DDN (Defense Data Network) Protocol Handbook. Volume 1. DoD Military Standard Protocols

DTIC Science & Technology

1985-12-01

official Military Standard communication protocols in use on the DDN are included, as are several ARPANET (Advanced Research Projects Agency Network... research protocols which are currently in use, and some protocols currently undergoing review. Tutorial information and auxiliary documents are also...compatible with DoD needs, by researchers wishing to improve the protocols, and by impleroentors of local area networks (LANs) wishing their

Validation of quantitative and qualitative methods for detecting allergenic ingredients in processed foods in Japan.

PubMed

Sakai, Shinobu; Adachi, Reiko; Akiyama, Hiroshi; Teshima, Reiko

2013-06-19

A labeling system for food allergenic ingredients was established in Japan in April 2002. To monitor the labeling, the Japanese government announced official methods for detecting allergens in processed foods in November 2002. The official methods consist of quantitative screening tests using enzyme-linked immunosorbent assays (ELISAs) and qualitative confirmation tests using Western blotting or polymerase chain reactions (PCR). In addition, the Japanese government designated 10 μg protein/g food (the corresponding allergenic ingredient soluble protein weight/food weight), determined by ELISA, as the labeling threshold. To standardize the official methods, the criteria for the validation protocol were described in the official guidelines. This paper, which was presented at the Advances in Food Allergen Detection Symposium, ACS National Meeting and Expo, San Diego, CA, Spring 2012, describes the validation protocol outlined in the official Japanese guidelines, the results of interlaboratory studies for the quantitative detection method (ELISA for crustacean proteins) and the qualitative detection method (PCR for shrimp and crab DNAs), and the reliability of the detection methods.

Prescriptions for uncomplicated malaria treatment among pregnant women in the Brazilian Amazon: evidences from the Mafalda Project.

PubMed

Luz, Tatiana Chama Borges; Miranda, Elaine Silva; Freitas, Letícia Figueira; Osório-de-Castro, Claudia Garcia Serpa

2013-06-01

To evaluate antimalarial prescriptions according to quality indicators and to describe adverse events reports among pregnant women with uncomplicated malaria. Descriptive study of medical files of pregnant women 15 years and older, residents in high-risk municipalities in the Brazilian Amazon. Antimalarial medicines were characterized by frequency of prescription, type of plasmodium and health care facilities where prescribing took place, and by possible adverse events. Variables were compared by Pearson's chi-square. A total of 262 medical files were evaluated. Most patients were diagnosed for Plasmodium vivax 71,2%. Chloroquine was the commonest prescribed antimalarial (65.6%). Of P. vivax prescriptions, 9.0%, and 16.2% of P. falciparum prescriptions presented antimalarials not recommended in the official protocol. Prescriptions for P. falciparum , in significantly higher proportion, did not adhere to the official protocol in regard to type of antimalarial and dose/duration of treatment (p = 0,001). They also lacked information on dose and dosing interval (p = 0,004). There were no significant differences among reference centers and basic health care units in respect to the prescribed antimalarials, to prescriptions containing antimalarials not recommended in the official protocol or in respect to lack of dosing information. Chloroquine was the antimalarial most related to the occurrence of adverse events. THE findings indicate that there are flaws in antimalarial prescribing for pregnant women, especially in respect to their adequacy to the official protocol.

First Results in the Use of Bovine Ear Notch Tag for Bovine Viral Diarrhoea Virus Detection and Genetic Analysis

PubMed Central

Quinet, Christian; Czaplicki, Guy; Dion, Elise; Dal Pozzo, Fabiana; Kurz, Anke; Saegerman, Claude

2016-01-01

Background Infection due to bovine viral diarrhoea virus (BVDV) is endemic in most cattle-producing countries throughout the world. The key elements of a BVDV control programme are biosecurity, elimination of persistently infected animals and surveillance. Bovine viral diarrhoea (BVD) is a notifiable disease in Belgium and an official eradication programme started from January 2015, based on testing ear notches sampled during the official identification and registration of calves at birth. An antigen-capture ELISA test based on the detection of BVDV Erns protein is used. Ear notch sample may also be used to characterize the genotype of the calf when appropriate elution/dilution buffer is added. Both BVDV antigen-ELISA analysis and animal traceability could be performed. Methodology With regards to the reference protocol used in the preparation of ear notch samples, alternative procedures were tested in terms of BVDV analytic sensitivity, diagnostic sensitivity and specificity, as well as quality and purity of animal DNA. Principal Findings/Significance The Allflex DNA Buffer D showed promising results in BVDV diagnosis and genome analyses, opening new perspectives for the livestock industry by the exploitation of the animal genome. Due to the high number of cattle involved in the Belgian official BVDV eradication programme based on ear notch tags sample, a large database on both BVDV status of newborn calves and cattle genome could be created for subsequent different uses (e.g. traceability, determination of parentage, genetic signatures throughout the genome associated with particular traits) evolving through a more integrated animal health. PMID:27764130

7 CFR 51.17 - Official sampling.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 2 2010-01-01 2010-01-01 false Official sampling. 51.17 Section 51.17 Agriculture... Inspection Service § 51.17 Official sampling. Samples may be officially drawn by any duly authorized... time and place of the sampling and the brands or other identifying marks of the containers from which...

7 CFR 51.17 - Official sampling.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 2 2011-01-01 2011-01-01 false Official sampling. 51.17 Section 51.17 Agriculture... Inspection Service § 51.17 Official sampling. Samples may be officially drawn by any duly authorized... time and place of the sampling and the brands or other identifying marks of the containers from which...

[The characterization of biosolids produced by the San Fernando wastewater treatment plant in Itagui, Antioquia, Colombia].

PubMed

Bedoya-Urrego, Katherine; Acevedo-Ruíz, José M; Peláez-Jaramillo, Carlos A; Agudelo-López, Sonia Del Pilar

2013-01-01

ABSTRACT Objective This study was aimed at evaluating pertinent physicochemical and microbiological (bacteria and parasites) parameters regarding the biosolids produced by the San Fernando wastewater treatment plant (WWTP) in Itagui, Antioquia, Colombia. Methods Twelve samples were collected and evaluated every month from January to December during 2010. The chemical, physical and microbiological tests followed the protocol described in Colombian technical guideline 5167. The protocol described in Mexican official Norm 004 (with some modifications) was used for identifying helminth ova and assessing their viability. Results All samples proved positive for Ascarislumbricoides, viable ova count ranging from 4 to 22 eggs/2gTS. Both Salmonella and Enterobacteriawere detected in all samples evaluated, the latter having 3,000 colony forming unit (CFU)/g minimum concentration. Biosolid sample values met the heavy metal concentration requirement established by national guidelines. There was no statistical association between rainfall and the pathogen's presence in the biosolids. Conclusion Our results suggested that the biosolids being produced by the San Fernando wastewater treatment plant (WWTP) could be used as organic fertilizer; however they should be treated/sanitized to meet the stipulations in Colombian technical guideline 5167.

Protocol for Addressing Induced Seismicity Associated with Enhanced Geothermal Systems

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

Majer, Ernie; Nelson, James; Robertson-Tait, Ann

2012-01-01

This Protocol is a living guidance document for geothermal developers, public officials, regulators and the general public that provides a set of general guidelines detailing useful steps to evaluate and manage the effects of induced seismicity related to EGS projects.

22 CFR 2.5 - Records.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 22 Foreign Relations 1 2013-04-01 2013-04-01 false Records. 2.5 Section 2.5 Foreign Relations DEPARTMENT OF STATE GENERAL PROTECTION OF FOREIGN DIGNITARIES AND OTHER OFFICIAL PERSONNEL § 2.5 Records. The Chief of Protocol shall maintain as a part of the official files of the Department of State a cumulative...

22 CFR 2.5 - Records.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 22 Foreign Relations 1 2014-04-01 2014-04-01 false Records. 2.5 Section 2.5 Foreign Relations DEPARTMENT OF STATE GENERAL PROTECTION OF FOREIGN DIGNITARIES AND OTHER OFFICIAL PERSONNEL § 2.5 Records. The Chief of Protocol shall maintain as a part of the official files of the Department of State a cumulative...

22 CFR 2.5 - Records.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 22 Foreign Relations 1 2011-04-01 2011-04-01 false Records. 2.5 Section 2.5 Foreign Relations DEPARTMENT OF STATE GENERAL PROTECTION OF FOREIGN DIGNITARIES AND OTHER OFFICIAL PERSONNEL § 2.5 Records. The Chief of Protocol shall maintain as a part of the official files of the Department of State a cumulative...

22 CFR 2.5 - Records.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 22 Foreign Relations 1 2010-04-01 2010-04-01 false Records. 2.5 Section 2.5 Foreign Relations DEPARTMENT OF STATE GENERAL PROTECTION OF FOREIGN DIGNITARIES AND OTHER OFFICIAL PERSONNEL § 2.5 Records. The Chief of Protocol shall maintain as a part of the official files of the Department of State a cumulative...

9 CFR 312.10 - Official mark for maintaining the identity and integrity of samples.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 9 Animals and Animal Products 2 2010-01-01 2010-01-01 false Official mark for maintaining the identity and integrity of samples. 312.10 Section 312.10 Animals and Animal Products FOOD SAFETY AND... § 312.10 Official mark for maintaining the identity and integrity of samples. The official mark for use...

9 CFR 312.10 - Official mark for maintaining the identity and integrity of samples.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 9 Animals and Animal Products 2 2013-01-01 2013-01-01 false Official mark for maintaining the identity and integrity of samples. 312.10 Section 312.10 Animals and Animal Products FOOD SAFETY AND... § 312.10 Official mark for maintaining the identity and integrity of samples. The official mark for use...

9 CFR 312.10 - Official mark for maintaining the identity and integrity of samples.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 9 Animals and Animal Products 2 2014-01-01 2014-01-01 false Official mark for maintaining the identity and integrity of samples. 312.10 Section 312.10 Animals and Animal Products FOOD SAFETY AND... § 312.10 Official mark for maintaining the identity and integrity of samples. The official mark for use...

9 CFR 312.10 - Official mark for maintaining the identity and integrity of samples.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 9 Animals and Animal Products 2 2012-01-01 2012-01-01 false Official mark for maintaining the identity and integrity of samples. 312.10 Section 312.10 Animals and Animal Products FOOD SAFETY AND... § 312.10 Official mark for maintaining the identity and integrity of samples. The official mark for use...

50 CFR 260.59 - How officially drawn samples are to be identified.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 7 2010-10-01 2010-10-01 false How officially drawn samples are to be identified. 260.59 Section 260.59 Wildlife and Fisheries NATIONAL MARINE FISHERIES SERVICE, NATIONAL OCEANIC... drawn samples are to be identified. Officially drawn samples shall be marked by the inspector or...

In Brief: Kyoto Protocol moves forward

NASA Astrophysics Data System (ADS)

Showstack, Randy

2004-10-01

The Russian cabinet's 30 September endorsement of the Kyoto Protocol to the United Nations Framework Convention on Climate Change (UNFCCC) likely clears the way for the treaty's ratification by that country's parliament and for its entry into force. The protocol enters into force when not less than 55 Parties to the Convention, including industrialized countries (so called ``Annex I Parties'') which accounted in total for at least 55 % of the total carbon dioxide emissions for 1990 from that group, officially have agreed to the treaty.

9 CFR 381.112 - Official mark for maintaining the identity and integrity of samples.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 9 Animals and Animal Products 2 2011-01-01 2011-01-01 false Official mark for maintaining the identity and integrity of samples. 381.112 Section 381.112 Animals and Animal Products FOOD SAFETY AND... Inspection Act shall bear the designation “Sample Seal” accompanied by the official USDA logo as shown below...

9 CFR 381.112 - Official mark for maintaining the identity and integrity of samples.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 9 Animals and Animal Products 2 2010-01-01 2010-01-01 false Official mark for maintaining the identity and integrity of samples. 381.112 Section 381.112 Animals and Animal Products FOOD SAFETY AND... mark for maintaining the identity and integrity of samples. The official mark for use in sealing...

9 CFR 381.112 - Official mark for maintaining the identity and integrity of samples.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 9 Animals and Animal Products 2 2013-01-01 2013-01-01 false Official mark for maintaining the identity and integrity of samples. 381.112 Section 381.112 Animals and Animal Products FOOD SAFETY AND... mark for maintaining the identity and integrity of samples. The official mark for use in sealing...

9 CFR 381.112 - Official mark for maintaining the identity and integrity of samples.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 9 Animals and Animal Products 2 2012-01-01 2012-01-01 false Official mark for maintaining the identity and integrity of samples. 381.112 Section 381.112 Animals and Animal Products FOOD SAFETY AND... mark for maintaining the identity and integrity of samples. The official mark for use in sealing...

9 CFR 381.112 - Official mark for maintaining the identity and integrity of samples.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 9 Animals and Animal Products 2 2014-01-01 2014-01-01 false Official mark for maintaining the identity and integrity of samples. 381.112 Section 381.112 Animals and Animal Products FOOD SAFETY AND... mark for maintaining the identity and integrity of samples. The official mark for use in sealing...

[Protocol for the treatment of severe acute pancreatitis with necrosis].

PubMed

Barreda, Luis; Targarona, Javier; Rodriguez, César

2005-01-01

The Severe Acute Pancreatic Unit of Edgardo Rebagliati Martins National Hospital was officially created in the year 2000. Up to date, we have cared for more than 195 patients with Pancreatic Necrosis. All of them have been treated under a management protocol presented by us. This has helped us to standardize treatment and also to compare results with work groups around the world. This Protocol comes from our own experience and that of our colleagues abroad with a wide knowledge in this kind of pathology abroad, with whom we maintain close ties.

Assuring bridge safety and serviceability in Europe

DOT National Transportation Integrated Search

2010-08-01

U.S. engineers need advanced tools and protocols to better assess and assure safety and serviceability of bridges. The Federal Highway Administration, American Association of State Highway and Transportation Officials, and National Cooperative Highwa...

Easy, fast and environmental friendly method for the simultaneous extraction of the 16 EPA PAHs using magnetic molecular imprinted polymers (mag-MIPs).

PubMed

Villar-Navarro, Mercedes; Martín-Valero, María Jesús; Fernández-Torres, Rut Maria; Callejón-Mochón, Manuel; Bello-López, Miguel Ángel

2017-02-15

An easy and environmental friendly method, based on the use of magnetic molecular imprinted polymers (mag-MIPs) is proposed for the simultaneous extraction of the 16 U.S. EPA polycyclic aromatic hydrocarbons (PAHs) priority pollutants. The mag-MIPs based extraction protocol is simple, more sensitive and low organic solvent consuming compared to official methods and also adequate for those PAHs more retained in the particulate matter. The new proposed extraction method followed by HPLC determination has been validated and applied to different types of water samples: tap water, river water, lake water and mineral water. Copyright © 2017 Elsevier B.V. All rights reserved.

US screening of international travelers for radioactive contamination after the Japanese nuclear plant disaster in March 2011.

PubMed

Wilson, Todd; Chang, Arthur; Berro, Andre; Still, Aaron; Brown, Clive; Demma, Andrew; Nemhauser, Jeffrey; Martin, Colleen; Salame-Alfie, Adela; Fisher-Tyler, Frieda; Smith, Lee; Grady-Erickson, Onalee; Alvarado-Ramy, Francisco; Brunette, Gary; Ansari, Armin; McAdam, David; Marano, Nina

2012-10-01

On March 11, 2011, a magnitude 9.0 earthquake and subsequent tsunami damaged nuclear reactors at the Fukushima Daiichi complex in Japan, resulting in radionuclide release. In response, US officials augmented existing radiological screening at its ports of entry (POEs) to detect and decontaminate travelers contaminated with radioactive materials. During March 12 to 16, radiation screening protocols detected 3 travelers from Japan with external radioactive material contamination at 2 air POEs. Beginning March 23, federal officials collaborated with state and local public health and radiation control authorities to enhance screening and decontamination protocols at POEs. Approximately 543 000 (99%) travelers arriving directly from Japan at 25 US airports were screened for radiation contamination from March 17 to April 30, and no traveler was detected with contamination sufficient to require a large-scale public health response. The response highlighted synergistic collaboration across government levels and leveraged screening methods already in place at POEs, leading to rapid protocol implementation. Policy development, planning, training, and exercising response protocols and the establishment of federal authority to compel decontamination of travelers are needed for future radiological responses. Comparison of resource-intensive screening costs with the public health yield should guide policy decisions, given the historically low frequency of contaminated travelers arriving during radiological disasters.

Volcano-hazards Education for Emergency Officials Through Study Trip Learning—The 2013 Colombia-USA Bi-national Exchange

NASA Astrophysics Data System (ADS)

Driedger, C. L.; Ewert, J. W.

2015-12-01

A central tenant of hazard communication is that colleagues with principal responsibilities for emergency planning and response sustain a 'long-term conversation' that builds trust, and increases understanding of hazards and successful protocols. This requires well maintained partnerships among a broad spectrum of officials who are knowledgeable about volcano hazards; credible within their communities; and who have personal and professional stake in their community's safety. It can require that volcano scientists facilitate learning opportunities for partners in emergency management who have little or no familiarity with eruption response. Scientists and officials from Colombia and the Cascades region of the United States recognized that although separated by geographic and cultural distance, their communities faced similar hazards from lahars. For the purpose of sharing best practices, the 2013 Colombia-USA Bi-national Exchange was organized by the US Geological Survey (USGS) and the Washington Emergency Management Division, with support from the US Agency for International Development (USAID). Nine Colombian emergency officials and scientists visited the U.S. to observe emergency response planning and protocols and to view the scale of a potential lahar disaster at Mount Rainier. Ten U.S. delegates visited Colombia to absorb best practices developed after the catastrophic 1985 eruption and lahars at Nevado del Ruiz. They observed the devastation and spoke with survivors, first responders, and emergency managers responsible for post-disaster recovery efforts. Delegates returned to their nations energized and with improved knowledge about volcanic crises and effective mitigation and response. In the U.S., trainings, hazard signage, evacuation routes and assembly points, and community websites have gained momentum. Colombian officials gained a deeper appreciation of and a renewed commitment to response planning, education, and disaster preparedness.

Extension of the validation of AOAC Official Method 2005.06 for dc-GTX2,3: interlaboratory study.

PubMed

Ben-Gigirey, Begoña; Rodríguez-Velasco, María L; Gago-Martínez, Ana

2012-01-01

AOAC Official Method(SM) 2005.06 for the determination of saxitoxin (STX)-group toxins in shellfish by LC with fluorescence detection with precolumn oxidation was previously validated and adopted First Action following a collaborative study. However, the method was not validated for all key STX-group toxins, and procedures to quantify some of them were not provided. With more STX-group toxin standards commercially available and modifications to procedures, it was possible to overcome some of these difficulties. The European Union Reference Laboratory for Marine Biotoxins conducted an interlaboratory exercise to extend AOAC Official Method 2005.06 validation for dc-GTX2,3 and to compile precision data for several STX-group toxins. This paper reports the study design and the results obtained. The performance characteristics for dc-GTX2,3 (intralaboratory and interlaboratory precision, recovery, and theoretical quantification limit) were evaluated. The mean recoveries obtained for dc-GTX2,3 were, in general, low (53.1-58.6%). The RSD for reproducibility (RSD(r)%) for dc-GTX2,3 in all samples ranged from 28.2 to 45.7%, and HorRat values ranged from 1.5 to 2.8. The article also describes a hydrolysis protocol to convert GTX6 to NEO, which has been proven to be useful for the quantification of GTX6 while the GTX6 standard is not available. The performance of the participant laboratories in the application of this method was compared with that obtained from the original collaborative study of the method. Intralaboratory and interlaboratory precision data for several STX-group toxins, including dc-NEO and GTX6, are reported here. This study can be useful for those laboratories determining STX-group toxins to fully implement AOAC Official Method 2005.06 for official paralytic shellfish poisoning control. However the overall quantitative performance obtained with the method was poor for certain toxins.

7 CFR 800.99 - Checkweighing sacked grain.

Code of Federal Regulations, 2010 CFR

2010-01-01

... the instructions. (c) Protecting samples and data. Official personnel and other employees of an agency or the Service shall protect official weight samples and data from manipulation, substitution, and improper and careless handling which might deprive the samples and sample data of their representativeness...

7 CFR 800.99 - Checkweighing sacked grain.

Code of Federal Regulations, 2011 CFR

2011-01-01

... the instructions. (c) Protecting samples and data. Official personnel and other employees of an agency or the Service shall protect official weight samples and data from manipulation, substitution, and improper and careless handling which might deprive the samples and sample data of their representativeness...

Monitoring forest areas from continental to territorial levels using a sample of medium spatial resolution satellite imagery

NASA Astrophysics Data System (ADS)

Eva, Hugh; Carboni, Silvia; Achard, Frédéric; Stach, Nicolas; Durieux, Laurent; Faure, Jean-François; Mollicone, Danilo

A global systematic sampling scheme has been developed by the UN FAO and the EC TREES project to estimate rates of deforestation at global or continental levels at intervals of 5 to 10 years. This global scheme can be intensified to produce results at the national level. In this paper, using surrogate observations, we compare the deforestation estimates derived from these two levels of sampling intensities (one, the global, for the Brazilian Amazon the other, national, for French Guiana) to estimates derived from the official inventories. We also report the precisions that are achieved due to sampling errors and, in the case of French Guiana, compare such precision with the official inventory precision. We extract nine sample data sets from the official wall-to-wall deforestation map derived from satellite interpretations produced for the Brazilian Amazon for the year 2002 to 2003. This global sampling scheme estimate gives 2.81 million ha of deforestation (mean from nine simulated replicates) with a standard error of 0.10 million ha. This compares with the full population estimate from the wall-to-wall interpretations of 2.73 million ha deforested, which is within one standard error of our sampling test estimate. The relative difference between the mean estimate from sampling approach and the full population estimate is 3.1%, and the standard error represents 4.0% of the full population estimate. This global sampling is then intensified to a territorial level with a case study over French Guiana to estimate deforestation between the years 1990 and 2006. For the historical reference period, 1990, Landsat-5 Thematic Mapper data were used. A coverage of SPOT-HRV imagery at 20 m × 20 m resolution acquired at the Cayenne receiving station in French Guiana was used for year 2006. Our estimates from the intensified global sampling scheme over French Guiana are compared with those produced by the national authority to report on deforestation rates under the Kyoto protocol rules for its overseas department. The latter estimates come from a sample of nearly 17,000 plots analyzed from same spatial imagery acquired between year 1990 and year 2006. This sampling scheme is derived from the traditional forest inventory methods carried out by IFN (Inventaire Forestier National). Our intensified global sampling scheme leads to an estimate of 96,650 ha deforested between 1990 and 2006, which is within the 95% confidence interval of the IFN sampling scheme, which gives an estimate of 91,722 ha, representing a relative difference from the IFN of 5.4%. These results demonstrate that the intensification of the global sampling scheme can provide forest area change estimates close to those achieved by official forest inventories (<6%), with precisions of between 4% and 7%, although we only estimate errors from sampling, not from the use of surrogate data. Such methods could be used by developing countries to demonstrate that they are fulfilling requirements for reducing emissions from deforestation in the framework of an REDD (Reducing Emissions from Deforestation in Developing Countries) mechanism under discussion within the United Nations Framework Convention on Climate Change (UNFCCC). Monitoring systems at national levels in tropical countries can also benefit from pan-tropical and regional observations, to ensure consistency between different national monitoring systems.

Specification, Synthesis, and Verification of Software-based Control Protocols for Fault-Tolerant Space Systems

DTIC Science & Technology

2016-08-16

Force Research Laboratory Space Vehicles Directorate AFRL /RVSV 3550 Aberdeen Ave, SE 11. SPONSOR/MONITOR’S REPORT Kirtland AFB, NM 87117-5776 NUMBER...Ft Belvoir, VA 22060-6218 1 cy AFRL /RVIL Kirtland AFB, NM 87117-5776 2 cys Official Record Copy AFRL /RVSV/Richard S. Erwin 1 cy... AFRL -RV-PS- AFRL -RV-PS- TR-2016-0112 TR-2016-0112 SPECIFICATION, SYNTHESIS, AND VERIFICATION OF SOFTWARE-BASED CONTROL PROTOCOLS FOR FAULT-TOLERANT

Analytical methods for the determination of personal care products in human samples: an overview.

PubMed

Jiménez-Díaz, I; Zafra-Gómez, A; Ballesteros, O; Navalón, A

2014-11-01

Personal care products (PCPs) are organic chemicals widely used in everyday human life. Nowadays, preservatives, UV-filters, antimicrobials and musk fragrances are widely used PCPs. Different studies have shown that some of these compounds can cause adverse health effects, such as genotoxicity, which could even lead to mutagenic or carcinogenic effects, or estrogenicity because of their endocrine disruption activity. Due to the absence of official monitoring protocols, there is an increasing demand of analytical methods that allow the determination of those compounds in human samples in order to obtain more information regarding their behavior and fate in the human body. The complexity of the biological matrices and the low concentration levels of these compounds make necessary the use of advanced sample treatment procedures that afford both, sample clean-up, to remove potentially interfering matrix components, as well as the concentration of analytes. In the present work, a review of the more recent analytical methods published in the scientific literature for the determination of PCPs in human fluids and tissue samples, is presented. The work focused on sample preparation and the analytical techniques employed. Copyright © 2014 Elsevier B.V. All rights reserved.

The Observation of Bahasa Indonesia Official Computer Terms Implementation in Scientific Publication

NASA Astrophysics Data System (ADS)

Gunawan, D.; Amalia, A.; Lydia, M. S.; Muthaqin, M. I.

2018-03-01

The government of the Republic of Indonesia had issued a regulation to substitute computer terms in foreign language that have been used earlier into official computer terms in Bahasa Indonesia. This regulation was stipulated in Presidential Decree No. 2 of 2001 concerning the introduction of official computer terms in Bahasa Indonesia (known as Senarai Padanan Istilah/SPI). After sixteen years, people of Indonesia, particularly for academics, should have implemented the official computer terms in their official publications. This observation is conducted to discover the implementation of official computer terms usage in scientific publications which are written in Bahasa Indonesia. The data source used in this observation are the publications by the academics, particularly in computer science field. The method used in the observation is divided into four stages. The first stage is metadata harvesting by using Open Archive Initiative - Protocol for Metadata Harvesting (OAI-PMH). Second, converting the harvested document (in pdf format) to plain text. The third stage is text-preprocessing as the preparation of string matching. Then the final stage is searching the official computer terms based on 629 SPI terms by using Boyer-Moore algorithm. We observed that there are 240,781 foreign computer terms in 1,156 scientific publications from six universities. This result shows that the foreign computer terms are still widely used by the academics.

9 CFR 381.146 - Sampling at official establishments.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 9 Animals and Animal Products 2 2010-01-01 2010-01-01 false Sampling at official establishments. 381.146 Section 381.146 Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE, DEPARTMENT OF... Establishments; Processing Inspection and Other Reinspections; Processing Requirements § 381.146 Sampling at...

9 CFR 381.146 - Sampling at official establishments.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 9 Animals and Animal Products 2 2011-01-01 2011-01-01 false Sampling at official establishments. 381.146 Section 381.146 Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE, DEPARTMENT OF... Establishments; Processing Inspection and Other Reinspections; Processing Requirements § 381.146 Sampling at...

Short communication: Chemical and sensory characteristics of Canestrato di Moliterno cheese manufactured in spring.

PubMed

Trani, A; Gambacorta, G; Loizzo, P; Cassone, A; Faccia, M

2016-08-01

Canestrato di Moliterno is an Italian Protected Geographical Indication hard cheese, made in winter and spring from a mixture of ewe and goat milks, that has been poorly investigated. The present study was aimed at characterizing the cheese made in the warm season. Two series of samples, ripened in traditional rooms called fondaco as indicated in the official protocol of production, were taken from the main certified producers. The cheeses were analyzed for gross composition; proteolysis and lipolysis; volatile fraction; and organoleptic features. Gross composition was not completely homogeneous among the samples, but primary proteolysis and lipolysis were quite uniform. We observed variations in secondary proteolysis, likely caused by fluctuations in environmental conditions in the fondaco. The sensory profiles of the samples were homogeneous: the cheese was soluble, greasy, and adhesive, with a sheepfold and buttery odor. The main taste attributes were fermented, pungent, and bitter. Overall, the results of this study provide an initial contribution to the characterization of Canestrato di Moliterno, and could be used to improve marketing strategies. Copyright © 2016 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Rail-dbGaP: analyzing dbGaP-protected data in the cloud with Amazon Elastic MapReduce.

PubMed

Nellore, Abhinav; Wilks, Christopher; Hansen, Kasper D; Leek, Jeffrey T; Langmead, Ben

2016-08-15

Public archives contain thousands of trillions of bases of valuable sequencing data. More than 40% of the Sequence Read Archive is human data protected by provisions such as dbGaP. To analyse dbGaP-protected data, researchers must typically work with IT administrators and signing officials to ensure all levels of security are implemented at their institution. This is a major obstacle, impeding reproducibility and reducing the utility of archived data. We present a protocol and software tool for analyzing protected data in a commercial cloud. The protocol, Rail-dbGaP, is applicable to any tool running on Amazon Web Services Elastic MapReduce. The tool, Rail-RNA v0.2, is a spliced aligner for RNA-seq data, which we demonstrate by running on 9662 samples from the dbGaP-protected GTEx consortium dataset. The Rail-dbGaP protocol makes explicit for the first time the steps an investigator must take to develop Elastic MapReduce pipelines that analyse dbGaP-protected data in a manner compliant with NIH guidelines. Rail-RNA automates implementation of the protocol, making it easy for typical biomedical investigators to study protected RNA-seq data, regardless of their local IT resources or expertise. Rail-RNA is available from http://rail.bio Technical details on the Rail-dbGaP protocol as well as an implementation walkthrough are available at https://github.com/nellore/rail-dbgap Detailed instructions on running Rail-RNA on dbGaP-protected data using Amazon Web Services are available at http://docs.rail.bio/dbgap/ : anellore@gmail.com or langmea@cs.jhu.edu Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

Prehospital care training in a rapidly developing economy: a multi-institutional study.

PubMed

Vyas, Dinesh; Hollis, Michael; Abraham, Rohit; Rustagi, Neeti; Chandra, Siddharth; Malhotra, Ajai; Rajpurohit, Vikas; Purohit, Harshada; Pal, Ranabir

2016-06-01

The trauma pandemic is one of the leading causes of death worldwide but especially in rapidly developing economies. Perhaps, a common cause of trauma-related mortality in these settings comes from the rapid expansion of motor vehicle ownership without the corresponding expansion of national prehospital training in developed countries. The resulting road traffic injuries often never make it to the hospital in time for effective treatment, resulting in preventable disability and death. The current article examines the development of a medical first responder training program that has the potential to reduce this unnecessary morbidity and mortality. An intensive training workshop has been differentiated into two progressive tiers: acute trauma training (ATT) and broad trauma training (BTT) protocols. These four-hour and two-day protocols, respectively, allow for the mass education of laypersons-such as police officials, fire brigade, and taxi and/or ambulance drivers-who are most likely to interact first with prehospital victims. Over 750 ATT participants and 168 BTT participants were trained across three Indian educational institutions at Jodhpur and Jaipur. Trainees were given didactic and hands-on education in a series of critical trauma topics, in addition to pretraining and post-training self-assessments to rate clinical confidence across curricular topics. Two-sample t-test statistical analyses were performed to compare pretraining and post-training confidence levels. Program development resulted in recruitment of a variety of career backgrounds for enrollment in both our ATT and BTT workshops. The workshops were run by local physicians from a wide spectrum of medical specialties and previously ATT-trained police officials. Statistically significant improvements in clinical confidence across all curricular topics for ATT and BTT protocols were identified (P < 0.0001). In addition, improvement in confidence after BTT training was similar in Jodhpur compared with Jaipur. These results suggest a promising level of reliability and reproducibility across different geographic areas in rapidly developing settings. Program expansion can offer an exponential growth in the training rate of medical first responders, which can help curb the trauma-related mortality in rapidly developing economies. Future directions will include clinical competency assessments and further progressive differentiation into higher tiers of trauma expertise. Published by Elsevier Inc.

Comprehensive measurement of total nondigestible carbohydrates in foods by enzymatic-gravimetric method and liquid chromatography.

PubMed

Nishibata, Toyohide; Tashiro, Kouichi; Kanahori, Sumiko; Hashizume, Chieko; Kitagawa, Machiko; Okuma, Kazuhiro; Gordon, Dennis T

2009-09-09

Total nondigestible carbohydrate (NDC) in foods was determined by combining, not modifications, AOAC Official Methods 991.43, 2001.03, and 2002.02. Total NDC included insoluble dietary fiber (IDF) + high-molecular-weight soluble dietary fiber (HMWSDF), nondigestible oligosaccharides (NDO) not precipitated in ethanol solution, and resistant starch (RS). Eight sources of NDC (cellulose, wheat bran, gum arabic, resistant maltodextrin, polydextrose, fructooligosaccharide, galactooligosaccharides, and RS) were incorporated in different combinations into standard formula bread samples. All of the NDC sources and bread samples were analyzed for their (1) IDF + HMWSDF content with corrections for residual RS amount using AOAC Official Method 991.43, (2) NDO by liquid chromatography (LC) in AOAC Official Method 2001.03, and (3) RS by AOAC Official Method 2002.02. The correlation coefficient (R(2)) comparing calculated amounts versus measured amounts of total NDC in 11 bread samples was 0.92. Analysis of commercial food samples was also well matched with the DF + NDO value on their nutritional label. Consequently, we confirmed a single measurement of LC can determine all NDO in foods, and total NDC in foods can be determined by unifying existing AOAC Official Methods.

