for fullerene research

NASA Astrophysics Data System (ADS)

Anderson, T. T.; Dyer, P. L.; Dykes, J. W.; Klavins, P.; Anderson, P. E.; Liu, J. Z.; Shelton, R. N.

1994-12-01

A modified Krätschmer-Huffman reactor for the mass production of fullerenes is presented. Fullerene mass production is fundamental for the synthesis of higher and endohedral fullerenes. The reactor employs mechanisms for continuous graphite-rod feeding and in situ slag removal. Soot collects into a Soxhlet extraction thimble which serves as a fore-line vacuum pump filter, thereby easing fullerene separation from soot. Thermal gravimetric analysis (TGA) for yield determination is reported. This TGA method is faster and uses smaller samples than Soxhlet extraction methods which rely on aromatic solvents. Production of 10 g of soot per hour is readily achieved utilizing this reactor. Fullerene yields of 20% are attained routinely.

INFORM: An interactive data collection and display program with debugging capability

NASA Technical Reports Server (NTRS)

Cwynar, D. S.

1980-01-01

A computer program was developed to aid ASSEMBLY language programmers of mini and micro computers in solving the man machine communications problems that exist when scaled integers are involved. In addition to producing displays of quasi-steady state values, INFORM provides an interactive mode for debugging programs, making program patches, and modifying the displays. Auxiliary routines SAMPLE and DATAO add dynamic data acquisition and high speed dynamic display capability to the program. Programming information and flow charts to aid in implementing INFORM on various machines together with descriptions of all supportive software are provided. Program modifications to satisfy the individual user's needs are considered.

Analysis of benzo(a)pyrene in airborne particulates by gas chromatography

NASA Technical Reports Server (NTRS)

Luedecke, E.

1976-01-01

A routine method was developed to measure benzo(a)pyrene in airborne particulates. Samples were collected on a filter and the organic portion was extracted with cyclohexane. The polynuclear hydrocarbon (PNHC) fraction was separated from the aliphatics by column chromatography. An internal standard was added to the extract and a portion of it was injected into a gas chromatograph. Although the gas chromatographic method has often been reported in the literature, satisfactory separation of benzo(a)pyrene and benzo(e)pyrene has not been achieved. With the introduction of a nematic liquid crystal as the stationary phase good separation is now possible.

Evaluation of quality-control data collected by the U.S. Geological Survey for routine water-quality activities at the Idaho National Laboratory, Idaho, 1996–2001

USGS Publications Warehouse

Rattray, Gordon W.

2012-01-01

The U.S. Geological Survey, in cooperation with the U.S. Department of Energy, collects surface water and groundwater samples at and near the Idaho National Laboratory as part of a routine, site-wide, water-quality monitoring program. Quality-control samples are collected as part of the program to ensure and document the quality of environmental data. From 1996 to 2001, quality-control samples consisting of 204 replicates and 27 blanks were collected at sampling sites. Paired measurements from replicates were used to calculate variability (as reproducibility and reliability) from sample collection and analysis of radiochemical, chemical, and organic constituents. Measurements from field and equipment blanks were used to estimate the potential contamination bias of constituents. The reproducibility of measurements of constituents was calculated from paired measurements as the normalized absolute difference (NAD) or the relative standard deviation (RSD). The NADs and RSDs, as well as paired measurements with censored or estimated concentrations for which NADs and RSDs were not calculated, were compared to specified criteria to determine if the paired measurements had acceptable reproducibility. If the percentage of paired measurements with acceptable reproducibility for a constituent was greater than or equal to 90 percent, then the reproducibility for that constituent was considered acceptable. The percentage of paired measurements with acceptable reproducibility was greater than or equal to 90 percent for all constituents except orthophosphate (89 percent), zinc (80 percent), hexavalent chromium (53 percent), and total organic carbon (TOC; 38 percent). The low reproducibility for orthophosphate and zinc was attributed to calculation of RSDs for replicates with low concentrations of these constituents. The low reproducibility for hexavalent chromium and TOC was attributed to the inability to preserve hexavalent chromium in water samples and high variability with the analytical method for TOC. The reliability of measurements of constituents was estimated from pooled RSDs that were calculated for discrete concentration ranges for each constituent. Pooled RSDs of 15 to 33 percent were calculated for low concentrations of gross-beta radioactivity, strontium-90, ammonia, nitrite, orthophosphate, nickel, selenium, zinc, tetrachloroethene, and toluene. Lower pooled RSDs of 0 to 12 percent were calculated for all other concentration ranges of these constituents, and for all other constituents, except for one concentration range for gross-beta radioactivity, chloride, and nitrate + nitrite; two concentration ranges for hexavalent chromium; and TOC. Pooled RSDs for the 50 to 60 picocuries per liter concentration range of gross-beta radioactivity (reported as cesium-137) and the 10 to 60 milligrams per liter (mg/L) concentration range of nitrate + nitrite (reported as nitrogen [N]) were 17 percent. Chloride had a pooled RSD of 14 percent for the 20 to less than 60 mg/L concentration range. High pooled RSDs of 40 and 51 percent were calculated for two concentration ranges for hexavalent chromium and of 60 percent for TOC. Measurements from (1) field blanks were used to estimate the potential bias associated with environmental samples from sample collection and analysis, (2) equipment blanks were used to estimate the potential bias from cross contamination of samples collected from wells where portable sampling equipment was used, and (3) a source-solution blank was used to verify that the deionized water source-solution was free of the constituents of interest. If more than one measurement was available, the bias was estimated using order statistics and the binomial probability distribution. The source-solution blank had a detectable concentration of hexavalent chromium of 2 micrograms per liter. If this bias was from a source other than the source solution, then about 84 percent of the 117 hexavalent chromium measurements from environmental samples could have a bias of 10 percent or more. Of the 14 field blanks that were collected, only chloride (0.2 milligrams per liter) and ammonia (0.03 milligrams per liter as nitrogen), in one blank each, had detectable concentrations. With an estimated confidencelevel of 95 percent, at least 80 percent of the 1,987 chloride concentrations measured from all environmental samples had a potential bias of less than 8 percent. The ammonia bias, which may have occurred at the analytical laboratory, could produce a potential bias of 5-100 percent in eight potentially affected ammonia measurements. Of the 11 equipment blanks that were collected, chloride was detected in 4 of these blanks, sodium in 3 blanks, and sulfate and hexavalent chromium were each detected in 1 blank. The concentration of hexavalent chromium in the equipment blank was the same concentration as in the source-solution blank collected on the same day, which indicates that the hexavalent chromium in the equipment blank is probably from a source other than the portable sampling equipment, such as the sample bottles or the source-solution water itself. The potential bias for chloride, sodium, and sulfate measurements was estimated for environmental samples that were collected using portable sampling equipment. For chloride, it was estimated with 93 percent confidence that at least 80 percent of the measurements had a bias of less than 18 percent. For sodium and sulfate, it was estimated with 91 percent confidence that at least 70 percent of the measurements had a bias of less than 12 and 5 percent, respectively.

The Use and Interpretation of Sodium Concentrations in Casual (Spot) Urine Collections for Population Surveillance and Partitioning of Dietary Iodine Intake Sources

PubMed Central

Conkle, Joel; van der Haar, Frits

2016-01-01

In 2013, the World Health Organization (WHO) called for joint surveillance of population salt and iodine intakes using urinary analysis. 24-h urine collection is considered the gold standard for salt intake assessment, but there is an emerging consensus that casual urine sampling can provide comparable information for population-level surveillance. Our review covers the use of the urinary sodium concentration (UNaC) and the urinary iodine concentration (UIC) from casual urine samples to estimate salt intakes and to partition the sources of iodine intakes. We reviewed literature on 24-h urinary sodium excretion (UNaE) and UNaC and documented the use of UNaC for national salt intake monitoring. We combined information from our review of urinary sodium with evidence on urinary iodine to assess the appropriateness of partitioning methods currently being adapted for cross-sectional survey analyses. At least nine countries are using casual urine collection for surveillance of population salt intakes; all these countries used single samples. Time trend analyses indicate that single UNaC can be used for monitoring changes in mean salt intakes. However; single UNaC suffers the same limitation as single UNaE; i.e., an estimate of the proportion excess salt intake can be biased due to high individual variability. There is evidence, albeit limited, that repeat UNaC sampling has good agreement at the population level with repeat UNaE collections; thus permitting an unbiased estimate of the proportion of excess salt intake. High variability of UIC and UNaC in single urine samples may also bias the estimates of dietary iodine intake sources. Our review concludes that repeated collection, in a sub-sample of individuals, of casual UNaC data would provide an immediate practical approach for routine monitoring of salt intake, because it overcomes the bias in estimates of excess salt intake. Thus we recommend more survey research to expand the evidence-base on predicted-UNaE from repeat casual UNaC sampling. We also conclude that the methodology for partitioning the sources of iodine intake based on the combination of UIC and UNaC measurements in casual urine samples can be improved by repeat collections of casual data; which helps to reduce regression dilution bias. We recommend more survey research to determine the effect of regression dilution bias and circadian rhythms on the partitioning of dietary iodine intake sources. PMID:28025546

Identification of novel serum peptide biomarkers for high-altitude adaptation: a comparative approach

PubMed Central

Yang, Juan; Li, Wenhua; Liu, Siyuan; Yuan, Dongya; Guo, Yijiao; Jia, Cheng; Song, Tusheng; Huang, Chen

2016-01-01

We aimed to identify serum biomarkers for screening individuals who could adapt to high-altitude hypoxia at sea level. HHA (high-altitude hypoxia acclimated; n = 48) and HHI (high-altitude hypoxia illness; n = 48) groups were distinguished at high altitude, routine blood tests were performed for both groups at high altitude and at sea level. Serum biomarkers were identified by comparing serum peptidome profiling between HHI and HHA groups collected at sea level. Routine blood tests revealed the concentration of hemoglobin and red blood cells were significantly higher in HHI than in HHA at high altitude. Serum peptidome profiling showed that ten significantly differentially expressed peaks between HHA and HHI at sea level. Three potential serum peptide peaks (m/z values: 1061.91, 1088.33, 4057.63) were further sequence identified as regions of the inter-α trypsin inhibitor heavy chain H4 fragment (ITIH4 347–356), regions of the inter-α trypsin inhibitor heavy chain H1 fragment (ITIH1 205–214), and isoform 1 of fibrinogen α chain precursor (FGA 588–624). Expression of their full proteins was also tested by ELISA in HHA and HHI samples collected at sea level. Our study provided a novel approach for identifying potential biomarkers for screening people at sea level who can adapt to high altitudes. PMID:27150491

A phase III, randomized controlled study to assess the safety and immunogenicity of a semi-synthetic diphtheria, tetanus and whole-cell pertussis vaccine in Indian infants.

PubMed

Sharma, Hitt; Patil, Vishwanath; Sharma, Dharambhushan; Kapre, Subhash; Jadhav, Suresh; Ravetkar, Satish; Kumar, Rakesh; Bahl, Sunil; Parekh, Sameer; Chakravarty, Anita

2012-09-21

Reactions to DTwP vaccine are well known and are a matter of great concern, much for the development of next generation combination vaccines. To avoid such reactions which occur from foreign compounds, WHO suggested manufacture of DTwP vaccine using semi-synthetic medium. The phase III trial reported here was conducted to assess the immunogenicity, tolerability and safety of a new DTwP vaccine manufactured using semi-synthetic medium for both tetanus and diphtheria toxoids in comparison with the routinely manufactured DTwP vaccine. In all, 331 infants aged 6-8 weeks were enrolled, out of which 308 completed the study. The vaccination was done at 6-10-14 weeks following EPI/WHO recommended immunization schedule. Blood samples were collected prior to the administration of first dose and one month after the third dose. Postvaccination, geometric mean titres for each component did not differ significantly amongst the two study groups. Though, the immunogenicity results were comparable between the two vaccines, the incidence of adverse events was comparatively low in semi-synthetic vaccine as against the routine vaccine group for all the three doses. The semi-synthetic DTwP vaccine was immunogenic and showed a significant lower incidence of local adverse events in comparison to the routine vaccine. This vaccine is now being used in the routine vaccination programme both as a triple antigen (DTwP alone) as well as a combination with Hepatitis B and/or Haemophilus influenzae type b vaccine. Copyright © 2012 Elsevier Ltd. All rights reserved.

Rapid determination of 226Ra in environmental samples

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

Maxwell, Sherrod L.; Culligan, Brian K.

A new rapid method for the determination of {sup 228}Ra in natural water samples has been developed at the SRNL/EBL (Savannah River National Lab/ Environmental Bioassay Laboratory) that can be used for emergency response or routine samples. While gamma spectrometry can be employed with sufficient detection limits to determine {sup 228}Ra in solid samples (via {sup 228}Ac) , radiochemical methods that employ gas flow proportional counting techniques typically provide lower MDA (Minimal Detectable Activity) levels for the determination of {sup 228}Ra in water samples. Most radiochemical methods for {sup 228}Ra collect and purify {sup 228}Ra and allow for {sup 228}Acmore » daughter ingrowth for ~36 hours. In this new SRNL/EBL approach, {sup 228}Ac is collected and purified from the water sample without waiting to eliminate this delay. The sample preparation requires only about 4 hours so that {sup 228}Ra assay results on water samples can be achieved in < 6 hours. The method uses a rapid calcium carbonate precipitation enhanced with a small amount of phosphate added to enhance chemical yields (typically >90%), followed by rapid cation exchange removal of calcium. Lead, bismuth, uranium, thorium and protactinium isotopes are also removed by the cation exchange separation. {sup 228}Ac is eluted from the cation resin directly onto a DGA Resin cartridge attached to the bottom of the cation column to purify {sup 228}Ac. DGA Resin also removes lead and bismuth isotopes, along with Sr isotopes and {sup 90}Y. La is used to determine {sup 228}Ac chemical yield via ICP-MS, but {sup 133}Ba can also be used instead if ICP-MS assay is not available. Unlike some older methods, no lead or strontium holdback carriers or continual readjustment of sample pH is required.« less

Usefulness of an injectable anaesthetic protocol for semen collection through urethral catheterisation in domestic cats.

PubMed

Pisu, Maria Carmela; Ponzio, Patrizia; Rovella, Chiara; Baravalle, Michela; Veronesi, Maria Cristina

2017-10-01

Objectives Although less often requested in comparison with dogs, the collection of semen in cats can be necessary for artificial insemination, for semen evaluation in tom cats used for breeding and for semen storage. Urethral catheterisation after pharmacological induction with medetomidine has proved to be useful for the collection of semen in domestic cats. However, most of the previously used protocols require the administration of high doses of medetomidine that can increase the risk of side effects, especially on the cardiovascular system. In routine clinical practice, one safe and useful injectable anaesthetic protocol for short-term clinical investigations or surgery in cats involves premedication with low intramuscular doses of dexmedetomidine with methadone, followed by intravenous propofol bolus injection. We aimed to assess the usefulness of this injectable anaesthetic protocol for semen collection, via urethral catheterisation, in domestic cats. Methods The study was performed on 38 purebred, adult cats, during the breeding season, and semen was collected via urethral catheterisation using an injectable anaesthesia protocol with methadone (0.2 mg/kg) and dexmedetomidine (5 µg/kg) premedication, followed by induction with propofol. Results The anaesthetic protocol used in the present study allowed the collection of large-volume semen samples, characterised by good parameters and without side effects. Conclusions and relevance The results from the present study suggest that the injectable anaesthetic protocol using methadone and dexmedetomidine premedication, followed by induction with propofol, could be suitable and safe for the collection of a good-quality semen sample, via urethral catheterisation, in domestic cats. It can therefore be used as an alternative to previous medetomidine-based sedation protocols.

Pre-analytical effects of pneumatic tube system transport on routine haematology and coagulation tests, global coagulation assays and platelet function assays.

PubMed

Le Quellec, Sandra; Paris, Mickaël; Nougier, Christophe; Sobas, Frédéric; Rugeri, Lucia; Girard, Sandrine; Bordet, Jean-Claude; Négrier, Claude; Dargaud, Yesim

2017-05-01

Pneumatic tube system (PTS) in hospitals is commonly used for the transport of blood samples to clinical laboratories, as it is rapid and cost-effective. The aim was to compare the effects on haematology samples of a newly acquired ~2km-long PTS that links 2 hospitals with usual transport (non-pneumatic tube system, NPTS). Complete blood cell count, routine coagulation assays, platelet function tests (PFT) with light-transmission aggregometry and global coagulation assays including ROTEM® and thrombin generation assay (TGA) were performed on blood samples from 30 healthy volunteers and 9 healthy volunteers who agreed to take aspirin prior to blood sampling. The turnaround time was reduced by 31% (p<0.001) with the use of PTS. No statistically significant difference was observed for most routine haematology assays including PFT, and ROTEM® analysis. A statistically significant, but not clinically relevant, shortening of the APTT after sample transport by PTS was found (mean±SD: 30s±1.8 vs. 29.5s±2.1 for NPTS). D-dimer levels were 7.4% higher after transport through PTS but were not discordant. A statistically significant increase of thrombin generation was found in both platelet poor- and platelet rich- plasma samples after PTS transport compared to NPTS transport. PTS is suitable for the transport of samples prior to routine haematology assays including PFT, but should not be used for samples intended for thrombin generation measurement. Copyright © 2017 Elsevier Ltd. All rights reserved.

Immunodetection and molecular determination of visceral and cutaneous Leishmania infection using patients' urine.

PubMed

Mirzaei, Asad; Ahmadipour, Fereshteh; Cannet, Arnaud; Marty, Pierre; Delaunay, Pascal; Perrin, Pascale; Dorkeld, Franck; Sereno, Denis; Akhoundi, Mohammad

2018-05-27

The diagnosis of leishmaniasis relies mainly on the use of invasive processes, to collect the biological material for detecting Leishmania parasites. Body fluids, which can be collected by non-invasive process, would greatly facilitate the leishmaniasis diagnosis. In the present study, we investigated the potency of urine immunoblotting to diagnose cutaneous and visceral leishmaniasis and we compared with routine molecular methods. A total of 80 samples, including 40 sera and their 40 corresponding urine samples were collected from 37 suspected patients with cutaneous and visceral leishmaniasis, and 3 healthy individuals (as control), in Ilam and Ardabil provinces of Iran. All sera and urine samples were analyzed, using immunoblotting. The confirmation of leishmaniasis infection was performed, using conventional and quantitative PCRs as well as by sequencing the amplicons. Among 37 suspected patients, 23 patients presented cutaneous lesions (CL) and 14 exhibited clinical symptoms reminiscent of visceral leishmaniasis (L. infantum). Among cutaneous patients, 15 were positive for zoonotic cutaneous leishmaniasis (L. major), and eight for anthroponotic cutaneous leishmaniasis (L. tropica). Molecular quantification of Leishmania parasites was performed on sera, urines and cutaneous biopsies of CL and VL patients, demonstrating that parasite load is lower in urines, compared to sera or biopsy. DNA can be detected in 20 out of 23 (86.9%) CL urine samples and in 13 out of 14 (92.8%) VL urine samples. Immunodetection analysis demonstrates that 22 out of 23 (95.6%) sera from CL patients and all patients suspected with VL are positive. For urine samples, 18 out of 23 (78.2%) urine of CL patients and 13 out of 14 (92.8%) urine of VL patients were positive, using Western blot. Therefore, immunodetection and molecular analysis using urine samples can be used as a diagnostic tool for surveying cutaneous and visceral leishmaniasis. Copyright © 2017. Published by Elsevier B.V.

First isolation of dengue virus from the 2010 epidemic in Nepal.

PubMed

Pandey, Basu D; Nabeshima, Takeshi; Pandey, Kishor; Rajendra, Saroj P; Shah, Yogendra; Adhikari, Bal R; Gupta, Govinda; Gautam, Ishan; Tun, Mya M N; Uchida, Reo; Shrestha, Mahendra; Kurane, Ichiro; Morita, Kouichi

2013-09-01

Dengue is an emerging disease in Nepal and was first observed as an outbreak in nine lowland districts in 2006. In 2010, however, a large epidemic of dengue occurred with 4,529 suspected and 917 serologically-confirmed cases and five deaths reported in government hospitals in Nepal. The collection of demographic information was performed along with an entomological survey and clinical evaluation of the patients. A total of 280 serum samples were collected from suspected dengue patients. These samples were subjected to routine laboratory investigations and IgM-capture ELISA for dengue serological identification, and 160 acute serum samples were used for virus isolation, RT-PCR, sequencing and phylogenetic analysis. The results showed that affected patients were predominately adults, and that 10% of the cases were classified as dengue haemorrhagic fever/ dengue shock syndrome. The genetic characterization of dengue viruses isolated from patients in four major outbreak areas of Nepal suggests that the DENV-1 strain was responsible for the 2010 epidemic. Entomological studies identified Aedes aegypti in all epidemic areas. All viruses belonged to a monophyletic single clade which is phylogenetically close to Indian viruses. The dengue epidemic started in the lowlands and expanded to the highland areas. To our knowledge, this is the first dengue isolation and genetic characterization reported from Nepal.

Progress Toward Poliomyelitis Eradication - Pakistan, January 2016-September 2017.

PubMed

Elhamidi, Youness; Mahamud, Abdirahman; Safdar, Muhammad; Al Tamimi, Wasan; Jorba, Jaume; Mbaeyi, Chukwuma; Hsu, Christopher H; Wadood, Zubair; Sharif, Salmaan; Ehrhardt, Derek

2017-11-24

In 1988, the World Health Assembly launched the Global Polio Eradication Initiative. Among the three wild poliovirus serotypes, only wild poliovirus (WPV) type 1 (WPV1) has been detected since 2012. Since 2014, Pakistan, Afghanistan, and Nigeria remain the only countries with continuing endemic WPV1 transmission. This report describes activities conducted and progress made toward the eradication of poliovirus in Pakistan during January 2016-July 2017 and provides an update to previous reports (1,2). In 2016, Pakistan reported 20 WPV1 cases, a 63% decrease compared with 54 cases in 2015 (3). As of September 25, 2017, five WPV1 cases have been reported in 2017, representing a 69% decline compared with 16 cases reported during the same period in 2016 (Figure 1). During January-September 2017, WPV1 was detected in 72 of 468 (15%) environmental samples collected, compared with 36 of 348 (9%) samples collected during the same period in 2016. WPV1 was detected in environmental samples in areas where no polio cases are being reported, which indicates that WPV1 transmission is continuing in some high-risk areas. Interruption of WPV transmission in Pakistan requires maintaining focus on reaching missed children (particularly among mobile populations), continuing community-based vaccination, implementing the 2017-2018 National Emergency Action Plan (4), and improving routine immunization services.

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

PubMed

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

2007-08-01

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

Chlamydia trachomatis infection in young pregnant women in Southern Brazil: a cross-sectional study.

PubMed

Silveira, Mariângela Freitas da; Sclowitz, Iândora Krolow Timm; Entiauspe, Ludmila Gonçalves; Mesenburg, Marilia Arndt; Stauffert, Dulce; Bicca, Guilherme Lucas de Oliveira; Pieniz, Carine; Manta, Adriane Brod

2017-02-13

This study estimated the prevalence of Chlamydia trachomatis infection during pregnancy in a sample of women up to 29 years of age in the city of Pelotas, Rio Grande do Sul State, Brazil, and investigated socio-demographic risk factors such as maternal age, marital status, maternal schooling, and family income. C. trachomatis infection was diagnosed with PCR using BD ProbeTecTM CT/GC Amplified DNA Assay. Socio-demographic, behavioral, and reproductive data were collected using structured questionnaires. All collections were performed by previously trained medical students. The study included a stratified probabilistic sample from four maternity hospitals in the city. The sample included 562 pregnant women, and prevalence of C. trachomatis infection was 12.3% (95%CI: 9.6-15.0). No significant association was identified between C. trachomatis infection and any of the target variables, including obstetric outcomes such as history of preterm delivery. Our findings in terms of low treatment adherence, only 43% of the women and 9.7% of partners, associated with high C. trachomatis prevalence, reinforce the need to implement routine screening for C. trachomatis during prenatal care. The attempt to diagnose and treat this infection after delivery, as in this study, limits the possibility of success.

Diagnosis of central nervous system relapse of pediatric acute lymphoblastic leukemia: Impact of routine cytological CSF analysis at the time of intrathecal chemotherapy.

PubMed

Gassas, Adam; Krueger, Joerg; Alvi, Saima; Sung, Lillian; Hitzler, Johanne; Lieberman, Lani

2014-12-01

Despite the success of central nervous system (CNS) directed therapy in pediatric acute lymphoblastic leukemia (ALL), relapse involving the CNS continues to be observed in 5-10% of children when utilizing standard intrathecal prophylactic chemotherapy. While most pediatric ALL treatment protocols mandate regular lumbar punctures (LP) for the intrathecal injection of chemotherapy, the value of routine cytological analysis of cerebrospinal fluid (CSF) during therapy is unknown. Our objective was to assess the diagnostic value of routine CSF analysis during ALL therapy. To allow for at least 10 years of follow up from ALL diagnosis, children (0-18 years) with ALL diagnosed and treated at SickKids, Toronto, Canada between 1994-2004 were studied. Medical records of patients with CNS relapse were examined to determine whether CNS relapse was diagnosed based on cytology of a routinely obtained CSF sample, a CSF sample obtained because of signs and symptoms or a CSF sample obtained after the diagnosis of a bone marrow relapse. Of 494 children treated for ALL, 31 (6.6%) developed a relapse of ALL involving the CNS. Twenty-two had an isolated CNS relapse and nine had a combined bone marrow and CNS relapse. Among patients with isolated CNS relapse, 73% (16/22) were diagnosed based on routine CSF samples obtained from asymptomatic children. Conversely, 89% (8/9) of children with combined bone marrow and CNS relapse presented with symptoms and signs that prompted CSF examination. Routine CSF examination at the time of LP for intrathecal chemotherapy is useful in detecting CNS relapse. © 2014 Wiley Periodicals, Inc.