78 FR 54945 - Privacy Act; System of Records: Protocol Records, State-33

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-06

... accounting of those U.S. government officials receiving gifts and decorations from foreign governments and to....C. 2625, 22 U.S.C. 4301 et seq. PURPOSE: The information in this system of records is an accounting... public and professional institutions possessing relevant information. SYSTEMS EXEMPTED FROM CERTAIN...

Panama: Owning the Canal

DTIC Science & Technology

2014-03-01

tourist destination. The handbook reveals “a Korean/American consortium signed a deal with the [Panamanian] Government to invest nearly $400 million...the official policy or position of the Department of Defense or the U.S. Government . IRB protocol number ____N/A____. 12a. DISTRIBUTION...Credible, and Capable Governments ........................102 VII. CONCLUSION

9 CFR 312.10 - Official mark for maintaining the identity and integrity of samples.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 9 Animals and Animal Products 2 2011-01-01 2011-01-01 false Official mark for maintaining the identity and integrity of samples. 312.10 Section 312.10 Animals and Animal Products FOOD SAFETY AND... of the Federal Meat Inspection Act shall bear the designation “Sample Seal” accompanied by the...

Cross-sectional study on awareness and knowledge of torture investigation and documentation among Greek doctors and senior medical students.

PubMed

Orfanou, Christina; Tsiamis, Costas; Karamagioli, Evika; Pikouli, Anastasia; Terzidis, Agis; Pikoulis, Emmanuel

2018-06-05

Doctors in Greece face the possibility of encountering a person that has suffered torture, especially since the high rates of refugees' and migrants' inflows that took place over the last years. In order to assess the awareness and the knowledge of doctors and senior medical students in Greece regarding a manual on effective investigation and documentation of torture such as Istanbul Protocol (official United Nation document since 1999), a cross-sectional study was conducted using a structured anonymous questionnaire. The sample was doctors practicing in public hospitals in Greece, doctors volunteering at a non-governmental organization (NGO) and undergraduate medical students in their final year of studies in the Medical School of National and Kapodistrian University of Athens. The data were analyzed using IBM SPSS version 23, using descriptive statistics and statistical significance tests.In a total of 289 participants, the mean total score of Istanbul Protocol knowledge was 4.43 ± 1.104 (the maximum possible score was 10) and the mean total score of Istanbul Protocol awareness was 2.04 ± 1.521 (the maximum possible score was 10). The most important conclusion was that among doctors and senior medical students, there seem to be knowledge, awareness, and information deficit about Istanbul Protocol and several issues relating to torture. The overall research outcome highlights the need for the development of a relevant informative/educational program, in order to cover the corresponding existing needs of the population of doctors in Greece.

Comparison of R5 and G12 Antibody-Based ELISA Used for the Determination of the Gluten Content in Official Food Samples

PubMed Central

Hochegger, Rupert; Mayer, Walter; Prochaska, Manuela

2015-01-01

Celiac Disease (CD) is one of the most common food intolerances. It comes along with serious damage of the mucosa in the small intestine and is caused by the storage proteins—termed “gluten”—of wheat, rye, barley and possibly oats. Sensitive individuals need to stick to a strict gluten-free diet. The gluten level in food products labeled as “gluten-free”, must not exceed 20 mg/kg. It is obvious that effective test methods are needed to accurately determine the gluten concentration in foods. The determination of the presence of gluten in foodstuffs is mainly done by means of an immunochemical method called ELISA (enzyme-linked immunosorbent assay). To check the suitability of a G12 antibody-based gluten detection kit for its use in official control systems a number of routine samples were tested in parallel with two different test kits, as would be done in a routine lab. The determination of the gluten content was performed on samples entering the official laboratory including samples from official control plans, commercially available and private samples to request gluten-free labels. The results obtained with the G12 antibody ELISA assay were comparable to the official R5 method. A validation of the two different methods was not part of this study. PMID:28231228

Application of the BMWP-Costa Rica biotic index in aquatic biomonitoring: sensitivity to collection method and sampling intensity.

PubMed

Gutiérrez-Fonseca, Pablo E; Lorion, Christopher M

2014-04-01

The use of aquatic macroinvertebrates as bio-indicators in water quality studies has increased considerably over the last decade in Costa Rica, and standard biomonitoring methods have now been formulated at the national level. Nevertheless, questions remain about the effectiveness of different methods of sampling freshwater benthic assemblages, and how sampling intensity may influence biomonitoring results. In this study, we compared the results of qualitative sampling using commonly applied methods with a more intensive quantitative approach at 12 sites in small, lowland streams on the southern Caribbean slope of Costa Rica. Qualitative samples were collected following the official protocol using a strainer during a set time period and macroinvertebrates were field-picked. Quantitative sampling involved collecting ten replicate Surber samples and picking out macroinvertebrates in the laboratory with a stereomicroscope. The strainer sampling method consistently yielded fewer individuals and families than quantitative samples. As a result, site scores calculated using the Biological Monitoring Working Party-Costa Rica (BMWP-CR) biotic index often differed greatly depending on the sampling method. Site water quality classifications using the BMWP-CR index differed between the two sampling methods for 11 of the 12 sites in 2005, and for 9 of the 12 sites in 2006. Sampling intensity clearly had a strong influence on BMWP-CR index scores, as well as perceived differences between reference and impacted sites. Achieving reliable and consistent biomonitoring results for lowland Costa Rican streams may demand intensive sampling and requires careful consideration of sampling methods.

Preparticipation Screening of Athletic Officials: SEC Football Referees at Risk.

PubMed

Turner, John L; Walters, Rod; Leski, Mark J; Saywell, Robert M; Wooldridge, J Scott

2003-03-01

Although preparticipation screening for athletes is commonplace, few studies have addressed the issue for those officiating at games. To review current data on physiologic stress on sports officials, to obtain prevalence data on health parameters for football officials, and to determine the outcomes when screening criteria are applied in preseason exams. A protocol was established using health history questionnaires and physical exams with laboratory screening to assess the health of all football officials working in the Southeastern Conference (SEC) from 1997 to 2000. The main outcome measure was the prevalence of cardiac risk factors as determined by American College of Sports Medicine guidelines. Initial screening of 102 football officials revealed that 10.1% of SEC referees had elevated systolic blood pressure, 13.9% had elevated diastolic blood pressure, and 3.8% had resting tachycardia. Average body mass index (BMI) was 28.6 kg/m2, with 87.3% having a BMI that exceeded 25 (overweight). About one-third (31.6%) had a BMI greater than 30 (obese). Total fasting cholesterol exceeded 200 mg/dL in 44.2%, HDL levels were below 35 mg/dL in 34.3%, and LDL levels were above 120 mg/dL in 62.3%. Compared with age-adjusted national data, there were more overweight and more obese officials, but they had lower systolic and diastolic blood pressures and lower mean total cholesterol levels. Using the Framingham Study prediction model to estimate coronary heart disease (CHD) risk, analysis revealed that referees had a lower risk than the national 10-year CHD risk but a higher risk compared with that of the low-risk population. These data reveal a greater need for graded exercise testing. The higher rates of obesity among officials will promote further screening for CHD risk factors.

40 CFR 1036.530 - Calculating greenhouse gas emission rates.

Code of Federal Regulations, 2013 CFR

2013-07-01

... measured test fuel properties as specified in this paragraph (b) to obtain the official emission results... differences in test fuels within a fuel type. Use good engineering judgment to develop and apply testing protocols to minimize the impact of variations in test fuels. (1) For liquid fuels, determine the net energy...

40 CFR 1036.530 - Calculating greenhouse gas emission rates.

Code of Federal Regulations, 2012 CFR

2012-07-01

... measured test fuel properties as specified in this paragraph (b) to obtain the official emission results... differences in test fuels within a fuel type. Use good engineering judgment to develop and apply testing protocols to minimize the impact of variations in test fuels. (1) For liquid fuels, determine the net energy...

40 CFR 1036.530 - Calculating greenhouse gas emission rates.

Code of Federal Regulations, 2014 CFR

2014-07-01

... measured test fuel properties as specified in this paragraph (b) to obtain the official emission results... differences in test fuels within a fuel type. Use good engineering judgment to develop and apply testing protocols to minimize the impact of variations in test fuels. (1) For liquid fuels, determine the net energy...

Biosecurity protocols for heritage gardens

Treesearch

Ian Wright; David Slawson

2010-01-01

This project aims to protect The National Trust (NT) from the increasing number of harmful plant pests and diseases that slip though official controls and threaten our gardens, plant collections and landscapes. During 2008, the National Trust (NT) with the seconded help of Dr. David Slawson, Head of Pest and Disease Identification Programme, Food and Environment...

A Failure to Communicate

ERIC Educational Resources Information Center

Fredette, Michelle

2011-01-01

In April, Asia officially ran out of Internet Protocol (IP) version 4 addresses--the computer equivalent of running out of telephone numbers. Over the next couple of years, the rest of the world will also run dry. Yet, unlike the Y2K bug that had some people convinced the sky would fall, this particular problem is generating little more than tired…

Hindering the illegal trade in dog and cat furs through a DNA-based protocol for species identification.

PubMed

Garofalo, Luisa; Mariacher, Alessia; Fanelli, Rita; Fico, Rosario; Lorenzini, Rita

2018-01-01

In Western countries dogs and cats are the most popular pets, and people are increasingly opposed to their rearing for the fur industry. In 2007, a Regulation of the European Union (EU) banned the use and trade of dog and cat furs, but an official analytical protocol to identify them as source species was not provided, and violations of law are still frequent in all Member States. In this paper we report on the development and validation of a simple and affordable DNA method for species detection in furs to use as an effective tool to combat illegal trade in fur products. A set of mitochondrial primers was designed for amplification of partial cytochrome b, control region and ND1 gene in highly degraded samples, like furs and pelts. Our amplification workflow involved the use of a non-specific primer pair to perform a first test to identify the species through sequencing, then the application of species-specific primer pairs to use in singleplex end-point PCRs as confirmation tests. The advantage of this two-step procedure is twofold: on the one hand it minimises the possibility of negative test results from degraded samples, since failure of amplification with a first set of primers can be offset by successful amplification of the second, and on the other it adds confidence and reliability to final authentication of species. All designed primers were validated on a reference collection of tissue samples, obtaining solid results in terms of specificity, sensitivity, repeatability and reproducibility. Application of the protocol on real caseworks from seized furs yielded successful results also from old and dyed furs, suggesting that age and chemical staining do not necessarily affect positive amplifications. Major pros of this approach are: (1) sensitive and informative primer sets for detection of species; (2) short PCR amplicons for the analysis of poor quality DNA; (3) binding primers that avoid contamination from human DNA; (4) user-friendly protocol for any laboratory equipped for analysis of low-copy-number DNA. Our molecular procedure proved to be a good starting point for enforcing the EU Regulation against dog and cat fur trade in forensic contexts where source attribution is essential to the assignment of responsibilities.

21 CFR 184.1979a - Reduced lactose whey.

Code of Federal Regulations, 2013 CFR

2013-04-01

....199 (dry sample), entitled “Fat in Dried Milk (45)—Official Final Action.” (iii) Ash content, 11 to 27...—Official Final Action” under the heading “Dried Milk, Nonfat Dry Milk, and Malted Milk.” (iv) Lactose... section 16.192, entitled “Moisture (41)—Official Final Action” under the heading “Dried Milk, Nonfat Dry...

21 CFR 184.1979a - Reduced lactose whey.

Code of Federal Regulations, 2012 CFR

2012-04-01

....199 (dry sample), entitled “Fat in Dried Milk (45)—Official Final Action.” (iii) Ash content, 11 to 27...—Official Final Action” under the heading “Dried Milk, Nonfat Dry Milk, and Malted Milk.” (iv) Lactose... section 16.192, entitled “Moisture (41)—Official Final Action” under the heading “Dried Milk, Nonfat Dry...

Efficacy of chloroquine for the treatment of uncomplicated Plasmodium falciparum malaria in Honduras.

PubMed

Mejia Torres, Rosa Elena; Banegas, Engels Ilich; Mendoza, Meisy; Diaz, Cesar; Bucheli, Sandra Tamara Mancero; Fontecha, Gustavo A; Alam, Md Tauqeer; Goldman, Ira; Udhayakumar, Venkatachalam; Zambrano, Jose Orlinder Nicolas

2013-05-01

Chloroquine (CQ) is officially used for the primary treatment of Plasmodium falciparum malaria in Honduras. In this study, the therapeutic efficacy of CQ for the treatment of uncomplicated P. falciparum malaria in the municipality of Puerto Lempira, Gracias a Dios, Honduras was evaluated using the Pan American Health Organization-World Health Organization protocol with a follow-up of 28 days. Sixty-eight patients from 6 months to 60 years of age microscopically diagnosed with uncomplicated P. falciparum malaria were included in the final analysis. All patients who were treated with CQ (25 mg/kg over 3 days) cleared parasitemia by day 3 and acquired no new P. falciparum infection within 28 days of follow-up. All the parasite samples sequenced for CQ resistance mutations (pfcrt) showed only the CQ-sensitive genotype (CVMNK). This finding shows that CQ remains highly efficacious for the treatment of uncomplicated P. falciparum malaria in Gracias a Dios, Honduras.

7 CFR 800.117 - Who shall perform original services.

Code of Federal Regulations, 2011 CFR

2011-01-01

... by another official agency upon approval from the Service. (3) Barge probe service. Any official agency may provide probe sampling and inspection service for barge-lots of grain with no restrictions due...

7 CFR 800.117 - Who shall perform original services.

Code of Federal Regulations, 2012 CFR

2012-01-01

... by another official agency upon approval from the Service. (3) Barge probe service. Any official agency may provide probe sampling and inspection service for barge-lots of grain with no restrictions due...

7 CFR 800.117 - Who shall perform original services.

Code of Federal Regulations, 2013 CFR

2013-01-01

... by another official agency upon approval from the Service. (3) Barge probe service. Any official agency may provide probe sampling and inspection service for barge-lots of grain with no restrictions due...

7 CFR 800.117 - Who shall perform original services.

Code of Federal Regulations, 2014 CFR

2014-01-01

... by another official agency upon approval from the Service. (3) Barge probe service. Any official agency may provide probe sampling and inspection service for barge-lots of grain with no restrictions due...

First Detection of Tetrodotoxin in Greek Shellfish by UPLC-MS/MS Potentially Linked to the Presence of the Dinoflagellate Prorocentrum minimum

PubMed Central

Vlamis, Aristidis; Katikou, Panagiota; Rodriguez, Ines; Rey, Verónica; Alfonso, Amparo; Papazachariou, Angelos; Zacharaki, Thetis; Botana, Ana M.; Botana, Luis M.

2015-01-01

During official shellfish control for the presence of marine biotoxins in Greece in year 2012, a series of unexplained positive mouse bioassays (MBA) for lipophilic toxins with nervous symptomatology prior to mice death was observed in mussels from Vistonikos Bay–Lagos, Rodopi. This atypical toxicity coincided with (a) absence or low levels of regulated and some non-regulated toxins in mussels and (b) the simultaneous presence of the potentially toxic microalgal species Prorocentrum minimum at levels up to 1.89 × 103 cells/L in the area’s seawater. Further analyses by different MBA protocols indicated that the unknown toxin was hydrophilic, whereas UPLC-MS/MS analyses revealed the presence of tetrodotoxins (TTXs) at levels up to 222.9 μg/kg. Reviewing of official control data from previous years (2006–2012) identified a number of sample cases with atypical positive to asymptomatic negative MBAs for lipophilic toxins in different Greek production areas, coinciding with periods of P. minimum blooms. UPLC-MS/MS analysis of retained sub-samples from these cases revealed that TTXs were already present in Greek shellfish since 2006, in concentrations ranging between 61.0 and 194.7 μg/kg. To our knowledge, this is the earliest reported detection of TTXs in European bivalve shellfish, while it is also the first work to indicate a possible link between presence of the toxic dinoflagellate P. minimum in seawater and that of TTXs in bivalves. Confirmed presence of TTX, a very heat-stable toxin, in filter-feeding mollusks of the Mediterranean Sea, even at lower levels to those inducing symptomatology to humans, indicates that this emerging risk should be seriously taken into account by the EU to protect the health of shellfish consumers. PMID:26008234

Assessing Crime as a Problem: The Relationship between Residents' Perception of Crime and Official Crime Rates over 25 Years

ERIC Educational Resources Information Center

Hipp, John R.

2013-01-01

This study compares the relationship between official crime rates in census tracts and resident perceptions of crime. Using a unique data set that links household-level data from the American Housing Survey metro samples over 25 years (1976-1999) with official crime rate data for census tracts in selected cities during selected years, this study…

Validation of the Italian version of the Movement Disorder Society--Unified Parkinson's Disease Rating Scale.

PubMed

Antonini, Angelo; Abbruzzese, Giovanni; Ferini-Strambi, Luigi; Tilley, Barbara; Huang, Jing; Stebbins, Glenn T; Goetz, Christopher G; Barone, Paolo; Bandettini di Poggio, Monica; Fabbrini, Giovanni; Di Stasio, Flavio; Tinazzi, Michele; Bovi, Tommaso; Ramat, Silvia; Meoni, Sara; Pezzoli, Gianni; Canesi, Margherita; Martinelli, Paolo; Maria Scaglione, Cesa Lorella; Rossi, Aroldo; Tambasco, Nicola; Santangelo, Gabriella; Picillo, Marina; Morgante, Letterio; Morgante, Francesca; Quatrale, Rocco; Sensi, MariaChiara; Pilleri, Manuela; Biundo, Roberta; Nordera, Giampietro; Caria, Antonella; Pacchetti, Claudio; Zangaglia, Roberta; Lopiano, Leonardo; Zibetti, Maurizio; Zappia, Mario; Nicoletti, Alessandra; Quattrone, Aldo; Salsone, Maria; Cossu, Gianni; Murgia, Daniela; Albanese, Alberto; Del Sorbo, Francesca

2013-05-01

The Movement Disorder Society-sponsored revision of the Unified Parkinson's Disease Rating Scale (MDS-UPDRS) has been available in English since 2008. As part of this process, the MDS-UPDRS organizing team developed guidelines for development of official non-English translations. We present here the formal process for completing officially approved non-English versions of the MDS-UPDRS and specifically focus on the first of these versions in Italian. The MDS-UPDRS was translated into Italian and tested in 377 native-Italian speaking PD patients. Confirmatory and exploratory factor analyses determined whether the factor structure for the English-language MDS-UPDRS could be confirmed in data collected using the Italian translation. To be designated an 'Official MDS translation,' the Comparative Fit Index (CFI) had to be ≥0.90 relative to the English-language version. For all four parts of the Italian MDS-UPDRS, the CFI, in comparison with the English-language data, was ≥0.94. Exploratory factor analyses revealed some differences between the two datasets, however these differences were considered to be within an acceptable range. The Italian version of the MDS-UPDRS reaches the criterion to be designated as an Official Translation and is now available for use. This protocol will serve as outline for further validation of this in multiple languages.

JPRS Report, China

DTIC Science & Technology

1990-01-08

Wash- ington in the middle of the presidential race between Bush and Dukakis, Deng Xiaoping violated diplomatic protocol by telling U.S. officials...explanation for their evil acts and failed to prevent some of his subordinates from publicly breaking with the CPC authorities and seeking political...want to guide the masses of workers toward the road of reform and the road of labor-capital cooperation to prevent them from developing revolutionary

The International Nexus Between Drugs and Terror: Lessons in Conflict and Diplomacy

DTIC Science & Technology

2010-12-01

claimed the intelligence recovered provided evidentiary documentation that there were verifiable links between the governments of both Ecuador and...not reflect the official policy or position of the Department of Defense or the U.S. Government . IRB Protocol number: N/A. 12a. DISTRIBUTION...Revolucionarias de Colombia) FBI Federal Bureau of Investigation GAO Government Accountability Office HRK Kurdistan Freedom Brigade (Hazen Rizgariya Kurdistan

Branched Nerve Allografts to Improve Outcomes in Facial Composite Tissue Transplantation

DTIC Science & Technology

2017-12-01

Ethicon, Inc. Somervile, N.J.). Postoperatively, animals were recovered per standard protocol in the animal care facility.  Experimental Design ...official Department of the Army position, policy or decision unless so designated by other documentation. REPORT DOCUMENTATION PAGE Form Approved OMB No...a human xenograft with or without oral Tacrolimus. Electrophysiologic assessments were performed pre -operatively and at the study endpoint (24 weeks

Prevention of Post-Traumatic Epilepsy by Transcranial Direct Current Stimulation

DTIC Science & Technology

2014-09-01

epidural fluid percussion itself. As an improvement on the classic LFPI procedure, we designed and validated a new protocol, termed rapid fluid ...plated on an 8X8 micoelectrode array (left) and bathed in oxygenated artificial cerebrospinal fluid . Cortical excitability was measured as the magnitude...not be construed as an official Department of the Army position, policy or decision unless so designated by other documentation. 1 REPORT

Illicit Networks: Targeting the Nexus Between Terrorists, Proliferators, and Narcotraffickers

DTIC Science & Technology

2010-12-01

the official policy or position of the Department of Defense or the U.S. government . IRB Protocol number: N/A 12a. DISTRIBUTION / AVAILABILITY...national and international security. These illicit networks exist within the shadows of legitimate trade and governance . They exploit an abundant...Current U.S. government efforts to counter these activities are similarly “stovepiped,” The term “cylinders of excellence” has been used to describe

Telecommunications Policy in the Caribbean: A Case Study of Telecommunications in Jamaica and Cuba

DTIC Science & Technology

2013-03-01

official policy or position of the Department of Defense or the U.S. Government . IRB Protocol number ____N/A____. 12a. DISTRIBUTION / AVAILABILITY...STATEMENT Approved for public release; distribution is unlimited 12b. DISTRIBUTION CODE A 13. ABSTRACT (maximum 200 words) Government influence and...nation’s ideology will dictate how governments interact with telecommunications providers and, ultimately, the telecommunications company’s ability to

Resolution of a disputed albendazole result in the UK Official Control System - time for more guidance?

PubMed

Walker, Michael; Gray, Kirstin; Hopley, Christopher; Mussell, Christopher; Clifford, Louise; Meinerikandathevan, Jayanie; Firpo, Leonardo; Topping, Joanna; Santacruz, Daniel

2017-04-01

Albendazole, one of the benzimidazole anthelmintics, is used in ruminants and has maximum residue limits in muscle, fat and other tissue owing to reported teratogenicity. Albendazole is extensively metabolised in domestic animals and humans with rapid conversion to a sulphoxide and subsequently sulphone and amino sulphone metabolites. Sulphoxide metabolites are responsible for the systemic biological activity of benzimidazole drugs. Herein we report a case of disputed results for albendazole in a consignment sampled at import in which the Official Analyst certified against the consignment for excess albendazole. A laboratory acting for the importer reported data below the MRL, including a finding of the parent drug which is not included in the residue definition. The Government Chemist has a statutory duty as a route of technical appeal in the UK Official Food Control system and the case was referred for referee analysis. We report our findings based on a LC-MS/MS method, which confirmed the official findings, did not reveal the presence of the parent drug but identified hot spots of albendazole marker residues in the consignment. We discuss the need for recommendations on official sampling at import and interpretation of results.

Validation of Single and Pooled Manure Drag Swabs for the Detection of Salmonella Serovar Enteritidis in Commercial Poultry Houses.

PubMed

Kinde, Hailu; Goodluck, Helen A; Pitesky, Maurice; Friend, Tom D; Campbell, James A; Hill, Ashley E

2015-12-01

Single swabs (cultured individually) are currently used in the Food and Drug Administration (FDA) official method for sampling the environment of commercial laying hens for the detection of Salmonella enterica ssp. serovar Enteritidis (Salmonella Enteritidis). The FDA has also granted provisional acceptance of the National Poultry Improvement Plan's (NPIP) Salmonella isolation and identification methodology for samples taken from table-egg layer flock environments. The NPIP method, as with the FDA method, requires single-swab culturing for the environmental sampling of laying houses for Salmonella Enteritidis. The FDA culture protocol requires a multistep culture enrichment broth, and it is more labor intensive than the NPIP culture protocol, which requires a single enrichment broth. The main objective of this study was to compare the FDA single-swab culturing protocol with that of the NPIP culturing protocol but using a four-swab pool scheme. Single and multi-laboratory testing of replicate manure drag swab sets (n  =  525 and 672, respectively) collected from a Salmonella Enteritidis-free commercial poultry flock was performed by artificially contaminating swabs with either Salmonella Enteritidis phage type 4, 8, or 13a at one of two inoculation levels: low, x¯  = 2.5 CFU (range 2.5-2.7), or medium, x¯  = 10.0 CFU (range 7.5-12). For each replicate, a single swab (inoculated), sets of two swabs (one inoculated and one uninoculated), and sets of four swabs (one inoculated and three uninoculated), testing was conducted using the FDA or NPIP culture method. For swabs inoculated with phage type 8, the NPIP method was more efficient (P < 0.05) for all swab sets at both inoculation levels than the reference method. The single swabs in the NPIP method were significantly (P < 0.05) better than four-pool swabs in detecting Salmonella Enteritidis at the lower inoculation level. In the collaborative study (n  =  13 labs) using Salmonella Enteritidis phage type 13a inoculated swabs, there was no significant difference (P > 0.05) between the FDA method (single swabs) and the pooled NPIP method (four-pool swabs). The study concludes that the pooled NPIP method is not significantly different from the FDA method for the detection of Salmonella Enteritidis in drag swabs in commercial poultry laying houses. Consequently based on the FDA's Salmonella Enteritidis rule for equivalency of different methods, the pooled NPIP method should be considered equivalent. Furthermore, the pooled NPIP method was more efficient and cost effective.

Evaluation of Protocol Uniformity Concerning Laparoscopic Cholecystectomy in The Netherlands

PubMed Central

Goossens, Richard H. M.; van Eijk, Daan J.; Lange, Johan F.

2008-01-01

Background Iatrogenic bile duct injury remains a current complication of laparoscopic cholecystectomy. One uniform and standardized protocol, based on the “critical view of safety” concept of Strasberg, should reduce the incidence of this complication. Furthermore, owing to the rapid development of minimally invasive surgery, technicians are becoming more frequently involved. To improve communication between the operating team and technicians, standardized actions should also be defined. The aim of this study was to compare existing protocols for laparoscopic cholecystectomy from various Dutch hospitals. Methods Fifteen Dutch hospitals were contacted for evaluation of their protocols for laparoscopic cholecystectomy. All evaluated protocols were divided into six steps and were compared accordingly. Results In total, 13 hospitals responded—5 academic hospitals, 5 teaching hospitals, 3 community hospitals—of which 10 protocols were usable for comparison. Concerning the trocar positions, only minor differences were found. The concept of “critical view of safety” was represented in just one protocol. Furthermore, the order of clipping and cutting the cystic artery and duct differed. Descriptions of instruments and apparatus were also inconsistent. Conclusions Present protocols differ too much to define a universal procedure among surgeons in The Netherlands. The authors propose one (inter)national standardized protocol, including standardized actions. This uniform standardized protocol has to be officially released and recommended by national scientific associations (e.g., the Dutch Society of Surgery) or international societies (e.g., European Association for Endoscopic Surgery and Society of American Gastrointestinal and Endoscopic Surgeons). The aim is to improve patient safety and professional communication, which are necessary for new developments. PMID:18224485

Design of a sampling plan to detect ochratoxin A in green coffee.

PubMed

Vargas, E A; Whitaker, T B; Dos Santos, E A; Slate, A B; Lima, F B; Franca, R C A

2006-01-01

The establishment of maximum limits for ochratoxin A (OTA) in coffee by importing countries requires that coffee-producing countries develop scientifically based sampling plans to assess OTA contents in lots of green coffee before coffee enters the market thus reducing consumer exposure to OTA, minimizing the number of lots rejected, and reducing financial loss for producing countries. A study was carried out to design an official sampling plan to determine OTA in green coffee produced in Brazil. Twenty-five lots of green coffee (type 7 - approximately 160 defects) were sampled according to an experimental protocol where 16 test samples were taken from each lot (total of 16 kg) resulting in a total of 800 OTA analyses. The total, sampling, sample preparation, and analytical variances were 10.75 (CV = 65.6%), 7.80 (CV = 55.8%), 2.84 (CV = 33.7%), and 0.11 (CV = 6.6%), respectively, assuming a regulatory limit of 5 microg kg(-1) OTA and using a 1 kg sample, Romer RAS mill, 25 g sub-samples, and high performance liquid chromatography. The observed OTA distribution among the 16 OTA sample results was compared to several theoretical distributions. The 2 parameter-log normal distribution was selected to model OTA test results for green coffee as it gave the best fit across all 25 lot distributions. Specific computer software was developed using the variance and distribution information to predict the probability of accepting or rejecting coffee lots at specific OTA concentrations. The acceptation probability was used to compute an operating characteristic (OC) curve specific to a sampling plan design. The OC curve was used to predict the rejection of good lots (sellers' or exporters' risk) and the acceptance of bad lots (buyers' or importers' risk).

Perspectives and Challenges of HMIS Officials in the Implementation of Health Management Information System (HMIS) with Reference to Maternal Health Services in Assam.

PubMed

Samal, Janmejaya; Dehury, Ranjit Kumar

2016-06-01

Health Management Information System (HMIS) is one of the important components of National Rural Health Mission (NRHM). The web portal of HMIS was launched by the Ministry of Health and Family Welfare (MOHFW), Govt. of India (GOI) in 21(st) Oct. 2008 to enable capturing of public health data from both public and private institutions in rural and urban areas across the country. The aim of the study was to assess the quality perspectives and challenges among HMIS officials in implementing HMIS at their respective levels, i.e. district and block level. We conducted a pilot qualitative study in two districts of Assam. HMIS officials working at district and block level were interviewed in-depth with the help of a semi-structured interview schedule which lasted from May to July 2014. Both HMIS and MCTS (Mother and Child Tracking System) formats were considered useful, by the HMIS officials, for data collection, planning at various levels, tracking maternal and neonatal deaths, institutional deliveries. HMIS officials reported that MCTS is useful for monitoring individual health status especially the status of the mother and child and HMIS being helpful as a health facility monitoring tool. The study used a small sample size, hence similar type of studies are required with large sample size to understand the perspectives and challenges of HMIS officials in the implementation of HMIS.

AFNOR validation of Premi Test, a microbiological-based screening tube-test for the detection of antimicrobial residues in animal muscle tissue.

PubMed

Gaudin, Valerie; Juhel-Gaugain, Murielle; Morétain, Jean-Pierre; Sanders, Pascal

2008-12-01

Premi Test contains viable spores of a strain of Bacillus stearothermophilus which is sensitive to antimicrobial residues, such as beta-lactams, tetracyclines, macrolides and sulphonamides. The growth of the strain is inhibited by the presence of antimicrobial residues in muscle tissue samples. Premi Test was validated according to AFNOR rules (French Association for Normalisation). The AFNOR validation was based on the comparison of reference methods (French Official method, i.e. four plate test (FPT) and the STAR protocol (five plate test)) with the alternative method (Premi Test). A preliminary study was conducted in an expert laboratory (Community Reference Laboratory, CRL) on both spiked and incurred samples (field samples). Several method performance criteria (sensitivity, specificity, relative accuracy) were estimated and are discussed, in addition to detection capabilities. Adequate agreement was found between the alternative method and the reference methods. However, Premi Test was more sensitive to beta-lactams and sulphonamides than the FPT. Subsequently, a collaborative study with 11 laboratories was organised by the CRL. Blank and spiked meat juice samples were sent to participants. The expert laboratory (CRL) statistically analysed the results. It was concluded that Premi Test could be used for the routine determination of antimicrobial residues in muscle of different animal origin with acceptable analytical performance. The detection capabilities of Premi Test for beta-lactams (amoxicillin, ceftiofur), one macrolide (tylosin) and tetracycline were at the level of the respective maximum residue limits (MRL) in muscle samples or even lower.

Comparison of three methods of DNA extraction from peripheral blood mononuclear cells and lung fragments of equines.

PubMed

Santos, E M; Paula, J F R; Motta, P M C; Heinemann, M B; Leite, R C; Haddad, J P A; Del Puerto, H L; Reis, J K P

2010-08-17

We compared three different protocols for DNA extraction from horse peripheral blood mononuclear cells (PBMC) and lung fragments, determining average final DNA concentration, purity, percentage of PCR amplification using beta-actin, and cost. Thirty-four samples from PBMC, and 33 samples from lung fragments were submitted to DNA extraction by three different protocols. Protocol A consisted of a phenol-chloroform and isoamylic alcohol extraction, Protocol B used alkaline extraction with NaOH, and Protocol C used the DNAzol((R)) reagent kit. Protocol A was the best option for DNA extraction from lung fragments, producing high DNA concentrations, with high sensitivity in PCR amplification (100%), followed by Protocols C and B. On the other hand, for PBMC samples, Protocol B gave the highest sensitivity in PCR amplification (100%), followed by Protocols C and A. We conclude that Protocol A should be used for PCR diagnosis from lung fragment samples, while Protocol B should be used for PBMC.

[Application of DNA extraction kit, 'GM quicker' for detection of genetically modified soybeans].