Comparison of microbiological diagnosis of urinary tract infection in young children by routine health service laboratories and a research laboratory: Diagnostic cohort study

PubMed Central

Birnie, Kate; Hay, Alastair D.; Wootton, Mandy; Howe, Robin; MacGowan, Alasdair; Whiting, Penny; Lawton, Michael; Delaney, Brendan; Downing, Harriet; Dudley, Jan; Hollingworth, William; Lisles, Catherine; Little, Paul; O’Brien, Kathryn; Pickles, Timothy; Rumsby, Kate; Thomas-Jones, Emma; Van der Voort, Judith; Waldron, Cherry-Ann; Harman, Kim; Hood, Kerenza; Butler, Christopher C.; Sterne, Jonathan A. C.

2017-01-01

Objectives To compare the validity of diagnosis of urinary tract infection (UTI) through urine culture between samples processed in routine health service laboratories and those processed in a research laboratory. Population and methods We conducted a prospective diagnostic cohort study in 4808 acutely ill children aged <5 years attending UK primary health care. UTI, defined as pure/predominant growth ≥105 CFU/mL of a uropathogen (the reference standard), was diagnosed at routine health service laboratories and a central research laboratory by culture of urine samples. We calculated areas under the receiver-operator curve (AUC) for UTI predicted by pre-specified symptoms, signs and dipstick test results (the “index test”), separately according to whether samples were obtained by clean catch or nappy (diaper) pads. Results 251 (5.2%) and 88 (1.8%) children were classified as UTI positive by health service and research laboratories respectively. Agreement between laboratories was moderate (kappa = 0.36; 95% confidence interval [CI] 0.29, 0.43), and better for clean catch (0.54; 0.45, 0.63) than nappy pad samples (0.20; 0.12, 0.28). In clean catch samples, the AUC was lower for health service laboratories (AUC = 0.75; 95% CI 0.69, 0.80) than the research laboratory (0.86; 0.79, 0.92). Values of AUC were lower in nappy pad samples (0.65 [0.61, 0.70] and 0.79 [0.70, 0.88] for health service and research laboratory positivity, respectively) than clean catch samples. Conclusions The agreement of microbiological diagnosis of UTI comparing routine health service laboratories with a research laboratory was moderate for clean catch samples and poor for nappy pad samples and reliability is lower for nappy pad than for clean catch samples. Positive results from the research laboratory appear more likely to reflect real UTIs than those from routine health service laboratories, many of which (particularly from nappy pad samples) could be due to contamination. Health service laboratories should consider adopting procedures used in the research laboratory for paediatric urine samples. Primary care clinicians should try to obtain clean catch samples, even in very young children. PMID:28199403

Development, validation, and application of a method for selected avermectin determination in rural waters using high performance liquid chromatography and fluorescence detection.

PubMed

Lemos, Maria Augusta Travassos; Matos, Camila Alves; de Resende, Michele Fabri; Prado, Rachel Bardy; Donagemma, Raquel Andrade; Netto, Annibal Duarte Pereira

2016-11-01

Avermectins (AVM) are macrocyclic lactones used in livestock and agriculture. A quantitative method of high performance liquid chromatography with fluorescence detection for the determination of eprinomectin, abamectin, doramectin and ivermectin in rural water samples was developed and validated. The method was employed to study samples collected in the Pito Aceso River microbasin, located in the Bom Jardim municipality, Rio de Janeiro State, Brazil. Samples were extracted by solid phase extraction using a polymeric stationary phase, the eluted fraction was re-concentrated under a gentle N2 flow and derivatized to allow AVM determination using liquid chromatography with fluorescence detection. The excitation and emission wavelengths of the derivatives were 365 and 470nm, respectively, and a total chromatographic run of 12min was achieved. Very low limits of quantification (22-58ngL(-1)) were found after re-concentration using N2. Recovery values varied from 85.7% to 119.2% with standard deviations between 1.2% and 10.2%. The validated method was applied in the determination of AVM in 15 water samples collected in the Pito Aceso River microbasin, but most of them were free of AVM or showed only trace levels of these compounds, except for a sample that contained doramectin (9.11µgL(-1)). The method is suitable for routine analysis with satisfactory recovery, sensitivity, and selectivity. Copyright © 2016 Elsevier Inc. All rights reserved.

Assessment and forensic application of laser-induced breakdown spectroscopy (LIBS) for the discrimination of Australian window glass.

PubMed

El-Deftar, Moteaa M; Speers, Naomi; Eggins, Stephen; Foster, Simon; Robertson, James; Lennard, Chris

2014-08-01

A commercially available laser-induced breakdown spectroscopy (LIBS) instrument was evaluated for the determination of elemental composition of twenty Australian window glass samples, consisting of 14 laminated samples and 6 non-laminated samples (or not otherwise specified) collected from broken windows at crime scenes. In this study, the LIBS figures of merit were assessed in terms of accuracy, limits of detection and precision using three standard reference materials (NIST 610, 612, and 1831). The discrimination potential of LIBS was compared to that obtained using laser ablation inductively coupled plasma mass spectrometry (LA-ICP-MS), X-ray microfluorescence spectroscopy (μXRF) and scanning electron microscopy energy dispersive X-ray spectrometry (SEM-EDX) for the analysis of architectural window glass samples collected from crime scenes in the Canberra region, Australia. Pairwise comparisons were performed using a three-sigma rule, two-way ANOVA and Tukey's HSD test at 95% confidence limit in order to investigate the discrimination power for window glass analysis. The results show that the elemental analysis of glass by LIBS provides a discrimination power greater than 97% (>98% when combined with refractive index data), which was comparable to the discrimination powers obtained by LA-ICP-MS and μXRF. These results indicate that LIBS is a feasible alternative to the more expensive LA-ICP-MS and μXRF options for the routine forensic analysis of window glass samples. Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.

Issue Management by School Superintendents: Final Report. Part II.

ERIC Educational Resources Information Center

Huff, Anne S.; Pondy, Louis R.

Four papers generated by a broader study of issues management in three suburban Chicago school districts are collected here. "Achieving Routine" focuses on the effective routinization of organizational change, in this case a curriculum decision, through the use of administrative mechanisms and the conceptual linkage of the new to…

75 FR 68358 - Proposed Data Collections Submitted for Public Comment and Recommendations

Federal Register 2010, 2011, 2012, 2013, 2014

2010-11-05

... care physicians who routinely provide an initial diagnosis of asthma and nurses who routinely provide... Care Providers Better Asthma Educators--New--National Center for Environmental Health (NCEH), Centers... have the disorder. Asthma accounts for 13.3 million health care visits and more than 3,400 deaths per...

Playing with Rules around Routines: Children Making Mealtimes Meaningful and Enjoyable

ERIC Educational Resources Information Center

Alcock, Sophie

2007-01-01

Children attending early childhood education and care centres spend a lot of time fitting in with institutional routines. This paper uses ethnographic methods and sociocultural activity theory to describe and analyse the processes whereby young children in an early childhood centre collectively created meaning and interest during potentially…

Use of routinely collected data on trihalomethane in drinking water for epidemiological purposes

PubMed Central

Keegan, T; Whitaker, H; Nieuwenhuijsen, M; Toledano, M; Elliott, P; Fawell, J; Wilkinson, M; Best, N

2001-01-01

OBJECTIVES—To explore the use of routinely collected trihalomethane (THM) measurements for epidemiological studies. Recently there has been interest in the relation between byproducts of disinfection of public drinking water and certain adverse reproductive outcomes, including stillbirth, congenital malformations, and low birth weight.
METHOD—Five years of THM readings (1992-6), collected for compliance with statutory limits, were analysed. One water company in the north west of England, divided into 288 water zones, provided 15 984 observations for statistical analysis. On average each zone was sampled 11.1 times a year. Five year, annual, monthly, and seasonal variation in THMs were examined as well as the variability within and between zones.
RESULTS—Between 1992 and 1996 the total THM (TTHM) annual zone means were less than half the statutory concentration, at approximately 46 µg/l. Differences in annual water zone means were within 7%. Over the study period, the maximum water zone mean fell from 142.2 to 88.1 µg/l. Mean annual concentrations for individual THMs (µg/l) were 36.6, 8.0, and 2.8 for chloroform, bromodichloromethane (BDCM), and dibromochloromethane (DBCM) respectively. Bromoform data were not analysed, because a high proportion of the data were below the detection limit. The correlation between chloroform and TTHM was 0.98, between BDCM and TTHM 0.62, and between DBCM and TTHM −0.09. Between zone variation was larger than within zone variation for chloroform and BDCM, but not for DBCM. There was only little seasonal variation (<3%). Monthly variation was found although there were no consistent trends within years.
CONCLUSION—In an area where the TTHM concentrations were less than half the statutory limit (48 µg/l) chloroform formed a high proportion of TTHM. The results of the correlation analysis suggest that TTHM concentrations provided a good indication of chloroform concentrations, a reasonable indication of BDCM concentrations, but no indication of DBCM. Zone means were similar over the years, but the maximum concentrations reduced considerably, which suggests that successful improvements in treatment have been made to reduce high TTHM concentrations in the area. For chloroform and BDCM, the main THMs, the component between water zones was greater than variation within water zones and explained most of the overall exposure variation. Variation between months and seasons was low and showed no clear trends within years. The results indicate that routinely collected data can be used to obtain exposure estimates for epidemiological studies at a small area level.


Keywords: chlorination byproducts; exposure; birth outcomes; routine data; trihalomethanes PMID:11404449

Diarrheagenic pathogens in adults attending a hospital in Singapore.

PubMed

Chau, Man Ling; Hartantyo, Sri Harminda Pahm; Yap, Min; Kang, Joanne Su Lin; Aung, Kyaw Thu; Gutiérrez, Ramona Alikiiteaga; Ng, Lee Ching; Tam, Clarence C; Barkham, Timothy

2016-01-28

Singapore's diarrhoeal notification system is based on specific pathogens. Official data may thus be skewed towards notifiable diseases. Limited information is available on the profiles of aetiological agents responsible for acute gastroenteritis (AGE) cases, especially among the adult population. To understand the frequency and distribution of potential causative agents of diarrheal disease in Singapore, we screened adults' stool samples collected from a large public hospital. The stool samples were screened for 18 diarrheagenic pathogens using a combination of commercial multiplex polymerase chain reaction (PCR), in-house singleplex PCR and immunochromatographic assays. One hundred adult faecal samples that were collected from October 2013 to January 2014 for routine diagnostic purposes and submitted for culture at Tan Tock Seng Hospital, Singapore were used. Pathogens were detected in 32% of the samples. The predominant organisms encountered were norovirus genogroup II (11%), Aeromonas spp. (9%) and Campylobacter spp. (5%). One sample was positive for both verocytotoxigenic E. coli (VTEC) and E. coli O157:H7. Two other samples were positive for VTEC only, and one other sample was positive for E. coli O157:H7 only. Astrovirus, C. perfringens, Shigella spp. and toxigenic C. difficile were each detected in 2% of the samples. Cryptosporidium parvum, Giardia lamblia, group A rotavirus, Salmonella spp. and Vibrio spp. were each detected in 1% of the samples. No L. monocytogenes, Y. enterocolitica, enteric adenovirus, or norovirus genogroup I were detected. Our preliminary findings suggest that pathogens causing non-notifiable diseases might have contributed considerably to the adult hospitalised AGE cases. However, as the samples were from an adult hospital, the data obtained may not be representative of the whole community. Thus, a larger study to collect clinical samples and risk exposure data from primary healthcare clinics and children hospital is planned for, to gain a more holistic perspective on the epidemiology of AGE in Singapore. A larger study may also offer valuable insights for improving the approach of microbiological surveillance of food, as well as strategizing inspection efforts along the food supply chain by public health authorities.

Multicenter performance evaluation of a second generation cortisol assay.

PubMed

Vogeser, Michael; Kratzsch, Jürgen; Ju Bae, Yoon; Bruegel, Mathias; Ceglarek, Uta; Fiers, Tom; Gaudl, Alexander; Kurka, Hedwig; Milczynski, Christoph; Prat Knoll, Cristina; Suhr, Anna C; Teupser, Daniel; Zahn, Ingrid; Ostlund, Richard E

2017-05-01

Untreated disorders of the adrenocortical system, such as Cushing's or Addison's disease, can be fatal, and accurate quantification of a patient's cortisol levels is vital for diagnosis. The objective of this study was to assess the analytical performance of a new fully-automated Elecsys® Cortisol II assay (second generation) to measure cortisol levels in serum and saliva. Four European investigational sites assessed the intermediate precision and reproducibility of the Cortisol II assay (Roche Diagnostics) under routine conditions. Method comparisons of the Cortisol II assay vs. liquid chromatography-tandem mass spectrometry (LC-MS/MS), the gold standard for cortisol measurement, were performed. Cortisol reference ranges from three US sites were determined using samples from self-reported healthy individuals. The coefficients of variation (CVs) for repeatability, intermediate precision, and reproducibility for serum samples were ≤2.6%, ≤5.8%, and ≤9.5%, respectively, and for saliva were ≤4.4% and ≤10.9%, and ≤11.4%, respectively. Agreement between the Cortisol II assay and LC-MS/MS in serum samples was close, with a slope of 1.02 and an intercept of 4.473 nmol/L. Reference range samples were collected from healthy individuals (n=300) and serum morning cortisol concentrations (5-95th percentile) were 166.1-507 nmol/L and afternoon concentrations were 73.8-291 nmol/L. Morning, afternoon, and midnight saliva concentrations (95th percentile) were 20.3, 6.94, and 7.56 nmol/L, respectively. The Cortisol II assay had good precision over the entire measuring range and had excellent agreement with LC-MS/MS. This test was found suitable for routine diagnostic application and will be valuable for the diagnosis of adrenocortical diseases.