PubMed

Sato, Noriko; Sugiura, Yoshitsugu; Tanaka, Toshitsugu

2012-01-01

Several DNA extraction methods have been officially introduced to detect genetically modified soybeans, but the choice of DNA extraction kits depend on the nature of the samples, such as grains or processed foods. To overcome this disadvantage, we examined whether the GM quicker kit is available for both grains and processed foods. We compared GM quicker with four approved DNA extraction kits in respect of DNA purity, copy numbers of lectin gene, and working time. We found that the DNA quality of GM quicker was superior to that of the other kits for grains, and the procedure was faster. However, in the case of processed foods, GM quicker was not superior to the other kits. We therefore investigated an unapproved GM quicker 3 kit, which is available for DNA extraction from processed foods, such as tofu and boiled soybeans. The GM quicker 3 kit provided good DNA quality from both grains and processed foods, so we made a minor modification of the GM quicker-based protocol that was suitable for processed foods, using GM quicker and its reagents. The modified method enhanced the performance of GM quicker with processed foods. We believe that GM quicker with the modified protocol is an excellent tool to obtain high-quality DNA from grains and processed foods for detection of genetically modified soybeans.

Efficacy of Chloroquine for the Treatment of Uncomplicated Plasmodium falciparum Malaria in Honduras

PubMed Central

Torres, Rosa Elena Mejia; Banegas, Engels Ilich; Mendoza, Meisy; Diaz, Cesar; Bucheli, Sandra Tamara Mancero; Fontecha, Gustavo A.; Alam, Md Tauqeer; Goldman, Ira; Udhayakumar, Venkatachalam; Zambrano, Jose Orlinder Nicolas

2013-01-01

Chloroquine (CQ) is officially used for the primary treatment of Plasmodium falciparum malaria in Honduras. In this study, the therapeutic efficacy of CQ for the treatment of uncomplicated P. falciparum malaria in the municipality of Puerto Lempira, Gracias a Dios, Honduras was evaluated using the Pan American Health Organization—World Health Organization protocol with a follow-up of 28 days. Sixty-eight patients from 6 months to 60 years of age microscopically diagnosed with uncomplicated P. falciparum malaria were included in the final analysis. All patients who were treated with CQ (25 mg/kg over 3 days) cleared parasitemia by day 3 and acquired no new P. falciparum infection within 28 days of follow-up. All the parasite samples sequenced for CQ resistance mutations (pfcrt) showed only the CQ-sensitive genotype (CVMNK). This finding shows that CQ remains highly efficacious for the treatment of uncomplicated P. falciparum malaria in Gracias a Dios, Honduras. PMID:23458957

Template-based protein structure modeling using the RaptorX web server.

PubMed

Källberg, Morten; Wang, Haipeng; Wang, Sheng; Peng, Jian; Wang, Zhiyong; Lu, Hui; Xu, Jinbo

2012-07-19

A key challenge of modern biology is to uncover the functional role of the protein entities that compose cellular proteomes. To this end, the availability of reliable three-dimensional atomic models of proteins is often crucial. This protocol presents a community-wide web-based method using RaptorX (http://raptorx.uchicago.edu/) for protein secondary structure prediction, template-based tertiary structure modeling, alignment quality assessment and sophisticated probabilistic alignment sampling. RaptorX distinguishes itself from other servers by the quality of the alignment between a target sequence and one or multiple distantly related template proteins (especially those with sparse sequence profiles) and by a novel nonlinear scoring function and a probabilistic-consistency algorithm. Consequently, RaptorX delivers high-quality structural models for many targets with only remote templates. At present, it takes RaptorX ~35 min to finish processing a sequence of 200 amino acids. Since its official release in August 2011, RaptorX has processed ~6,000 sequences submitted by ~1,600 users from around the world.

Template-based protein structure modeling using the RaptorX web server

PubMed Central

Källberg, Morten; Wang, Haipeng; Wang, Sheng; Peng, Jian; Wang, Zhiyong; Lu, Hui; Xu, Jinbo

2016-01-01

A key challenge of modern biology is to uncover the functional role of the protein entities that compose cellular proteomes. To this end, the availability of reliable three-dimensional atomic models of proteins is often crucial. This protocol presents a community-wide web-based method using RaptorX (http://raptorx.uchicago.edu/) for protein secondary structure prediction, template-based tertiary structure modeling, alignment quality assessment and sophisticated probabilistic alignment sampling. RaptorX distinguishes itself from other servers by the quality of the alignment between a target sequence and one or multiple distantly related template proteins (especially those with sparse sequence profiles) and by a novel nonlinear scoring function and a probabilistic-consistency algorithm. Consequently, RaptorX delivers high-quality structural models for many targets with only remote templates. At present, it takes RaptorX ~35 min to finish processing a sequence of 200 amino acids. Since its official release in August 2011, RaptorX has processed ~6,000 sequences submitted by ~1,600 users from around the world. PMID:22814390

Guidelines and sample protocol for sampling forest gaps.

Treesearch

J.R. Runkle

1992-01-01

A protocol for sampling forest canopy gaps is presented. Methods used in published gap studies are reviewed. The sample protocol will be useful in developing a broader understanding of forest structure and dynamics through comparative studies across different forest ecosystems.

It's Time to Develop a New "Draft Test Protocol" for a Mars Sample Return Mission (or Two…).

PubMed

Rummel, John D; Kminek, Gerhard

2018-04-01

The last time NASA envisioned a sample return mission from Mars, the development of a protocol to support the analysis of the samples in a containment facility resulted in a "Draft Test Protocol" that outlined required preparations "for the safe receiving, handling, testing, distributing, and archiving of martian materials here on Earth" (Rummel et al., 2002 ). This document comprised a specific protocol to be used to conduct a biohazard test for a returned martian sample, following the recommendations of the Space Studies Board of the US National Academy of Sciences. Given the planned launch of a sample-collecting and sample-caching rover (Mars 2020) in 2 years' time, and with a sample return planned for the end of the next decade, it is time to revisit the Draft Test Protocol to develop a sample analysis and biohazard test plan to meet the needs of these future missions. Key Words: Biohazard detection-Mars sample analysis-Sample receiving facility-Protocol-New analytical techniques-Robotic sample handling. Astrobiology 18, 377-380.

Phase II Clinical Trial of Intraoral Grafting of Human Tissue Engineered Oral Mucosa

DTIC Science & Technology

2017-10-01

experimental arm subject in the small defect study. A protocol amendment in early 2017revised the study inclusionary criteria to include all non ...construed as an official Department of the Army position, policy or decision unless so designated by other documentation. REPORT DOCUMENTATION PAGE...group phase II study to assess the safety and efficacy for use of human EVPOME for soft tissue intraoral grafting procedures compared to the “gold

An Influence Analysis of Dissuading Nation States from Producing and Proliferating Weapons of Mass Destruction (WMD)

DTIC Science & Technology

2011-03-01

author and do not reflect the official policy or position of the Department of Defense or the U.S. Government. IRB Protocol number ______N/A__________...18 5. Lead Up to the Fission Device Test 1974 .........................................22 6. Maintaining Nuclear Policy 1974-1998...out to produce nuclear energy for research and civilian energy consumption. Its government maintained a policy of peace nuclear energy usage unless

Field Screening Method for 2,4-Dinitrotoluene in Soil

DTIC Science & Technology

1991-10-01

to be used for advertising or promotional purposes. Citation of brand names doesnot constitute an official endorsement or approval of the use of such... processed according to the tions of the protocols and results are shown in Table 8. method. After colordevelopment, four individuals were ANOVA...repeat process througho.: 30-minute pe- again for I minute. The solutions are filtered and the riod. absorbance read again at 570 nm. If 2,4-DNT is

Stemming the Flow of Improvised Explosive Device Making Materials through Global Export Control Regimes

DTIC Science & Technology

2012-09-01

reflect the official policy or position of the Department of Defense or the U.S. Government. IRB Protocol number ______N/A______. 12a. DISTRIBUTION...Warfare DHS Department of Homeland Security DoD Department of Defense DTMF Dual-Tone Multi-Frequency EOD Explosive Ordnance Disposal EU European...Organization JMTC Joint Multinational Training Command JTF Joint Task Force MANPADS Man Portable Air Defense Systems MERC Multilateral Export Control

Brazils Rise to Global Power

DTIC Science & Technology

2014-06-01

not reflect the official policy or position of the Department of Defense or the U.S. Government . IRB protocol number ____N/A____. 12a...economic power status, since the country is also a member of the Group of 8 (G-8), a forum for the governments of the world’s eight most powerful economies...English. This may pose methodological problems since the author will be relying largely on data published by the Brazilian government . Even with this

Return of the Bear Russia’s Ties with Former Soviet Allies in Latin America

DTIC Science & Technology

2016-03-01

Defense or the U.S. Government . IRB Protocol number ____N/A____. 12a. DISTRIBUTION / AVAILABILITY STATEMENT Approved for public release...some government officials and scholars may be overlooking. Moreover, the literature does not clearly assess the degree of closeness between Russia and...Peoples of Our America (ALBA)—that is, Venezuela, Nicaragua, Bolivia, Ecuador , Cuba, and some other Caribbean island states—are firm.9 Regarding the

Positive Communications: The Keystone of Counterinsurgency Strategy

DTIC Science & Technology

2013-12-01

and do not reflect the official policy or position of the Department of Defense or the U.S. government. IRB protocol number ____N/A____. 12a...temporal data to isolate the casual effect of population engagements and radio broadcasts in relation to levels of insurgent violence over time and space...casual effect of population engagements and radio broadcasts in relation to levels of insurgent violence over time and space. The evidence supports our

Sampling protocol for post-landfall Deepwater Horizon oil release, Gulf of Mexico, 2010

USGS Publications Warehouse

Wilde, F.D.; Skrobialowski, S.C.; Hart, J.S.

2010-01-01

The protocols and procedures described in this report are designed to be used by U.S. Geological Survey (USGS) field teams for the collection of environmental data and samples in coastal areas affected by the 2010 Deepwater Horizon oil spill in the Gulf of Mexico. This sampling protocol focuses specifically on sampling for water, sediments, benthic invertebrates, and microorganisms (ambient bacterial populations) after shoreline arrival of petroleum-associated product on beach, barrier island, and wetland environments of the Gulf of Mexico coastal states. Deployment to sampling sites, site setup, and sample collection in these environments necessitates modifications to standard USGS sampling procedures in order to address the regulatory, logistical, and legal requirements associated with samples collected in oil-impacted coastal areas. This document, therefore, has been written as an addendum to the USGS National Field Manual for the Collection of Water-Quality Data (NFM) (http://pubs.water.usgs.gov/twri9A/), which provides the basis for training personnel in the use of standard USGS sampling protocols. The topics covered in this Gulf of Mexico oil-spill sampling protocol augment NFM protocols for field-deployment preparations, health and safety precautions, sampling and quality-assurance procedures, and decontamination requirements under potentially hazardous environmental conditions. Documentation procedures and maintenance of sample integrity by use of chain-of-custody procedures also are described in this protocol.

Endogenous levels of nitrites and nitrates in wide consumption foodstuffs: Results of five years of official controls and monitoring.

PubMed

Iammarino, Marco; Di Taranto, Aurelia; Cristino, Marianna

2013-10-15

The massive introduction of nitrogen fertilisers, necessary to maximise the global food production, has brought about an increase of the residual amounts of nitrites and nitrates in the products. Notoriously, these compounds may exercise toxic effects. In this work the results obtained from 5years of official controls and monitoring focused on tracing quantifiable amounts of nitrites and nitrates in 1785 samples of meat, dairy, fish products and leafy vegetables are reported. A widespread presence of nitrates at low concentrations in foodstuffs was verified. High concentrations of nitrates were registered in some leafy vegetables and mussels samples, while high nitrites concentrations were registered in some spinach samples. The results confirmed the necessity to develop most controls and suggest the introduction of new legal limits related to some combinations contaminant/matrix. Such new limits may fill legislative gaps that may cause wrong interpretations of the results obtained during official controls. Copyright © 2012 Elsevier Ltd. All rights reserved.

Perspectives and Challenges of HMIS Officials in the Implementation of Health Management Information System (HMIS) with Reference to Maternal Health Services in Assam

PubMed Central

Dehury, Ranjit Kumar

2016-01-01

Introduction Health Management Information System (HMIS) is one of the important components of National Rural Health Mission (NRHM). The web portal of HMIS was launched by the Ministry of Health and Family Welfare (MOHFW), Govt. of India (GOI) in 21st Oct. 2008 to enable capturing of public health data from both public and private institutions in rural and urban areas across the country. Aim The aim of the study was to assess the quality perspectives and challenges among HMIS officials in implementing HMIS at their respective levels, i.e. district and block level. Materials and Methods We conducted a pilot qualitative study in two districts of Assam. HMIS officials working at district and block level were interviewed in-depth with the help of a semi-structured interview schedule which lasted from May to July 2014. Results Both HMIS and MCTS (Mother and Child Tracking System) formats were considered useful, by the HMIS officials, for data collection, planning at various levels, tracking maternal and neonatal deaths, institutional deliveries. HMIS officials reported that MCTS is useful for monitoring individual health status especially the status of the mother and child and HMIS being helpful as a health facility monitoring tool. Conclusion The study used a small sample size, hence similar type of studies are required with large sample size to understand the perspectives and challenges of HMIS officials in the implementation of HMIS. PMID:27504314

Mars Sample Handling Protocol Workshop Series: Workshop 4

NASA Technical Reports Server (NTRS)

Race Margaret S. (Editor); DeVincenzi, Donald L. (Editor); Rummel, John D. (Editor); Acevedo, Sara E. (Editor)

2001-01-01

In preparation for missions to Mars that will involve the return of samples to Earth, it will be necessary to prepare for the receiving, handling, testing, distributing, and archiving of martian materials here on Earth. Previous groups and committees have studied selected aspects of sample return activities, but specific detailed protocols for the handling and testing of returned samples must still be developed. To further refine the requirements for sample hazard testing and to develop the criteria for subsequent release of sample materials from quarantine, the NASA Planetary Protection Officer convened a series of workshops in 2000-2001. The overall objective of the Workshop Series was to produce a Draft Protocol by which returned martian sample materials can be assessed for biological hazards and examined for evidence of life (extant or extinct) while safeguarding the purity of the samples from possible terrestrial contamination. This report also provides a record of the proceedings of Workshop 4, the final Workshop of the Series, which was held in Arlington, Virginia, June 5-7, 2001. During Workshop 4, the sub-groups were provided with a draft of the protocol compiled in May 2001 from the work done at prior Workshops in the Series. Then eight sub-groups were formed to discuss the following assigned topics: Review and Assess the Draft Protocol for Physical/Chemical Testing Review and Assess the Draft Protocol for Life Detection Testing Review and Assess the Draft Protocol for Biohazard Testing Environmental and Health/Monitoring and Safety Issues Requirements of the Draft Protocol for Facilities and Equipment Contingency Planning for Different Outcomes of the Draft Protocol Personnel Management Considerations in Implementation of the Draft Protocol Draft Protocol Implementation Process and Update Concepts This report provides the first complete presentation of the Draft Protocol for Mars Sample Handling to meet planetary protection needs. This Draft Protocol, which was compiled from deliberations and recommendations from earlier Workshops in the Series, represents a consensus that emerged from the discussions of all the sub-groups assembled over the course of the five Workshops of the Series. These discussions converged on a conceptual approach to sample handling, as well as on specific analytical requirements. Discussions also identified important issues requiring attention, as well as research and development needed for protocol implementation.

Evaluation of storage and filtration protocols for alpine/subalpine lake water quality samples

Treesearch

John L. Korfmacher; Robert C. Musselman

2007-01-01

Many government agencies and other organizations sample natural alpine and subalpine surface waters using varying protocols for sample storage and filtration. Simplification of protocols would be beneficial if it could be shown that sample quality is unaffected. In this study, samples collected from low ionic strength waters in alpine and subalpine lake inlets...

Effects of child maltreatment and inherited liability on antisocial development: an official records study.

PubMed

Jonson-Reid, Melissa; Presnall, Ned; Drake, Brett; Fox, Louis; Bierut, Laura; Reich, Wendy; Kane, Phyllis; Todd, Richard D; Constantino, John N

2010-04-01

Evidence is steadily accumulating that a preventable environmental hazard, child maltreatment, exerts causal influences on the development of long-standing patterns of antisocial behavior in humans. The relationship between child maltreatment and antisocial outcome, however, has never previously been tested in a large-scale study in which official reports (rather than family member reports) of child abuse and neglect were incorporated, and genetic influences comprehensively controlled for. We cross-referenced official report data on child maltreatment from the Missouri Division of Social Services (DSS) with behavioral data from 4,432 epidemiologically ascertained Missouri twins from the Missouri Twin Registry (MOTWIN). We performed a similar procedure for a clinically ascertained sample of singleton children ascertained from families affected by alcohol dependence participating in the Collaborative Study on the Genetics of Alcoholism (COGA; n = 428) to determine whether associations observed in the general population held true in an "enriched" sample at combined inherited and environmental risk for antisocial development. For both the twin and clinical samples, the additive effects (not interactive effects) of maltreatment and inherited liability on antisocial development were confirmed and were highly statistically significant. Child maltreatment exhibited causal influence on antisocial outcome when controlling for inherited liability in both the general population and in a clinically ascertained sample. Official report maltreatment data represents a critical resource for resolving competing hypotheses on genetic and environmental causation of child psychopathology, and for assessing intervention outcomes in efforts to prevent antisocial development.

Adaptation of occupants with its environment in the official residence (case study: Housing of TNI AD Gaperta)

NASA Astrophysics Data System (ADS)

Nirfalini Aulia, Dwira; Aritonang, Cindy

2018-03-01

An official residence is a housing provided by the state and used as a residence occupied by the official duties of officials and civil servants during their service in the city. The property rights of the official residence have limit, only valid while the residents serve in the city. The process of adaptation becomes indispensable because, in the early days of occupying the housing, residents will face a new social environment, which may be different from their previous environment. Furthermore, backgrounds such as economic, cultural, and social factors of each occupant will also determine the adaptation process that occurs. This research aims to find out and analyze adaptation process of the official residence’s dwellers to its environment. This study used the descriptive-qualitative method by interviewing ten occupants who selected by purposive sampling method. Results of research indicated that the most adaptation process occurs adaptation by the reaction such as adding the number of room and service area.

7 CFR 301.92-11 - Inspection and sampling protocols.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 5 2010-01-01 2010-01-01 false Inspection and sampling protocols. 301.92-11 Section... Inspection and sampling protocols. Type(s) of plants in the nursery Type(s) of plants shipped interstate... interstate. (1) Annual inspection, sampling, and testing—(i) Inspection. The nursery must be inspected...

7 CFR 301.92-11 - Inspection and sampling protocols.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 5 2011-01-01 2011-01-01 false Inspection and sampling protocols. 301.92-11 Section... Inspection and sampling protocols. Type(s) of plants in the nursery Type(s) of plants shipped interstate... interstate. (1) Annual inspection, sampling, and testing—(i) Inspection. The nursery must be inspected...

Evaluation of the VIDAS Listeria (LIS) immunoassay for the detection of Listeria in foods using demi-Fraser and Fraser enrichment broths, as modification of AOAC Official Method 999.06 (AOAC Official Method 2004.06).

PubMed

Silbernagel, Karen M; Jechorek, Robert P; Kaufer, Amanda L; Johnson, Ronald L; Aleo, V; Brown, B; Buen, M; Buresh, J; Carson, M; Franklin, J; Ham, P; Humes, L; Husby, G; Hutchins, J; Jechorek, R; Jenkins, J; Kaufer, A; Kexel, N; Kora, L; Lam, L; Lau, D; Leighton, S; Loftis, M; Luc, S; Martin, J; Nacar, I; Nogle, J; Park, J; Schultz, A; Seymore, D; Smith, C; Smith, J; Thou, P; Ulmer, M; Voss, R; Weaver, V

2005-01-01

A multilaboratory study was conducted to compare the VIDAS LIS immunoassay with the standard cultural methods for the detection of Listeria in foods using an enrichment modification of AOAC Official Method 999.06. The modified enrichment protocol was implemented to harmonize the VIDAS LIS assay with the VIDAS LMO2 assay. Five food types--brie cheese, vanilla ice cream, frozen green beans, frozen raw tilapia fish, and cooked roast beef--at 3 inoculation levels, were analyzed by each method. A total of 15 laboratories representing government and industry participated. In this study, 1206 test portions were tested, of which 1170 were used in the statistical analysis. There were 433 positive by the VIDAS LIS assay and 396 positive by the standard culture methods. A Chi-square analysis of each of the 5 food types, at the 3 inoculation levels tested, was performed. The resulting average Chi square analysis, 0.42, indicated that, overall, there are no statistical differences between the VIDAS LIS assay and the standard methods at the 5% level of significance.

Get with the System: General Systems Theory for Business Officials.

ERIC Educational Resources Information Center

Graczyk, Sandra L.

1993-01-01

An introduction to general systems theory and an overview of vocabulary and concepts are presented to introduce school business officials to systems thinking and to foster its use as an analytical tool. The theory is then used to analyze a sample problem: planning changes to a district's administrative computer system. (eight references) (MLF)

A comparison of single and multiple stressor protocols to assess acute stress in a coastal shark species, Rhizoprionodon terraenovae.

PubMed

Hoffmayer, Eric R; Hendon, Jill M; Parsons, Glenn R; Driggers, William B; Campbell, Matthew D

2015-10-01

Elasmobranch stress responses are traditionally measured in the field by either singly or serially sampling an animal after a physiologically stressful event. Although capture and handling techniques are effective at inducing a stress response, differences in protocols could affect the degree of stress experienced by an individual, making meaningful comparisons between the protocols difficult, if not impossible. This study acutely stressed Atlantic sharpnose sharks, Rhizoprionodon terraenovae, by standardized capture (rod and reel) and handling methods and implemented either a single or serial blood sampling protocol to monitor four indicators of the secondary stress response. Single-sampled sharks were hooked and allowed to swim around the boat until retrieved for a blood sample at either 0, 15, 30, 45, or 60 min post-hooking. Serially sampled sharks were retrieved, phlebotomized, released while still hooked, and subsequently resampled at 15, 30, 45, and 60 min intervals post-hooking. Blood was analyzed for hematocrit, and plasma glucose, lactate, and osmolality levels. Although both single and serial sampling protocols resulted in an increase in glucose, no significant difference in glucose level was found between protocols. Serially sampled sharks exhibited cumulatively heightened levels for lactate and osmolality at all time intervals when compared to single-sampled animals at the same time. Maximal concentration differences of 217.5, 9.8, and 41.6 % were reported for lactate, osmolality, and glucose levels, respectively. Hematocrit increased significantly over time for the single sampling protocol but did not change significantly during the serial sampling protocol. The differences in resultant blood chemistry levels between implemented stress protocols and durations are significant and need to be considered when assessing stress in elasmobranchs.

A Draft Test Protocol for Detecting Possible Biohazards in Martian Samples Returned to Earth

NASA Technical Reports Server (NTRS)

Rummel, John D. (Editor); Race, Margaret S.; DeVincenzi, Donald L.; Schad, P. Jackson; Stabekis, Pericles D.; Viso, Michel; Acevedo, Sara E.

2002-01-01

This document presents the first complete draft of a protocol for detecting possible biohazards in Mars samples returned to Earth: it is the final product of the Mars Sample Handling Protocol Workshop Series. convened in 2000-2001 by NASA's Planetary Protection Officer. The goal of the five-workshop Series vas to develop a comprehensive protocol by which returned martian sample materials could be assessed k r the presence of any biological hazard(s) while safeguarding the purity of the samples from possible terrestrial contamination.

77 FR 5492 - Magnuson-Stevens Act Provisions; General Provisions for Domestic Fisheries; Application for...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-02-03

... assess the performance of an approved sampling protocol and to allow for continued sample collection and... developmental sampling protocol. While this application was being reviewed and was available for public comment, the sampling protocol being tested was adopted into the National Shellfish Sanitation Program by the...

Autophagy and TGF-Beta Antagonist Signaling in Breast Cancer at Premetastatic Sites

DTIC Science & Technology

2015-06-01

dormant legions. These inhibitors will be the drug leads for further medicinal chemistry and preclinical/clinical studies. 4 Body Overview Over the...autophagy, largely due to unexpected half-year delay of the official approval of our ACURO animal protocol . Below we report our progress, starting with...sections taken at various times after tail vein injection will enable us to verify that the anti-Coco MAb does not affect extravasation or homing but

Study of Managerial Challenges Confronting a New Agency: The Case of the Malaysian Maritime Enforcement Agency

DTIC Science & Technology

2015-06-01

of the author and do not reflect the official policy or position of the Department of Defense or the U.S. Government . IRB Protocol number ____N...maximum 200 words) The government of Malaysia decided to establish a new dedicated agency for law enforcement in the Malaysian Maritime Zone, in...CONFRONTING A NEW AGENCY: THE CASE OF THE MALAYSIAN MARITIME ENFORCEMENT AGENCY ABSTRACT The government of Malaysia decided to establish a

Shaping the National Guard in a Post-War Environment

DTIC Science & Technology

2012-09-01

IRR Individual Ready Reserve xiv JCS Joint Chiefs of Staff JFHQ Joint Forces Headquarters JTF Joint Task Force LAPD Los Angeles ... changing -of- the -guard/. 35 budget is a mirror of 2010, with future budgets projected to be capped at 2009 levels . In a troubled economy, DoD is...thesis are those of the author and do not reflect the official policy or position of the Department of Defense or the U.S. Government. IRB Protocol

Altered standards of care during an influenza pandemic: identifying ethical, legal, and practical principles to guide decision making.

PubMed

Levin, Donna; Cadigan, Rebecca Orfaly; Biddinger, Paul D; Condon, Suzanne; Koh, Howard K

2009-12-01

Although widespread support favors prospective planning for altered standards of care during mass casualty events, the literature includes few, if any, accounts of groups that have formally addressed the overarching policy considerations at the state level. We describe the planning process undertaken by public health officials in the Commonwealth of Massachusetts, along with community and academic partners, to explore the issues surrounding altered standards of care in the event of pandemic influenza. Throughout 2006, the Massachusetts Department of Public Health and the Harvard School of Public Health Center for Public Health Preparedness jointly convened a working group comprising ethicists, lawyers, clinicians, and local and state public health officials to consider issues such as allocation of antiviral medications, prioritization of critical care, and state seizure of private assets. Community stakeholders were also engaged in the process through facilitated discussion of case scenarios focused on these and other issues. The objective of this initiative was to establish a framework and some fundamental principles that would subsequently guide the process of establishing specific altered standards of care protocols. The group collectively identified 4 goals and 7 principles to guide the equitable allocation of limited resources and establishment of altered standards of care protocols. Reviewing and analyzing this process to date may serve as a resource for other states.

Longitudinal analysis of serological tests officially adopted by the Brazilian Ministry of Health for the diagnosis of canine visceral leishmaniasis in dogs vaccinated with Leishmune®.

PubMed

Marcondes, Mary; de Lima, Valéria Marçal Félix; de Araújo, Maria de Fátima Lereno; Hiramoto, Roberto Mitsuyoshi; Tolezano, José Eduardo; Vieira, Rafael F C; Biondo, Alexander W

2013-11-08

Development of vaccines against canine visceral leishmaniasis (CVL) may provide a prophylactic barrier, but antibody response detected by standard diagnostic techniques may not separate vaccinated from naturally infected dogs. Moreover, anti-Leishmania antibody levels in vaccinated dogs may be detectable for months. Accordingly, the aim of the present study was to comparatively evaluate an "in-house" ELISA with three serological tests officially adopted by the Brazilian Ministry of Health for the diagnosis of CVL in dogs vaccinated with Leishmune(®). A total of 18 mongrel dogs were submitted to a complete protocol of the vaccine, monitored and evaluated in 5 times (T0-T4) up to 180 days after T0. Twenty-one days after the first dose (T1), 50% of the dogs were seropositive by the "in-house" ELISA and 5.5% by IFAT, while by the official ELISA and DPP(®) CVL rapid test all dogs tested negative. At time T2, 42 days after of the first dose, 100%, 83.3%, 11.1%, and 5.5% of the dogs were seropositive by the "in-house" ELISA, IFAT, official ELISA kit and the DPP(®) CVL rapid test, respectively. Ninety days after the first dose (T3), 100%, 83.3%, 72.2% and 33.3% of the dogs were seropositive by the "in-house" ELISA, official ELISA kit, IFAT, and the DPP(®) CVL rapid test, respectively. Finally, at time T4, 88.8%, 33.3%, 11.1% and 5.5% of the dogs were seropositive by the "in-house" ELISA, official ELISA kit, DPP(®) CVL rapid test and IFAT, respectively. In conclusion, dogs vaccinated with Leishmune(®) cross-react by an "in-house" ELISA and by the three official Brazilian serological tests for the diagnosis of canine visceral leishmaniasis up to six months after the first vaccine dose, and may be mistakenly diagnosed and removed. Copyright © 2013 Elsevier B.V. All rights reserved.

Recommended protocols for sampling macrofungi

Treesearch

Gregory M. Mueller; John Paul Schmit; Sabine M. Hubndorf Leif Ryvarden; Thomas E. O' Dell; D. Jean Lodge; Patrick R. Leacock; Milagro Mata; Loengrin Umania; Qiuxin (Florence) Wu; Daniel L. Czederpiltz

2004-01-01

This chapter discusses several issues regarding reommended protocols for sampling macrofungi: Opportunistic sampling of macrofungi, sampling conspicuous macrofungi using fixed-size, sampling small Ascomycetes using microplots, and sampling a fixed number of downed logs.

National Sample Assessment Protocols

ERIC Educational Resources Information Center

Ministerial Council on Education, Employment, Training and Youth Affairs (NJ1), 2012

2012-01-01

These protocols represent a working guide for planning and implementing national sample assessments in connection with the national Key Performance Measures (KPMs). The protocols are intended for agencies involved in planning or conducting national sample assessments and personnel responsible for administering associated tenders or contracts,…

A Draft Test Protocol for Detecting Possible Biohazards in Martian Samples Returned to Earth

NASA Technical Reports Server (NTRS)

Rummel, John D.; Race, Margaret S.; DeVinenzi, Donald L.; Schad, P. Jackson; Stabekis, Pericles D.; Viso, Michel; Acevedo, Sara E.

2002-01-01

This document presents the first complete draft of a protocol for detecting possible biohazards in Mars samples returned to Earth; it is the final product of the Mars Sample Handling Protocol Workshop Series, convened in 2000-2001 by NASA's Planetary Protection Officer. The goal of the five-workshop Series vas to develop a comprehensive protocol by which returned martian sample materials could be assessed for the presence of any biological hazard(s) while safeguarding the purity of the samples from possible terrestrial contamination The reference numbers for the proceedings from the five individual Workshops.

English Language Teaching in Spain: Do Textbooks Comply with the Official Methodological Regulations? A Sample Analysis

ERIC Educational Resources Information Center

Criado, Raquel; Sanchez, Aquilino

2009-01-01

The goal of this paper is to verify up to what point ELT textbooks used in Spanish educational settings comply with the official regulations prescribed, which fully advocate the Communicative Language Teaching Method (CLT). For that purpose, seven representative coursebooks of different educational levels and modalities in Spain--secondary, upper…

Salmonella detection in poultry samples. Comparison of two commercial real-time PCR systems with culture methods for the detection of Salmonella spp. in environmental and fecal samples of poultry.

PubMed

Sommer, D; Enderlein, D; Antakli, A; Schönenbrücher, H; Slaghuis, J; Redmann, T; Lierz, M

2012-01-01

The efficiency of two commercial PCR methods based on real-time technology, the foodproof® Salmonella detection system and the BAX® PCR Assay Salmonella system was compared to standardized culture methods (EN ISO 6579:2002 - Annex D) for the detection of Salmonella spp. in poultry samples. Four sample matrices (feed, dust, boot swabs, feces) obtained directly from poultry flocks, as well as artificially spiked samples of the same matrices, were used. All samples were tested for Salmonella spp. using culture methods first as the gold standard. In addition samples spiked with Salmonella Enteridis were tested to evaluate the sensitivity of both PCR methods. Furthermore all methods were evaluated in an annual ring-trial of the National Salmonella Reference Laboratory of Germany. Salmonella detection in the matrices feed, dust and boot swabs were comparable in both PCR systems whereas the results from feces differed markedly. The quality, especially the freshness, of the fecal samples had an influence on the sensitivity of the real-time PCR and the results of the culture methods. In fresh fecal samples an initial spiking level of 100cfu/25g Salmonella Enteritidis was detected. Two-days-dried fecal samples allowed the detection of 14cfu/25g. Both real- time PCR protocols appear to be suitable for the detection of Salmonella spp. in all four matrices. The foodproof® system detected eight samples more to be positive compared to the BAX® system, but had a potential false positive result in one case. In 7-days-dried samples none of the methods was able to detect Salmonella likely through letal cell damage. In general the advantage of PCR analyses over the culture method is the reduction of working time from 4-5 days to only 2 days. However, especially for the analysis of fecal samples official validation should be conducted according to the requirement of EN ISO6579:2002 - Annex D.