A molecular approach for the rapid, selective and sensitive detection of Exophiala jeanselmei in environmental samples: development and performance assessment of a real-time PCR assay.

PubMed

Libert, X; Chasseur, C; Packeu, A; Bureau, F; Roosens, N H; De Keersmaecker, S J C

2016-02-01

Exophiala jeanselmei is an opportunistic pathogenic black yeast growing in humid environments such as water reservoirs of air-conditioning systems. Because this fungal contaminant could be vaporized into the air and subsequently cause health problems, its monitoring is recommended. Currently, this monitoring is based on culture and microscopic identification which are complex, sometimes ambiguous and time-demanding, i.e., up to 21 days. Therefore, molecular, culture-independent methods could be more advantageous for the monitoring of E. jeanselmei. In this study, we developed a SYBR®green real-time PCR assay based on the internal transcribed spacer 2 from the 18S ribosomal DNA complex for the specific detection of E. jeanselmei. The selectivity (100 %), PCR efficiency (95.5 %), dynamic range and repeatability of this qPCR assay were subsequently evaluated. The limit of detection for this qPCR assay was determined to be 1 copy of genomic DNA of E. jeanselmei. Finally, water samples collected from cooling reservoirs were analyzed using this qPCR assay to deliver a proof of concept for the molecular detection of E. jeanselmei in environmental samples. The results obtained by molecular analysis were compared with those of classical methods (i.e., culture and microscopic identification) used in routine analysis and were 100 % matching. This comparison demonstrated that this SYBR®green qPCR assay can be used as a molecular alternative for monitoring and routine investigation of samples contaminated by E. jeanselmei, while eliminating the need for culturing and thereby considerably decreasing the required analysis time to 2 days.

Validity of Targeted Next-Generation Sequencing in Routine Care for Identifying Clinically Relevant Molecular Profiles in Non-Small-Cell Lung Cancer: Results of a 2-Year Experience on 1343 Samples.

PubMed

Legras, Antoine; Barritault, Marc; Tallet, Anne; Fabre, Elizabeth; Guyard, Alice; Rance, Bastien; Digan, William; Pecuchet, Nicolas; Giroux-Leprieur, Etienne; Julie, Catherine; Jouveshomme, Stéphane; Duchatelle, Véronique; Giraudet, Véronique; Gibault, Laure; Cazier, Alain; Pastre, Jean; Le Pimpec-Barthes, Françoise; Laurent-Puig, Pierre; Blons, Hélène

2018-05-19

Theranostic assays are based on single-gene testing, but the ability of next-generation sequencing (NGS) to interrogate numerous genetic alterations will progressively replace single-gene assays. Although NGS was evaluated to screen for theranostic mutations, its usefulness in clinical practice on large series of samples remains to be demonstrated. NGS performance was assessed following guidelines. TaqMan probes and NGS were compared for their ability to detect EGFR and KRAS mutations, and NGS mutation profiles were analyzed on a large series of non-small-cell lung cancers (n = 1343). The R 2 correlation between expected and measured allelic ratio, using commercial samples, was >0.96. Mutation detection threshold was 2% for 10 ng of DNA input. κ Scores for TaqMan versus NGS were 0.99 (95% CI, 0.97-1.00) for EGFR and 0.98 (95% CI, 0.97-1.00) for KRAS after exclusion of rare EGFR (n = 40) and KRAS (n = 60) mutations. NGS identified 693 and 292 mutations in validated and potential oncogenic drivers, respectively. Significant associations were found between EGFR and PI3KCA or CTNNB1 and between KRAS and STK11. Potential oncogenic driver mutations or gene amplifications were more frequent in validated oncogenic driver nonmutated samples. This work is a proof of concept that targeted NGS is accessible in routine screening, including large screening, at reasonable cost. Clinical data should be collected and implemented in specific databases to make molecular data meaningful for direct patients' benefit. Copyright © 2018. Published by Elsevier Inc.

Data acquisition and PV module power production in upgraded TEP/AzRISE solar test yard

NASA Astrophysics Data System (ADS)

Bennett, Whit E.; Fishgold, Asher D.; Lai, Teh; Potter, Barrett G.; Simmons-Potter, Kelly

2017-08-01

The Tucson Electric Power (TEP)/University of Arizona AzRISE (Arizona Research Institute for Solar Energy) solar test yard is continuing efforts to improve standardization and data acquisition reliability throughout the facility. Data reliability is ensured through temperature-insensitive data acquisition devices with battery backups in the upgraded test yard. Software improvements allow for real-time analysis of collected data, while uploading to a web server. Sample data illustrates high fidelity monitoring of the burn-in period of a polycrystalline silicon photovoltaic module test string with no data failures over 365 days of data collection. In addition to improved DAQ systems, precision temperature monitoring has been implemented so that PV module backside temperatures are routinely obtained. Weather station data acquired at the test yard provides local ambient temperature, humidity, wind speed, and irradiance measurements that have been utilized to enable characterization of PV module performance over an extended test period

Effects of urbanization on stream water quality in the city of Atlanta, Georgia, USA

USGS Publications Warehouse

Peters, N.E.

2009-01-01

A long-term stream water quality monitoring network was established in the city of Atlanta, Georgia during 2003 to assess baseline water quality conditions and the effects of urbanization on stream water quality. Routine hydrologically based manual stream sampling, including several concurrent manual point and equal width increment sampling, was conducted ???12 times annually at 21 stations, with drainage areas ranging from 3.7 to 232 km2. Eleven of the stations are real-time (RT) stations having continuous measures of stream stage/ discharge, pH, dissolved oxygen, specific conductance, water temperature and turbidity, and automatic samplers for stormwater collection. Samples were analyzed for field parameters, and a broad suite of water quality and sediment-related constituents. Field parameters and concentrations of major ions, metals, nutrient species and coliform bacteria among stations were evaluated and with respect to watershed characteristics and plausible sources from 2003 through September 2007. Most constituent concentrations are much higher than nearby reference streams. Concentrations are statistically different among stations for several constituents, despite high variability both within and among stations. Routine manual sampling, automatic sampling during stormflows and RT water quality monitoring provided sufficient information about urban stream water quality variability to evaluate causes of water quality differences among streams. Fecal coliform bacteria concentrations of most samples exceeded Georgia's water quality standard for any water-usage class. High chloride concentrations occur at three stations and are hypothesized to be associated with discharges of chlorinated combined sewer overflows, drainage of swimming pool(s) and dissolution and transport during rainstorms of CaCl2, a deicing salt applied to roads during winter storms. One stream was affected by dissolution and transport of ammonium alum [NH4Al(SO4)2] from an alum-manufacturing plant; streamwater has low pH (<5), low alkalinity and high metals concentrations. Several trace metals exceed acute and chronic water quality standards and high concentrations are attributed to washoff from impervious surfaces.

A Case of Human Infection by Rickettsia slovaca in Greece.

PubMed

Kostopoulou, Vasiliki; Chochlakis, Dimosthenis; Kanta, Chrysoula; Katsanou, Andromachi; Rossiou, Konstantina; Rammos, Aidonis; Papadopoulos, Spyridon-Filippos; Katsarou, Theodora; Tselentis, Yannis; Psaroulaki, Anna; Boukas, Chrysostomos

2016-07-22

Although tick-borne rickettsiosis is endemic in Greece, until recently, human samples arriving at the National Reference Centre under suspicion of rickettsial infection were routinely tested only for Rickettsia typhi and R. conorii. However, identification of additional rickettsia species in ticks prompted revision of the protocol in 2010. Until that year, all human samples received by the laboratory were tested for antibodies against R. conorii and R. typhi only. Now, tests for R. slovaca, R. felis, and R. mongolotimonae are all included in routine analysis. The current description of a human R. slovaca case is possible as a result of these changes in routine testing.

Investigating socio-economic inequity in access to and expenditures on routine immunization services in Anambra state.

PubMed

Sibeudu, Florence T; Uzochukwu, Benjamin S C; Onwujekwe, Obinna E

2017-02-01

Addressing existing inequities in the utilization of priority health services such as routine immunization is a current public health priority. Increasing access to routine immunization from the current low levels amongst all socio-economic status groups in Nigeria is challenging. However, little is known on the level of SES inequity in utilization of routine immunization services and such information which will inform the development of strategies for ensuring equitable provision of routine immunization services in the country. The study was a cross sectional household survey, which was undertaken in two randomly selected communities in Anambra State, southeast Nigeria. A pre-tested interviewer administered questionnaire was used to collect data on levels of access to RI by children under-2 years from randomly selected households. In each household, data was collected from the primary care givers or their representative (in their absence). The relationship between access to routine immunization and socio-economic status of households and other key variables was explored in data analysis. Households from high socio-economic status (well-off) groups utilized routine immunization services more than those that belong to low socio-economic status (poor) groups (X 2  = 9.97, p < 0.002). It was found that higher percentage of low socio-economic status households compared to the high socio-economic status households received routine immunization services at public health facilities. Households that belong to low socio-economic status groups had to travel longer distance to get to health facilities consequently incurring some transportation cost. The mean expenditures on service charge for routine immunization services (mostly informal payments) and transportation were US$1.84 and US$1.27 respectively. Logistic regression showed that access to routine immunization was positively related to socio-economic status and negatively related to distant of a household to a health facility. Ability to pay affects access to services, even when such services are free at point of consumption with lower socio-economic status groups having less access to services and also having other constraints such as transportation. Hence, innovative provision methods that will bring routine immunization services closer to the people and eliminate all formal and informal user fees for routine immunization will help to increase and improve equitable coverage with routine immunization services.

Factors Affecting Detection of Hepatitis E Virus on Canadian Retail Pork Chops and Pork Livers Assayed Using Real-Time RT-PCR.

PubMed

Wilhelm, B J; Leblanc, D; Avery, B; Pearl, D L; Houde, A; Rajić, A; McEwen, S A

2016-03-01

We collected 599 Canadian retail pork chops and 283 pork livers routinely (usually weekly) from April 2011 to March 2012 using the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) retail sampling platform. Samples were assayed using validated real-time (q) reverse transcriptase polymerase chain reaction (RT-PCR) and nested classical RT-PCR for the detection of hepatitis E virus (HEV), porcine enteric calicivirus (PEC) and rotavirus (RV). The presence of Escherichia coli, Salmonella spp. and Campylobacter spp. was measured on a subset of our samples. Exact logistic regression models were fitted for predictors for HEV detection, for each assay. For both assays, sample type (pork chop versus liver) was a significant predictor for HEV RNA detection. For nested classical RT-PCR but not qRT-PCR, region of sample collection was a significant predictor (P = 0.008) of HEV detection. Odds of HEV detection were greatest in spring relative to other seasons. E. coli was a significant predictor for HEV RNA detection using the qRT-PCR (P = 0.03). Overall, the prevalence of E. coli, Salmonella spp. and Campylobacter spp. was significantly greater than HEV, PEC or RV on our retail pork samples. Our sparse data set for the detection of PEC and RV precluded modelling of risk factors for the detection of these viruses. © 2015 Zoonoses and Public Health © 2015 Her Majesty the Queen in Right of Canada Reproduced with the permission of the Minister of the Public Health Agency of Canada.

[Factors associated with the use of dental health services].

PubMed

Dho, María Silvina

2018-02-01

This paper seeks to analyze the factors associated with the use of dental health services (UDHS) by adults in the city of Corrientes, Argentina. A cross-sectional study was conducted. Information concerning the study variables was collected via a home survey. The sample size was established with a 95% confidence interval level (381 individuals). A simple random sampling design was used, which was complemented with a non-probability quota sampling. The data was analyzed using SPSS version 21.0 and Epidat version 3.1 softwares. Socio-economic level, dental health coverage, perception of oral health care, perception of oral health, knowledge about oral health, and oral hygiene habits were significantly associated with the UDHS over the last twelve months. These same factors, excluding dental health coverage and knowledge about oral health, were associated with the UDHS for routine dental check-ups. Measures should be implemented to increase the UDHS for prevention purposes in men and women of all socio-economic levels, particularly in less-privileged individuals.

Optimization and Standardization of Fluorescent Cell Barcoding for Multiplexed Flow Cytometric Phenotyping

PubMed Central

Giudice, Valentina; Feng, Xingmin; Kajigaya, Sachiko; Young, Neal S.; Biancotto, Angélique

2017-01-01

Fluorescent cell barcoding (FCB) is a cell-based multiplexing technique for high-throughput flow cytometry. Barcoded samples can be stained and acquired collectively, minimizing staining variability and antibody consumption, and decreasing required sample volumes. Combined with functional measurements, FCB can be used for drug screening, signaling profiling, and cytokine detection, but technical issues are present. We optimized the FCB technique for routine utilization using DyLight 350, DyLight 800, Pacific Orange, and CBD500 for barcoding six, nine, or 36 human peripheral blood specimens. Working concentrations of FCB dyes ranging from 0 to 500 μg/ml were tested, and viability dye staining was optimized to increase robustness of data. A five-color staining with surface markers for Vβ usage analysis in CD4+ and CD8+ T cells was achieved in combination with nine sample barcoding. We provide improvements of the FCB technique that should be useful for multiplex drug screening and for lymphocyte characterization and perturbations in the diagnosis and during the course of disease. PMID:28692789

Recovery and Stability of Δ9-Tetrahydrocannabinol Using the Oral-Eze® Oral Fluid Collection System and Intercept® Oral Specimen Collection Device.