Personnel-General: A Guide to Protocol and Etiquette for Official Entertainment

DTIC Science & Technology

2001-12-11

they are not announced and will have to seek out their host and apologize for their tardiness . At a large function it may not be possible for...X PANAMA X 31DA PAM 600–60 • 11 December 2001 Table 7–1 Record of dietary restrictions—Continued PARAGUAY X PERU X PHILIPPINES X POLAND X PORTUGAL X...President of the Republic of Peru PHILIPPINES His Excellency, the President of the Republic of the Philippines POLAND His Excellency, the President of

Increased Vulnerability to Soman Exposure in Aged Compared to Adult F344 Rats

DTIC Science & Technology

2016-10-01

or the U.S. Government. The experimental protocol was approved by the Animal Care and Use Committee at the United States Army Medical Research...Laboratory Animals and the Animal Welfare Act of 1966 (P.L. 89-544), as amended. The use of trade names does not constitute an official endorsement or...medical countermeasures to CWNAs has been conducted on young adult male animal models of CWNA exposure, focusing on the potential for drug therapies to

A System Dynamics Approach to the Efficacy of Oxime Therapy in Sub Lethal Exposure to Sarin Gas

DTIC Science & Technology

2015-06-18

effective treatments , including antidotes, is considered to contribute to this high mortality rate (Buckley et al., 2004:1231). The efficacy of current...officials to reduce the risk associated with high -consequence threats”. Nerve agents, such as Sarin gas, are considered high consequence threats...The threat of use of agents such as Sarin is as much a threat today as any other time in our history. However, the suggested treatment protocol is

Soil Carbon Variability and Change Detection in the Forest Inventory Analysis Database of the United States

NASA Astrophysics Data System (ADS)

Wu, A. M.; Nater, E. A.; Dalzell, B. J.; Perry, C. H.

2014-12-01

The USDA Forest Service's Forest Inventory Analysis (FIA) program is a national effort assessing current forest resources to ensure sustainable management practices, to assist planning activities, and to report critical status and trends. For example, estimates of carbon stocks and stock change in FIA are reported as the official United States submission to the United Nations Framework Convention on Climate Change. While the main effort in FIA has been focused on aboveground biomass, soil is a critical component of this system. FIA sampled forest soils in the early 2000s and has remeasurement now underway. However, soil sampling is repeated on a 10-year interval (or longer), and it is uncertain what magnitude of changes in soil organic carbon (SOC) may be detectable with the current sampling protocol. We aim to identify the sensitivity and variability of SOC in the FIA database, and to determine the amount of SOC change that can be detected with the current sampling scheme. For this analysis, we attempt to answer the following questions: 1) What is the sensitivity (power) of SOC data in the current FIA database? 2) How does the minimum detectable change in forest SOC respond to changes in sampling intervals and/or sample point density? Soil samples in the FIA database represent 0-10 cm and 10-20 cm depth increments with a 10-year sampling interval. We are investigating the variability of SOC and its change over time for composite soil data in each FIA region (Pacific Northwest, Interior West, Northern, and Southern). To guide future sampling efforts, we are employing statistical power analysis to examine the minimum detectable change in SOC storage. We are also investigating the sensitivity of SOC storage changes under various scenarios of sample size and/or sample frequency. This research will inform the design of future FIA soil sampling schemes and improve the information available to international policy makers, university and industry partners, and the public.

A multigear protocol for sampling crayfish assemblages in Gulf of Mexico coastal streams

Treesearch

William R. Budnick; William E. Kelso; Susan B. Adams; Michael D. Kaller

2018-01-01

Identifying an effective protocol for sampling crayfish in streams that vary in habitat and physical/chemical characteristics has proven problematic. We evaluated an active, combined-gear (backpack electrofishing and dipnetting) sampling protocol in 20 Coastal Plain streams in Louisiana. Using generalized linear models and rarefaction curves, we evaluated environmental...

7 CFR 58.56 - Incubation of product samples.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 3 2012-01-01 2012-01-01 false Incubation of product samples. 58.56 Section 58.56 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Standards... Packaging Products with Official Identification § 58.56 Incubation of product samples. (a) Samples of...

7 CFR 58.56 - Incubation of product samples.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 3 2013-01-01 2013-01-01 false Incubation of product samples. 58.56 Section 58.56 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Standards... Packaging Products with Official Identification § 58.56 Incubation of product samples. (a) Samples of...

7 CFR 58.56 - Incubation of product samples.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 3 2011-01-01 2011-01-01 false Incubation of product samples. 58.56 Section 58.56 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Standards... Packaging Products with Official Identification § 58.56 Incubation of product samples. (a) Samples of...

7 CFR 58.56 - Incubation of product samples.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 3 2010-01-01 2010-01-01 false Incubation of product samples. 58.56 Section 58.56 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Standards... Packaging Products with Official Identification § 58.56 Incubation of product samples. (a) Samples of...

7 CFR 58.56 - Incubation of product samples.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 3 2014-01-01 2014-01-01 false Incubation of product samples. 58.56 Section 58.56 Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Standards... Packaging Products with Official Identification § 58.56 Incubation of product samples. (a) Samples of...

7 CFR 94.3 - Analyses performed and locations of laboratories.

Code of Federal Regulations, 2011 CFR

2011-01-01

... applicable plant on the official certificate. (b) Mandatory egg product samples for Salmonella are required... recognized laboratories for analyzing routine egg product samples for Salmonella. (c) Mandatory egg product...

Gaps in the Substance Use Disorder Treatment Referral Process: Provider Perceptions.

PubMed

Blevins, Claire E; Rawat, Nishi; Stein, Michael D

2018-05-07

The demand for substance use disorder treatment is increasing, fueled by the opioid epidemic and the Affordable Care Act mandate to treat substance use disorders. The increased demand for treatment, however, is not being met by a corresponding increase in access to or availability of treatment. This report focuses specifically on the treatment referral process, which we have identified as 1 of the key barriers to timely and effective treatment. Difficulties in referral to substance use disorder treatment are examined through the lens of providers who make referrals (ie, referral source) and individuals who work in substance use disorder facilities (ie, referral recipient). Administrative officials, emergency department physicians, addiction physicians, government officials, providers, insurance officials, and mental health advocates (n = 59) were interviewed on the referral process protocol, challenges for providers and others making referrals, and issues with substance use treatment facility intake procedures. Several main themes were identified as barriers in the process: difficulties in determining patient eligibility, lack of transparency regarding treatment capacity, referral source knowledge/understanding of options, and issues with communication between referral source and recipient. We then proposed several solutions to address specific barriers. Current gaps in the referral process cause delays to care. Improving systems would involve addressing these themes and expanding the use of appropriate treatments for the many patients in need.

7 CFR 61.33 - Equipment of sampler; contents of certificate.

Code of Federal Regulations, 2013 CFR

2013-01-01

... sampler shall have available suitable triers or sampling tools, sample containers, scales, seed cleaners, seed mixers, and air-tight containers for enclosing and forwarding the official samples to licensed... identification of the lot from which the sample was drawn; (d) The date on which the sample was drawn; (e) The...

Interdisciplinary consensus on the uses and technique of MR-guided vacuum-assisted breast biopsy (VAB): results of a European consensus meeting.

PubMed

Heywang-Köbrunner, Sylvia H; Sinnatamby, Ruchi; Lebeau, Annette; Lebrecht, Antje; Britton, Peter D; Schreer, Ingrid

2009-11-01

Quality assurance of MR-guided vacuum-assisted breast biopsy (VAB). A consensus was achieved based on the existing literature and experience of an interdisciplinary group comprising European specialists in breast imaging and VAB. Full imaging work-up must be completed according to existing standards before an indication for MR-guided VAB is established. The procedure should be reserved for lesions demonstrable by MRI alone. Acquisition of >24 cores (11-Gauge) should be routinely attempted, with the intention of sufficiently removing small lesions for accurate diagnosis. Following biopsy the patient should be re-imaged to demonstrate the biopsy site and its proximity to the lesion and hence the likely accuracy of the sampling. All patients should be discussed in a regular interdisciplinary conference and a documented consensus reached regarding patient management. Regular audit and review of all MR-guided VAB results and subsequent follow-up are recommended. This consensus includes protocols for the indication, performance parameters, interdisciplinary interpretation therapeutic recommendation, documentation and follow-up of MR-guided VAB. It does not replace official recommendations for percutaneous biopsy.

Parameters for determining inoculated pack/challenge study protocols.

PubMed

2010-01-01

The National Advisory Committee on Microbiological Criteria for Foods developed guidelines for conducting challenge studies on pathogen inhibition and inactivation studies in a variety of foods. The document is intended for use by the food industry, including food processors, food service operators, and food retailers; federal, state, and local food safety regulators; public health officials; food testing laboratories; and process authorities. The document is focused on and limited to bacterial inactivation and growth inhibition and does not make specific recommendations with respect to public health. The Committee concluded that challenge studies should be designed considering the most current advances in methodologies, current thinking on pathogens of concern, and an understanding of the product preparation, variability, and storage conditions. Studies should be completed and evaluated under the guidance of an expert microbiologist in a qualified laboratory and should include appropriate statistical design and data analyses. This document provides guidelines for choice of microorganisms for studies, inoculum preparation, inoculum level, methods of inoculation, incubation temperatures and times, sampling considerations, and interpreting test results. Examples of appropriately designed growth inhibition and inactivation studies are provided.

16 CFR 1500.214 - Examinations and investigations; samples.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Examinations and investigations; samples... § 1500.214 Examinations and investigations; samples. When any officer or employee of the Commission...” includes examinations and tests. (b) The owner of a hazardous substance of which an official sample is...

A distance limited method for sampling downed coarse woody debris

Treesearch

Jeffrey H. Gove; Mark J. Ducey; Harry T. Valentine; Michael S. Williams

2012-01-01

A new sampling method for down coarse woody debris is proposed based on limiting the perpendicular distance from individual pieces to a randomly chosen sample point. Two approaches are presented that allow different protocols to be used to determine field measurements; estimators for each protocol are also developed. Both protocols are compared via simulation against...

[Examination of analytical method for triphenyltin (TPT) and tributyltin (TBT) to revise the official methods based on "Act on the Control of Household Products Containing Harmful Substances"].

PubMed

Kawakami, Tsuyoshi; Isama, Kazuo; Nakashima, Harunobu; Yoshida, Jin; Ooshima, Tomoko; Ohno, Hiroyuki; Uemura, Hitoshi; Shioda, Hiroko; Kikuchi, Yoko; Matsuoka, Atsuko; Nishimura, Tetsuji

2012-01-01

The use of triphenyltin (TPT) and tributyltin (TBT) in some household products is banned by "Act on the Control of Household Products Containing Harmful Substances" in Japan. To revise the official analytical method, the method for detecting these organotin compounds was examined in six laboratories using a textile product, water-based adhesive, oil-based paint, which contained known amounts of TPT and TBT (0.1, 1.0, 10 μg/g). TPT and TBT were measured by GC-MS after ethyl-derivation with sodium tetraethylborate. The TBT recoveries in the samples were 70-120%. The TPT recoveries in the water-based adhesive samples were 80-110%, while its concentrations in the textile product and oil-based paint samples decreased because of dephenylation during storage. However, the precision of the method examined was satisfactory because most coefficients of variation for TPT and TBT in the samples were less than 10%. Furthermore, the revised method was able to detect concentrations lower than the officially regulated value. However, the sample matrix and the condition of analytical instrument might affect the estimated TPT and TBT concentrations. Therefore, the revised method may not be suitable for quantitative tests; rather, it can be employed to judge the acceptable levels of these organotin compounds by comparing the values of control sample containing regulated amounts of TPT and TBT with those for an unknown sample, with deuterated TPT and TBT as surrogate substances. It is desirable that TPT in textile and oil-based paint samples are analyzed immediately after the samples obtained because of the decomposition of TPT.

7 CFR 29.34 - Sample seal.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 2 2011-01-01 2011-01-01 false Sample seal. 29.34 Section 29.34 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... INSPECTION Regulations Definitions § 29.34 Sample seal. A seal approved by the Director for sealing official...

7 CFR 29.34 - Sample seal.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 2 2010-01-01 2010-01-01 false Sample seal. 29.34 Section 29.34 Agriculture Regulations of the Department of Agriculture AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing... INSPECTION Regulations Definitions § 29.34 Sample seal. A seal approved by the Director for sealing official...

Youth Attitude Tracking Study II Wave 17 -- Fall 1986.

DTIC Science & Technology

1987-06-01

decision, unless so designated by other official documentation. TABLE OF CONTENTS Page PREFACE ................................................. xi...Segmentation Analyses .......................... 2-7 .3. METHODOLOGY OF YATS II....................................... 3-1 A. Sampling Design Overview...Sampling Design , Estimation Procedures and Estimated Sampling Errors ................................. A-i Appendix B: Data Collection Procedures

The GLOBE/Madagascar Malaria Project: Creating Student/Educator/Scientist Partnerships With Regional Impact

NASA Astrophysics Data System (ADS)

Brooks, D.; Boger, R.; Rafalimanana, A.

2006-05-01

Malaria is a parasitic disease spread by mosquitoes in the genus Anopheles. It causes more than 300,000,000 acute illnesses and more than one million deaths annually, including the death of one African child every 30 seconds. Recent epidemiological trends include increases in malaria mortality and the emergence of drug-resistant parasites. Some experts believe that predicted climate changes during the 21st century will bring malaria to areas where it is not now common. The GLOBE Program is currently collaborating with students, educators, scientists, health department officials, and government officials in Madagascar to develop a program that combines existing GLOBE protocols for measuring atmospheric and water quality parameters with a new protocol for collecting and identifying mosquito larvae at the genus (Anopheles and non-Anopheles) level. There are dozens of Anopheles species and sub-species that are adapted to a wide range of micro-environmental conditions encountered in Madagascar's variable climate. Local data collection is essential because mosquitoes typically spend their entire lives within a few kilometers of their breeding sites. The GLOBE Program provides an ideal framework for such a project because it offers a highly structured system for defining experiment protocols that ensure consistent procedures, a widely dispersed network of observing sites, and a centralized data collection and reporting system. Following a series of training activities in 2005, students in Madagascar are now beginning to collect data. Basic environmental parameters and first attempts at larvae collection and identification are presented. Results from this project can be used to increase public awareness of malaria, to provide new scientific data concerning environmental impacts on mosquito breeding, and to provide better information for guiding effective mitigation strategies. Problems encountered include difficulties in visiting and communicating with remote school sites. These are typical problems in developing tropical countries where malaria is endemic and their solution benefits the entire scientific and educational infrastructure in those countries.

VALIDATION OF ANALYTICAL METHODS AND INSTRUMENTATION FOR BERYLLIUM MEASUREMENT: REVIEW AND SUMMARY OF AVAILABLE GUIDES, PROCEDURES, AND PROTOCOLS

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

Ekechukwu, A

Method validation is the process of evaluating whether an analytical method is acceptable for its intended purpose. For pharmaceutical methods, guidelines from the United States Pharmacopeia (USP), International Conference on Harmonisation (ICH), and the United States Food and Drug Administration (USFDA) provide a framework for performing such valications. In general, methods for regulatory compliance must include studies on specificity, linearity, accuracy, precision, range, detection limit, quantitation limit, and robustness. Elements of these guidelines are readily adapted to the issue of validation for beryllium sampling and analysis. This document provides a listing of available sources which can be used to validatemore » analytical methods and/or instrumentation for beryllium determination. A literature review was conducted of available standard methods and publications used for method validation and/or quality control. A comprehensive listing of the articles, papers and books reviewed is given in the Appendix. Available validation documents and guides are listed therein; each has a brief description of application and use. In the referenced sources, there are varying approches to validation and varying descriptions of the valication process at different stages in method development. This discussion focuses on valication and verification of fully developed methods and instrumentation that have been offered up for use or approval by other laboratories or official consensus bodies such as ASTM International, the International Standards Organization (ISO) and the Association of Official Analytical Chemists (AOAC). This review was conducted as part of a collaborative effort to investigate and improve the state of validation for measuring beryllium in the workplace and the environment. Documents and publications from the United States and Europe are included. Unless otherwise specified, all referenced documents were published in English.« less

7 CFR 800.82 - Sampling provisions by level of service.

Code of Federal Regulations, 2014 CFR

2014-01-01

... criteria, and a sample obtained with a probe at the time of the reinspection or appeal, generally, shall be... instances where original inspection results are based on samples obtained by probe, the decision as to whether file samples or new samples obtained by probe are to be used shall be made by the official...

Correlation Between Iron and alpha and pi Glutathione-S-Transferase Levels in Humans

DTIC Science & Technology

2012-09-01

assays were performed as described in the Biotrin High Sensitivity Alpha GST EIA kit protocol. First, serum samples were diluted 1:10 with wash solution...immunosorbent assays were performed as described in the Biotrin Pi GST EIA kit protocol. First, plasma samples were diluted 1:5 with sample diluent...immunosorbent assays were performed as described in the AssayMax Human Transferrin ELISA kit protocol. First, serum samples were diluted 1:2000 with MIX

Methods for Monitoring Fish Communities of Buffalo National River and Ozark National Scenic Riverways in the Ozark Plateaus of Arkansas and Missouri: Version 1.0

USGS Publications Warehouse

Petersen, James C.; Justus, B.G.; Dodd, H.R.; Bowles, D.E.; Morrison, L.W.; Williams, M.H.; Rowell, G.A.

2008-01-01

Buffalo National River located in north-central Arkansas, and Ozark National Scenic Riverways, located in southeastern Missouri, are the two largest units of the National Park Service in the Ozark Plateaus physiographic province. The purpose of this report is to provide a protocol that will be used by the National Park Service to sample fish communities and collect related water-quality, habitat, and stream discharge data of Buffalo National River and Ozark National Scenic Riverways to meet inventory and long-term monitoring objectives. The protocol includes (1) a protocol narrative, (2) several standard operating procedures, and (3) supplemental information helpful for implementation of the protocol. The protocol narrative provides background information about the protocol such as the rationale of why a particular resource or resource issue was selected for monitoring, information concerning the resource or resource issue of interest, a description of how monitoring results will inform management decisions, and a discussion of the linkages between this and other monitoring projects. The standard operating procedures cover preparation, training, reach selection, water-quality sampling, fish community sampling, physical habitat collection, measuring stream discharge, equipment maintenance and storage, data management and analysis, reporting, and protocol revision procedures. Much of the information in the standard operating procedures was gathered from existing protocols of the U.S. Geological Survey National Water Quality Assessment program or other sources. Supplemental information that would be helpful for implementing the protocol is included. This information includes information on fish species known or suspected to occur in the parks, sample sites, sample design, fish species traits, index of biotic integrity metrics, sampling equipment, and field forms.

Determination of proline in honey: comparison between official methods, optimization and validation of the analytical methodology.

PubMed

Truzzi, Cristina; Annibaldi, Anna; Illuminati, Silvia; Finale, Carolina; Scarponi, Giuseppe

2014-05-01

The study compares official spectrophotometric methods for the determination of proline content in honey - those of the International Honey Commission (IHC) and the Association of Official Analytical Chemists (AOAC) - with the original Ough method. Results show that the extra time-consuming treatment stages added by the IHC method with respect to the Ough method are pointless. We demonstrate that the AOACs method proves to be the best in terms of accuracy and time saving. The optimized waiting time for the absorbance recording is set at 35min from the removal of reaction tubes from the boiling bath used in the sample treatment. The optimized method was validated in the matrix: linearity up to 1800mgL(-1), limit of detection 20mgL(-1), limit of quantification 61mgL(-1). The method was applied to 43 unifloral honey samples from the Marche region, Italy. Copyright © 2013 Elsevier Ltd. All rights reserved.

Tissue Sampling Guides for Porcine Biomedical Models.

PubMed

Albl, Barbara; Haesner, Serena; Braun-Reichhart, Christina; Streckel, Elisabeth; Renner, Simone; Seeliger, Frank; Wolf, Eckhard; Wanke, Rüdiger; Blutke, Andreas

2016-04-01

This article provides guidelines for organ and tissue sampling adapted to porcine animal models in translational medical research. Detailed protocols for the determination of sampling locations and numbers as well as recommendations on the orientation, size, and trimming direction of samples from ∼50 different porcine organs and tissues are provided in the Supplementary Material. The proposed sampling protocols include the generation of samples suitable for subsequent qualitative and quantitative analyses, including cryohistology, paraffin, and plastic histology; immunohistochemistry;in situhybridization; electron microscopy; and quantitative stereology as well as molecular analyses of DNA, RNA, proteins, metabolites, and electrolytes. With regard to the planned extent of sampling efforts, time, and personnel expenses, and dependent upon the scheduled analyses, different protocols are provided. These protocols are adjusted for (I) routine screenings, as used in general toxicity studies or in analyses of gene expression patterns or histopathological organ alterations, (II) advanced analyses of single organs/tissues, and (III) large-scale sampling procedures to be applied in biobank projects. Providing a robust reference for studies of porcine models, the described protocols will ensure the efficiency of sampling, the systematic recovery of high-quality samples representing the entire organ or tissue as well as the intra-/interstudy comparability and reproducibility of results. © The Author(s) 2016.

Lead Sampling Protocols: Why So Many and What Do They Tell You?

EPA Science Inventory

Sampling protocols can be broadly categorized based on their intended purpose of 1) Pb regulatory compliance/corrosion control efficacy, 2) Pb plumbing source determination or Pb type identification, and 3) Pb exposure assessment. Choosing the appropriate protocol is crucial to p...

NHEXAS PHASE I MARYLAND STUDY--LIST OF AVAILABLE DOCUMENTS: PROTOCOLS AND SOPS

EPA Science Inventory

This document lists available protocols and SOPs for the NHEXAS Phase I Maryland study. It identifies protocols and SOPs for the following study components: (1) Sample collection and field operations, (2) Sample analysis and general laboratory procedures, (3) Data Analysis Proced...

Early-life exposure to air pollutants and adverse pregnancy outcomes: protocol for a prospective cohort study in Beijing

PubMed Central

Song, Jing; Wei, Ling; Ma, Ying; Tian, Ning; Huang, Shi Yun; Dai, Yin Mei; Zhao, Li Hong; Kong, Yuan Yuan

2017-01-01

Introduction The association between early exposure to ambient air pollution and adverse pregnancy outcomes in China is unclear. This study will assess the risk of early-life exposure to air pollutants in Beijing and explore the viability of 8-hydroxydeoxyguanosine (8-OHdG) as a biological indicator to assess oxidative stress induced by early-life exposure to air pollution. Methods and analysis Here, 2500 women with singleton pregnancies and their infants will be recruited from the Beijing Obstetrics and Gynecology Hospital. We will collect nine types of biological samples, including maternal serum, urine, placental tissue, umbilical cord tissue and umbilical cord blood during all three trimesters. The air pollution data (particulate matter (PM)2.5, PM10 and similar factors) will be recorded at official fixed-site monitoring stations closest to where the pregnant women live. We plan to assess the effect of air pollutants on adverse pregnancy outcomes and infant respiratory and circulatory disease using Cox regression and competitive risk analysis and explore possible critical windows of exposure during pregnancy using daily pollutant concentrations averaged over various periods of pregnancy combined with individual activity and physiological parameters. Maternal and umbilical cord blood samples (1000 samples) will be randomly selected for 8-OHdG assays to assess the correlation between exposures to air pollutants and oxidative stress. We will determine whether air pollutant exposure or 8-OHdG levels are associated with adverse pregnancy outcomes. SPSS and SAS statistical software will be used for data analysis. Cox regression and competing risk analysis will be used to compute the HR and population attributable risk. Ethics and dissemination This research protocol has already been approved by the Medical Ethics Committee of Beijing Obstetrics and Gynecology Hospital. Written informed consent will be obtained from all study participants prior to enrolment. The results will be published in peer-reviewed journals or disseminated through conference presentations. Trial registration number This study has been registered in WHO International Clinical Trial Register—Chinese Clinical Trial Registry under registration number ChiCTR-ROC-16010181 (http :// www.chictr.org.cn / showproj.aspx ?proj=17328). PMID:28871018

Implications Of The Security Cooperation Office Transition in Afghanistan For Special Operations Forces: An Abbreviated Report of the Study’s Primary Findings

DTIC Science & Technology

2017-01-01

for working in an interagency environment can lead to mission success. From the Iraq case study , one former U.S. Forces–Iraq official felt that...of six historical case studies in which the mission of special operations forces (SOF) in country transitioned over time to some level of inclusion...explanation of the methodology applied for case study selec- tion, as well as adopted interview protocols, are provided in the long- form version of

Confocal Raman Microspectroscopy: The Measurement of VX Depth Profiles in Hairless Guinea Pig Skin and the Evaluation of RSDL

DTIC Science & Technology

2015-02-01

Defense, or the U.S. Government. The experimental protocol was approved by the Animal Care and Use Committee at the United States Army Medical Research...Laboratory Animals and the Animal Welfare Act of 1966 (P.L. 89-544), as amended. The use of trade names does not constitute an official endorsement or...neat VX (0.3 µl, 13-14 x LD50), using a specially designed template that allowed repeated Raman measurements on the same skin location. Animals were

Expansion of U.S. emergency medical service routing for stroke care: 2000-2010.

PubMed

Hanks, Natalie; Wen, Ge; He, Shuhan; Song, Sarah; Saver, Jeffrey L; Cen, Steven; Kim-Tenser, May; Mack, William; Sanossian, Nerses

2014-07-01

Organized stroke systems of care include preferential emergency medical services (EMS) routing to deliver suspected stroke patients to designated hospitals. To characterize the growth and implementation of EMS routing of stroke nationwide, we describe the proportion of stroke hospitalizations in the United States (U.S.) occurring within regions having adopted these protocols. We collected data on ischemic stroke using International Classification of Diseases-9 (ICD-9) coding from the Healthcare Cost and Utilization Project Nationwide Inpatient Sample (NIS) database from the years 2000-2010. The NIS contains all discharge data from 1,051 hospitals located in 45 states, approximating a 20% stratified sample. We obtained data on EMS systems of care from a review of archives, reports, and interviews with state emergency medical services (EMS) officials. A county or state was considered to be in transition if the protocol was adopted in the calendar year, with establishment in the year following transition. Nationwide, stroke hospitalizations remained constant over the course of the study period: 583,000 in 2000 and 573,000 in 2010. From 2000-2003 there were no states or counties participating in the NIS with EMS systems of care. The proportion of U.S. stroke hospitalizations occurring in jurisdictions with established EMS regional systems of acute stroke care increased steadily from 2004 to 2010 (1%, 13%, 28%, 30%, 30%, 34%, 49%). In 2010, 278,538 stroke hospitalizations, 49% of all U.S. stroke hospitalizations, occurred in areas with established EMS routing, with an additional 18,979 (3%) patients in regions undergoing a transition to EMS routing. In 2010, a majority of stroke patients in the U.S. were hospitalized in states with established or transitioning to organized stroke systems of care. This milestone coverage of half the U.S. population is a major advance in systematic stroke care and emphasizes the need for novel approaches to further extend access to stroke center care to all patients.

The do-not-resuscitate order in teaching hospitals.

PubMed

Evans, A L; Brody, B A

1985-04-19

We studied the use of do-not-resuscitate (DNR) orders at three teaching hospitals that did not have official protocols for such orders to see whether their use meets the goals (decision making before a crisis and promoting patient autonomy) that have been identified for such orders. We found that 20% of all patients had or were being considered for DNR orders, that the patient and/or family was usually involved (83%) in the decision not to resuscitate, but rarely involved (25%) in decisions to resuscitate, or in cases of no decision, that a wide range of care was provided to patients with a DNR status, and that partial resuscitative efforts would be employed in some cases. Our main conclusion in light of our findings is that DNR orders are currently not fulfilling their major goals. We offer six proposals for improving future DNR protocols.

Representativeness of laboratory sampling procedures for the analysis of trace metals in soil.

PubMed

Dubé, Jean-Sébastien; Boudreault, Jean-Philippe; Bost, Régis; Sona, Mirela; Duhaime, François; Éthier, Yannic

2015-08-01

This study was conducted to assess the representativeness of laboratory sampling protocols for purposes of trace metal analysis in soil. Five laboratory protocols were compared, including conventional grab sampling, to assess the influence of sectorial splitting, sieving, and grinding on measured trace metal concentrations and their variability. It was concluded that grinding was the most important factor in controlling the variability of trace metal concentrations. Grinding increased the reproducibility of sample mass reduction by rotary sectorial splitting by up to two orders of magnitude. Combined with rotary sectorial splitting, grinding increased the reproducibility of trace metal concentrations by almost three orders of magnitude compared to grab sampling. Moreover, results showed that if grinding is used as part of a mass reduction protocol by sectorial splitting, the effect of sieving on reproducibility became insignificant. Gy's sampling theory and practice was also used to analyze the aforementioned sampling protocols. While the theoretical relative variances calculated for each sampling protocol qualitatively agreed with the experimental variances, their quantitative agreement was very poor. It was assumed that the parameters used in the calculation of theoretical sampling variances may not correctly estimate the constitutional heterogeneity of soils or soil-like materials. Finally, the results have highlighted the pitfalls of grab sampling, namely, the fact that it does not exert control over incorrect sampling errors and that it is strongly affected by distribution heterogeneity.

9 CFR 327.11 - Receipts to importers for import product samples.

Code of Federal Regulations, 2010 CFR

2010-01-01

... product samples. 327.11 Section 327.11 Animals and Animal Products FOOD SAFETY AND INSPECTION SERVICE... laboratory examination are to be used exclusively for that purpose, official receipts shall be issued and... collected, date of collection, and that the sample was collected for laboratory examination. The duplicate...

[Breastfeeding indicators produced at time of vaccination in four Primary Care Centres in southern Santiago, Chile].

PubMed

Glisser, Mario Boris; Barragán, Tatiana del Carmen; Weisstaub, Gerardo

2016-01-01

To compare official breastfeeding (BF) data with those obtained by interviews conducted during regular vaccination visits. A pilot descriptive study with convenience sampling was conducted by interviewing guardians of children attending vaccination in four Primary Care Centres in south Santiago. BF prevalence indicators were calculated and stratified by age and education of mothers. A comparison was made between the results and the official ones reported by each Centre. Chi-squared (X2) was calculated to evaluate differences (P<.05) RESULTS: A total of 1990 cases were analysed, in which exclusive BF prevalence was 43.4%, 34.2% and 8.8%, at 2, 4, and 6 months, respectively. At the sixth month, official data (41%) was significantly higher (P<.001). Mothers with less than 12 years of schooling have a lower prevalence of exclusive BF at the 4th month than those with higher education (28.4% vs. 37.8%, respectively, P<.05). Even considering the small size of the sample studied, exclusive BF prevalence obtained is surprisingly lower than official reported data. That difference might be explained by: (a) children brought to vaccinations are roughly two fold the number brought to well-child clinics and, (b) potential bias in official data obtained by staff in charge of promotion and education on BF practices, which could distort the results. Further studies are needed to improve the methodology for collecting and analysis BF data. Copyright © 2015 Sociedad Chilena de Pediatría. Publicado por Elsevier España, S.L.U. All rights reserved.

Optimization of Sample Preparation for the Identification and Quantification of Saxitoxin in Proficiency Test Mussel Sample using Liquid Chromatography-Tandem Mass Spectrometry

PubMed Central

Harju, Kirsi; Rapinoja, Marja-Leena; Avondet, Marc-André; Arnold, Werner; Schär, Martin; Burrell, Stephen; Luginbühl, Werner; Vanninen, Paula

2015-01-01

Saxitoxin (STX) and some selected paralytic shellfish poisoning (PSP) analogues in mussel samples were identified and quantified with liquid chromatography-tandem mass spectrometry (LC-MS/MS). Sample extraction and purification methods of mussel sample were optimized for LC-MS/MS analysis. The developed method was applied to the analysis of the homogenized mussel samples in the proficiency test (PT) within the EQuATox project (Establishment of Quality Assurance for the Detection of Biological Toxins of Potential Bioterrorism Risk). Ten laboratories from eight countries participated in the STX PT. Identification of PSP toxins in naturally contaminated mussel samples was performed by comparison of product ion spectra and retention times with those of reference standards. The quantitative results were obtained with LC-MS/MS by spiking reference standards in toxic mussel extracts. The results were within the z-score of ±1 when compared to the results measured with the official AOAC (Association of Official Analytical Chemists) method 2005.06, pre-column oxidation high-performance liquid chromatography with fluorescence detection (HPLC-FLD). PMID:26610567

Sticky trap and stem-tap sampling protocols for the Asian citrus psyllid (Hemiptera: Psyllidae)

USDA-ARS?s Scientific Manuscript database

Sampling statistics were obtained to develop a sampling protocol for estimating numbers of adult Diaphorina citri in citrus using two different sampling methods: yellow sticky traps and stem–tap samples. A 4.0 ha block of mature orange trees was stratified into ten 0.4 ha strata and sampled using...

Protocol for determining bull trout presence

USGS Publications Warehouse

Peterson, James; Dunham, Jason B.; Howell, Philip; Thurow, Russell; Bonar, Scott

2002-01-01

The Western Division of the American Fisheries Society was requested to develop protocols for determining presence/absence and potential habitat suitability for bull trout. The general approach adopted is similar to the process for the marbled murrelet, whereby interim guidelines are initially used, and the protocols are subsequently refined as data are collected. Current data were considered inadequate to precisely identify suitable habitat but could be useful in stratifying sampling units for presence/absence surveys. The presence/absence protocol builds on previous approaches (Hillman and Platts 1993; Bonar et al. 1997), except it uses the variation in observed bull trout densities instead of a minimum threshold density and adjusts for measured differences in sampling efficiency due to gear types and habitat characteristics. The protocol consists of: 1. recommended sample sizes with 80% and 95% detection probabilities for juvenile and resident adult bull trout for day and night snorkeling and electrofishing adjusted for varying habitat characteristics for 50m and 100m sampling units, 2. sampling design considerations, including possible habitat characteristics for stratification, 3. habitat variables to be measured in the sampling units, and 3. guidelines for training sampling crews. Criteria for habitat strata consist of coarse, watershed-scale characteristics (e.g., mean annual air temperature) and fine-scale, reach and habitat-specific features (e.g., water temperature, channel width). The protocols will be revised in the future using data from ongoing presence/absence surveys, additional research on sampling efficiencies, and development of models of habitat/species occurrence.

A new real-time PCR protocol for detection of avian haemosporidians.

PubMed

Bell, Jeffrey A; Weckstein, Jason D; Fecchio, Alan; Tkach, Vasyl V

2015-07-19

Birds possess the most diverse assemblage of haemosporidian parasites; including three genera, Plasmodium, Haemoproteus, and Leucocytozoon. Currently there are over 200 morphologically identified avian haemosporidian species, although true species richness is unknown due to great genetic diversity and insufficient sampling in highly diverse regions. Studies aimed at surveying haemosporidian diversity involve collecting and screening samples from hundreds to thousands of individuals. Currently, screening relies on microscopy and/or single or nested standard PCR. Although effective, these methods are time and resource consuming, and in the case of microscopy require substantial expertise. Here we report a newly developed real-time PCR protocol designed to quickly and reliably detect all three genera of avian haemosporidians in a single biochemical reaction. Using available DNA sequences from avian haemosporidians we designed primers R330F and R480RL, which flank a 182 base pair fragment of mitochondrial conserved rDNA. These primers were initially tested using real-time PCR on samples from Malawi, Africa, previously screened for avian haemosporidians using traditional nested PCR. Our real time protocol was further tested on 94 samples from the Cerrado biome of Brazil, previously screened using a single PCR assay for haemosporidian parasites. These samples were also amplified using modified nested PCR protocols, allowing for comparisons between the three different screening methods (single PCR, nested PCR, real-time PCR). The real-time PCR protocol successfully identified all three genera of avian haemosporidians from both single and mixed infections previously detected from Malawi. There was no significant difference between the three different screening protocols used for the 94 samples from the Brazilian Cerrado (χ(2) = 0.3429, df = 2, P = 0.842). After proving effective, the real-time protocol was used to screen 2113 Brazilian samples, identifying 693 positive samples. Our real-time PCR assay proved as effective as two widely used molecular screening techniques, single PCR and nested PCR. However, the real-time protocol has the distinct advantage of detecting all three genera in a single reaction, which significantly increases efficiency by greatly decreasing screening time and cost. Our real-time PCR protocol is therefore a valuable tool in the quickly expanding field of avian haemosporidian research.

The validity of open-source data when assessing jail suicides.

PubMed

Thomas, Amanda L; Scott, Jacqueline; Mellow, Jeff

2018-05-09

The Bureau of Justice Statistics' Deaths in Custody Reporting Program is the primary source for jail suicide research, though the data is restricted from general dissemination. This study is the first to examine whether jail suicide data obtained from publicly available sources can help inform our understanding of this serious public health problem. Of the 304 suicides that were reported through the DCRP in 2009, roughly 56 percent (N = 170) of those suicides were identified through the open-source search protocol. Each of the sources was assessed based on how much information was collected on the incident and the types of variables available. A descriptive analysis was then conducted on the variables that were present in both data sources. The four variables present in each data source were: (1) demographic characteristics of the victim, (2) the location of occurrence within the facility, (3) the location of occurrence by state, and (4) the size of the facility. Findings demonstrate that the prevalence and correlates of jail suicides are extremely similar in both open-source and official data. However, for almost every variable measured, open-source data captured as much information as official data did, if not more. Further, variables not found in official data were identified in the open-source database, thus allowing researchers to have a more nuanced understanding of the situational characteristics of the event. This research provides support for the argument in favor of including open-source data in jail suicide research as it illustrates how open-source data can be used to provide additional information not originally found in official data. In sum, this research is vital in terms of possible suicide prevention, which may be directly linked to being able to manipulate environmental factors.

Quarantine and protocol

NASA Technical Reports Server (NTRS)

1981-01-01

The purpose of the Orbiting Quarantine Facility is to provide maximum protection of the terrestrial biosphere by ensuring that the returned Martian samples are safe to bring to Earth. The protocol designed to detect the presence of biologically active agents in the Martian soil is described. The protocol determines one of two things about the sample: (1) that it is free from nonterrestrial life forms and can be sent to a terrestrial containment facility where extensive chemical, biochemical, geological, and physical investigations can be conducted; or (2) that it exhibits "biological effects" of the type that dictate second order testing. The quarantine protocol is designed to be conducted on a small portion of the returned sample, leaving the bulk of the sample undisturbed for study on Earth.

COMPARISON OF USEPA FIELD SAMPLING METHODS FOR BENTHIC MACROINVERTEBRATE STUDIES

EPA Science Inventory

Two U.S. Environmental Protection Agency (USEPA) macroinvertebrate sampling protocols were compared in the Mid-Atlantic Highlands region. The Environmental Monitoring and Assessment Program (EMAP) wadeable streams protocol results in a single composite sample from nine transects...

A Field Comparison of Sampling Protocols for Measuring Lead in Drinking Water

EPA Science Inventory

US EPA Region 5 conducted a sampling study that demonstrates existing sampling protocols used for the Lead and Copper Rule (LCR) underestimate peak and probable mass of lead released in a system with lead service lines (LSLs). This comparative stagnation sampling was conducted i...

7 CFR 160.31 - Time and manner of sampling.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Agriculture Regulations of the Department of Agriculture (Continued) AGRICULTURAL MARKETING SERVICE (Standards, Inspections, Marketing Practices), DEPARTMENT OF AGRICULTURE (CONTINUED) NAVAL STORES REGULATIONS AND..., samples of naval stores to be used for official inspection and certification shall be taken direct from...

Judges' Agreement and Disagreement Patterns When Encoding Verbal Protocols.

ERIC Educational Resources Information Center

Schael, Jocelyne; Dionne, Jean-Paul

The basis of agreement or disagreement among judges/evaluators when applying a coding scheme to concurrent verbal protocols was studied. The sample included 20 university graduates, from varied backgrounds; 10 subjects had and 10 subjects did not have experience in protocol analysis. The total sample was divided into four balanced groups according…

Thermogravimetric Analysis of Single-Wall Carbon Nanotubes

NASA Technical Reports Server (NTRS)

Arepalli, Sivram; Nikolaev, Pavel; Gorelik, Olga

2010-01-01

An improved protocol for thermogravimetric analysis (TGA) of samples of single-wall carbon nanotube (SWCNT) material has been developed to increase the degree of consistency among results so that meaningful comparisons can be made among different samples. This improved TGA protocol is suitable for incorporation into the protocol for characterization of carbon nanotube material. In most cases, TGA of carbon nanotube materials is performed in gas mixtures that contain oxygen at various concentrations. The improved protocol is summarized.

[Performance comparison of material tests for cadmium and lead in food contact plastics].

PubMed

Mutsuga, Motoh; Abe, Tomoyuki; Abe, Yutaka; Ishii, Rie; Itoh, Yuko; Ohno, Hiroyuki; Ohno, Yuichiro; Ozaki, Asako; Kakihara, Yoshiteru; Kaneko, Reiko; Kawamura, Yoko; Shibata, Hiroshi; Sekido, Haruko; Sonobe, Hironori; Takasaka, Noriko; Tajima, Yoshiyasu; Tanaka, Aoi; Nomura, Chie; Hikida, Akinori; Matsuyama, Sigetomo; Murakami, Ryo; Yamaguchi, Miku; Wada, Takenari; Watanabe, Kazunari; Akiyama, Hiroshi

2014-01-01

Based on the Japanese Food Sanitation Law, the performances of official and alternative material test methods for cadmium (Cd) and lead (Pb) in food contact plastics were compared. Nineteen laboratories participated to an interlaboratory study, and quantified Cd and Pb in three PVC pellets. in the official method, a sample is digested with H2SO4, taken up in HCl, and evaporated to dryness on a water bath, then measured by atomic absorption spectrometry (AAS) or inductively coupled plasma-optical emission spectrometry (ICP-OES). Statistical treatment revealed that the trueness, repeatability (RSDr) and reproducibility (RSDr) were 86-95%, 3.1-9.4% and 8.6-22.1%, respectively. The values of the performance parameters fulfilled the requirements , and the performances met the test specifications. The combination of evaporation to dryness on a hot plate and measurement by AAS or ICP-OES is applicable as an alternative method. However, the trueness and RSDr were inferior to those of the official method. The performance parameters obtained by using the microwave digestion method (MW method) to prepare test solution were better than those of the official method. Thus, the MW method is available as an alternative method. Induced coupled plasma-mass spectrometry (ICP-MS) is also available as an alternative method. However, it is necessary to ensure complete digestion of the sample.

‘If you pay, we'll operate immediately'

PubMed Central

Miller, W.; Grodeland, A.; Koshechkina, T.

2000-01-01

Objectives—To study the attitudes of health care staff in four postcommunist countries towards taking gifts from their clients—and their confessed experience of actually taking such gifts. Design—Survey questionnaire administered to officials including health care staff, supplemented by focus-group discussions with the general public. Setting – Ukraine, Bulgaria, Slovakia and the Czech Republic. Participants—A quota sample of 1,307 officials including 292 health care staff, supplemented by stratified national random samples of 4,778 ordinary members of the public and in-depth interviews or focus-group discussions involving another 323. Main measurements—Explicit justifications and willingness to accept offers, reported frequency of offers, and personal confessions to accepting "money and expensive presents" as well as smaller gifts. Results—Health care staff were far more inclined than the average official or public servant to accept "money or an expensive present" if offered, far more inclined to justify asking clients for "extra payments", and far more inclined to confess that they had actually taken gifts from clients recently. Judged by their own confessions, hospital doctors were only rivalled by traffic police and customs officials for taking money or expensive gifts from their clients. Conclusions—Poor pay does not explain why doctors so often took large gifts from their clients. Moral self justification, opportunity, and bargaining power are much more effective explanations. Key Words: Gifts • justification • gratitude • extortion • confession PMID:11055030

KENNEDY SPACE CENTER, FLA. - Key officials are poised to cut the ribbon officially dedicating the new Security gates on Kennedy Parkway (Gate 2) and NASA Parkway (Gate 3). From left are Wally Schroeder, with Jones, Edmunds & Associates; Bobby Porter, with Oneida Construction; Daniel Tweed, NASA project manager; Jim Kennedy, Center director; and William Sample, SGS deputy program manager. The new gates were activated Aug. 1, allowing the general public to have access to the new Space Commerce Way, which will provide access to the Research Park and KSC Visitor Complex, and providing an alternate route for the general public between Titusville and Merritt Island that is accessible 24 hours a day. The gates are staffed 24 hours daily.

NASA Image and Video Library

2003-08-27

KENNEDY SPACE CENTER, FLA. - Key officials are poised to cut the ribbon officially dedicating the new Security gates on Kennedy Parkway (Gate 2) and NASA Parkway (Gate 3). From left are Wally Schroeder, with Jones, Edmunds & Associates; Bobby Porter, with Oneida Construction; Daniel Tweed, NASA project manager; Jim Kennedy, Center director; and William Sample, SGS deputy program manager. The new gates were activated Aug. 1, allowing the general public to have access to the new Space Commerce Way, which will provide access to the Research Park and KSC Visitor Complex, and providing an alternate route for the general public between Titusville and Merritt Island that is accessible 24 hours a day. The gates are staffed 24 hours daily.

Homogenization of sample absorption for the imaging of large and dense fossils with synchrotron microtomography.

PubMed

Sanchez, Sophie; Fernandez, Vincent; Pierce, Stephanie E; Tafforeau, Paul

2013-09-01

Propagation phase-contrast synchrotron radiation microtomography (PPC-SRμCT) has proved to be very successful for examining fossils. Because fossils range widely in taphonomic preservation, size, shape and density, X-ray computed tomography protocols are constantly being developed and refined. Here we present a 1-h procedure that combines a filtered high-energy polychromatic beam with long-distance PPC-SRμCT (sample to detector: 4-16 m) and an attenuation protocol normalizing the absorption profile (tested on 13-cm-thick and 5.242 g cm(-3) locally dense samples but applicable to 20-cm-thick samples). This approach provides high-quality imaging results, which show marked improvement relative to results from images obtained without the attenuation protocol in apparent transmission, contrast and signal-to-noise ratio. The attenuation protocol involves immersing samples in a tube filled with aluminum or glass balls in association with a U-shaped aluminum profiler. This technique therefore provides access to a larger dynamic range of the detector used for tomographic reconstruction. This protocol homogenizes beam-hardening artifacts, thereby rendering it effective for use with conventional μCT scanners.

FIELD SAMPLING PROTOCOLS AND ANALYSIS

EPA Science Inventory

I have been asked to speak again to the environmental science class regarding actual research scenarios related to my work at Kerr Lab. I plan to discuss sampling protocols along with various field analyses performed during sampling activities. Many of the students have never see...

New secure communication-layer standard for medical image management (ISCL)

NASA Astrophysics Data System (ADS)

Kita, Kouichi; Nohara, Takashi; Hosoba, Minoru; Yachida, Masuyoshi; Yamaguchi, Masahiro; Ohyama, Nagaaki

1999-07-01

This paper introduces a summary of the standard draft of ISCL 1.00 which will be published by MEDIS-DC officially. ISCL is abbreviation of Integrated Secure Communication Layer Protocols for Secure Medical Image Management Systems. ISCL is a security layer which manages security function between presentation layer and TCP/IP layer. ISCL mechanism depends on basic function of a smart IC card and symmetric secret key mechanism. A symmetry key for each session is made by internal authentication function of a smart IC card with a random number. ISCL has three functions which assure authentication, confidently and integrity. Entity authentication process is done through 3 path 4 way method using functions of internal authentication and external authentication of a smart iC card. Confidentially algorithm and MAC algorithm for integrity are able to be selected. ISCL protocols are communicating through Message Block which consists of Message Header and Message Data. ISCL protocols are evaluating by applying to regional collaboration system for image diagnosis, and On-line Secure Electronic Storage system for medical images. These projects are supported by Medical Information System Development Center. These project shows ISCL is useful to keep security.

Maltreatment histories of aging out foster youth: A comparison of official investigated reports and self-reports of maltreatment prior to and during out-of-home care.

PubMed

Havlicek, Judy; Courtney, Mark E

2016-02-01

This study compared official investigated reports of child maltreatment with retrospective self-reports prior to and during out-of-home care for a sample of foster youth who reached the age of majority in out-of-home care in Illinois. Using matched administrative and self-reported data for 474 youth who completed a baseline interview in the Midwest Evaluation of Adult Functioning of Former Foster Youth (i.e. the Midwest study) at ages 17-18, and 386 youth who completed a follow up interview at age 19, this study finds that official reports and self-reports of maltreatment prior to and during out-of-home care differ significantly. Findings from this study add insight into measurement discrepancies, and help to inform understanding of the extent of maltreatment experienced by this sub-sample of young people exiting out-of-home care in adulthood. Study findings have implications for independent living policy and practice in child welfare. Copyright © 2015 Elsevier Ltd. All rights reserved.

Protocol for Microplastics Sampling on the Sea Surface and Sample Analysis

PubMed Central

Kovač Viršek, Manca; Palatinus, Andreja; Koren, Špela; Peterlin, Monika; Horvat, Petra; Kržan, Andrej

2016-01-01

Microplastic pollution in the marine environment is a scientific topic that has received increasing attention over the last decade. The majority of scientific publications address microplastic pollution of the sea surface. The protocol below describes the methodology for sampling, sample preparation, separation and chemical identification of microplastic particles. A manta net fixed on an »A frame« attached to the side of the vessel was used for sampling. Microplastic particles caught in the cod end of the net were separated from samples by visual identification and use of stereomicroscopes. Particles were analyzed for their size using an image analysis program and for their chemical structure using ATR-FTIR and micro FTIR spectroscopy. The described protocol is in line with recommendations for microplastics monitoring published by the Marine Strategy Framework Directive (MSFD) Technical Subgroup on Marine Litter. This written protocol with video guide will support the work of researchers that deal with microplastics monitoring all over the world. PMID:28060297

Protocol for Microplastics Sampling on the Sea Surface and Sample Analysis.

PubMed

Kovač Viršek, Manca; Palatinus, Andreja; Koren, Špela; Peterlin, Monika; Horvat, Petra; Kržan, Andrej

2016-12-16

Microplastic pollution in the marine environment is a scientific topic that has received increasing attention over the last decade. The majority of scientific publications address microplastic pollution of the sea surface. The protocol below describes the methodology for sampling, sample preparation, separation and chemical identification of microplastic particles. A manta net fixed on an »A frame« attached to the side of the vessel was used for sampling. Microplastic particles caught in the cod end of the net were separated from samples by visual identification and use of stereomicroscopes. Particles were analyzed for their size using an image analysis program and for their chemical structure using ATR-FTIR and micro FTIR spectroscopy. The described protocol is in line with recommendations for microplastics monitoring published by the Marine Strategy Framework Directive (MSFD) Technical Subgroup on Marine Litter. This written protocol with video guide will support the work of researchers that deal with microplastics monitoring all over the world.

Dual-view plane illumination microscopy for rapid and spatially isotropic imaging

PubMed Central

Kumar, Abhishek; Wu, Yicong; Christensen, Ryan; Chandris, Panagiotis; Gandler, William; McCreedy, Evan; Bokinsky, Alexandra; Colón-Ramos, Daniel A; Bao, Zhirong; McAuliffe, Matthew; Rondeau, Gary; Shroff, Hari

2015-01-01

We describe the construction and use of a compact dual-view inverted selective plane illumination microscope (diSPIM) for time-lapse volumetric (4D) imaging of living samples at subcellular resolution. Our protocol enables a biologist with some prior microscopy experience to assemble a diSPIM from commercially available parts, to align optics and test system performance, to prepare samples, and to control hardware and data processing with our software. Unlike existing light sheet microscopy protocols, our method does not require the sample to be embedded in agarose; instead, samples are prepared conventionally on glass coverslips. Tissue culture cells and Caenorhabditis elegans embryos are used as examples in this protocol; successful implementation of the protocol results in isotropic resolution and acquisition speeds up to several volumes per s on these samples. Assembling and verifying diSPIM performance takes ~6 d, sample preparation and data acquisition take up to 5 d and postprocessing takes 3–8 h, depending on the size of the data. PMID:25299154

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.

A Draft Protocol for Detecting Possible Biohazards in Martian Samples Returned to Earth

NASA Technical Reports Server (NTRS)

Viso, M.; DeVincenzi, D. L.; Race, M. S.; Schad, P. J.; Stabekis, P. D.; Acevedo, S. E.; Rummel, J. D.

2002-01-01

In preparation for missions to Mars that will involve the return of samples, it is necessary to prepare for the safe receiving, handling, testing, distributing, and archiving of martian materials here on Earth. Previous groups and committees have studied selected aspects of sample return activities, but a specific protocol for handling and testing of returned -=1 samples from Mars remained to be developed. To refine the requirements for Mars sample hazard testing and to develop criteria for the subsequent release of sample materials from precautionary containment, NASA Planetary Protection Officer, working in collaboration with CNES, convened a series of workshops to produce a Protocol by which returned martian sample materials could be assessed for biological hazards and examined for evidence of life (extant or extinct), while safeguarding the samples from possible terrestrial contamination. The Draft Protocol was then reviewed by an Oversight and Review Committee formed specifically for that purpose and composed of senior scientists. In order to preserve the scientific value of returned martian samples under safe conditions, while avoiding false indications of life within the samples, the Sample Receiving Facility (SRF) is required to allow handling and processing of the Mars samples to prevent their terrestrial contamination while maintaining strict biological containment. It is anticipated that samples will be able to be shipped among appropriate containment facilities wherever necessary, under procedures developed in cooperation with international appropriate institutions. The SRF will need to provide different types of laboratory environments for carrying out, beyond sample description and curation, the various aspects of the protocol: Physical/Chemical analysis, Life Detection testing, and Biohazard testing. The main principle of these tests will be described and the criteria for release will be discussed, as well as the requirements for the SRF and its personnel.

Sensitivity comparison of sequential monadic and side-by-side presentation protocols in affective consumer testing.

PubMed

Colyar, Jessica M; Eggett, Dennis L; Steele, Frost M; Dunn, Michael L; Ogden, Lynn V

2009-09-01

The relative sensitivity of side-by-side and sequential monadic consumer liking protocols was compared. In the side-by-side evaluation, all samples were presented at once and evaluated together 1 characteristic at a time. In the sequential monadic evaluation, 1 sample was presented and evaluated on all characteristics, then returned before panelists received and evaluated another sample. Evaluations were conducted on orange juice, frankfurters, canned chili, potato chips, and applesauce. Five commercial brands, having a broad quality range, were selected as samples for each product category to assure a wide array of consumer liking scores. Without their knowledge, panelists rated the same 5 retail brands by 1 protocol and then 3 wk later by the other protocol. For 3 of the products, both protocols yielded the same order of overall liking. Slight differences in order of overall liking for the other 2 products were not significant. Of the 50 pairwise overall liking comparisons, 44 were in agreement. The different results obtained by the 2 protocols in order of liking and significance of paired comparisons were due to the experimental variation and differences in sensitivity. Hedonic liking scores were subjected to statistical power analyses and used to calculate minimum number of panelists required to achieve varying degrees of sensitivity when using side-by-side and sequential monadic protocols. In most cases, the side-by-side protocol was more sensitive, thus providing the same information with fewer panelists. Side-by-side protocol was less sensitive in cases where sensory fatigue was a factor.

Human DNA extraction from whole saliva that was fresh or stored for 3, 6 or 12 months using five different protocols

PubMed Central

GARBIERI, Thais Francini; BROZOSKI, Daniel Thomas; DIONÍSIO, Thiago José; SANTOS, Carlos Ferreira; NEVES, Lucimara Teixeira das

2017-01-01

Abstract Saliva when compared to blood collection has the following advantages: it requires no specialized personnel for collection, allows for remote collection by the patient, is painless, well accepted by participants, has decreased risks of disease transmission, does not clot, can be frozen before DNA extraction and possibly has a longer storage time. Objective and Material and Methods This study aimed to compare the quantity and quality of human DNA extracted from saliva that was fresh or frozen for three, six and twelve months using five different DNA extraction protocols: protocol 1 – Oragene™ commercial kit, protocol 2 – QIAamp DNA mini kit, protocol 3 – DNA extraction using ammonium acetate, protocol 4 – Instagene™ Matrix and protocol 5 – Instagene™ Matrix diluted 1:1 using proteinase K and 1% SDS. Briefly, DNA was analyzed using spectrophotometry, electrophoresis and PCR. Results Results indicated that time spent in storage typically decreased the DNA quantity with the exception of protocol 1. The purity of DNA was generally not affected by storage times for the commercial based protocols, while the purity of the DNA samples extracted by the noncommercial protocols typically decreased when the saliva was stored longer. Only protocol 1 consistently extracted unfragmented DNA samples. In general, DNA samples extracted through protocols 1, 2, 3 and 4, regardless of storage time, were amplified by human specific primers whereas protocol 5 produced almost no samples that were able to be amplified by human specific primers. Depending on the protocol used, it was possible to extract DNA in high quantities and of good quality using whole saliva, and furthermore, for the purposes of DNA extraction, saliva can be reliably stored for relatively long time periods. Conclusions In summary, a complicated picture emerges when taking into account the extracted DNA’s quantity, purity and quality; depending on a given researchers needs, one protocol’s particular strengths and costs might be the deciding factor for its employment. PMID:28403355

NHEXAS PHASE I REGION 5 STUDY--STANDARD OPERATING PROCEDURE--HANDLING QUALITY CONTROL SAMPLES IN THE FIELD (RTI/ACS-AP-209-090)

EPA Science Inventory

This protocol describes how quality control samples should be handled in the field, and was designed as a quick reference source for the field staff. The protocol describes quality control samples for air-VOCs, air-particles, water samples, house dust, soil, urine, blood, hair, a...

Protocol for Detection of Yersinia pestis in Environmental ...

EPA Pesticide Factsheets

Methods Report This is the first ever open-access and detailed protocol available to all government departments and agencies, and their contractors to detect Yersinia pestis, the pathogen that causes plague, from multiple environmental sample types including water. Each analytical method includes sample processing procedure for each sample type in a step-by-step manner. It includes real-time PCR, traditional microbiological culture, and the Rapid Viability PCR (RV-PCR) analytical methods. For large volume water samples it also includes an ultra-filtration-based sample concentration procedure. Because of such a non-restrictive availability of this protocol to all government departments and agencies, and their contractors, the nation will now have increased laboratory capacity to analyze large number of samples during a wide-area plague incident.

Processing Protocol for Soil Samples Potentially ...

EPA Pesticide Factsheets

Method Operating Procedures This protocol describes the processing steps for 45 g and 9 g soil samples potentially contaminated with Bacillus anthracis spores. The protocol is designed to separate and concentrate the spores from bulk soil down to a pellet that can be used for further analysis. Soil extraction solution and mechanical shaking are used to disrupt soil particle aggregates and to aid in the separation of spores from soil particles. Soil samples are washed twice with soil extraction solution to maximize recovery. Differential centrifugation is used to separate spores from the majority of the soil material. The 45 g protocol has been demonstrated by two laboratories using both loamy and sandy soil types. There were no significant differences overall between the two laboratories for either soil type, suggesting that the processing protocol would be robust enough to use at multiple laboratories while achieving comparable recoveries. The 45 g protocol has demonstrated a matrix limit of detection at 14 spores/gram of soil for loamy and sandy soils.

Processing protocol for soil samples potentially contaminated with Bacillus anthracis spores [HS7.52.02 - 514

USGS Publications Warehouse

Silvestri, Erin E.; Griffin, Dale W.

2017-01-01

This protocol describes the processing steps for 45 g and 9 g soil samples potentially contaminated with Bacillus anthracis spores. The protocol is designed to separate and concentrate the spores from bulk soil down to a pellet that can be used for further analysis. Soil extraction solution and mechanical shaking are used to disrupt soil particle aggregates and to aid in the separation of spores from soil particles. Soil samples are washed twice with soil extraction solution to maximize recovery. Differential centrifugation is used to separate spores from the majority of the soil material. The 45 g protocol has been demonstrated by two laboratories using both loamy and sandy soil types. There were no significant differences overall between the two laboratories for either soil type, suggesting that the processing protocol would be robust enough to use at multiple laboratories while achieving comparable recoveries. The 45 g protocol has demonstrated a matrix limit of detection at 14 spores/gram of soil for loamy and sandy soils.

7 CFR 868.61 - How to request appeal inspection service.

Code of Federal Regulations, 2010 CFR

2010-01-01

... application shall be made: (i) Before the rice has left the place where the inspection being appealed was... inspection be based on: (i) The file sample or (ii) a new sample. However, an appeal inspection shall be based on a new sample only if the lot can positively be identified by official personnel as the one that...

7 CFR 868.61 - How to request appeal inspection service.

Code of Federal Regulations, 2011 CFR

2011-01-01

... application shall be made: (i) Before the rice has left the place where the inspection being appealed was... inspection be based on: (i) The file sample or (ii) a new sample. However, an appeal inspection shall be based on a new sample only if the lot can positively be identified by official personnel as the one that...

Economical impact associated with a biological therapy prioritization protocol in patients with rheumatoid arthritis in the Hospital of Sagunto.

PubMed

Borrás-Blasco, Joaquín; Casterá, M Dolores-Elvira; Cortes, Xavier; Rosique-Robles, J Dolores; Abad, F Javier

2014-11-01

Until 2010 the cost of biological treatments in Rheumatoid Arthritis (RA) was increasing annually by 15% in our hospital. In 1st January 2011, a Hospital Commission of Biological Therapies involving rheumatology and pharmacy services was created to improve the management of biological drugs and a biological therapy prioritization protocol in RA patients was also established to improve the efficient usage of biological drugs in RA. To evaluate the economic impact associated with a biological therapy prioritization protocol for RA patients in the Hospital of Sagunto. Observational, ambispective study comparing the associated cost of RA patients treated with biological drugs in the pre-protocol (2009 - 2010) versus post-protocol periods (2011 - 2012). RA patients treated with Abatacept (ABA), Adalimumab (ADA), Etanercept (ETN) or Infliximab (IFX) for at least 6 months during the study period (2009 - 2012) were included. In 2012, Tocilizumab (TCZ) was also included in the prioritization protocol. Prioritization protocol was established based on both clinical and economical aspects and supervised case by case by our Commission. Cost savings and economic impact were calculated using Spanish official prices. In the pre-protocol period (2009 - 2010), total expenses were increasing by €110,000, up to €1,761,000 in 2010 (€11,362 pat/year). After protocol implementation, total expenses decreased by 53,676€ on the 2010 - 2011 period, and 149,200€ on the 2011 - 2012 period. On the 2010 - 2011 period the cost of biological therapy per patient-year decreased 355€ (11,007€ pat/year) and additional 653€ (up to 10,354€ pat/year) by 2012, with a cumulative effect of the protocol implementation of 1,008€ per patient-year. In the pre-protocol period (2009), the annual cost/patient was 10.812€ with ETN, 10.942€ with IFX, 12.961€ with ADA and 12.739€ with ABA. By 1st January 2013, the annual cost per patient was 9,469€ with ETN, 10,579€ with IFX, 11,117€ with ADA, 13,540€ with ABA and 14,932€ with TCZ. The creation of our Commission of Biological Therapies is key to rational management of RA patients and optimization of resources, allowing us to save 200,000€ after 2-year efficiency protocol implementation.

Childhood predictors and age 48 outcomes of self-reports and official records of offending

PubMed Central

DUBOW, ERIC F.; HUESMANN, L. ROWELL; BOXER, PAUL; SMITH, CATHY

2014-01-01

Background The key question is: are self-reports and official records equally valid indicators of criminal offending? Aims We examine the correspondence between self-reports and official records of offending, the similarity of childhood and adolescent individual and contextual predictors of both measures of offending, and the similarity of age 48 correlates of both measures of offending. Methods Men (N = 436) from the Columbia County Longitudinal Study, a sample of all 3rd graders in Columbia County, New York, in 1959–60, participated. The youth, their peers and their parents were interviewed when the youth were age 8; the youth were later interviewed at ages 19, 30 and 48. Results We found moderate to high correspondence between self-reports of having been in trouble with the law and official arrest records. Lifetime self-reports and official records of offending were generally predicted by the same childhood and adolescent variables, and were correlated with many of the same adult outcome measures. By age 48, life-course non-offenders defined by either self-reports or official records had better outcomes than offenders. Conclusions The results validate the use of adolescent and adult self-reports of offending, and the early identification of individuals at risk for adult criminal behaviour through childhood parent and peer reports and adolescent self and peer reports. PMID:25294162

Childhood predictors and age 48 outcomes of self-reports and official records of offending.

PubMed

Dubow, Eric F; Huesmann, L Rowell; Boxer, Paul; Smith, Cathy

2014-10-01

The key question is: are self-reports and official records equally valid indicators of criminal offending? We examine the correspondence between self-reports and official records of offending, the similarity of childhood and adolescent individual and contextual predictors of both measures of offending, and the similarity of age 48 correlates of both measures of offending. Men (N=436) from the Columbia County Longitudinal Study, a sample of all 3rd graders in Columbia County, New York, in 1959-60, participated. The youth, their peers and their parents were interviewed when the youth were age 8; the youth were later interviewed at ages 19, 30 and 48. We found moderate to high correspondence between self-reports of having been in trouble with the law and official arrest records. Lifetime self-reports and official records of offending were generally predicted by the same childhood and adolescent variables, and were correlated with many of the same adult outcome measures. By age 48, life-course non-offenders defined by either self-reports or official records had better outcomes than offenders. The results validate the use of adolescent and adult self-reports of offending, and the early identification of individuals at risk for adult criminal behaviour through childhood parent and peer reports and adolescent self and peer reports. Copyright © 2014 John Wiley & Sons, Ltd.

A simplified protocol for molecular identification of Eimeria species in field samples.

PubMed

Haug, Anita; Thebo, Per; Mattsson, Jens G

2007-05-15

This study aimed to find a fast, sensitive and efficient protocol for molecular identification of chicken Eimeria spp. in field samples. Various methods for each of the three steps of the protocol were evaluated: oocyst wall rupturing methods, DNA extraction methods, and identification of species-specific DNA sequences by PCR. We then compared and evaluated five complete protocols. Three series of oocyst suspensions of known number of oocysts from Eimeria mitis, Eimeria praecox, Eimeria maxima and Eimeria tenella were prepared and ground using glass beads or mini-pestle. DNA was extracted from ruptured oocysts using commercial systems (GeneReleaser, Qiagen Stoolkit and Prepman) or phenol-chloroform DNA extraction, followed by identification of species-specific ITS-1 sequences by optimised single species PCR assays. The Stoolkit and Prepman protocols showed insufficient repeatability, and the former was also expensive and relatively time-consuming. In contrast, both the GeneReleaser protocol and phenol-chloroform protocols were robust and sensitive, detecting less than 0.4 oocysts of each species per PCR. Finally, we evaluated our new protocol on 68 coccidia positive field samples. Our data suggests that rupturing the oocysts by mini-pestle grinding, preparing the DNA with GeneReleaser, followed by optimised single species PCR assays, makes a robust and sensitive procedure for identifying chicken Eimeria species in field samples. Importantly, it also provides minimal hands-on-time in the pre-PCR process, lower contamination risk and no handling of toxic chemicals.

Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples.