PubMed

Samano, Kimberly L; Anne, Lakshmi; Johnson, Ted; Tang, Kenneth; Sample, R H Barry

2015-10-01

Oral fluid (OF) is increasingly used for clinical, forensic and workplace drug testing as an alternative to urine. Uncertainties surrounding OF collection device performance, drug stability and testing reproducibility may be partially responsible for delays in the implementation of OF testing in regulated drug testing programs. Stability of Δ(9)-tetrahydrocannabinol (THC) fortified and authentic specimens was examined after routine collection, transport and laboratory testing. Acceptable recovery and stability were observed when THC-fortified OF (1.5 and 4.5 ng/mL) was applied to Oral-Eze devices. Neat OF samples collected with Oral-Eze, processed per the package insert, and fortified with THC (3 and 6 ng/mL) were stable (±20%) at room temperature (21-25°C), refrigerated (2-8°C) and frozen (-25 to -15°C) conditions up to 1 month, while samples collected with Intercept devices showed decreases at refrigerated and room temperatures. After long-term refrigerated or frozen storage, maximum reductions in THC concentrations were 42% for Oral-Eze and 69% for Intercept. After ≥1 year frozen storage, 80.7% of laboratory specimens positive for THC (3 ng/mL cut-off) by GC-MS were reconfirmed positive (within 25%), with an average THC decrease of 4.2%. Specimens (n = 47) processed with Oral-Eze (diluted) and tested via enzyme immunoassay were concordant with LC-MS-MS results and showed 100% sensitivity and 95% specificity. Paired specimens collected with Oral-Eze and Intercept exhibited 98% overall agreement between the immunoassay test systems. Collectively, these data demonstrate consistent and reproducible recovery and stability of THC in OF after collection, transport and laboratory testing using the Oral-Eze OF Collection System. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Evaluation of quality-control data collected by the U.S. Geological Survey for routine water-quality activities at the Idaho National Laboratory and vicinity, southeastern Idaho, 2002-08

USGS Publications Warehouse

Rattray, Gordon W.

2014-01-01

Quality-control (QC) samples were collected from 2002 through 2008 by the U.S. Geological Survey, in cooperation with the U.S. Department of Energy, to ensure data robustness by documenting the variability and bias of water-quality data collected at surface-water and groundwater sites at and near the Idaho National Laboratory. QC samples consisted of 139 replicates and 22 blanks (approximately 11 percent of the number of environmental samples collected). Measurements from replicates were used to estimate variability (from field and laboratory procedures and sample heterogeneity), as reproducibility and reliability, of water-quality measurements of radiochemical, inorganic, and organic constituents. Measurements from blanks were used to estimate the potential contamination bias of selected radiochemical and inorganic constituents in water-quality samples, with an emphasis on identifying any cross contamination of samples collected with portable sampling equipment. The reproducibility of water-quality measurements was estimated with calculations of normalized absolute difference for radiochemical constituents and relative standard deviation (RSD) for inorganic and organic constituents. The reliability of water-quality measurements was estimated with pooled RSDs for all constituents. Reproducibility was acceptable for all constituents except dissolved aluminum and total organic carbon. Pooled RSDs were equal to or less than 14 percent for all constituents except for total organic carbon, which had pooled RSDs of 70 percent for the low concentration range and 4.4 percent for the high concentration range. Source-solution and equipment blanks were measured for concentrations of tritium, strontium-90, cesium-137, sodium, chloride, sulfate, and dissolved chromium. Field blanks were measured for the concentration of iodide. No detectable concentrations were measured from the blanks except for strontium-90 in one source solution and one equipment blank collected in September and October 2004, respectively. The detectable concentrations of strontium-90 in the blanks probably were from a small source of strontium-90 contamination or large measurement variability, or both. Order statistics and the binomial probability distribution were used to estimate the magnitude and extent of any potential contamination bias of tritium, strontium-90, cesium-137, sodium, chloride, sulfate, dissolved chromium, and iodide in water-quality samples. These statistical methods indicated that, with (1) 87 percent confidence, contamination bias of cesium-137 and sodium in 60 percent of water-quality samples was less than the minimum detectable concentration or reporting level; (2) 92‒94 percent confidence, contamination bias of tritium, strontium-90, chloride, sulfate, and dissolved chromium in 70 percent of water-quality samples was less than the minimum detectable concentration or reporting level; and (3) 75 percent confidence, contamination bias of iodide in 50 percent of water-quality samples was less than the reporting level for iodide. These results support the conclusion that contamination bias of water-quality samples from sample processing, storage, shipping, and analysis was insignificant and that cross-contamination of perched groundwater samples collected with bailers during 2002–08 was insignificant.

External evaluation of the Dimension Vista 1500® intelligent lab system.

PubMed

Bruneel, Arnaud; Dehoux, Monique; Barnier, Anne; Boutten, Anne

2012-09-01

Dimension Vista® analyzer combines four technologies (photometry, nephelometry, V-LYTE® integrated multisensor potentiometry, and LOCI® chemiluminescence) into one high-throughput system. We assessed analytical performance of assays routinely performed in our emergency laboratory according to the VALTEC protocol, and practicability. Precision was good for most parameters. Analytical domain was large and suitable for undiluted analysis in most clinical settings encountered in our hospital. Data were comparable and correlated to our routine analyzers (Roche Modular DP®, Abbott AXSYM®, Siemens Dimension® RxL, and BN ProSpec®). Performance of nephelometric and LOCI modules was excellent. Functional sensitivity of high-sensitivity C-reactive protein and cardiac troponin I were 0.165 mg/l and 0.03 ng/ml, respectively (coefficient of variation; CV < 10%). The influence of interfering substances (i.e., hemoglobin, bilirubin, or lipids) was moderate, and Dimension Vista® specifically alerted for interference according to HIL (hemolysis, icterus, lipemia) indices. Good instrument performance and full functionality (no reagent or sample carryover in the conditions evaluated, effective sample-volume detection, and clot detection) were confirmed. Simulated routine testing demonstrated excellent practicability, throughput, ease of use of software and security. Performance and practicability of Dimension Vista® are highly suitable for both routine and emergency use. Since no volume detection and thus no warning is available on limited sample racks, pediatric samples require special caution to the Siemens protocol to be analyzed in secured conditions. Our experience in routine practice is also discussed, i.e., the impact of daily workload, "manual" steps resulting from dilutions and pediatric samples, maintenances, flex hydration on instrument's performance on throughput and turnaround time. © 2012 Wiley Periodicals, Inc.

PopAffiliator: online calculator for individual affiliation to a major population group based on 17 autosomal short tandem repeat genotype profile.

PubMed

Pereira, Luísa; Alshamali, Farida; Andreassen, Rune; Ballard, Ruth; Chantratita, Wasun; Cho, Nam Soo; Coudray, Clotilde; Dugoujon, Jean-Michel; Espinoza, Marta; González-Andrade, Fabricio; Hadi, Sibte; Immel, Uta-Dorothee; Marian, Catalin; Gonzalez-Martin, Antonio; Mertens, Gerhard; Parson, Walther; Perone, Carlos; Prieto, Lourdes; Takeshita, Haruo; Rangel Villalobos, Héctor; Zeng, Zhaoshu; Zhivotovsky, Lev; Camacho, Rui; Fonseca, Nuno A

2011-09-01

Because of their sensitivity and high level of discrimination, short tandem repeat (STR) maker systems are currently the method of choice in routine forensic casework and data banking, usually in multiplexes up to 15-17 loci. Constraints related to sample amount and quality, frequently encountered in forensic casework, will not allow to change this picture in the near future, notwithstanding the technological developments. In this study, we present a free online calculator named PopAffiliator ( http://cracs.fc.up.pt/popaffiliator ) for individual population affiliation in the three main population groups, Eurasian, East Asian and sub-Saharan African, based on genotype profiles for the common set of STRs used in forensics. This calculator performs affiliation based on a model constructed using machine learning techniques. The model was constructed using a data set of approximately fifteen thousand individuals collected for this work. The accuracy of individual population affiliation is approximately 86%, showing that the common set of STRs routinely used in forensics provide a considerable amount of information for population assignment, in addition to being excellent for individual identification.

Activity Settings and Daily Routines in Preschool Classrooms: Diverse Experiences in Early Learning Settings for Low-Income Children

ERIC Educational Resources Information Center

Fuligni, Allison Sidle; Howes, Carollee; Huang, Yiching; Hong, Sandra Soliday; Lara-Cinisomo, Sandraluz

2012-01-01

This paper examines activity settings and daily classroom routines experienced by 3- and 4-year-old low-income children in public center-based preschool programs, private center-based programs, and family child care homes. Two daily routine profiles were identified using a time-sampling coding procedure: a High Free-Choice pattern in which…

Rapid MALDI-TOF Mass Spectrometry Strain Typing during a Large Outbreak of Shiga-Toxigenic Escherichia coli

PubMed Central

Christner, Martin; Trusch, Maria; Rohde, Holger; Kwiatkowski, Marcel; Schlüter, Hartmut; Wolters, Manuel; Aepfelbacher, Martin; Hentschke, Moritz

2014-01-01

Background In 2011 northern Germany experienced a large outbreak of Shiga-Toxigenic Escherichia coli O104:H4. The large amount of samples sent to microbiology laboratories for epidemiological assessment highlighted the importance of fast and inexpensive typing procedures. We have therefore evaluated the applicability of a MALDI-TOF mass spectrometry based strategy for outbreak strain identification. Methods Specific peaks in the outbreak strain’s spectrum were identified by comparative analysis of archived pre-outbreak spectra that had been acquired for routine species-level identification. Proteins underlying these discriminatory peaks were identified by liquid chromatography tandem mass spectrometry and validated against publicly available databases. The resulting typing scheme was evaluated against PCR genotyping with 294 E. coli isolates from clinical samples collected during the outbreak. Results Comparative spectrum analysis revealed two characteristic peaks at m/z 6711 and m/z 10883. The underlying proteins were found to be of low prevalence among genome sequenced E. coli strains. Marker peak detection correctly classified 292 of 293 study isolates, including all 104 outbreak isolates. Conclusions MALDI-TOF mass spectrometry allowed for reliable outbreak strain identification during a large outbreak of Shiga-Toxigenic E. coli. The applied typing strategy could probably be adapted to other typing tasks and might facilitate epidemiological surveys as part of the routine pathogen identification workflow. PMID:25003758

Monocyte chemotactic protein-3: possible involvement in apical periodontitis chemotaxis.

PubMed

Dezerega, A; Osorio, C; Mardones, J; Mundi, V; Dutzan, N; Franco, M; Gamonal, J; Oyarzún, A; Overall, C M; Hernández, M

2010-10-01

To study the expression of monocyte chemotactic protein-3 (MCP-3, also known as chemokine CCL-7) in tissue from apical lesions (AL) and to associate MCP-3 expression with symptomatic or asymptomatic apical periodontitis. To determine the expression of MCP-3 in AL, biopsies obtained during tooth extraction procedures were fixed, subjected to routine processing and diagnosed as apical granuloma (AG) (n = 7) or radicular cyst (RC) (n = 5). As controls, apical periodontal ligament (PDL) specimens from healthy premolars extracted for orthodontics reasons were included (n = 7). All specimens were immunostained for MCP-3 and examined under a light microscope. In addition, homogenates from AL (n = 14) and healthy PDL samples (n = 7) were studied through immunowestern blot. Finally, periapical exudates samples were collected from root canals of teeth having diagnosis of symptomatic (n = 14) and asymptomatic apical periodontitis (n = 14) during routine endodontic treatments and analysed by immunowestern blot and densitometry.   MCP-3 was detected in AG and RC and localized mainly to inflammatory leucocytes, whereas no expression was observed in healthy PDLs. MCP-3 was also detected in periapical exudate, and its levels were significantly higher in symptomatic than in asymptomatic apical periodontitis. MCP-3 was expressed in AL and its levels associated with clinical symptoms. MCP-3 might play a role in disease pathogenesis, possibly by stimulating mononuclear chemotaxis. © 2010 International Endodontic Journal.

The significance of routines in nursing practice.

PubMed

Rytterström, Patrik; Unosson, Mitra; Arman, Maria

2011-12-01

The aim of this study was to illuminate the significance of routines in nursing practice. Clinical nursing is performed under the guidance of routines to varying degrees. In the nursing literature, routine is described as having both negative and positive aspects, but use of the term is inconsistent, and empirical evidence is sparse. In the research on organisational routines, a distinction is made between routine as a rule and routine as action. A qualitative design using a phenomenological-hermeneutic approach. Data collection from three focus groups focused on nurses' experience of routines. Seventeen individual interviews from a previous study focusing on caring culture were also analysed in a secondary qualitative analysis. All participants were employed as 'qualified nursing pool' nurses. Routines are experienced as pragmatic, obstructive and meaningful. The aim of the pragmatic routine was to ensure that daily working life works; this routine is practised more on the basis of rational arguments and obvious intentions. The obstructive routine had negative consequences for nursing practice and was described as nursing losing its humanity and violating the patient's integrity. The meaningful routine involved becoming one with the routine and for the nurses, it felt right and meaningful to adapt to it. Routines become meaningful when the individual action is in harmony with the cultural pattern on which the nursing work is based. Instead of letting contemporary practice passively become routine, routines can be assessed and developed using research and theoretical underpinnings as a starting point for nursing practice. Leaders have a special responsibility to develop and support meaningful routines. One approach could be to let wards examine their routines from a patient perspective on the basis of the themes of pragmatic, meaningful and obstructive routine. © 2010 Blackwell Publishing Ltd.

Vaccination Week in the Americas, 2011: an opportunity to assess the routine vaccination program in the Bolivarian Republic of Venezuela.

PubMed

Sánchez, Daniel; Sodha, Samir V; Kurtis, Hannah J; Ghisays, Gladys; Wannemuehler, Kathleen A; Danovaro-Holliday, M Carolina; Ropero-Álvarez, Alba María

2015-04-17

Vaccination Week in the Americas (VWA) is an annual initiative in countries and territories of the Americas every April to highlight the work of national expanded programs on immunization (EPI) and increase access to vaccination services for high-risk population groups. In 2011, as part of VWA, Venezuela targeted children aged less than 6 years in 25 priority border municipalities using social mobilization to increase institution-based vaccination. Implementation of social communication activities was decentralized to the local level. We conducted a survey in one border municipality of Venezuela to evaluate the outcome of VWA 2011 and provide a snapshot of the overall performance of the routine EPI at that level. We conducted a coverage survey, using stratified cluster sampling, in the Venezuelan municipality of Bolivar (bordering Colombia) in August 2011. We collected information for children aged <6 years through caregiver interviews and transcription of vaccination card data. We estimated each child's eligibility to receive a specific vaccine dose during VWA 2011 and whether or not they were actually vaccinated during VWA activities. We also estimated baseline vaccination coverage, timeliness and 95% confidence intervals (CI), and used chi-square tests to compare coverage across age cohorts, taking into account the sampling design. We surveyed 839 children from 698 households; 93% of children had a vaccination card. Among households surveyed, 216 (31%) caregivers reported having heard about a vaccination activity during April or May 2011. Of the 528 children eligible to receive a vaccine during VWA, 24% received at least one dose, while 13% received all doses due. Overall, baseline coverage with routine vaccines, as measured by the survey, was >85%, with a few exceptions. Low levels of VWA awareness among caregivers probably contributed to the limited vaccination of eligible children during the VWA activities in Bolivar in 2011. However, vaccine coverage for most EPI vaccines was high. Additionally, high vaccination card availability and high participation in VWA among those caregivers aware of it in 2011 suggest public trust in the EPI program in the municipality. Health authorities have used survey findings to inform changes to the routine EPI and better VWA implementation in subsequent years.

Environmental stress in the Gulf of Mexico and its potential impact on public health

PubMed Central

Turner, J.; Walter, L.; Lathan, N.; Thorpe, D.; Ogbevoen, P.; Daye, J.; Alcorn, D.; Wilson, S.; Semien, J.; Richard, T.; Johnson, T.; McCabe, K.; Estrada, J.J.; Galvez, F.; Velasco, C.; Reiss, K.

2017-01-01

The Deepwater Horizon (DWH) oil spill in the Gulf of Mexico was the largest maritime oil spill in history resulting in the accumulation of genotoxic substances in the air, soil, and water. This has potential far-reaching health impacts on cleanup field workers and on the populations living in the contaminated coastal areas. We have employed portable airborne particulate matter samplers (SKC Biosampler Impinger) and a genetically engineered bacterial reporter system (umu-ChromoTest from EBPI) to determine levels of genotoxicity of air samples collected from highly contaminated areas of coastal Louisiana including Grand Isle, Port Fourchon, and Elmer's Island in the spring, summer and fall of 2011, 2012, 2013 and 2014. Air samples collected from a non-contaminated area, Sea Rim State Park, Texas, served as a control for background airborne genotoxic particles. In comparison to controls, air samples from the contaminated areas demonstrated highly significant increases in genotoxicity with the highest values registered during the month of July in 2011, 2013, and 2014, in all three locations. This seasonal trend was disrupted in 2012, when the highest genotoxicity values were detected in October, which correlated with hurricane Isaac landfall in late August of 2012, about five weeks before a routine collection of fall air samples. Our data demonstrate: (i) high levels of air genotoxicity in the monitored areas over last four years post DWH oil spill; (ii) airborne particulate genotoxicity peaks in summers and correlates with high temperatures and high humidity; and (iii) this seasonal trend was disrupted by the hurricane Isaac landfall, which further supports the concept of a continuous negative impact of the oil spill in this region. PMID:26745734

Environmental stress in the Gulf of Mexico and its potential impact on public health.

PubMed

Singleton, B; Turner, J; Walter, L; Lathan, N; Thorpe, D; Ogbevoen, P; Daye, J; Alcorn, D; Wilson, S; Semien, J; Richard, T; Johnson, T; McCabe, K; Estrada, J J; Galvez, F; Velasco, C; Reiss, K

2016-04-01

The Deepwater Horizon (DWH) oil spill in the Gulf of Mexico was the largest maritime oil spill in history resulting in the accumulation of genotoxic substances in the air, soil, and water. This has potential far-reaching health impacts on cleanup field workers and on the populations living in the contaminated coastal areas. We have employed portable airborne particulate matter samplers (SKC Biosampler Impinger) and a genetically engineered bacterial reporter system (umu-ChromoTest from EBPI) to determine levels of genotoxicity of air samples collected from highly contaminated areas of coastal Louisiana including Grand Isle, Port Fourchon, and Elmer's Island in the spring, summer and fall of 2011, 2012, 2013 and 2014. Air samples collected from a non-contaminated area, Sea Rim State Park, Texas, served as a control for background airborne genotoxic particles. In comparison to controls, air samples from the contaminated areas demonstrated highly significant increases in genotoxicity with the highest values registered during the month of July in 2011, 2013, and 2014, in all three locations. This seasonal trend was disrupted in 2012, when the highest genotoxicity values were detected in October, which correlated with hurricane Isaac landfall in late August of 2012, about five weeks before a routine collection of fall air samples. Our data demonstrate: (i) high levels of air genotoxicity in the monitored areas over last four years post DWH oil spill; (ii) airborne particulate genotoxicity peaks in summers and correlates with high temperatures and high humidity; and (iii) this seasonal trend was disrupted by the hurricane Isaac landfall, which further supports the concept of a continuous negative impact of the oil spill in this region. Copyright © 2015 Elsevier Inc. All rights reserved.

Evaluation of Chicken IgY Generated Against Canine Parvovirus Viral-Like Particles and Development of Enzyme-Linked Immunosorbent Assay and Immunochromatographic Assay for Canine Parvovirus Detection.

PubMed

He, Jinxin; Wang, Yuan; Sun, Shiqi; Zhang, Xiaoying

2015-11-01

Immunoglobulin Y (IgY) antibodies were generated against canine parvovirus virus-like particles (CPV-VLPs) antigen using chickens. Anti-CPV-VLPs-IgY was extracted from hen egg yolk and used for developing enzyme-linked immunosorbent assay (ELISA) and immunochromatographic assay (ICA) for the detection of CPV in dog feces. The cutoff negative values for anti-CPV-VLPs-IgY were determined using negative fecal samples (already confirmed by polymerase chain reaction [PCR]). In both ELISA and ICA, there was no cross-reaction with other diarrheal pathogens. Thirty-four fecal samples were collected from dogs with diarrhea, of which 26.47% were confirmed as CPV-positive samples by PCR, while 29.41% and 32.35% of the samples were found to be positive by ELISA and ICA, respectively. The developed ELISA and ICA exhibited 97.06% and 94.12% conformity with PCR. Higher sensitivity and specificity were observed for IgY-based ELISA and ICA. Thus, they could be suitable for routine use in the diagnosis of CPV in dogs.

Detection of genogroup IV norovirus in wastewater and river water in Japan.

PubMed

Kitajima, M; Haramoto, E; Phanuwan, C; Katayama, H; Ohgaki, S

2009-11-01

To test wastewater and river water in Japan for genogroup IV norovirus (GIV NoV). Influent and effluent samples from a wastewater treatment plant and the Tamagawa River water samples were collected monthly for a year. The water samples were concentrated by the adsorption-elution method, using an HA electronegative filter with acid rinse procedure, followed by quantitative detection of GIV NoV using TaqMan-based real-time RT-PCR. Both wastewater and river water samples showed a high positive ratio of GIV NoV during winter and spring. The highest concentration in wastewater and river water was 6.9 x 10(4) and 1.5 x 10(4) copies l(-1), respectively. Presence of GIV NoV in the environments demonstrates that not only GI and GII NoVs but also GIV strains are circulating and that routine monitoring of GIV NoV in water environments is recommended to understand its epidemics, environmental distribution and potential health risks. This is the first study providing quantitative data on the occurrence of GIV NoV in environmental water over a 1-year period.

An eight-year survey of the intestinal parasites of carnivores, hoofed mammals, primates, ratites and reptiles in the Ljubljana zoo in Slovenia.

PubMed

Kvapil, Pavel; Kastelic, Marjan; Dovc, Alenka; Bartova, Eva; Cizek, Petr; Lima, Natacha; Strus, Spela

2017-04-21

Problems with parasitic infections and their interspecies transmissions are common in zoological gardens and could pose serious health damage to captive animals. This study presents results of eight-year monitoring of intestinal parasites in animals from Zoo Ljubljana, Slovenia. A total of 741 faecal samples from 40 animal species were collected two to four times per year and examined microscopically. Intestinal parasites were detected in 45% of samples, with detection of helminths (Cestoda, Nematoda - Ascaridida, Enoplida, Strongylida, Oxyurida, Rhabditida and Trichurida) and protists (Apicomplexa and Ciliophora) in 25% and 13% of samples, respectively; mixed infection was found in 7% of samples. The mostly infected were ungulates (61%), followed by reptiles (44%), ratites (29%), primates (22%) and carnivores (7%). During the observation period, the number of infected animal species increased from 8 to 25. This is the first long-term monitoring study of intestinal parasites in zoo animals from Slovenia. Routine monitoring of parasitic infection and regular deworming and hygienic measures are necessary to prevent gastrointestinal infections in captive animals.

Critical evaluation of monitoring strategy for the multi-residue determination of 90 chiral and achiral micropollutants in effluent wastewater.

PubMed

Petrie, Bruce; Proctor, Kathryn; Youdan, Jane; Barden, Ruth; Kasprzyk-Hordern, Barbara

2017-02-01

It is essential to monitor the release of organic micropollutants from wastewater treatment plants (WWTPs) for developing environmental risk assessment and assessing compliance with legislative regulation. In this study the impact of sampling strategy on the quantitative determination of micropollutants in effluent wastewater was investigated. An extended list of 90 chiral and achiral micropollutants representing a broad range of biological and physico-chemical properties were studied simultaneously for the first time. During composite sample collection micropollutants can degrade resulting in the under-estimation of concentration. Cooling collected sub-samples to 4°C stabilised ≥81 of 90 micropollutants to acceptable levels (±20% of the initial concentration) in the studied effluents. However, achieving stability for all micropollutants will require an integrated approach to sample collection (i.e., multi-bottle sampling with more than one stabilisation method applied). Full-scale monitoring of effluent revealed time-paced composites attained similar information to volume-paced composites (influent wastewater requires a sampling mode responsive to flow variation). The option of monitoring effluent using time-paced composite samplers is advantageous as not all WWTPs have flow controlled samplers or suitable sites for deploying portable flow meters. There has been little research to date on the impact of monitoring strategy on the determination of chiral micropollutants at the enantiomeric level. Variability in wastewater flow results in a dynamic hydraulic retention time within the WWTP (and upstream sewerage system). Despite chiral micropollutants being susceptible to stereo-selective degradation, no diurnal variability in their enantiomeric distribution was observed. However, unused medication can be directly disposed into the sewer network creating short-term (e.g., daily) changes to their enantiomeric distribution. As enantio-specific toxicity is observed in the environment, similar resolution of enantio-selective analysis to more routinely applied achiral methods is needed throughout the monitoring period for accurate risk assessment. Copyright © 2016 British Geological Survey, NERC. Published by Elsevier B.V. All rights reserved.