PubMed

Lewandowska, Dagmara W; Zagordi, Osvaldo; Geissberger, Fabienne-Desirée; Kufner, Verena; Schmutz, Stefan; Böni, Jürg; Metzner, Karin J; Trkola, Alexandra; Huber, Michael

2017-08-08

Sequence-specific PCR is the most common approach for virus identification in diagnostic laboratories. However, as specific PCR only detects pre-defined targets, novel virus strains or viruses not included in routine test panels will be missed. Recently, advances in high-throughput sequencing allow for virus-sequence-independent identification of entire virus populations in clinical samples, yet standardized protocols are needed to allow broad application in clinical diagnostics. Here, we describe a comprehensive sample preparation protocol for high-throughput metagenomic virus sequencing using random amplification of total nucleic acids from clinical samples. In order to optimize metagenomic sequencing for application in virus diagnostics, we tested different enrichment and amplification procedures on plasma samples spiked with RNA and DNA viruses. A protocol including filtration, nuclease digestion, and random amplification of RNA and DNA in separate reactions provided the best results, allowing reliable recovery of viral genomes and a good correlation of the relative number of sequencing reads with the virus input. We further validated our method by sequencing a multiplexed viral pathogen reagent containing a range of human viruses from different virus families. Our method proved successful in detecting the majority of the included viruses with high read numbers and compared well to other protocols in the field validated against the same reference reagent. Our sequencing protocol does work not only with plasma but also with other clinical samples such as urine and throat swabs. The workflow for virus metagenomic sequencing that we established proved successful in detecting a variety of viruses in different clinical samples. Our protocol supplements existing virus-specific detection strategies providing opportunities to identify atypical and novel viruses commonly not accounted for in routine diagnostic panels.

A MORE COST-EFFECTIVE EMAP-ESTUARIES BENTHIC MACROFAUNAL SAMPLING PROTOCOL

EPA Science Inventory

The standard benthic macrofaunal sampling protocol in the U.S. Environmental Protection Agency's Pacific Coast Environmental Monitoring and Assessment Program (EMAP) is to collect a minimum of 30 random benthic samples per reporting unit (e.g., estuary) using a 0.1 m2 grab and to...

It's Time to Develop a New "Draft Test Protocol" for a Mars Sample Return Mission (or Two....)

NASA Astrophysics Data System (ADS)

Rummel, J. D.

2018-04-01

A Mars Sample Return (MSR) will involve analysis of those samples in containment, including their safe receiving, handling, testing, and archiving. With an MSR planned for the end of the next decade, it is time to update the existing MSR protocol.

Jens Esmark's Christiania (Oslo) meteorological observations 1816-1838: the first long-term continuous temperature record from the Norwegian capital homogenized and analysed

NASA Astrophysics Data System (ADS)

Hestmark, Geir; Nordli, Øyvind

2016-11-01

In 2010 we rediscovered the complete set of meteorological observation protocols made by Jens Esmark (1762-1839) during his years of residence in the Norwegian capital of Oslo (then Christiania). From 1 January 1816 to 25 January 1839, Esmark at his house in Øvre Voldgate in the morning, early afternoon and late evening recorded air temperature with state-of-the-art thermometers. He also noted air pressure, cloud cover, precipitation and wind directions, and experimented with rain gauges and hygrometers. From 1818 to the end of 1838 he twice a month provided weather tables to the official newspaper Den Norske Rigstidende, and thus acquired a semi-official status as the first Norwegian state meteorologist. This paper evaluates the quality of Esmark's temperature observations and presents new metadata, new homogenization and analysis of monthly means. Three significant shifts in the measurement series were detected, and suitable corrections are proposed. The air temperature in Oslo during this period is shown to exhibit a slow rise from 1816 towards 1825, followed by a slighter fall again towards 1838.

How do nurses, midwives and health visitors contribute to protocol-based care? A synthesis of the UK literature.

PubMed

Ilott, Irene; Booth, Andrew; Rick, Jo; Patterson, Malcolm

2010-06-01

To explore how nurses, midwives and health visitors contribute to the development, implementation and audit of protocol-based care. Protocol-based care refers to the use of documents that set standards for clinical care processes with the intent of reducing unacceptable variations in practice. Documents such as protocols, clinical guidelines and care pathways underpin evidence-based practice throughout the world. An interpretative review using the five-stage systematic literature review process. The data sources were the British Nursing Index, CINAHL, EMBASE, MEDLINE and Web of Science from onset to 2005. The Journal of Integrated Care Pathways was hand searched (1997-June 2006). Thirty three studies about protocol-based care in the United Kingdom were appraised using the Qualitative Assessment and Review Instrument (QARI version 2). The literature was synthesized inductively and deductively, using an official 12-step guide for development as a framework for the deductive synthesis. Most papers were descriptive, offering practitioner knowledge and positive findings about a locally developed and owned protocol-based care. The majority were instigated in response to clinical need or service re-design. Development of protocol-based care was a non-linear, idiosyncratic process, with steps omitted, repeated or completed in a different order. The context and the multiple purposes of protocol-based care influenced the development process. Implementation and sustainability were rarely mentioned, or theorised as a change. The roles and activities of nurses were so understated as to be almost invisible. There were notable gaps in the literature about the resource use costs, the engagement of patients in the decision-making process, leadership and the impact of formalisation and new roles on inter-professional relations. Documents that standardise clinical care are part of the history of nursing as well as contemporary evidence-based care and expanded roles. Considering the proliferation and contested nature of protocol-based care, the dearth of literature about the contribution, experience and outcomes for nurses, midwives and health visitors is noteworthy and requires further investigation. (c) 2010 Elsevier Ltd. All rights reserved.

Improving Leishmania Species Identification in Different Types of Samples from Cutaneous Lesions

PubMed Central

Cruz-Barrera, Mónica L.; Ovalle-Bracho, Clemencia; Ortegon-Vergara, Viviana; Pérez-Franco, Jairo E.

2015-01-01

The discrimination of Leishmania species from patient samples has epidemiological and clinical relevance. In this study, different gene target PCR-restriction fragment length polymorphism (RFLP) protocols were evaluated for their robustness as Leishmania species discriminators in 61 patients with cutaneous leishmaniasis. We modified the hsp70-PCR-RFLP protocol and found it to be the most reliable protocol for species identification. PMID:25609727

Quantification of the overall measurement uncertainty associated with the passive moss biomonitoring technique: Sample collection and processing.

PubMed

Aboal, J R; Boquete, M T; Carballeira, A; Casanova, A; Debén, S; Fernández, J A

2017-05-01

In this study we examined 6080 data gathered by our research group during more than 20 years of research on the moss biomonitoring technique, in order to quantify the variability generated by different aspects of the protocol and to calculate the overall measurement uncertainty associated with the technique. The median variance of the concentrations of different pollutants measured in moss tissues attributed to the different methodological aspects was high, reaching values of 2851 (ng·g -1 ) 2 for Cd (sample treatment), 35.1 (μg·g -1 ) 2 for Cu (sample treatment), 861.7 (ng·g -1 ) 2 and for Hg (material selection). These variances correspond to standard deviations that constitute 67, 126 and 59% the regional background levels of these elements in the study region. The overall measurement uncertainty associated with the worst experimental protocol (5 subsamples, refrigerated, washed, 5 × 5 m size of the sampling area and once a year sampling) was between 2 and 6 times higher than that associated with the optimal protocol (30 subsamples, dried, unwashed, 20 × 20 m size of the sampling area and once a week sampling), and between 1.5 and 7 times higher than that associated with the standardized protocol (30 subsamples and once a year sampling). The overall measurement uncertainty associated with the standardized protocol could generate variations of between 14 and 47% in the regional background levels of Cd, Cu, Hg, Pb and Zn in the study area and much higher levels of variation in polluted sampling sites. We demonstrated that although the overall measurement uncertainty of the technique is still high, it can be reduced by using already well defined aspects of the protocol. Further standardization of the protocol together with application of the information on the overall measurement uncertainty would improve the reliability and comparability of the results of different biomonitoring studies, thus extending use of the technique beyond the context of scientific research. Copyright © 2017 Elsevier Ltd. All rights reserved.

Western Australian Public Opinions of a Minimum Pricing Policy for Alcohol: Study Protocol

PubMed Central

Keatley, David A; Daube, Mike; Hardcastle, Sarah J

2015-01-01

Background Excessive alcohol consumption has significant adverse economic, social, and health outcomes. Recent estimates suggest that the annual economic costs of alcohol in Australia are up to AUD $36 billion. Policies influencing price have been demonstrated to be very effective in reducing alcohol consumption and alcohol-related harms. Interest in minimum pricing has gained traction in recent years. However, there has been little research investigating the level of support for the public interest case of minimum pricing in Australia. Objective This article describes protocol for a study exploring Western Australian (WA) public knowledge, understanding, and reaction to a proposed minimum price policy per standard drink. Methods The study will employ a qualitative methodological design. Participants will be recruited from a wide variety of backgrounds, including ethnic minorities, blue and white collar workers, unemployed, students, and elderly/retired populations to participate in focus groups. Focus group participants will be asked about their knowledge of, and initial reactions to, the proposed policy and encouraged to discuss how such a proposal may affect their own alcohol use and alcohol consumption at the population level. Participants will also be asked to discuss potential avenues for increasing acceptability of the policy. The focus groups will adopt a semi-structured, open-ended approach guided by a question schedule. The schedule will be based on feedback from pilot samples, previous research, and a steering group comprising experts in alcohol policy and pricing. Results The study is expected to take approximately 14 months to complete. Conclusions The findings will be of considerable interest and relevance to government officials, policy makers, researchers, advocacy groups, alcohol retail and licensed establishments and organizations, city and town planners, police, and other stakeholder organizations. PMID:26582408

Western Australian Public Opinions of a Minimum Pricing Policy for Alcohol: Study Protocol.

PubMed

Keatley, David A; Carragher, Natacha; Chikritzhs, Tanya; Daube, Mike; Hardcastle, Sarah J; Hagger, Martin S

2015-11-18

Excessive alcohol consumption has significant adverse economic, social, and health outcomes. Recent estimates suggest that the annual economic costs of alcohol in Australia are up to AUD $36 billion. Policies influencing price have been demonstrated to be very effective in reducing alcohol consumption and alcohol-related harms. Interest in minimum pricing has gained traction in recent years. However, there has been little research investigating the level of support for the public interest case of minimum pricing in Australia. This article describes protocol for a study exploring Western Australian (WA) public knowledge, understanding, and reaction to a proposed minimum price policy per standard drink. The study will employ a qualitative methodological design. Participants will be recruited from a wide variety of backgrounds, including ethnic minorities, blue and white collar workers, unemployed, students, and elderly/retired populations to participate in focus groups. Focus group participants will be asked about their knowledge of, and initial reactions to, the proposed policy and encouraged to discuss how such a proposal may affect their own alcohol use and alcohol consumption at the population level. Participants will also be asked to discuss potential avenues for increasing acceptability of the policy. The focus groups will adopt a semi-structured, open-ended approach guided by a question schedule. The schedule will be based on feedback from pilot samples, previous research, and a steering group comprising experts in alcohol policy and pricing. The study is expected to take approximately 14 months to complete. The findings will be of considerable interest and relevance to government officials, policy makers, researchers, advocacy groups, alcohol retail and licensed establishments and organizations, city and town planners, police, and other stakeholder organizations.

Predicting Adolescent and Adult Antisocial Behavior among Adjudicated Delinquent Females

ERIC Educational Resources Information Center

Cernkovich, Stephen A.; Lanctot, Nadine; Giordano, Peggy C.

2008-01-01

Studies identifying the mechanisms underlying the causes and consequences of antisocial behavior among female delinquents as they transit to adulthood are scarce and have important limitations: Most are based on official statistics, they typically are restricted to normative samples, and rarely do they gather prospective data from samples of…

7 CFR 61.9 - Cost of review.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 3 2010-01-01 2010-01-01 false Cost of review. 61.9 Section 61.9 Agriculture... FOR SALE FOR CRUSHING PURPOSES (INSPECTION, SAMPLING AND CERTIFICATION) Regulations Administrative and General § 61.9 Cost of review. In cases of review of the grade of any official sample of cottonseed...

21 CFR 184.1979b - Reduced minerals whey.

Code of Federal Regulations, 2010 CFR

2010-04-01

...) Lactose content, maximum 85 percent—as determined by the methods prescribed in section 16.057 (liquid sample), entitled “Gravimetric Method—Official Final Action” under the heading “Lactose,” or in section 31.061 (dry sample), entitled “Lane-Eynon General Volumetric Method” under the heading “Lactose...

21 CFR 184.1979b - Reduced minerals whey.

Code of Federal Regulations, 2011 CFR

2011-04-01

...) Lactose content, maximum 85 percent—as determined by the methods prescribed in section 16.057 (liquid sample), entitled “Gravimetric Method—Official Final Action” under the heading “Lactose,” or in section 31.061 (dry sample), entitled “Lane-Eynon General Volumetric Method” under the heading “Lactose...

Results of a Saxitoxin Proficiency Test Including Characterization of Reference Material and Stability Studies

PubMed Central

Harju, Kirsi; Rapinoja, Marja-Leena; Avondet, Marc-André; Arnold, Werner; Schär, Martin; Luginbühl, Werner; Kremp, Anke; Suikkanen, Sanna; Kankaanpää, Harri; Burrell, Stephen; Söderström, Martin; Vanninen, Paula

2015-01-01

A saxitoxin (STX) proficiency test (PT) was organized as part of the Establishment of Quality Assurance for the Detection of Biological Toxins of Potential Bioterrorism Risk (EQuATox) project. The aim of this PT was to provide an evaluation of existing methods and the European laboratories’ capabilities for the analysis of STX and some of its analogues in real samples. Homogenized mussel material and algal cell materials containing paralytic shellfish poisoning (PSP) toxins were produced as reference sample matrices. The reference material was characterized using various analytical methods. Acidified algal extract samples at two concentration levels were prepared from a bulk culture of PSP toxins producing dinoflagellate Alexandrium ostenfeldii. The homogeneity and stability of the prepared PT samples were studied and found to be fit-for-purpose. Thereafter, eight STX PT samples were sent to ten participating laboratories from eight countries. The PT offered the participating laboratories the possibility to assess their performance regarding the qualitative and quantitative detection of PSP toxins. Various techniques such as official Association of Official Analytical Chemists (AOAC) methods, immunoassays, and liquid chromatography-mass spectrometry were used for sample analyses. PMID:26602927

Calibrated work function mapping by Kelvin probe force microscopy

NASA Astrophysics Data System (ADS)

Fernández Garrillo, Pablo A.; Grévin, Benjamin; Chevalier, Nicolas; Borowik, Łukasz

2018-04-01

We propose and demonstrate the implementation of an alternative work function tip calibration procedure for Kelvin probe force microscopy under ultrahigh vacuum, using monocrystalline metallic materials with known crystallographic orientation as reference samples, instead of the often used highly oriented pyrolytic graphite calibration sample. The implementation of this protocol allows the acquisition of absolute and reproducible work function values, with an improved uncertainty with respect to unprepared highly oriented pyrolytic graphite-based protocols. The developed protocol allows the local investigation of absolute work function values over nanostructured samples and can be implemented in electronic structures and devices characterization as demonstrated over a nanostructured semiconductor sample presenting Al0.7Ga0.3As and GaAs layers with variable thickness. Additionally, using our protocol we find that the work function of annealed highly oriented pyrolytic graphite is equal to 4.6 ± 0.03 eV.

Effectiveness of the Preservation Protocol within EPA Method 200.8 for Soluble and Particulate Lead Recovery in Drinking Water

EPA Science Inventory

The purpose of this project was to investigate the effectiveness of the sample preservation protocol outlined in Method 200.8 in recovering lead from water samples. Lead recoveries were studied in various water samples spiked with lead by evaluating lead sorption and desorption f...

21 CFR 660.36 - Samples and protocols.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 7 2011-04-01 2010-04-01 true Samples and protocols. 660.36 Section 660.36 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) BIOLOGICS... Research Sample Custodian (ATTN: HFM-672) (see mailing addresses in § 600.2 of this chapter), within 30...

BIASES IN CASTNET FILTER PACK RESULTS ASSOCIATED WITH SAMPLING PROTOCOL

EPA Science Inventory

In the current study, single filter weekly (w) results are compared with weekly results aggregated from day and night (dn) weekly samples. Comparisons of the two sampling protocols for all major constituents (SO42-, NO3-, NH4+, HNO3, and SO2) show median bias (MB) of < 5 nmol m-3...

National Human Trafficking Initiatives: Dimensions of Policy Diffusion1

PubMed Central

Yoo, Eun-hye; Boyle, Elizabeth Heger

2014-01-01

The implementation of criminal law involves formal law enforcement, education and public outreach aimed at preventing criminal activity, and providing services for victims. Historically, quantitative research on global trends has tended to focus on a single policy dimension, potentially masking the unique factors that affect the diffusion of each policy dimension independently. Using an ordered-probit model to analyze new human trafficking policy data on national prosecution, prevention, and victim-protection efforts, we find that global ties and domestic interest groups matter more in areas where international law is less defined. While prosecution, officially mandated by the Trafficking Protocol, was relatively impervious to global ties and domestic interest groups, both trafficking prevention and victim protection were associated with these factors. Our findings also suggest that fear of repercussions is not a major driver of state actions to combat trafficking—neither ratification of the Trafficking Protocol nor levels of United States aid were associated with greater implementation of anti-trafficking measures. PMID:26538806

National Human Trafficking Initiatives: Dimensions of Policy Diffusion.

PubMed

Yoo, Eun-Hye; Boyle, Elizabeth Heger

2015-01-01

The implementation of criminal law involves formal law enforcement, education and public outreach aimed at preventing criminal activity, and providing services for victims. Historically, quantitative research on global trends has tended to focus on a single policy dimension, potentially masking the unique factors that affect the diffusion of each policy dimension independently. Using an ordered-probit model to analyze new human trafficking policy data on national prosecution, prevention, and victim-protection efforts, we find that global ties and domestic interest groups matter more in areas where international law is less defined. While prosecution, officially mandated by the Trafficking Protocol, was relatively impervious to global ties and domestic interest groups, both trafficking prevention and victim protection were associated with these factors. Our findings also suggest that fear of repercussions is not a major driver of state actions to combat trafficking-neither ratification of the Trafficking Protocol nor levels of United States aid were associated with greater implementation of anti-trafficking measures.

43 CFR Appendix A to Part 10 - Sample Summary

Code of Federal Regulations, 2010 CFR

2010-10-01

... specific circumstances of each case. Before November 17, 1993 Chairman or Other Authorized Official Indian..., tools, household equipment, clothing, travel and transportation, personal adornment, smoking, toys, and...

Adequacy of dietary intakes and poverty in India: trends in the 1990s.

PubMed

Mahal, Ajay; Karan, Anup K

2008-03-01

Linear programming methods, indicators of nutritional adequacy from the Indian Council of Medical Research and household expenditure survey data from the National Sample Survey Organization were used to construct poverty lines for India. Poverty ratios were calculated for 1993--1994 and 1999--2000 on the basis of nutritional adequacy poverty lines and compared to official estimates of poverty based on energy requirements. Nutritional adequacy poverty lines are higher than official poverty lines, particularly in rural areas. The application of nutritional adequacy poverty lines points to greater rural-urban poverty differences than in official estimates. Declines in rural poverty during the 1990s were also slower under the nutritional adequacy definition, especially in south India. There is a greater degree of rural-urban and regional bias in nutritional adequacy poverty reduction than suggested by official data. Inter-state variations in changes in nutritional poverty and official poverty in the 1990s are largely explained by differences in assumptions on overall price movements. However, relative price movements in food items also played a role, particularly the slow increase in prices of cereals and edible oils in comparison to the prices of pulses, and in some southern states, compared to milk and vegetable prices as well.

Strategies for Achieving High Sequencing Accuracy for Low Diversity Samples and Avoiding Sample Bleeding Using Illumina Platform

PubMed Central

Mitra, Abhishek; Skrzypczak, Magdalena; Ginalski, Krzysztof; Rowicka, Maga

2015-01-01

Sequencing microRNA, reduced representation sequencing, Hi-C technology and any method requiring the use of in-house barcodes result in sequencing libraries with low initial sequence diversity. Sequencing such data on the Illumina platform typically produces low quality data due to the limitations of the Illumina cluster calling algorithm. Moreover, even in the case of diverse samples, these limitations are causing substantial inaccuracies in multiplexed sample assignment (sample bleeding). Such inaccuracies are unacceptable in clinical applications, and in some other fields (e.g. detection of rare variants). Here, we discuss how both problems with quality of low-diversity samples and sample bleeding are caused by incorrect detection of clusters on the flowcell during initial sequencing cycles. We propose simple software modifications (Long Template Protocol) that overcome this problem. We present experimental results showing that our Long Template Protocol remarkably increases data quality for low diversity samples, as compared with the standard analysis protocol; it also substantially reduces sample bleeding for all samples. For comprehensiveness, we also discuss and compare experimental results from alternative approaches to sequencing low diversity samples. First, we discuss how the low diversity problem, if caused by barcodes, can be avoided altogether at the barcode design stage. Second and third, we present modified guidelines, which are more stringent than the manufacturer’s, for mixing low diversity samples with diverse samples and lowering cluster density, which in our experience consistently produces high quality data from low diversity samples. Fourth and fifth, we present rescue strategies that can be applied when sequencing results in low quality data and when there is no more biological material available. In such cases, we propose that the flowcell be re-hybridized and sequenced again using our Long Template Protocol. Alternatively, we discuss how analysis can be repeated from saved sequencing images using the Long Template Protocol to increase accuracy. PMID:25860802

Clauser-Horne-Shimony-Holt versus three-party pseudo-telepathy: on the optimal number of samples in device-independent quantum private query

NASA Astrophysics Data System (ADS)

Basak, Jyotirmoy; Maitra, Subhamoy

2018-04-01

In device-independent (DI) paradigm, the trustful assumptions over the devices are removed and CHSH test is performed to check the functionality of the devices toward certifying the security of the protocol. The existing DI protocols consider infinite number of samples from theoretical point of view, though this is not practically implementable. For finite sample analysis of the existing DI protocols, we may also consider strategies for checking device independence other than the CHSH test. In this direction, here we present a comparative analysis between CHSH and three-party Pseudo-telepathy game for the quantum private query protocol in DI paradigm that appeared in Maitra et al. (Phys Rev A 95:042344, 2017) very recently.

Comparison of two DNA extraction protocols from leave samples of Cotinus coggygria, Citrus sinensis and Genus juglans.

PubMed

Fallah, F; Minaei Chenar, H; Amiri, H; Omodipour, S; Shirbande Ghods, F; Kahrizi, D; Sohrabi, M; Ghorbani, T; Kazemi, E

2017-02-28

High quality DNA is essential for molecular research. Secondary metabolites can affect the quantity and quality DNA. In current research two DNA isolation methods including CTAB and Delaporta (protocols 1 & 2 respectively) were applied in three leave samples from Cotinus coggygria, Citrus sinensis and Genus juglans that their leaves are rich of secondary metabolites. We successfully isolated DNA from C. coggygria, C. sinensis and Genus Juglans using the two protocols described above. Good quality DNA was isolated from C. coggygria, C. sinensis and Genus Juglans using protocol 1, while protocol 2 failed to produce usable DNA from these sources. The highest amount of DNA (1.3-1.6) was obtained from them using protocol 1. As we discovered, procedure 1 may work better for plants with secondary metabolites.

Distributional assumptions in food and feed commodities- development of fit-for-purpose sampling protocols.

PubMed

Paoletti, Claudia; Esbensen, Kim H

2015-01-01

Material heterogeneity influences the effectiveness of sampling procedures. Most sampling guidelines used for assessment of food and/or feed commodities are based on classical statistical distribution requirements, the normal, binomial, and Poisson distributions-and almost universally rely on the assumption of randomness. However, this is unrealistic. The scientific food and feed community recognizes a strong preponderance of non random distribution within commodity lots, which should be a more realistic prerequisite for definition of effective sampling protocols. Nevertheless, these heterogeneity issues are overlooked as the prime focus is often placed only on financial, time, equipment, and personnel constraints instead of mandating acquisition of documented representative samples under realistic heterogeneity conditions. This study shows how the principles promulgated in the Theory of Sampling (TOS) and practically tested over 60 years provide an effective framework for dealing with the complete set of adverse aspects of both compositional and distributional heterogeneity (material sampling errors), as well as with the errors incurred by the sampling process itself. The results of an empirical European Union study on genetically modified soybean heterogeneity, Kernel Lot Distribution Assessment are summarized, as they have a strong bearing on the issue of proper sampling protocol development. TOS principles apply universally in the food and feed realm and must therefore be considered the only basis for development of valid sampling protocols free from distributional constraints.

High sensitivity Troponin T: an audit of implementation of its protocol in a district general hospital.

PubMed

Kalim, Shahid; Nazir, Shaista; Khan, Zia Ullah

2013-01-01

Protocols based on newer high sensitivity Troponin T (hsTropT) assays can rule in a suspected Acute Myocardial Infarction (AMI) as early as 3 hours. We conducted this study to audit adherence to our Trust's newly introduced AMI diagnostic protocol based on paired hsTropT testing at 0 and 3 hours. We retrospectively reviewed data of all patients who had hsTropT test done between 1st and 7th May 2012. Patient's demographics, utility of single or paired samples, time interval between paired samples, patient's presenting symptoms and ECG findings were noted and their means, medians, Standard deviations and proportions were calculated. A total of 66 patients had hsTropT test done during this period. Mean age was 63.30 +/- 17.46 years and 38 (57.57%) were males. Twenty-four (36.36%) patients had only single, rather than protocol recommended paired hsTropT samples, taken. Among the 42 (63.63%) patients with paired samples, the mean time interval was found to be 4.41 +/- 5.7 hours. Contrary to the recommendations, 15 (22.73%) had a very long whereas 2 (3.03%) had a very short time interval between two samples. A subgroup analysis of patients with single samples, found only 2 (3.03%) patient with ST-segment elevation, appropriate for single testing. Our study confirmed that in a large number of patients the protocol for paired sampling or a recommended time interval of 3 hours between 2 samples was not being followed.

Performance of Identifiler Direct and PowerPlex 16 HS on the Applied Biosystems 3730 DNA Analyzer for processing biological samples archived on FTA cards.

PubMed

Laurin, Nancy; DeMoors, Anick; Frégeau, Chantal

2012-09-01

Direct amplification of STR loci from biological samples collected on FTA cards without prior DNA purification was evaluated using Identifiler Direct and PowerPlex 16 HS in conjunction with the use of a high throughput Applied Biosystems 3730 DNA Analyzer. In order to reduce the overall sample processing cost, reduced PCR volumes combined with various FTA disk sizes were tested. Optimized STR profiles were obtained using a 0.53 mm disk size in 10 μL PCR volume for both STR systems. These protocols proved effective in generating high quality profiles on the 3730 DNA Analyzer from both blood and buccal FTA samples. Reproducibility, concordance, robustness, sample stability and profile quality were assessed using a collection of blood and buccal samples on FTA cards from volunteer donors as well as from convicted offenders. The new developed protocols offer enhanced throughput capability and cost effectiveness without compromising the robustness and quality of the STR profiles obtained. These results support the use of these protocols for processing convicted offender samples submitted to the National DNA Data Bank of Canada. Similar protocols could be applied to the processing of casework reference samples or in paternity or family relationship testing. Copyright © 2012 Elsevier Ireland Ltd. All rights reserved.

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.

Environmental DNA sampling protocol - filtering water to capture DNA from aquatic organisms

USGS Publications Warehouse

Laramie, Matthew B.; Pilliod, David S.; Goldberg, Caren S.; Strickler, Katherine M.

2015-09-29

Environmental DNA (eDNA) analysis is an effective method of determining the presence of aquatic organisms such as fish, amphibians, and other taxa. This publication is meant to guide researchers and managers in the collection, concentration, and preservation of eDNA samples from lentic and lotic systems. A sampling workflow diagram and three sampling protocols are included as well as a list of suggested supplies. Protocols include filter and pump assembly using: (1) a hand-driven vacuum pump, ideal for sample collection in remote sampling locations where no electricity is available and when equipment weight is a primary concern; (2) a peristaltic pump powered by a rechargeable battery-operated driver/drill, suitable for remote sampling locations when weight consideration is less of a concern; (3) a 120-volt alternating current (AC) powered peristaltic pump suitable for any location where 120-volt AC power is accessible, or for roadside sampling locations. Images and detailed descriptions are provided for each step in the sampling and preservation process.

Early-life exposure to air pollutants and adverse pregnancy outcomes: protocol for a prospective cohort study in Beijing.

PubMed

Song, Jing; Chen, Yi; Wei, Ling; Ma, Ying; Tian, Ning; Huang, Shi Yun; Dai, Yin Mei; Zhao, Li Hong; Kong, Yuan Yuan

2017-09-03

The association between early exposure to ambient air pollution and adverse pregnancy outcomes in China is unclear. This study will assess the risk of early-life exposure to air pollutants in Beijing and explore the viability of 8-hydroxydeoxyguanosine (8-OHdG) as a biological indicator to assess oxidative stress induced by early-life exposure to air pollution. Here , 2500 women with singleton pregnancies and their infants will be recruited from the Beijing Obstetrics and Gynecology Hospital. We will collect nine types of biological samples, including maternal serum, urine, placental tissue, umbilical cord tissue and umbilical cord blood during all three trimesters. The air pollution data (particulate matter (PM)2.5, PM10 and similar factors) will be recorded at official fixed-site monitoring stations closest to where the pregnant women live. We plan to assess the effect of air pollutants on adverse pregnancy outcomes and infant respiratory and circulatory disease using Cox regression and competitive risk analysis and explore possible critical windows of exposure during pregnancy using daily pollutant concentrations averaged over various periods of pregnancy combined with individual activity and physiological parameters. Maternal and umbilical cord blood samples (1000 samples) will be randomly selected for 8-OHdG assays to assess the correlation between exposures to air pollutants and oxidative stress. We will determine whether air pollutant exposure or 8-OHdG levels are associated with adverse pregnancy outcomes. SPSS and SAS statistical software will be used for data analysis. Cox regression and competing risk analysis will be used to compute the HR and population attributable risk. This research protocol has already been approved by the Medical Ethics Committee of Beijing Obstetrics and Gynecology Hospital. Written informed consent will be obtained from all study participants prior to enrolment. The results will be published in peer-reviewed journals or disseminated through conference presentations. This study has been registered in WHO International Clinical Trial Register-Chinese Clinical Trial Registry under registrationnumber ChiCTR-ROC-16010181 (http :// www.chictr.org.cn / showproj.aspx ?proj=17328). © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2017. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Performance assessment of two lysis methods for direct identification of yeasts from clinical blood cultures using MALDI-TOF mass spectrometry.

PubMed

Jeddi, Fakhri; Yapo-Kouadio, Gisèle Cha; Normand, Anne-Cécile; Cassagne, Carole; Marty, Pierre; Piarroux, Renaud

2017-02-01

In cases of fungal infection of the bloodstream, rapid species identification is crucial to provide adapted therapy and thereby ameliorate patient outcome. Currently, the commercial Sepsityper kit and the sodium-dodecyl sulfate (SDS) method coupled with MALDI-TOF mass spectrometry are the most commonly reported lysis protocols for direct identification of fungi from positive blood culture vials. However, the performance of these two protocols has never been compared on clinical samples. Accordingly, we performed a two-step survey on two distinct panels of clinical positive blood culture vials to identify the most efficient protocol, establish an appropriate log score (LS) cut-off, and validate the best method. We first compared the performance of the Sepsityper and the SDS protocols on 71 clinical samples. For 69 monomicrobial samples, mass spectrometry LS values were significantly higher with the SDS protocol than with the Sepsityper method (P < .0001), especially when the best score of four deposited spots was considered. Next, we established the LS cut-off for accurate identification at 1.7, based on specimen DNA sequence data. Using this LS cut-off, 66 (95.6%) and 46 (66.6%) isolates were correctly identified at the species level with the SDS and the Sepsityper protocols, respectively. In the second arm of the survey, we validated the SDS protocol on an additional panel of 94 clinical samples. Ninety-two (98.9%) of 93 monomicrobial samples were correctly identified at the species level (median LS = 2.061). Overall, our data suggest that the SDS method yields more accurate species identification of yeasts, than the Sepsityper protocol. © The Author 2016. Published by Oxford University Press on behalf of The International Society for Human and Animal Mycology. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.

40 CFR 86.1845-04 - Manufacturer in-use verification testing requirements.

Code of Federal Regulations, 2014 CFR

2014-07-01

... of test vehicles in the sample comply with the sample size requirements of this section. Any post... HDV must test, or cause to have tested, a specified number of vehicles. Such testing must be conducted... first test will be considered the official results for the test vehicle, regardless of any test results...

32 CFR Appendix A to Part 504 - Request For Basic Identifying Account Data-Sample Format

Code of Federal Regulations, 2010 CFR

2010-07-01

..., you are requested to provide the following account information: (name, address, account number, and... complied with as to this request for account information. (Official Signature Block) ___ Under section 3417... 32 National Defense 3 2010-07-01 2010-07-01 true Request For Basic Identifying Account Data-Sample...

7 CFR 800.86 - Inspection of shiplot, unit train, and lash barge grain in single lots.

Code of Federal Regulations, 2010 CFR

2010-01-01

... prescribed in the instructions. (b) Application procedure. Applications for the official inspection of... statistical acceptance sampling and inspection plan according to the provisions of this section and procedures... inspection as part of a single lot and accepted by a statistical acceptance sampling and inspection plan...

21 CFR 2.10 - Examination and investigation samples.

Code of Federal Regulations, 2014 CFR

2014-04-01

... for analysis, the term analysis includes examinations and tests. (3) The owner of a food, drug, or... official sample of a food, drug, or cosmetic for analysis under the act, he shall collect at least twice... use as trial exhibits. (c) After the Food and Drug Administration has completed such analysis of an...

21 CFR 2.10 - Examination and investigation samples.

Code of Federal Regulations, 2012 CFR

2012-04-01

... for analysis, the term analysis includes examinations and tests. (3) The owner of a food, drug, or... official sample of a food, drug, or cosmetic for analysis under the act, he shall collect at least twice... use as trial exhibits. (c) After the Food and Drug Administration has completed such analysis of an...