Value of Routine Dengue Diagnostic Tests in Urine and Saliva Specimens

PubMed Central

Andries, Anne-Claire; Duong, Veasna; Ly, Sowath; Cappelle, Julien; Kim, Kim Srorn; Lorn Try, Patrich; Ros, Sopheaktra; Ong, Sivuth; Huy, Rekol; Horwood, Paul; Flamand, Marie; Sakuntabhai, Anavaj; Tarantola, Arnaud; Buchy, Philippe

2015-01-01

Background Dengue laboratory diagnosis is essentially based on detection of the virus, its components or antibodies directed against the virus in blood samples. Blood, however, may be difficult to draw in some patients, especially in children, and sampling during outbreak investigations or epidemiological studies may face logistical challenges or limited compliance to invasive procedures from subjects. The aim of this study was to assess the possibility of using saliva and urine samples instead of blood for dengue diagnosis. Methodology/Principal Findings Serial plasma, urine and saliva samples were collected at several time-points between the day of admission to hospital until three months after the onset of fever in children with confirmed dengue disease. Quantitative RT-PCR, NS1 antigen capture and ELISA serology for anti-DENV antibody (IgG, IgM and IgA) detection were performed in parallel on the three body fluids. RT-PCR and NS1 tests demonstrated an overall sensitivity of 85.4%/63.4%, 41.6%/14.5% and 39%/28.3%, in plasma, urine and saliva specimens, respectively. When urine and saliva samples were collected at the same time-points and tested concurrently, the diagnostic sensitivity of RNA and NS1 detection assays was 69.1% and 34.4%, respectively. IgG/IgA detection assays had an overall sensitivity of 54.4%/37.4%, 38.5%/26.8% and 52.9%/28.6% in plasma, urine and saliva specimens, respectively. IgM were detected in 38.1% and 36% of the plasma and saliva samples but never in urine. Conclusions Although the performances of the different diagnostic methods were not as good in saliva and urine as in plasma specimens, the results obtained by qRT-PCR and by anti-DENV antibody ELISA could well justify the use of these two body fluids to detect dengue infection in situations when the collection of blood specimens is not possible. PMID:26406240

Fixing Formalin: A Method to Recover Genomic-Scale DNA Sequence Data from Formalin-Fixed Museum Specimens Using High-Throughput Sequencing

PubMed Central

Hykin, Sarah M.; Bi, Ke; McGuire, Jimmy A.

2015-01-01

For 150 years or more, specimens were routinely collected and deposited in natural history collections without preserving fresh tissue samples for genetic analysis. In the case of most herpetological specimens (i.e. amphibians and reptiles), attempts to extract and sequence DNA from formalin-fixed, ethanol-preserved specimens—particularly for use in phylogenetic analyses—has been laborious and largely ineffective due to the highly fragmented nature of the DNA. As a result, tens of thousands of specimens in herpetological collections have not been available for sequence-based phylogenetic studies. Massively parallel High-Throughput Sequencing methods and the associated bioinformatics, however, are particularly suited to recovering meaningful genetic markers from severely degraded/fragmented DNA sequences such as DNA damaged by formalin-fixation. In this study, we compared previously published DNA extraction methods on three tissue types subsampled from formalin-fixed specimens of Anolis carolinensis, followed by sequencing. Sufficient quality DNA was recovered from liver tissue, making this technique minimally destructive to museum specimens. Sequencing was only successful for the more recently collected specimen (collected ~30 ybp). We suspect this could be due either to the conditions of preservation and/or the amount of tissue used for extraction purposes. For the successfully sequenced sample, we found a high rate of base misincorporation. After rigorous trimming, we successfully mapped 27.93% of the cleaned reads to the reference genome, were able to reconstruct the complete mitochondrial genome, and recovered an accurate phylogenetic placement for our specimen. We conclude that the amount of DNA available, which can vary depending on specimen age and preservation conditions, will determine if sequencing will be successful. The technique described here will greatly improve the value of museum collections by making many formalin-fixed specimens available for genetic analysis. PMID:26505622

Fixing Formalin: A Method to Recover Genomic-Scale DNA Sequence Data from Formalin-Fixed Museum Specimens Using High-Throughput Sequencing.

PubMed

Hykin, Sarah M; Bi, Ke; McGuire, Jimmy A

2015-01-01

For 150 years or more, specimens were routinely collected and deposited in natural history collections without preserving fresh tissue samples for genetic analysis. In the case of most herpetological specimens (i.e. amphibians and reptiles), attempts to extract and sequence DNA from formalin-fixed, ethanol-preserved specimens-particularly for use in phylogenetic analyses-has been laborious and largely ineffective due to the highly fragmented nature of the DNA. As a result, tens of thousands of specimens in herpetological collections have not been available for sequence-based phylogenetic studies. Massively parallel High-Throughput Sequencing methods and the associated bioinformatics, however, are particularly suited to recovering meaningful genetic markers from severely degraded/fragmented DNA sequences such as DNA damaged by formalin-fixation. In this study, we compared previously published DNA extraction methods on three tissue types subsampled from formalin-fixed specimens of Anolis carolinensis, followed by sequencing. Sufficient quality DNA was recovered from liver tissue, making this technique minimally destructive to museum specimens. Sequencing was only successful for the more recently collected specimen (collected ~30 ybp). We suspect this could be due either to the conditions of preservation and/or the amount of tissue used for extraction purposes. For the successfully sequenced sample, we found a high rate of base misincorporation. After rigorous trimming, we successfully mapped 27.93% of the cleaned reads to the reference genome, were able to reconstruct the complete mitochondrial genome, and recovered an accurate phylogenetic placement for our specimen. We conclude that the amount of DNA available, which can vary depending on specimen age and preservation conditions, will determine if sequencing will be successful. The technique described here will greatly improve the value of museum collections by making many formalin-fixed specimens available for genetic analysis.

Study design requirements for RNA sequencing-based breast cancer diagnostics.

PubMed

Mer, Arvind Singh; Klevebring, Daniel; Grönberg, Henrik; Rantalainen, Mattias

2016-02-01

Sequencing-based molecular characterization of tumors provides information required for individualized cancer treatment. There are well-defined molecular subtypes of breast cancer that provide improved prognostication compared to routine biomarkers. However, molecular subtyping is not yet implemented in routine breast cancer care. Clinical translation is dependent on subtype prediction models providing high sensitivity and specificity. In this study we evaluate sample size and RNA-sequencing read requirements for breast cancer subtyping to facilitate rational design of translational studies. We applied subsampling to ascertain the effect of training sample size and the number of RNA sequencing reads on classification accuracy of molecular subtype and routine biomarker prediction models (unsupervised and supervised). Subtype classification accuracy improved with increasing sample size up to N = 750 (accuracy = 0.93), although with a modest improvement beyond N = 350 (accuracy = 0.92). Prediction of routine biomarkers achieved accuracy of 0.94 (ER) and 0.92 (Her2) at N = 200. Subtype classification improved with RNA-sequencing library size up to 5 million reads. Development of molecular subtyping models for cancer diagnostics requires well-designed studies. Sample size and the number of RNA sequencing reads directly influence accuracy of molecular subtyping. Results in this study provide key information for rational design of translational studies aiming to bring sequencing-based diagnostics to the clinic.

Analysis of fingerprint samples, testing various conditions, for forensic DNA identification.

PubMed

Ostojic, Lana; Wurmbach, Elisa

2017-01-01

Fingerprints can be of tremendous value for forensic biology, since they can be collected from a wide variety of evident types, such as handles of weapons, tools collected in criminal cases, and objects with no apparent staining. DNA obtained from fingerprints varies greatly in quality and quantity, which ultimately affects the quality of the resulting STR profiles. Additional difficulties can arise when fingerprint samples show mixed STR profiles due to the handling of multiple persons. After applying a tested protocol for sample collection (swabbing with 5% Triton X-100), DNA extraction (using an enzyme that works at elevated temperatures), and PCR amplification (AmpFlSTR® Identifiler® using 31cycles) extensive analysis was performed to better understand the challenges inherent to fingerprint samples, with the ultimate goal of developing valuable profiles (≥50% complete). The impact of time on deposited fingerprints was investigated, revealing that while the quality of profiles deteriorated, full STR profiles could still be obtained from samples after 40days of storage at room temperature. By comparing the STR profiles from fingerprints of the dominant versus the non-dominant hand, we found a slightly better quality from the non-dominant hand, which was not always significant. Substrates seem to have greater effects on fingerprints. Tests on glass, plastic, paper and metal (US Quarter dollar, made of Cu and Ni), common substrates in offices and homes, showed best results for glass, followed by plastic and paper, while almost no profiles were obtained from a Quarter dollar. Important for forensic casework, we also assessed three-person mixtures of touched fingerprint samples. Unlike routinely used approaches for sampling evidence, the surface of an object (bottle) was sectioned into six equal parts and separate samples were taken from each section. The samples were processed separately for DNA extraction and STR amplification. The results included a few single source profiles and distinguishable two person mixtures. On average, this approach led to two profiles ≥50% complete per touched object. Some STR profiles were obtained more than once thereby increasing the confidence. Copyright © 2016 The Chartered Society of Forensic Sciences. Published by Elsevier Ireland Ltd. All rights reserved.

Automated Microflow NMR: Routine Analysis of Five-Microliter Samples

PubMed Central

Jansma, Ariane; Chuan, Tiffany; Geierstanger, Bernhard H.; Albrecht, Robert W.; Olson, Dean L.; Peck, Timothy L.

2006-01-01

A microflow CapNMR probe double-tuned for 1H and 13C was installed on a 400-MHz NMR spectrometer and interfaced to an automated liquid handler. Individual samples dissolved in DMSO-d6 are submitted for NMR analysis in vials containing as little as 10 μL of sample. Sets of samples are submitted in a low-volume 384-well plate. Of the 10 μL of sample per well, as with vials, 5 μL is injected into the microflow NMR probe for analysis. For quality control of chemical libraries, 1D NMR spectra are acquired under full automation from 384-well plates on as many as 130 compounds within 24 h using 128 scans per spectrum and a sample-to-sample cycle time of ∼11 min. Because of the low volume requirements and high mass sensitivity of the microflow NMR system, 30 nmol of a typical small molecule is sufficient to obtain high-quality, well-resolved, 1D proton or 2D COSY NMR spectra in ∼6 or 20 min of data acquisition time per experiment, respectively. Implementation of pulse programs with automated solvent peak identification and suppression allow for reliable data collection, even for samples submitted in fully protonated DMSO. The automated microflow NMR system is controlled and monitored using web-based software. PMID:16194121

Factors associated with long turnaround time for early infant diagnosis of HIV in Myanmar.

PubMed

Thiha, Soe; Shewade, Hemant Deepak; Philip, Sairu; Aung, Thet Ko; Kyaw, Nang Thu Thu; Oo, Myo Minn; Kyaw, Khine Wut Yee; Wint War, May; Oo, Htun Nyunt

2017-01-01

A previous review of early infant diagnosis (EID) using polymerase chain reaction technology (PCR) under integrated HIV care (IHC) program in Myanmar revealed a low uptake of timely (within 6 to 8 weeks of babies' age) EID and a long turnaround time (TAT) of receiving results. This study aimed to determine the proportion and factors associated with the composite outcome of a long TAT (≥7 weeks; from sample collection to receipt of result by mother) or nonreceipt of result among HIV-exposed babies whose blood samples were collected for PCR at <9 months of age under the IHC program, Myanmar (2013-15). Cohort study involving record review of routinely collected data. A predictive Poisson regression model with robust variance estimates was fitted for risk factors of long TAT or nonreceipt of result. Blood samples of 1 000 babies were collected; among them, long TAT or nonreceipt of results was seen in 690 (69%), and this was more than 50% across all subgroups. Babies with a mother's CD4 count of 100-350 cells/mm 3 at enrollment [adjusted RR (0.95 confidence intervals, CI): 0.8 (0.7, 0.9)] had a 20% lower risk of long TAT or nonreceipt of results when compared with ≥350 cells/mm 3 . Distance between ART center and PCR facility ≥105 km [adjusted RR (0.95 CI): 1.2 (1.1, 1.4)], when compared with <105 km, was associated with 20% higher risk of long TAT or nonreceipt of results. The proportion of babies with long TAT or nonreceipt of result by the mother was high. Point-of-care testing for EID may reduce TAT/nonreceipt of results by the mother. Health system, laboratory, and logistic factors such as sample transportation, laboratory procedures, and result dispatching associated with long TAT should be further explored.

Sampling scheme for pyrethroids on multiple surfaces on commercial aircrafts.

PubMed

Mohan, Krishnan R; Weisel, Clifford P

2010-06-01

A wipe sampler for the collection of permethrin from soft and hard surfaces has been developed for use in aircraft. "Disinsection" or application of pesticides, predominantly pyrethrods, inside commercial aircraft is routinely required by some countries and is done on an as-needed basis by airlines resulting in potential pesticide dermal and inhalation exposures to the crew and passengers. A wipe method using filter paper and water was evaluated for both soft and hard aircraft surfaces. Permethrin was analyzed by GC/MS after its ultrasonication extraction from the sampling medium into hexane and volume reduction. Recoveries, based on spraying known levels of permethrin, were 80-100% from table trays, seat handles and rugs; and 40-50% from seat cushions. The wipe sampler is easy to use, requires minimum training, is compatible with the regulations on what can be brought through security for use on commercial aircraft, and readily adaptable for use in residential and other settings.

Quantitative determination of the major saponin mixture bacoside A in Bacopa monnieri by HPLC.