9 CFR 145.83 - Terminology and classification; flocks and products.

Code of Federal Regulations, 2012 CFR

2012-01-01

...-typhoid control under official supervision; (B) All hatchery supply flocks within the State are qualified as U.S. Pullorum-Typhoid Clean or have met equivalent requirements for pullorum-typhoid control under... laboratory and any group D Salmonella samples have been serotyped: (A) A 25-gram sample of meconium from the...

9 CFR 145.83 - Terminology and classification; flocks and products.

Code of Federal Regulations, 2011 CFR

2011-01-01

...-typhoid control under official supervision; (B) All hatchery supply flocks within the State are qualified as U.S. Pullorum-Typhoid Clean or have met equivalent requirements for pullorum-typhoid control under... laboratory and any group D Salmonella samples have been serotyped: (A) A 25-gram sample of meconium from the...

9 CFR 145.83 - Terminology and classification; flocks and products.

Code of Federal Regulations, 2014 CFR

2014-01-01

...-typhoid control under official supervision; (B) All hatchery supply flocks within the State are qualified as U.S. Pullorum-Typhoid Clean or have met equivalent requirements for pullorum-typhoid control under... laboratory and any group D Salmonella samples have been serotyped: (A) A 25-gram sample of meconium from the...

78 FR 59621 - Extension of the Current Fees for the Accredited Laboratory Program

Federal Register 2010, 2011, 2012, 2013, 2014

2013-09-27

... regulatory samples of raw or processed meat and poultry products, and through which a check sample program... Laboratory Program. Such accreditation allows laboratories to conduct analyses of official meat and poultry... employer. List of Subjects in 9 CFR Part 391 Fees and charges, Government employees, Meat inspection...

9 CFR 439.53 - Revocation of accreditation.

Code of Federal Regulations, 2014 CFR

2014-01-01

... ACCREDITATION OF NON-FEDERAL CHEMISTRY LABORATORIES § 439.53 Revocation of accreditation. The accreditation of a... has: (1) Altered any official sample or analytical finding; or (2) Substituted any analytical result...

9 CFR 439.53 - Revocation of accreditation.

Code of Federal Regulations, 2012 CFR

2012-01-01

... ACCREDITATION OF NON-FEDERAL CHEMISTRY LABORATORIES § 439.53 Revocation of accreditation. The accreditation of a... has: (1) Altered any official sample or analytical finding; or (2) Substituted any analytical result...

9 CFR 439.53 - Revocation of accreditation.

Code of Federal Regulations, 2013 CFR

2013-01-01

... ACCREDITATION OF NON-FEDERAL CHEMISTRY LABORATORIES § 439.53 Revocation of accreditation. The accreditation of a... has: (1) Altered any official sample or analytical finding; or (2) Substituted any analytical result...

9 CFR 439.53 - Revocation of accreditation.

Code of Federal Regulations, 2011 CFR

2011-01-01

... ACCREDITATION OF NON-FEDERAL CHEMISTRY LABORATORIES § 439.53 Revocation of accreditation. The accreditation of a... has: (1) Altered any official sample or analytical finding; or (2) Substituted any analytical result...

7 CFR 52.36 - How officially drawn samples are to be identified.

Code of Federal Regulations, 2010 CFR

2010-01-01

... UNDER THE AGRICULTURAL MARKETING ACT OF 1946 PROCESSED FRUITS AND VEGETABLES, PROCESSED PRODUCTS THEREOF, AND CERTAIN OTHER PROCESSED FOOD PRODUCTS 1 Regulations Governing Inspection and Certification...

Optimization of Native and Formaldehyde iPOND Techniques for Use in Suspension Cells.

PubMed

Wiest, Nathaniel E; Tomkinson, Alan E

2017-01-01

The isolation of proteins on nascent DNA (iPOND) technique developed by the Cortez laboratory allows a previously unparalleled ability to examine proteins associated with replicating and newly synthesized DNA in mammalian cells. Both the original, formaldehyde-based iPOND technique and a more recent derivative, accelerated native iPOND (aniPOND), have mostly been performed in adherent cell lines. Here, we describe modifications to both protocols for use with suspension cell lines. These include cell culture, pulse, and chase conditions that optimize sample recovery in both protocols using suspension cells and several key improvements to the published aniPOND technique that reduce sample loss, increase signal to noise, and maximize sample recovery. Additionally, we directly and quantitatively compare the iPOND and aniPOND protocols to test the strengths and limitations of both. Finally, we present a detailed protocol to perform the optimized aniPOND protocol in suspension cell lines. © 2017 Elsevier Inc. All rights reserved.

Corrosion and mechanical performance of AZ91 exposed to simulated inflammatory conditions.

PubMed

Brooks, Emily K; Der, Stephanie; Ehrensberger, Mark T

2016-03-01

Magnesium (Mg) and its alloys, including Mg-9%Al-1%Zn (AZ91), are biodegradable metals with potential use as temporary orthopedic implants. Invasive orthopedic procedures can provoke an inflammatory response that produces hydrogen peroxide (H2O2) and an acidic environment near the implant. This study assessed the influence of inflammation on both the corrosion and mechanical properties of AZ91. The AZ91 samples in the inflammatory protocol were immersed for three days in a complex biologically relevant electrolyte (AMEM culture media) that contained serum proteins (FBS), 150 mM of H2O2, and was titrated to a pH of 5. The control protocol immersed AZ91 samples in the same biologically relevant electrolyte (AMEM & FBS) but without H2O2 and the acid titration. After 3 days all samples were switched into fresh AMEM & FBS for an additional 3-day immersion. During the initial immersion, inflammatory protocol samples showed increased corrosion rate determined by mass loss testing, increased Mg and Al ion released to solution, and a completely corroded surface morphology as compared to the control protocol. Although corrosion in both protocols slowed once the test electrolyte solution was replaced at 3 days, the samples originally exposed to the simulated inflammatory conditions continued to display enhanced corrosion rates as compared to the control protocol. These lingering effects may indicate the initial inflammatory corrosion processes modified components of the surface oxide and corrosion film or initiated aggressive localized processes that subsequently left the interface more vulnerable to continued enhanced corrosion. The electrochemical properties of the interfaces were also evaluated by EIS, which found that the corrosion characteristics of the AZ91 samples were potentially influenced by the role of intermediate adsorption layer processes. The increased corrosion observed for the inflammatory protocol did not affect the flexural mechanical properties of the AZ91 at any time point assessed. Copyright © 2015 Elsevier B.V. All rights reserved.

Two Decades into the LCR: What We Do and Still Don’t Know to Solve Lead Problems

EPA Science Inventory

Site selection and sampling protocol biases in LCR samplingunderestimate peak lead and copper concentrations whilemissing erratic lead release episodes resulting from distributionsystem chemical and physical disturbances. Possible sitetargeting and sampling protocol changes could...

Vascular Blood Collection protocol samples into MELFI

NASA Image and Video Library

2011-10-18

iss029e028495 (10/18/2011) --- Japan Aerospace Exploration Agency astronaut Satoshi Furukawa,Expedition 29 flight engineer,prepares to put samples from the CSA (Canadian Space Agency) Vascular Blood Collection protocol into the MELFI-1 (Minus Eighty Laboratory Freezer for ISS 1) unit.

Two Decades into the LCR: What We Do and Still Don’t Know to Solve Lead Problems - abstract

EPA Science Inventory

Site selection and sampling protocol biases in LCR samplingunderestimate peak lead and copper concentrations whilemissing erratic lead release episodes resulting from distributionsystem chemical and physical disturbances. Possible sitetargeting and sampling protocol changes could...

NHEXAS PHASE I ARIZONA STUDY--LIST OF STANDARD OPERATING PROCEDURES

EPA Science Inventory

This document lists available protocols and SOPs for the NHEXAS Phase I Arizona study. It identifies protocols and SOPs for the following study components: (1) Sample collection and field operations, (2) Sample analysis, (3) General laboratory procedures, (4) Quality Assurance, (...

Directive counseling on long-acting contraception.

PubMed Central

Moskowitz, E; Jennings, B

1996-01-01

National rates of unintended births are a major public health concern. The availability of highly effective long-acting contraceptives has prompted some public officials to promote the coercive use of these methods to reduce such problems as intergenerational poverty and child abuse. Broad-brush public policies that require long-term contraceptive use are unethical. However, persuasion to use these methods can be appropriate. One place for exerting ethically justified influence is in family planning counseling. The dominant nondirective counseling model, which excludes the possibility of vigorous persuasion, is overly rigid. Family planning professionals should develop practice protocols that permit and guide the exercise of directive counseling to use long-acting contraception. PMID:8659650

Energy efficiency as a commodity: The emergence of a secondary market for efficiency savings in commercial buildings

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

Kats, G.H.; Rosenfield, A.H.; McIntosh, T.A.

1997-06-01

The energy efficiency industry is constrained by lack of financing. For example, in the United States, commercial and public buildings need an investment of $100 billion for cost-effective retrofits with an average payback of about four years. But the current level of financing is stagnant at only about 34% of this level per year. The U.S. Department of Energy (DOE) has led the development of the North American Energy Measurement and Verification Protocol (NEMVP). This Protocol will increase the reliability and quality of estimated efficiency savings and improve realized savings. A critical element in the development of low cost financingmore » and a secondary market--whether for homes or credit card debt--is the adoption of protocols to provide uniformity and reliability of the product. This is also true of energy efficiency installations, which have been characterized by inconsistency in the installation methodologies and, frequently, unreliability of savings. This Protocol, published in April 1996, is a DOE-led effort involving American Society of Heating, Refrigerating, and Air-Conditioning Engineers, Inc. ASHRAE, National Association of Energy Service Companies NAESCO, National Association of Regulatory Utility Commissioners NARUC, National Association of State Energy Officials NASEO, US Environmental Protection Agency EPA, Canada`s Canadian Association of Energy Service Companies CAESCO, and Mexico`s Comision Nacional Para El Ahorro De Energia CONAE and Fideicomiso De Apoyo Al Programa De Ahorro De Energia Del Sector Electrico FIDE. DOE has begun to build on this Protocol to develop new forms of lower-cost financing including, ultimately, development of a secondary market for energy efficiency. This could double financing for building energy efficiency within five years.« less

Sampled-data-based consensus and containment control of multiple harmonic oscillators: A motion-planning approach

NASA Astrophysics Data System (ADS)

Liu, Yongfang; Zhao, Yu; Chen, Guanrong

2016-11-01

This paper studies the distributed consensus and containment problems for a group of harmonic oscillators with a directed communication topology. First, for consensus without a leader, a class of distributed consensus protocols is designed by using motion planning and Pontryagin's principle. The proposed protocol only requires relative information measurements at the sampling instants, without requiring information exchange over the sampled interval. By using stability theory and the properties of stochastic matrices, it is proved that the distributed consensus problem can be solved in the motion planning framework. Second, for the case with multiple leaders, a class of distributed containment protocols is developed for followers such that their positions and velocities can ultimately converge to the convex hull formed by those of the leaders. Compared with the existing consensus algorithms, a remarkable advantage of the proposed sampled-data-based protocols is that the sampling periods, communication topologies and control gains are all decoupled and can be separately designed, which relaxes many restrictions in controllers design. Finally, some numerical examples are given to illustrate the effectiveness of the analytical results.

7 CFR 52.37 - How official samples are to be identified and shipped.

Code of Federal Regulations, 2010 CFR

2010-01-01

... UNDER THE AGRICULTURAL MARKETING ACT OF 1946 PROCESSED FRUITS AND VEGETABLES, PROCESSED PRODUCTS THEREOF, AND CERTAIN OTHER PROCESSED FOOD PRODUCTS 1 Regulations Governing Inspection and Certification...

Sampling protocol, estimation, and analysis procedures for the down woody materials indicator of the FIA program

Treesearch

Christopher W. Woodall; Vicente J. Monleon

2008-01-01

The USDA Forest Service's Forest Inventory and Analysis program conducts an inventory of forests of the United States including down woody materials (DWM). In this report we provide the rationale and context for a national inventory of DWM, describe the components sampled, discuss the sampling protocol used and corresponding estimation procedures, and provide...

Simple Sodium Dodecyl Sulfate-Assisted Sample Preparation Method for LC-MS-based Proteomic Applications

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

Zhou, Jianying; Dann, Geoffrey P.; Shi, Tujin

2012-03-10

Sodium dodecyl sulfate (SDS) is one of the most popular laboratory reagents used for highly efficient biological sample extraction; however, SDS presents a significant challenge to LC-MS-based proteomic analyses due to its severe interference with reversed-phase LC separations and electrospray ionization interfaces. This study reports a simple SDS-assisted proteomic sample preparation method facilitated by a novel peptide-level SDS removal protocol. After SDS-assisted protein extraction and digestion, SDS was effectively (>99.9%) removed from peptides through ion substitution-mediated DS- precipitation with potassium chloride (KCl) followed by {approx}10 min centrifugation. Excellent peptide recovery (>95%) was observed for less than 20 {mu}g of peptides.more » Further experiments demonstrated the compatibility of this protocol with LC-MS/MS analyses. The resulting proteome coverage from this SDS-assisted protocol was comparable to or better than those obtained from other standard proteomic preparation methods in both mammalian tissues and bacterial samples. These results suggest that this SDS-assisted protocol is a practical, simple, and broadly applicable proteomic sample processing method, which can be particularly useful when dealing with samples difficult to solubilize by other methods.« less

DNA elution from buccal cells stored on Whatman FTA Classic Cards using a modified methanol fixation method.

PubMed

Johanson, Helene C; Hyland, Valentine; Wicking, Carol; Sturm, Richard A

2009-04-01

We describe here a method for DNA elution from buccal cells and whole blood both collected onto Whatman FTA technology, using methanol fixation followed by an elution PCR program. Extracted DNA is comparable in quality to published Whatman FTA protocols, as judged by PCR-based genotyping. Elution of DNA from the dried sample is a known rate-limiting step in the published Whatman FTA protocol; this method enables the use of each 3-mm punch of sample for several PCR reactions instead of the standard, one PCR reaction per sample punch. This optimized protocol therefore extends the usefulness and cost effectiveness of each buccal swab sample collected, when used for nucleic acid PCR and genotyping.

Avoidance of harvesting and sampling artefacts in hydraulic analyses: a protocol tested on Malus domestica

PubMed Central

Beikircher, Barbara; Mayr, Stefan

2016-01-01

A prerequisite for reliable hydraulic measurements is an accurate collection of the plant material. Thereby, the native hydraulic state of the sample has to be preserved during harvesting (i.e., cutting the plant or plant parts) and preparation (i.e., excising the target section). This is particularly difficult when harvesting has to be done under transpiring conditions. In this article, we present a harvesting and sampling protocol designed for hydraulic measurements on Malus domestica Borkh. and checked for possible sampling artefacts. To test for artefacts, we analysed the percentage loss of hydraulic conductivity, maximum specific conductivity and water contents of bark and wood of branches, taking into account conduit length, time of day of harvesting, different shoot ages and seasonal effects. Our results prove that use of appropriate protocols can avoid artefactual embolization or refilling even when the xylem is under tension at harvest. The presented protocol was developed for Malus but may also be applied for other angiosperms with similar anatomy and refilling characteristics. PMID:26705311

Rapid Waterborne Pathogen Detection with Mobile Electronics.

PubMed

Wu, Tsung-Feng; Chen, Yu-Chen; Wang, Wei-Chung; Kucknoor, Ashwini S; Lin, Che-Jen; Lo, Yu-Hwa; Yao, Chun-Wei; Lian, Ian

2017-06-09

Pathogen detection in water samples, without complex and time consuming procedures such as fluorescent-labeling or culture-based incubation, is essential to public safety. We propose an immunoagglutination-based protocol together with the microfluidic device to quantify pathogen levels directly from water samples. Utilizing ubiquitous complementary metal-oxide-semiconductor (CMOS) imagers from mobile electronics, a low-cost and one-step reaction detection protocol is developed to enable field detection for waterborne pathogens. 10 mL of pathogen-containing water samples was processed using the developed protocol including filtration enrichment, immune-reaction detection and imaging processing. The limit of detection of 10 E. coli O157:H7 cells/10 mL has been demonstrated within 10 min of turnaround time. The protocol can readily be integrated into a mobile electronics such as smartphones for rapid and reproducible field detection of waterborne pathogens.

FISH-in-CHIPS: A Microfluidic Platform for Molecular Typing of Cancer Cells.

PubMed

Perez-Toralla, Karla; Mottet, Guillaume; Tulukcuoglu-Guneri, Ezgi; Champ, Jérôme; Bidard, François-Clément; Pierga, Jean-Yves; Klijanienko, Jerzy; Draskovic, Irena; Malaquin, Laurent; Viovy, Jean-Louis; Descroix, Stéphanie

2017-01-01

Microfluidics offer powerful tools for the control, manipulation, and analysis of cells, in particular for the assessment of cell malignancy or the study of cell subpopulations. However, implementing complex biological protocols on chip remains a challenge. Sample preparation is often performed off chip using multiple manually performed steps, and protocols usually include different dehydration and drying steps that are not always compatible with a microfluidic format.Here, we report the implementation of a Fluorescence in situ Hybridization (FISH) protocol for the molecular typing of cancer cells in a simple and low-cost device. The geometry of the chip allows integrating the sample preparation steps to efficiently assess the genomic content of individual cells using a minute amount of sample. The FISH protocol can be fully automated, thus enabling its use in routine clinical practice.

Near-optimal protocols in complex nonequilibrium transformations

DOE PAGES

Gingrich, Todd R.; Rotskoff, Grant M.; Crooks, Gavin E.; ...

2016-08-29

The development of sophisticated experimental means to control nanoscale systems has motivated efforts to design driving protocols that minimize the energy dissipated to the environment. Computational models are a crucial tool in this practical challenge. In this paper, we describe a general method for sampling an ensemble of finite-time, nonequilibrium protocols biased toward a low average dissipation. In addition, we show that this scheme can be carried out very efficiently in several limiting cases. As an application, we sample the ensemble of low-dissipation protocols that invert the magnetization of a 2D Ising model and explore how the diversity of themore » protocols varies in response to constraints on the average dissipation. In this example, we find that there is a large set of protocols with average dissipation close to the optimal value, which we argue is a general phenomenon.« less

Exploring the Implementation of Steganography Protocols on Quantum Audio Signals

NASA Astrophysics Data System (ADS)

Chen, Kehan; Yan, Fei; Iliyasu, Abdullah M.; Zhao, Jianping

2018-02-01

Two quantum audio steganography (QAS) protocols are proposed, each of which manipulates or modifies the least significant qubit (LSQb) of the host quantum audio signal that is encoded as an FRQA (flexible representation of quantum audio) audio content. The first protocol (i.e. the conventional LSQb QAS protocol or simply the cLSQ stego protocol) is built on the exchanges between qubits encoding the quantum audio message and the LSQb of the amplitude information in the host quantum audio samples. In the second protocol, the embedding procedure to realize it implants information from a quantum audio message deep into the constraint-imposed most significant qubit (MSQb) of the host quantum audio samples, we refer to it as the pseudo MSQb QAS protocol or simply the pMSQ stego protocol. The cLSQ stego protocol is designed to guarantee high imperceptibility between the host quantum audio and its stego version, whereas the pMSQ stego protocol ensures that the resulting stego quantum audio signal is better immune to illicit tampering and copyright violations (a.k.a. robustness). Built on the circuit model of quantum computation, the circuit networks to execute the embedding and extraction algorithms of both QAS protocols are determined and simulation-based experiments are conducted to demonstrate their implementation. Outcomes attest that both protocols offer promising trade-offs in terms of imperceptibility and robustness.

USGS/EPA collection protocol for bacterial pathogens in soil

USGS Publications Warehouse

Griffin, Dale W.; Shaefer, F.L.; Charlena Bowling,; Dino Mattorano,; Tonya Nichols,; Erin Silvestri,

2014-01-01

This Sample Collection Procedure (SCP) describes the activities and considerations for the collection of bacterial pathogens from representative surface soil samples (0-5 cm). This sampling depth can be reached without the use of a drill rig, direct-push technology, or other mechanized equipment. This procedure can be used in most soil types but is limited to sampling at or near the ground surface. This protocol has components for two different types of sampling applications: (1) typical sampling, when there is no suspicion of contamination (e.g., surveillance or background studies); and (2) in response to known or suspected accidental contamination (e.g., the presence of animal carcasses). This protocol does not cover sampling in response to a suspected bioterrorist or intentional release event. Surface material is removed to the required depth (0-5 cm) and clean trowel or 50 ml sample tube is used to collect the sample. Sample containers are sealed, bagged, and shipped to the laboratory for analysis. Associated documentation, including a Field Data Log and Chain-of-Custody are also included in this document.

Optimization of scat detection methods for a social ungulate, the wild pig, and experimental evaluation of factors affecting detection of scat

USGS Publications Warehouse

Keiter, David A.; Cunningham, Fred L.; Rhodes, Olin E.; Irwin, Brian J.; Beasley, James

2016-01-01

Collection of scat samples is common in wildlife research, particularly for genetic capture-mark-recapture applications. Due to high degradation rates of genetic material in scat, large numbers of samples must be collected to generate robust estimates. Optimization of sampling approaches to account for taxa-specific patterns of scat deposition is, therefore, necessary to ensure sufficient sample collection. While scat collection methods have been widely studied in carnivores, research to maximize scat collection and noninvasive sampling efficiency for social ungulates is lacking. Further, environmental factors or scat morphology may influence detection of scat by observers. We contrasted performance of novel radial search protocols with existing adaptive cluster sampling protocols to quantify differences in observed amounts of wild pig (Sus scrofa) scat. We also evaluated the effects of environmental (percentage of vegetative ground cover and occurrence of rain immediately prior to sampling) and scat characteristics (fecal pellet size and number) on the detectability of scat by observers. We found that 15- and 20-m radial search protocols resulted in greater numbers of scats encountered than the previously used adaptive cluster sampling approach across habitat types, and that fecal pellet size, number of fecal pellets, percent vegetative ground cover, and recent rain events were significant predictors of scat detection. Our results suggest that use of a fixed-width radial search protocol may increase the number of scats detected for wild pigs, or other social ungulates, allowing more robust estimation of population metrics using noninvasive genetic sampling methods. Further, as fecal pellet size affected scat detection, juvenile or smaller-sized animals may be less detectable than adult or large animals, which could introduce bias into abundance estimates. Knowledge of relationships between environmental variables and scat detection may allow researchers to optimize sampling protocols to maximize utility of noninvasive sampling for wild pigs and other social ungulates.

Optimization of Scat Detection Methods for a Social Ungulate, the Wild Pig, and Experimental Evaluation of Factors Affecting Detection of Scat.

PubMed

Keiter, David A; Cunningham, Fred L; Rhodes, Olin E; Irwin, Brian J; Beasley, James C

2016-01-01

Collection of scat samples is common in wildlife research, particularly for genetic capture-mark-recapture applications. Due to high degradation rates of genetic material in scat, large numbers of samples must be collected to generate robust estimates. Optimization of sampling approaches to account for taxa-specific patterns of scat deposition is, therefore, necessary to ensure sufficient sample collection. While scat collection methods have been widely studied in carnivores, research to maximize scat collection and noninvasive sampling efficiency for social ungulates is lacking. Further, environmental factors or scat morphology may influence detection of scat by observers. We contrasted performance of novel radial search protocols with existing adaptive cluster sampling protocols to quantify differences in observed amounts of wild pig (Sus scrofa) scat. We also evaluated the effects of environmental (percentage of vegetative ground cover and occurrence of rain immediately prior to sampling) and scat characteristics (fecal pellet size and number) on the detectability of scat by observers. We found that 15- and 20-m radial search protocols resulted in greater numbers of scats encountered than the previously used adaptive cluster sampling approach across habitat types, and that fecal pellet size, number of fecal pellets, percent vegetative ground cover, and recent rain events were significant predictors of scat detection. Our results suggest that use of a fixed-width radial search protocol may increase the number of scats detected for wild pigs, or other social ungulates, allowing more robust estimation of population metrics using noninvasive genetic sampling methods. Further, as fecal pellet size affected scat detection, juvenile or smaller-sized animals may be less detectable than adult or large animals, which could introduce bias into abundance estimates. Knowledge of relationships between environmental variables and scat detection may allow researchers to optimize sampling protocols to maximize utility of noninvasive sampling for wild pigs and other social ungulates.

An Organic Decontamination Method for Sampling Devices used in Life-detection Studies

NASA Technical Reports Server (NTRS)

Eigenbrode, Jennifer; Maule, Jake; Wainwright, Norm; Steele, Andrew; Amundsen, Hans E.F.

2008-01-01

Organic decontamination of sampling and storage devices are crucial steps for life-detection, habitability, and ecological investigations of extremophiles living in the most inhospitable niches of Earth, Mars and elsewhere. However, one of the main stumbling blocks for Mars-analogue life-detection studies in terrestrial remote field-sites is the capability to clean instruments and sampling devices to organic levels consistent with null values. Here we present a new seven-step, multi-reagent cleaning and decontamination protocol that was adapted and tested on a glacial ice-coring device and on a rover-guided scoop used for sediment sampling both deployed multiple times during two field seasons of the Arctic Mars Analog Svalbard Expedition AMASE). The effectiveness of the protocols for both devices was tested by (1)in situ metabolic measurements via APT, (2)in situ lipopolysacchride (LPS) quantifications via low-level endotoxin assays, and(3) laboratory-based molecular detection via gas chromatography-mass spectrometry. Our results show that the combination and step-wise application of disinfectants with oxidative and solvation properties for sterilization are effective at removing cellular remnants and other organic traces to levels necessary for molecular organic- and life-detection studies. The validation of this seven-step protocol - specifically for ice sampling - allows us to proceed with confidence in kmskia4 analogue investigations of icy environments. However, results from a rover scoop test showed that this protocol is also suitable for null-level decontamination of sample acquisition devices. Thus, this protocol may be applicable to a variety of sampling devices and analytical instrumentation used for future astrobiology missions to Enceladus, and Europa, as well as for sample-return missions.

[Helminth prevalence in a waste-water plant at El Rosal, Cundinamarca].

PubMed

Ortiz, Carolina; López, Myriam C; Rivas, Favio A

2012-01-01

Assessing helminth egg prevalence in sludge and raw and treated wastewater from a wastewater treatment system located in the village of El Rosal, Cundinamarca. 30 wastewater and 10 sludge samples from the El Rosal plant were taken during a 10-week period. The sludge and water samples were processed according to the Bailinger and the official Mexican standard methodology, respectively. Egg viability was determined by the method described by Victórica & Galván and the Mexican official standard. Descriptive statistics were used for analysing data. 100 % of the untreated wastewater samples showed the presence of eggs and at least one viable helminth egg/litre was found in 90 % of them. 90 % of the treated wastewater samples were positive for the presence of eggs, finding that 70 % had at least one viable egg. All raw wastewater samples being dumped directly into the stream were positive for helminths; the same situation was found at the time of the viability test. All sludge samples were positive for helminths, finding that 100 % of these had at least one viable egg. Using this water for crop irrigation and using the sludge as fertiliser is a potential risk for public health. The sludge can only be used in forestry activities, as long as it does not come into contact with humans.

DEVELOPMENT OF LARGE RIVER BIOASSESSMENT PROTOCOLS (LR-BPS) FOR BENTHIC MACROINVERTEBRATES IN EPA REGION 5

EPA Science Inventory

Non-wadeable rivers have been largely overlooked by bioassessment programs because of sampling difficulties and a lack of appropriate methods and biological indicators. We are in the process of developing a Large River Bioassessment Protocol (LR-BP) for sampling macroinvertebrat...

U.S.-MEXICO BORDER PROGRAM ARIZONA BORDER STUDY--LIST OF STANDARD OPERATING PROCEDURES

EPA Science Inventory

This document lists available protocols and SOPs for the U.S.-Mexico Border Program study. It identifies protocols and SOPs for the following study components: (1) Sample collection and field operations, (2) Sample analysis, (3) General laboratory procedures, (4) Quality Assuranc...

Preparedness for climate change among local health department officials in New York state: a comparison with national survey results.

PubMed

Carr, Jessie L; Sheffield, Perry E; Kinney, Patrick L

2012-01-01

Climate-change adaptation strategies that address locally specific climate hazards are critical for preventing negative health outcomes, and local public health care officials are key foci for adaptation planning. To assess New York State Local Health Department officials' perceptions and preparedness related to climate-sensitive health areas, and compare these with a national sample. Online survey instrument, originally used in a national survey of local health department (LHD) officials. New York State. Eligible participants included all New York State city and county LHD officials, 1 respondent per LHD. LHD officials' perceptions of (1) local climate-related public health effects, (2) preparation status and programming areas of LHDs, and (3) necessary resources to better address climate-related health risks. : Survey participants, representing a 54% response rate (with 93% of respondents completing more than 90% of the questions), perceived climate change as relevant to public health, and most noted that some of their existing programs already use or are planning to use climate adaptation strategies. Overall, fewer New York State respondents identified concerns or related expertise compared with the previous national survey. Many respondents expressed uncertainty regarding necessary additional resources. This type of assessment makes clear the high variability in perceived impacts and capacity at the level of LHD jurisdictions, and underscores the importance of sustained support for local climate-change preparedness programming. The implications of these findings are germane to other states with similar decentralized jurisdiction of public health. Findings from such surveys can bolster existing LHD programs, as well as inform long-term and emergency planning for climate change.

The use of medical care and out-of-pocket payments in Russia.

PubMed

Zasimova, Liudmila

2016-07-01

Despite the constitutional right of all Russian citizens to free medical care, out-of-pocket payment is a widespread phenomenon for all types of medical treatment. The aims of this paper are twofold: To present new evidence on the use of, and payment for, outpatient and inpatient treatment in Russia; and to compare the motivations behind both official and informal payments for outpatient services provided in public medical institutions. This study uses data from a quantitative household survey conducted in April 2014. The sample comprised 1602 individuals aged ⩾ 18 years, representing the entire adult population of the Russian Federation. We studied three types of medical care: inpatient treatment, outpatient treatment and medicines. Our study found that 22.2% of patients pay for outpatient services, 37.5% pay for inpatient services and 91.5% pay for outpatient medicinal treatment. The informal payments are almost equally met in both outpatient (13.4%) and inpatient (12.2%) care; while the official payments are more common in inpatient care (25.2%), compared to outpatient care (8.8%). The main reasons for informal payment include: improvements in the quality of care and gratitude for medical staff. The official payments are more frequently motivated by an inability to receive a certain treatment free of charge. CONCLUSIONS THIS STUDY DEMONSTRATES THAT BOTH OFFICIAL AND INFORMAL PAYMENTS FOR MEDICAL TREATMENT ARE WIDESPREAD IN RUSSIA INFORMAL PAYMENTS ARE STRONGLY PREFERRED OVER OFFICIAL PAYMENTS FOR OUTPATIENT CARE, WHILE OFFICIAL PAYMENTS DOMINATE IN INPATIENT CARE. © 2016 the Nordic Societies of Public Health.

Optimization of a Sample Processing Protocol for Recovery of ...

EPA Pesticide Factsheets

Journal Article Following a release of Bacillus anthracis spores into the environment, there is a potential for lasting environmental contamination in soils. There is a need for detection protocols for B. anthracis in environmental matrices. However, identification of B. anthracis within a soil is a difficult task. Processing soil samples helps to remove debris, chemical components, and biological impurities that can interfere with microbiological detection. This study aimed to optimize a previously used indirect processing protocol, which included a series of washing and centrifugation steps.

Cardiology electrocardiogram overreads rarely influence patient care outcome.

PubMed

Proano, Lawrence; Sucov, Andrew; Woolard, Robert

2014-11-01

The value of electrocardiogram (ECG) overreads of emergency department (ED) tracings have been questioned in the literature. This review was designed to assess the validity of this criticism. In this university teaching hospital ED, following the normal quality assurance protocol, each abnormal ECG is reviewed the following day against the corresponding chart; and if the official reading from cardiology is discordant from the initial clinical one, the patient and/or their physician is contacted. If necessary, the patient is instructed to return to the ED or to their private physician's office. This study is a retrospective review of those ECG overreads for a 21-month period, as well as a summary of those patients who required follow-up care. There were 38,490 patients seen with ECGs performed during the study interval. Of these, 16,011 were discharged and 22,479 were admitted from a total patient volume of 117,407. Of those 16,011 patients discharged, follow-up was deemed necessary in 22 patients whose official readings were discordant from the interpretation of the original clinician. Three patients were lost to follow-up (no phone, no address). Review of the tracings and patient/physician follow-up of the 19 remaining patients resulted in a significant change of therapy in 2 patients (admission). The remainder of the abnormal tracings were deemed, after patient or private physician follow-up, to be not significant or to mandate no change in management. Official cardiology overreads seldom affect the clinical outcome of patient care delivered in the ED setting. Copyright © 2014 Elsevier Inc. All rights reserved.

VALIDATION OF ANALYTICAL METHODS AND INSTRUMENTATION FOR BERYLLIUM MEASUREMENT: REVIEW AND SUMMARY OF AVAILABLE GUIDES, PROCEDURES, AND PROTOCOLS

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

Ekechukwu, A.