PubMed

Deepak, M; Sangli, G K; Arun, P C; Amit, A

2005-01-01

Bacoside A, the putative bioactive component of the Indian medicinal plant Bacopa monnieri, was found to be a mixture of saponins with bacoside A3 (1), bacopaside II (2), jujubogenin isomer of bacopasaponin C (3) and bacopasaponin C (4) as major constituents. An HPLC method together with an optimised extraction procedure was developed for the estimation of 1-4 in B. monnieri to enable standardisation of the latter. Concentration ranges of the analytes in samples of B. monnieri collected from different regions of India were 0.14-0.85% (w/w) (1), 0.12-0.69% (2), 0.05-0.72% (3) and 0.05-0.44% (4). The importance of using bacoside A, with known concentrations of 1-4, as a reference standard for the routine analysis of B. monnieri is highlighted. Two common flavonoids, luteolin and apigenin, were present in all samples of B. monnieri.

Routine single particle CryoEM sample and grid characterization by tomography

PubMed Central

Noble, Alex J; Brasch, Julia; Chase, Jillian; Acharya, Priyamvada; Tan, Yong Zi; Zhang, Zhening; Kim, Laura Y; Scapin, Giovanna; Rapp, Micah; Eng, Edward T; Rice, William J; Cheng, Anchi; Negro, Carl J; Shapiro, Lawrence; Kwong, Peter D; Jeruzalmi, David; des Georges, Amedee; Potter, Clinton S

2018-01-01

Single particle cryo-electron microscopy (cryoEM) is often performed under the assumption that particles are not adsorbed to the air-water interfaces and in thin, vitreous ice. In this study, we performed fiducial-less tomography on over 50 different cryoEM grid/sample preparations to determine the particle distribution within the ice and the overall geometry of the ice in grid holes. Surprisingly, by studying particles in holes in 3D from over 1000 tomograms, we have determined that the vast majority of particles (approximately 90%) are adsorbed to an air-water interface. The implications of this observation are wide-ranging, with potential ramifications regarding protein denaturation, conformational change, and preferred orientation. We also show that fiducial-less cryo-electron tomography on single particle grids may be used to determine ice thickness, optimal single particle collection areas and strategies, particle heterogeneity, and de novo models for template picking and single particle alignment. PMID:29809143

Estimation of the Rate of Unrecognized Cross-Contamination with Mycobacterium tuberculosis in London Microbiology Laboratories

PubMed Central

Ruddy, M.; McHugh, T. D.; Dale, J. W.; Banerjee, D.; Maguire, H.; Wilson, P.; Drobniewski, F.; Butcher, P.; Gillespie, S. H.

2002-01-01

Isolates from patients with confirmed tuberculosis from London were collected over 2.5 years between 1995 and 1997. Restriction fragment length polymorphism (RFLP) analysis was performed by the international standard technique as part of a multicenter epidemiological study. A total of 2,779 samples representing 2,500 individual patients from 56 laboratories were examined. Analysis of these samples revealed a laboratory cross-contamination rate of between 0.54%, when only presumed cases of cross-contamination were considered, and 0.93%, when presumed and possible cases were counted. Previous studies suggest an extremely wide range of laboratory cross-contamination rates of between 0.1 and 65%. These data indicate that laboratory cross-contamination has not been a common problem in routine practice in the London area, but in several incidents patients did receive full courses of therapy that were probably unnecessary. PMID:12409381

Second trimester serum cortisol and preterm birth: an analysis by timing and subtype.

PubMed

Bandoli, Gretchen; Jelliffe-Pawlowski, Laura L; Feuer, Sky K; Liang, Liang; Oltman, Scott P; Paynter, Randi; Ross, Kharah M; Schetter, Christine Dunkel; Ryckman, Kelli K; Chambers, Christina D

2018-05-24

We hypothesized second trimester serum cortisol would be higher in spontaneous preterm births compared to provider-initiated (previously termed 'medically indicated') preterm births. We used a nested case-control design with a sample of 993 women with live births. Cortisol was measured from serum samples collected as part of routine prenatal screening. We tested whether mean-adjusted cortisol fold-change differed by gestational age at delivery or preterm birth subtype using multivariable linear regression. An inverse association between cortisol and gestational age category (trend p = 0.09) was observed. Among deliveries prior to 37 weeks, the mean-adjusted cortisol fold-change values were highest for preterm premature rupture of the membranes (1.10), followed by premature labor (1.03) and provider-initiated preterm birth (1.01), although they did not differ statistically. Cortisol continues to be of interest as a marker of future preterm birth. Augmentation with additional biomarkers should be explored.

A survey on uncertainty in bioassay measurements carried out within the OMINEX project.

PubMed

Hurtgen, C; Cossonnet, C

2003-01-01

One of the topics covered by the OMINEX (Optimisation of Monitoring for Internal Exposure) project was to look at the bioassay measurements performed in the European laboratories. Questionnaires on bioassay measurements by alpha spectrometry or inductively coupled plasma-mass spectrometry (ICP-MS) were sent to European laboratories. The main objective was to collect information on analytical procedures and on the uncertainties associated with bioassay results. Alpha spectrometry is the technique most often used for the determination of alpha emitters, such as actinides in biological samples. ICP-MS is not used much as yet for routine measurements of actinides in biological samples, but is very sensitive for measurements of long-lived radionuclides. The different parameters influencing the uncertainties on the results and the minimum detectable amount have been investigated. Optimum conditions for achieving low result uncertainties and high sensitivity are given for alpha spectrometry and ICP-MS.

Histopathological study of the mite biting (Dermanyssus gallinae) in poultry skin

PubMed Central

Hobbenaghi, Rahim; Tavassoli, Mousa; Alimehr, Manochehr; Shokrpoor, Sara; Ghorbanzadeghan, Mohammad

2012-01-01

The red mite of poultry, Dremanyssus gallinae, is the most important hematophagous ectoparasite of poultry. In this study, pathologic changes of its biting on the poultry skin have been investigated. Thirty-two (Control = 16 and Treatment = 16) four weeks old Ross broilers (308) were infested with the mite on skin of hock joins. Samples were collected after 1, 24, 72 hours and 10 days. The skin samples were fixed in 10% buffered formalin and histological sections were prepared using routine Hematoxylin & Eosin staining method. Results showed that in all cases, except within first hour of infestation, lymphocytic infiltration was always a constant pathologic feature. Necrosis of feather's follicles was a prominent pathologic feature ensued due to vascular disturbances and resulted in loss of feather. Hyperkeratosis, parakeratosis and acanthosis were observed after 72 hours. These findings reveal that mite biting induces local epidermal hyperplasia. PMID:25610570

Histopathological study of the mite biting (Dermanyssus gallinae) in poultry skin.

PubMed

Hobbenaghi, Rahim; Tavassoli, Mousa; Alimehr, Manochehr; Shokrpoor, Sara; Ghorbanzadeghan, Mohammad

2012-01-01

The red mite of poultry, Dremanyssus gallinae, is the most important hematophagous ectoparasite of poultry. In this study, pathologic changes of its biting on the poultry skin have been investigated. Thirty-two (Control = 16 and Treatment = 16) four weeks old Ross broilers (308) were infested with the mite on skin of hock joins. Samples were collected after 1, 24, 72 hours and 10 days. The skin samples were fixed in 10% buffered formalin and histological sections were prepared using routine Hematoxylin & Eosin staining method. Results showed that in all cases, except within first hour of infestation, lymphocytic infiltration was always a constant pathologic feature. Necrosis of feather's follicles was a prominent pathologic feature ensued due to vascular disturbances and resulted in loss of feather. Hyperkeratosis, parakeratosis and acanthosis were observed after 72 hours. These findings reveal that mite biting induces local epidermal hyperplasia.

Prevalence of psychiatric disorders in the Texas juvenile correctional system.

PubMed

Harzke, Amy Jo; Baillargeon, Jacques; Baillargeon, Gwen; Henry, Judith; Olvera, Rene L; Torrealday, Ohiana; Penn, Joseph V; Parikh, Rajendra

2012-04-01

Most studies assessing the burden of psychiatric disorders in juvenile correctional facilities have been based on small or male-only samples or have focused on a single disorder. Using electronic data routinely collected by the Texas juvenile correctional system and its contracted medical provider organization, we estimated the prevalence of selected psychiatric disorders among youths committed to Texas juvenile correctional facilities between January 1, 2004, and December 31, 2008 (N = 11,603). Ninety-eight percent were diagnosed with at least one of the disorders. Highest estimated prevalence was for conduct disorder (83.2%), followed by any substance use disorder (75.6%), any bipolar disorder (19.4%), attention-deficit/hyperactivity disorder (18.3%), and any depressive disorder (12.6%). The estimated prevalence of psychiatric disorders among these youths was exceptionally high and showed patterns by sex, race/ethnicity, and age that were both consistent and inconsistent with other juvenile justice samples.

Fast Bayesian Inference of Copy Number Variants using Hidden Markov Models with Wavelet Compression

PubMed Central

Wiedenhoeft, John; Brugel, Eric; Schliep, Alexander

2016-01-01

By integrating Haar wavelets with Hidden Markov Models, we achieve drastically reduced running times for Bayesian inference using Forward-Backward Gibbs sampling. We show that this improves detection of genomic copy number variants (CNV) in array CGH experiments compared to the state-of-the-art, including standard Gibbs sampling. The method concentrates computational effort on chromosomal segments which are difficult to call, by dynamically and adaptively recomputing consecutive blocks of observations likely to share a copy number. This makes routine diagnostic use and re-analysis of legacy data collections feasible; to this end, we also propose an effective automatic prior. An open source software implementation of our method is available at http://schlieplab.org/Software/HaMMLET/ (DOI: 10.5281/zenodo.46262). This paper was selected for oral presentation at RECOMB 2016, and an abstract is published in the conference proceedings. PMID:27177143

The cost structure of routine infant immunization services: a systematic analysis of six countries

PubMed Central

Geng, Fangli; Suharlim, Christian; Brenzel, Logan; Resch, Stephen C; Menzies, Nicolas A

2017-01-01

Abstract Little information exists on the cost structure of routine infant immunization services in low- and middle-income settings. Using a unique dataset of routine infant immunization costs from six countries, we estimated how costs were distributed across budget categories and programmatic activities, and investigated how the cost structure of immunization sites varied by country and site characteristics. The EPIC study collected data on routine infant immunization costs from 319 sites in Benin, Ghana, Honduras, Moldova, Uganda, Zambia, using a standardized approach. For each country, we estimated the economic costs of infant immunization by administrative level, budget category, and programmatic activity from a programme perspective. We used regression models to describe how costs within each category were related to site operating characteristics and efficiency level. Site-level costs (incl. vaccines) represented 77–93% of national routine infant immunization costs. Labour and vaccine costs comprised 14–69% and 13–69% of site-level cost, respectively. The majority of site-level resources were devoted to service provision (facility-based or outreach), comprising 48–78% of site-level costs across the six countries. Based on the regression analyses, sites with the highest service volume had a greater proportion of costs devoted to vaccines, with vaccine costs per dose relatively unaffected by service volume but non-vaccine costs substantially lower with higher service volume. Across all countries, more efficient sites (compared with sites with similar characteristics) had a lower cost share devoted to labour. The cost structure of immunization services varied substantially between countries and across sites within each country, and was related to site characteristics. The substantial variation observed in this sample suggests differences in operating model for otherwise similar sites, and further understanding of these differences could reveal approaches to improve efficiency and performance of immunization sites. PMID:28575193

The cost structure of routine infant immunization services: a systematic analysis of six countries.

PubMed

Geng, Fangli; Suharlim, Christian; Brenzel, Logan; Resch, Stephen C; Menzies, Nicolas A

2017-10-01

Little information exists on the cost structure of routine infant immunization services in low- and middle-income settings. Using a unique dataset of routine infant immunization costs from six countries, we estimated how costs were distributed across budget categories and programmatic activities, and investigated how the cost structure of immunization sites varied by country and site characteristics. The EPIC study collected data on routine infant immunization costs from 319 sites in Benin, Ghana, Honduras, Moldova, Uganda, Zambia, using a standardized approach. For each country, we estimated the economic costs of infant immunization by administrative level, budget category, and programmatic activity from a programme perspective. We used regression models to describe how costs within each category were related to site operating characteristics and efficiency level. Site-level costs (incl. vaccines) represented 77-93% of national routine infant immunization costs. Labour and vaccine costs comprised 14-69% and 13-69% of site-level cost, respectively. The majority of site-level resources were devoted to service provision (facility-based or outreach), comprising 48-78% of site-level costs across the six countries. Based on the regression analyses, sites with the highest service volume had a greater proportion of costs devoted to vaccines, with vaccine costs per dose relatively unaffected by service volume but non-vaccine costs substantially lower with higher service volume. Across all countries, more efficient sites (compared with sites with similar characteristics) had a lower cost share devoted to labour. The cost structure of immunization services varied substantially between countries and across sites within each country, and was related to site characteristics. The substantial variation observed in this sample suggests differences in operating model for otherwise similar sites, and further understanding of these differences could reveal approaches to improve efficiency and performance of immunization sites. © The Author 2017. Published by Oxford University Press in association with The London School of Hygiene and Tropical Medicine.