This document proposes to provide a listing of available sources which can be used to validate analytical methods and/or instrumentation for beryllium determination. A literature review was conducted of available standard methods and publications used for method validation and/or quality control. A comprehensive listing of the articles, papers, and books reviewed is given in Appendix 1. Available validation documents and guides are listed in the appendix; each has a brief description of application and use. In the referenced sources, there are varying approaches to validation and varying descriptions of validation at different stages in method development. This discussion focuses onmore » validation and verification of fully developed methods and instrumentation that have been offered up for use or approval by other laboratories or official consensus bodies such as ASTM International, the International Standards Organization (ISO) and the Association of Official Analytical Chemists (AOAC). This review was conducted as part of a collaborative effort to investigate and improve the state of validation for measuring beryllium in the workplace and the environment. Documents and publications from the United States and Europe are included. Unless otherwise specified, all documents were published in English.« less

Metabolic profiling of body fluids and multivariate data analysis.

PubMed

Trezzi, Jean-Pierre; Jäger, Christian; Galozzi, Sara; Barkovits, Katalin; Marcus, Katrin; Mollenhauer, Brit; Hiller, Karsten

2017-01-01

Metabolome analyses of body fluids are challenging due pre-analytical variations, such as pre-processing delay and temperature, and constant dynamical changes of biochemical processes within the samples. Therefore, proper sample handling starting from the time of collection up to the analysis is crucial to obtain high quality samples and reproducible results. A metabolomics analysis is divided into 4 main steps: 1) Sample collection, 2) Metabolite extraction, 3) Data acquisition and 4) Data analysis. Here, we describe a protocol for gas chromatography coupled to mass spectrometry (GC-MS) based metabolic analysis for biological matrices, especially body fluids. This protocol can be applied on blood serum/plasma, saliva and cerebrospinal fluid (CSF) samples of humans and other vertebrates. It covers sample collection, sample pre-processing, metabolite extraction, GC-MS measurement and guidelines for the subsequent data analysis. Advantages of this protocol include: •Robust and reproducible metabolomics results, taking into account pre-analytical variations that may occur during the sampling process•Small sample volume required•Rapid and cost-effective processing of biological samples•Logistic regression based determination of biomarker signatures for in-depth data analysis.

76 FR 24862 - Proposed Information Collection; Comment Request; Protocol for Access to Tissue Specimen Samples...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-05-03

... Collection; Comment Request; Protocol for Access to Tissue Specimen Samples From the National Marine Mammal Tissue Bank AGENCY: National Oceanic and Atmospheric Administration (NOAA), Commerce. ACTION: Notice... National Marine Mammal Tissue Bank (NMMTB) was established by the National Marine Fisheries Service (NMFS...

A MORE COST-EFFECTIVE EMAP BENTHIC MACROFAUNAL SAMPLING PROTOCOL

EPA Science Inventory

Benthic macrofaunal sampling protocols in the U.S. Environmental Protection Agency's Environmental Monitoring and Assessment Program (EMAP) are to collect 30 to 50 random benthic macrofauna [defined as animals retained on a 0.5 mm (East and Gulf Coasts, USA) or a 1.0 mm mesh siev...

STANDARD MEASUREMENT PROTOCOLS - FLORIDA RADON RESEARCH PROGRAM

EPA Science Inventory

The manual, in support of the Florida Radon Research Program, contains standard protocols for key measurements where data quality is vital to the program. t contains two sections. he first section, soil measurements, contains field sampling protocols for soil gas permeability and...

Automated Dissolution for Enteric-Coated Aspirin Tablets: A Case Study for Method Transfer to a RoboDis II.

PubMed

Ibrahim, Sarah A; Martini, Luigi

2014-08-01

Dissolution method transfer is a complicated yet common process in the pharmaceutical industry. With increased pharmaceutical product manufacturing and dissolution acceptance requirements, dissolution testing has become one of the most labor-intensive quality control testing methods. There is an increased trend for automation in dissolution testing, particularly for large pharmaceutical companies to reduce variability and increase personnel efficiency. There is no official guideline for dissolution testing method transfer from a manual, semi-automated, to automated dissolution tester. In this study, a manual multipoint dissolution testing procedure for an enteric-coated aspirin tablet was transferred effectively and reproducibly to a fully automated dissolution testing device, RoboDis II. Enteric-coated aspirin samples were used as a model formulation to assess the feasibility and accuracy of media pH change during continuous automated dissolution testing. Several RoboDis II parameters were evaluated to ensure the integrity and equivalency of dissolution method transfer from a manual dissolution tester. This current study provides a systematic outline for the transfer of the manual dissolution testing protocol to an automated dissolution tester. This study further supports that automated dissolution testers compliant with regulatory requirements and similar to manual dissolution testers facilitate method transfer. © 2014 Society for Laboratory Automation and Screening.

Microbial Groundwater Sampling Protocol for Fecal-Rich Environments

PubMed Central

Harter, Thomas; Watanabe, Naoko; Li, Xunde; Atwill, Edward R; Samuels, William

2014-01-01

Inherently, confined animal farming operations (CAFOs) and other intense fecal-rich environments are potential sources of groundwater contamination by enteric pathogens. The ubiquity of microbial matter poses unique technical challenges in addition to economic constraints when sampling wells in such environments. In this paper, we evaluate a groundwater sampling protocol that relies on extended purging with a portable submersible stainless steel pump and Teflon® tubing as an alternative to equipment sterilization. The protocol allows for collecting a large number of samples quickly, relatively inexpensively, and under field conditions with limited access to capacity for sterilizing equipment. The protocol is tested on CAFO monitoring wells and considers three cross-contamination sources: equipment, wellbore, and ambient air. For the assessment, we use Enterococcus, a ubiquitous fecal indicator bacterium (FIB), in laboratory and field tests with spiked and blank samples, and in an extensive, multi-year field sampling campaign on 17 wells within 2 CAFOs. The assessment shows that extended purging can successfully control for equipment cross-contamination, but also controls for significant contamination of the well-head, within the well casing and within the immediate aquifer vicinity of the well-screen. Importantly, our tests further indicate that Enterococcus is frequently entrained in water samples when exposed to ambient air at a CAFO during sample collection. Wellbore and air contamination pose separate challenges in the design of groundwater monitoring strategies on CAFOs that are not addressed by equipment sterilization, but require adequate QA/QC procedures and can be addressed by the proposed sampling strategy. PMID:24903186

A novel method of genomic DNA extraction for Cactaceae1

PubMed Central

Fehlberg, Shannon D.; Allen, Jessica M.; Church, Kathleen

2013-01-01

• Premise of the study: Genetic studies of Cactaceae can at times be impeded by difficult sampling logistics and/or high mucilage content in tissues. Simplifying sampling and DNA isolation through the use of cactus spines has not previously been investigated. • Methods and Results: Several protocols for extracting DNA from spines were tested and modified to maximize yield, amplification, and sequencing. Sampling of and extraction from spines resulted in a simplified protocol overall and complete avoidance of mucilage as compared to typical tissue extractions. Sequences from one nuclear and three plastid regions were obtained across eight genera and 20 species of cacti using DNA extracted from spines. • Conclusions: Genomic DNA useful for amplification and sequencing can be obtained from cactus spines. The protocols described here are valuable for any cactus species, but are particularly useful for investigators interested in sampling living collections, extensive field sampling, and/or conservation genetic studies. PMID:25202521

Diverse protocols for correlative super-resolution fluorescence imaging and electron microscopy of chemically fixed samples

PubMed Central

Kopek, Benjamin G.; Paez-Segala, Maria G.; Shtengel, Gleb; Sochacki, Kem A.; Sun, Mei G.; Wang, Yalin; Xu, C. Shan; van Engelenburg, Schuyler B.; Taraska, Justin W.; Looger, Loren L.; Hess, Harald F.

2017-01-01

Our groups have recently developed related approaches for sample preparation for super-resolution imaging within endogenous cellular environments using correlative light and electron microscopy (CLEM). Four distinct techniques for preparing and acquiring super-resolution CLEM datasets on aldehyde-fixed specimens are provided, including Tokuyasu cryosectioning, whole-cell mount, cell unroofing and platinum replication, and resin embedding and sectioning. Choice of the best protocol for a given application depends on a number of criteria that are discussed in detail. Tokuyasu cryosectioning is relatively rapid but is limited to small, delicate specimens. Whole-cell mount has the simplest sample preparation but is restricted to surface structures. Cell unroofing and platinum replica creates high-contrast, 3-dimensional images of the cytoplasmic surface of the plasma membrane, but is more challenging than whole-cell mount. Resin embedding permits serial sectioning of large samples, but is limited to osmium-resistant probes, and is technically difficult. Expected results from these protocols include super-resolution localization (~10–50 nm) of fluorescent targets within the context of electron microscopy ultrastructure, which can help address cell biological questions. These protocols can be completed in 2–7 days, are compatible with a number of super-resolution imaging protocols, and are broadly applicable across biology. PMID:28384138

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

PubMed

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

2018-01-01

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

Use of a Filter Cartridge for Filtration of Water Samples and Extraction of Environmental DNA.

PubMed

Miya, Masaki; Minamoto, Toshifumi; Yamanaka, Hiroki; Oka, Shin-Ichiro; Sato, Keiichi; Yamamoto, Satoshi; Sado, Tetsuya; Doi, Hideyuki

2016-11-25

Recent studies demonstrated the use of environmental DNA (eDNA) from fishes to be appropriate as a non-invasive monitoring tool. Most of these studies employed disk fiber filters to collect eDNA from water samples, although a number of microbial studies in aquatic environments have employed filter cartridges, because the cartridge has the advantage of accommodating large water volumes and of overall ease of use. Here we provide a protocol for filtration of water samples using the filter cartridge and extraction of eDNA from the filter without having to cut open the housing. The main portions of this protocol consists of 1) filtration of water samples (water volumes ≤4 L or >4 L); (2) extraction of DNA on the filter using a roller shaker placed in a preheated incubator; and (3) purification of DNA using a commercial kit. With the use of this and previously-used protocols, we perform metabarcoding analysis of eDNA taken from a huge aquarium tank (7,500 m 3 ) with known species composition, and show the number of detected species per library from the two protocols as the representative results. This protocol has been developed for metabarcoding eDNA from fishes, but is also applicable to eDNA from other organisms.

The DNA isolation method has effect on allele drop-out and on the results of fluorescent PCR and DNA fragment analysis.

PubMed

Nagy, Bálint; Bán, Zoltán; Papp, Zoltán

2005-10-01

The quality and the quantity of isolated DNA have an effect on PCR amplifications. The authors studied three DNA isolation protocols (resin binding method using fresh and frozen amniotic fluid samples, and silica adsorption method using fresh samples) on the quantity and on the quality of the isolated DNA. Amniotic fluid samples were obtained from 20 pregnant women. The isolated DNA concentrations were determined by real-time fluorimeter using SYBRGreen I method. Each sample was studied for the presence of 8 STR markers. The authors compared the number of the detected alleles, electrophoretograms and peak areas. There was a significant difference between the concentration of the obtained DNA and in the peak areas between the three isolation protocols. The numbers of detected alleles were different, we observed the most allele drop outs in the resin type DNA isolation protocol from the fresh sample (detected allele numbers 182), followed by resin binding protocol from the frozen samples (detected allele number 243) and by the silica adsorption method (detected allele number 264). The authors demonstrated that the DNA isolation method has an effect on the quantity and quality of the isolated DNA, and on further PCR amplifications.

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.

Digital gene expression analysis with sample multiplexing and PCR duplicate detection: A straightforward protocol.

PubMed

Rozenberg, Andrey; Leese, Florian; Weiss, Linda C; Tollrian, Ralph

2016-01-01

Tag-Seq is a high-throughput approach used for discovering SNPs and characterizing gene expression. In comparison to RNA-Seq, Tag-Seq eases data processing and allows detection of rare mRNA species using only one tag per transcript molecule. However, reduced library complexity raises the issue of PCR duplicates, which distort gene expression levels. Here we present a novel Tag-Seq protocol that uses the least biased methods for RNA library preparation combined with a novel approach for joint PCR template and sample labeling. In our protocol, input RNA is fragmented by hydrolysis, and poly(A)-bearing RNAs are selected and directly ligated to mixed DNA-RNA P5 adapters. The P5 adapters contain i5 barcodes composed of sample-specific (moderately) degenerate base regions (mDBRs), which later allow detection of PCR duplicates. The P7 adapter is attached via reverse transcription with individual i7 barcodes added during the amplification step. The resulting libraries can be sequenced on an Illumina sequencer. After sample demultiplexing and PCR duplicate removal with a free software tool we designed, the data are ready for downstream analysis. Our protocol was tested on RNA samples from predator-induced and control Daphnia microcrustaceans.

Non-Uniformly Sampled MR Correlated Spectroscopic Imaging in Breast Cancer and Nonlinear Reconstruction

DTIC Science & Technology

2017-10-01

AWARD NUMBER: W81XWH-16-1-0524 TITLE: Non-Uniformly Sampled MR Correlated Spectroscopic Imaging in Breast Cancer and Nonlinear Reconstruction...author(s) and should not be construed as an official Department of the Army position, policy or decision unless so designated by other...COVERED 30 Sep 2016 - 29 Sep 2017 5a. CONTRACT NUMBER 4. TITLE AND SUBTITLE Non-Uniformly Sampled MR Correlated Spectroscopic Imaging in Breast

Crystallization of Macromolecules

PubMed Central

Friedmann, David; Messick, Troy; Marmorstein, Ronen

2014-01-01

X-ray crystallography has evolved into a very powerful tool to determine the three-dimensional structure of macromolecules and macromolecular complexes. The major bottleneck in structure determination by X-ray crystallography is the preparation of suitable crystalline samples. This unit outlines steps for the crystallization of a macromolecule, starting with a purified, homogeneous sample. The first protocols describe preparation of the macromolecular sample (i.e., proteins, nucleic acids, and macromolecular complexes). The preparation and assessment of crystallization trials is then described, along with a protocol for confirming whether the crystals obtained are composed of macromolecule as opposed to a crystallization reagent . Next, the optimization of crystallization conditions is presented. Finally, protocols that facilitate the growth of larger crystals through seeding are described. PMID:22045560

Development of an efficient real-time quantitative PCR protocol for detection of Xanthomonas arboricola pv. pruni in Prunus species.

PubMed

Palacio-Bielsa, Ana; Cubero, Jaime; Cambra, Miguel A; Collados, Raquel; Berruete, Isabel M; López, María M

2011-01-01

Xanthomonas arboricola pv. pruni, the causal agent of bacterial spot disease of stone fruit, is considered a quarantine organism by the European Union and the European and Mediterranean Plant Protection Organization (EPPO). The bacterium can undergo an epiphytic phase and/or be latent and can be transmitted by plant material, but currently, only visual inspections are used to certify plants as being X. arboricola pv. pruni free. A novel and highly sensitive real-time TaqMan PCR detection protocol was designed based on a sequence of a gene for a putative protein related to an ABC transporter ATP-binding system in X. arboricola pv. pruni. Pathogen detection can be completed within a few hours with a sensitivity of 10(2) CFU ml(-1), thus surpassing the sensitivity of the existing conventional PCR. Specificity was assessed for X. arboricola pv. pruni strains from different origins as well as for closely related Xanthomonas species, non-Xanthomonas species, saprophytic bacteria, and healthy Prunus samples. The efficiency of the developed protocol was evaluated with field samples of 14 Prunus species and rootstocks. For symptomatic leaf samples, the protocol was very efficient even when washed tissues of the leaves were directly amplified without any previous DNA extraction. For samples of 117 asymptomatic leaves and 285 buds, the protocol was more efficient after a simple DNA extraction, and X. arboricola pv. pruni was detected in 9.4% and 9.1% of the 402 samples analyzed, respectively, demonstrating its frequent epiphytic or endophytic phase. This newly developed real-time PCR protocol can be used as a quantitative assay, offers a reliable and sensitive test for X. arboricola pv. pruni, and is suitable as a screening test for symptomatic as well as asymptomatic plant material.

Consensus for second-order multi-agent systems with position sampled data

NASA Astrophysics Data System (ADS)

Wang, Rusheng; Gao, Lixin; Chen, Wenhai; Dai, Dameng

2016-10-01

In this paper, the consensus problem with position sampled data for second-order multi-agent systems is investigated. The interaction topology among the agents is depicted by a directed graph. The full-order and reduced-order observers with position sampled data are proposed, by which two kinds of sampled data-based consensus protocols are constructed. With the provided sampled protocols, the consensus convergence analysis of a continuous-time multi-agent system is equivalently transformed into that of a discrete-time system. Then, by using matrix theory and a sampled control analysis method, some sufficient and necessary consensus conditions based on the coupling parameters, spectrum of the Laplacian matrix and sampling period are obtained. While the sampling period tends to zero, our established necessary and sufficient conditions are degenerated to the continuous-time protocol case, which are consistent with the existing result for the continuous-time case. Finally, the effectiveness of our established results is illustrated by a simple simulation example. Project supported by the Natural Science Foundation of Zhejiang Province, China (Grant No. LY13F030005) and the National Natural Science Foundation of China (Grant No. 61501331).

Robust DNA Isolation and High-throughput Sequencing Library Construction for Herbarium Specimens.

PubMed

Saeidi, Saman; McKain, Michael R; Kellogg, Elizabeth A

2018-03-08

Herbaria are an invaluable source of plant material that can be used in a variety of biological studies. The use of herbarium specimens is associated with a number of challenges including sample preservation quality, degraded DNA, and destructive sampling of rare specimens. In order to more effectively use herbarium material in large sequencing projects, a dependable and scalable method of DNA isolation and library preparation is needed. This paper demonstrates a robust, beginning-to-end protocol for DNA isolation and high-throughput library construction from herbarium specimens that does not require modification for individual samples. This protocol is tailored for low quality dried plant material and takes advantage of existing methods by optimizing tissue grinding, modifying library size selection, and introducing an optional reamplification step for low yield libraries. Reamplification of low yield DNA libraries can rescue samples derived from irreplaceable and potentially valuable herbarium specimens, negating the need for additional destructive sampling and without introducing discernible sequencing bias for common phylogenetic applications. The protocol has been tested on hundreds of grass species, but is expected to be adaptable for use in other plant lineages after verification. This protocol can be limited by extremely degraded DNA, where fragments do not exist in the desired size range, and by secondary metabolites present in some plant material that inhibit clean DNA isolation. Overall, this protocol introduces a fast and comprehensive method that allows for DNA isolation and library preparation of 24 samples in less than 13 h, with only 8 h of active hands-on time with minimal modifications.

An optimised protocol for molecular identification of Eimeria from chickens☆

PubMed Central

Kumar, Saroj; Garg, Rajat; Moftah, Abdalgader; Clark, Emily L.; Macdonald, Sarah E.; Chaudhry, Abdul S.; Sparagano, Olivier; Banerjee, Partha S.; Kundu, Krishnendu; Tomley, Fiona M.; Blake, Damer P.

2014-01-01

Molecular approaches supporting identification of Eimeria parasites infecting chickens have been available for more than 20 years, although they have largely failed to replace traditional measures such as microscopy and pathology. Limitations of microscopy-led diagnostics, including a requirement for specialist parasitological expertise and low sample throughput, are yet to be outweighed by the difficulties associated with accessing genomic DNA from environmental Eimeria samples. A key step towards the use of Eimeria species-specific PCR as a sensitive and reproducible discriminatory tool for use in the field is the production of a standardised protocol that includes sample collection and DNA template preparation, as well as primer selection from the numerous PCR assays now published. Such a protocol will facilitate development of valuable epidemiological datasets which may be easily compared between studies and laboratories. The outcome of an optimisation process undertaken in laboratories in India and the UK is described here, identifying four steps. First, samples were collected into a 2% (w/v) potassium dichromate solution. Second, oocysts were enriched by flotation in saturated saline. Third, genomic DNA was extracted using a QIAamp DNA Stool mini kit protocol including a mechanical homogenisation step. Finally, nested PCR was carried out using previously published primers targeting the internal transcribed spacer region 1 (ITS-1). Alternative methods tested included sample processing in the presence of faecal material, DNA extraction using a traditional phenol/chloroform protocol, the use of SCAR multiplex PCR (one tube and two tube versions) and speciation using the morphometric tool COCCIMORPH for the first time with field samples. PMID:24138724

Development of an HPV Educational Protocol for Adolescents

PubMed Central

Wetzel, Caitlin; Tissot, Abbigail; Kollar, Linda M.; Hillard, Paula A.; Stone, Rachel; Kahn, Jessica A.

2007-01-01

Study Objectives To develop an educational protocol about HPV and Pap tests for adolescents, to evaluate the protocol for understandability and clarity, and to evaluate the protocol for its effectiveness in increasing knowledge about HPV. Design In phase 1, investigators and adolescents developed the protocol. In phase 2, adolescents evaluated the protocol qualitatively, investigators evaluated its effectiveness in increasing HPV knowledge in a sample of adolescents, and the protocol was revised. In phase 3, investigators evaluated the effectiveness of the revised protocol in an additional adolescent sample. Setting Urban, hospital-based teen health center. Participants A total of 252 adolescent girls and boys in the three study phases. Main Outcome Measures Pre- and post-protocol knowledge about HPV, measured using a 10- or 11-item scale. Results Scores on the HPV knowledge scale increased significantly (p<.0001) among adolescents who participated in phases 2 and 3 after they received the protocol. Initial differences in scores based on race, insurance type and condom use were not noted post-protocol. Conclusion The protocol significantly increased knowledge scores about HPV in this population, regardless of sociodemographic characteristics and risk behaviors. Effective, developmentally appropriate educational protocols about HPV and Pap tests are particularly important in clinical settings as cervical cancer screening guidelines evolve, HPV DNA testing is integrated into screening protocols, and HPV vaccines become available. In-depth, one-on-one education about HPV may also prevent adverse psychosocial responses and promote healthy sexual and Pap screening behaviors in adolescents with abnormal HPV or Pap test results. Synopsis The investigators developed an educational protocol about HPV and Pap tests and evaluated its effectiveness in increasing knowledge about HPV among adolescents. PMID:17868894

[Determination of markers from characteristic HPLC chromatogram of phenols in three official origins of Ephedrae Herba and quantitative analysis of four phenols].

PubMed

Zuo, Xue; Hong, Hao; Zang, Xin-yu; Xu, Feng; Shang, Ming-ying; Wang, Xuan; Cai, Shao-qing

2015-12-01

This study is to establish the characteristic HPLC chromatogram of phenols in Ephedrae Herba, from which to pick out the marker peaks, followed by the analysis of the regularity of their distribution and content in the herbaceous stems of Ephedra sinica, E. intermedia and E. equisetina. The HPLC-DAD method for the characteristic chromatogram as well as quantitative analysis was established. The separation was carried out on a YMC-Pack ODS-A column (4.6 mm x 250 mm, 5 µm), eluted with the mobile phases as 0.01% formic acid aqueous solution (A) and acetonitrile (B) in a linear gradient (0-10 min, 17% B; 10-25 min, 17%-19% B; 25- 33 min, 19%-48% B; 33-35 min, 48%-51% B; 35-44 min, 51% B). The flow rate was kept at 1.0 mL · min⁻¹. The column tem- perature was 40 °C, and the detection wavelength was set at 350 nm (0-16 min) and 330 nm (16-44 min). Forty-six batches of collected samples from three official origins of Ephedrae Herba were detected, whose liquid chromatograms proven to be helpful to the differentiation of different origins. With principal component analysis and the analysis of distribution of peak area, twelve key peaks from the chromatogram were discussed in details on their contributions to the characteristics and differences of three official origins of the herb: peak area of peak 10, 11, 12 were found out to be significantly higher in E. equisetina than in other two origins, whose sum (higher than 146 mAU in E. equisetina) was useful for the discrimination between E. equisetina and the other two origins; peak area of 1 and 4 were respectively higher in E. sinica and E. intermedia than in other official origins, indicating their important effect on the differen- tiation of corresponding origins; peak 8 and 9 were picked out as two characteristic common peaks in three official origins of the herb, whose peak area showed little difference among different origins; further, peak area of other key peaks in the chromatogram also showed some difference among three origins, which make contributions to the differentiation of origins as well. Then, four phenols as 2"-O-α- L-rhamnosyl-isovitexin (1), vitexin (2), pollenitin B (5) and herbacetin-7-O-β-D-glucoside (6) were quantitative analyzed with the above-mentioned method, with good linear relationship and accuracy (recoveries in a range of 97.8%-102.5%). The content of the four phenols were firstly reported in Ephedrae Herba from official origins, which were respectively trace-1.55 (1), trace-0.160 (2), trace-0.284 (5) and trace-0.620 (6) mg · g⁻¹ in all of the tested samples. In addition, the content of these phenols showed differences in three official origins, especially 1, whose content in E. sinica [(0.670 ± 0.88) mg ± g⁻¹] were significantly higher than in other two origins (lower than 0.16 mg ± g⁻¹ besides sample Ei-060630-2-2), and 6, whose average content in E. equisetina [(0.260 ± 0.039 2) mg · g⁻¹] were twice as high as in E. sinica [(0.120 ± 0.270) mg · g⁻¹] and E. intermedia [(0.136 ± 0.485) mg g⁻¹], indicating the important effects of the two constituents on the differentiation among three official origins of the herb. The method established for the characteristic HPLC chromatogram and quantitative analysis of phenols was simple and accurate, and the marker constituents selected may provide new guides for the discrimination of official origins as well as the improvement of quality criteria of EphedraeHerba.

Optimization of a sample processing protocol for recovery of Bacillus anthracis spores from soil

USGS Publications Warehouse

Silvestri, Erin E.; Feldhake, David; Griffin, Dale; Lisle, John T.; Nichols, Tonya L.; Shah, Sanjiv; Pemberton, A; Schaefer III, Frank W

2016-01-01

Following a release of Bacillus anthracis spores into the environment, there is a potential for lasting environmental contamination in soils. There is a need for detection protocols for B. anthracis in environmental matrices. However, identification of B. anthracis within a soil is a difficult task. Processing soil samples helps to remove debris, chemical components, and biological impurities that can interfere with microbiological detection. This study aimed to optimize a previously used indirect processing protocol, which included a series of washing and centrifugation steps. Optimization of the protocol included: identifying an ideal extraction diluent, variation in the number of wash steps, variation in the initial centrifugation speed, sonication and shaking mechanisms. The optimized protocol was demonstrated at two laboratories in order to evaluate the recovery of spores from loamy and sandy soils. The new protocol demonstrated an improved limit of detection for loamy and sandy soils over the non-optimized protocol with an approximate matrix limit of detection at 14 spores/g of soil. There were no significant differences overall between the two laboratories for either soil type, suggesting that the processing protocol will be robust enough to use at multiple laboratories while achieving comparable recoveries.

7 CFR 28.25 - Samples for Form A determination.

Code of Federal Regulations, 2014 CFR

2014-01-01

... each side of the bale, and the portion of cotton removed from each cut should be broken in half across... provided the outside portion from each side is submitted for the official classification. (d) Dressing...

7 CFR 28.25 - Samples for Form A determination.

Code of Federal Regulations, 2012 CFR

2012-01-01

... each side of the bale, and the portion of cotton removed from each cut should be broken in half across... provided the outside portion from each side is submitted for the official classification. (d) Dressing...

7 CFR 28.25 - Samples for Form A determination.

Code of Federal Regulations, 2013 CFR

2013-01-01

... each side of the bale, and the portion of cotton removed from each cut should be broken in half across... provided the outside portion from each side is submitted for the official classification. (d) Dressing...

Slow histidine H/D exchange protocol for thermodynamic analysis of protein folding and stability using mass spectrometry.

PubMed

Tran, Duc T; Banerjee, Sambuddha; Alayash, Abdu I; Crumbliss, Alvin L; Fitzgerald, Michael C

2012-02-07

Described here is a mass spectrometry-based protocol to study the thermodynamic stability of proteins and protein-ligand complexes using the chemical denaturant dependence of the slow H/D exchange reaction of the imidazole C(2) proton in histidine side chains. The protocol is developed using several model protein systems including: ribonuclease (Rnase) A, myoglobin, bovine carbonic anhydrase (BCA) II, hemoglobin (Hb), and the hemoglobin-haptoglobin (Hb-Hp) protein complex. Folding free energies consistent with those previously determined by other more conventional techniques were obtained for the two-state folding proteins, Rnase A and myoglobin. The protocol successfully detected a previously observed partially unfolded intermediate stabilized in the BCA II folding/unfolding reaction, and it could be used to generate a K(d) value of 0.24 nM for the Hb-Hp complex. The compatibility of the protocol with conventional mass spectrometry-based proteomic sample preparation and analysis methods was also demonstrated in an experiment in which the protocol was used to detect the binding of zinc to superoxide dismutase in the yeast cell lysate sample. The yeast cell sample analyses also helped define the scope of the technique, which requires the presence of globally protected histidine residues in a protein's three-dimensional structure for successful application. © 2011 American Chemical Society

Comparison of two cooling protocols for llama semen: with and without collagenase and seminal plasma in the medium.

PubMed

Carretero, M I; Giuliano, S M; Arraztoa, C C; Santa Cruz, R C; Fumuso, F G; Neild, D M

2017-08-01

Seminal plasma (SP) of South American Camelids could interfere with the interaction of spermatozoa with the extenders; therefore it becomes necessary to improve semen management using enzymatic treatment. Our objective was to compare two cooling protocols for llama semen. Twelve ejaculates were incubated in 0.1% collagenase and then were divided into two aliquots. One was extended in lactose and egg yolk (LEY) (Protocol A: collagenase and SP present). The other aliquot was centrifuged, and the pellet was resuspended in LEY (Protocol B: collagenase and SP absent). Both samples were maintained at 5°C during 24 hr. Routine and DNA evaluations were carried out in raw and cooled semen. Both cooling protocols maintained sperm viability, membrane function and DNA fragmentation, with Protocol A showing a significantly lowered total and progressive motility (p < .05) and Protocol B showing a significant increase in chromatin decondensation (p < .05). Protocol A avoids centrifugation, reducing processing times and making application in the field simpler. However, as neither protocol showed a significant superiority over the other, studies should be carried out in vivo to evaluate the effect on pregnancy rates of the presence of collagenase and SP in semen samples prior to either cooling or freeze-thawing. © 2016 Blackwell Verlag GmbH.

Comparison of Cryopreservation Protocols (Single and Two-steps) and Thawing (Fast and Slow) for Canine Sperm.

PubMed

Brito, Maíra M; Lúcio, Cristina F; Angrimani, Daniel S R; Losano, João Diego A; Dalmazzo, Andressa; Nichi, Marcílio; Vannucchi, Camila I

2017-01-02

In addition to the existence of several cryopreservation protocols, no systematic research has been carried out in order to confirm the suitable protocol for canine sperm. This study aims to assess the effect of adding 5% glycerol during cryopreservation at 37°C (one-step) and 5°C (two-steps), in addition of testing two thawing protocols (37°C for 30 seconds, and 70°C for 8 seconds). We used 12 sperm samples divided into four experimental groups: Single-Step - Slow Thawing Group; Two-Step - Slow Thawing Group; Single-Step - Fast Thawing Group; and Two-Step - Fast Thawing Group. Frozen-thawed samples were submitted to automated analysis of sperm motility, evaluation of plasmatic membrane integrity, acrosomal integrity, mitochondrial activity, sperm morphology, sperm susceptibility to oxidative stress, and sperm binding assay to perivitellinic membrane of chicken egg yolk. Considering the comparison between freezing protocols, no statistical differences were verified for any of the response variables. When comparison between thawing protocols was performed, slow thawing protocol presented higher sperm count bound to perivitelline membrane of chicken egg yolk, compared to fast thawing protocol. Regardless of the freezing process, the slow thawing protocol can be recommended for the large scale cryopreservation of canine semen, since it shows a consistent better functional result.

Development of bull trout sampling protocols

Treesearch

R. F. Thurow; J. T. Peterson; J. W. Guzevich

2001-01-01

This report describes results of research conducted in Washington in 2000 through Interagency Agreement #134100H002 between the U.S. Fish and Wildlife Service (USFWS) and the U.S. Forest Service Rocky Mountain Research Station (RMRS). The purpose of this agreement is to develop a bull trout (Salvelinus confluentus) sampling protocol by integrating...

21 CFR 184.1979a - Reduced lactose whey.

Code of Federal Regulations, 2014 CFR

2014-04-01

... Action” under the heading “Fat,” or in section 16.199 (dry sample), entitled “Fat in Dried Milk (45...,” or in section 16.196 (dry sample), entitled “Ash—Official Final Action” under the heading “Dried Milk, Nonfat Dry Milk, and Malted Milk.” (iv) Lactose content, not more than 60 percent—as determined by the...

Assessment of levels of bacterial contamination of large wild game meat in Europe.

PubMed

Membré, Jeanne-Marie; Laroche, Michel; Magras, Catherine

2011-08-01

The variations in prevalence and levels of pathogens and fecal contamination indicators in large wild game meat were studied to assess their potential impact on consumers. This analysis was based on hazard analysis, data generation and statistical analysis. A total of 2919 meat samples from three species (red deer, roe deer, wild boar) were collected at French game meat traders' facilities using two sampling protocols. Information was gathered on the types of meat cuts (forequarter or haunch; first sampling protocol) or type of retail-ready meat (stewing meat or roasting meat; second protocol), and also on the meat storage conditions (frozen or chilled), country of origin (eight countries) and shooting season (autumn, winter, spring). The samples were analyzed in both protocols for detection and enumeration of Escherichia coli, coagulase+staphylococci and Clostridium perfringens. In addition, detection and enumeration of thermotolerant coliforms and Listeria monocytogenes were performed for samples collected in the first and second protocols, respectively. The levels of bacterial contamination of the raw meat were determined by performing statistical analysis involving probabilistic techniques and Bayesian inference. C. perfringens was found in the highest numbers for the three indicators of microbial quality, hygiene and good handling, and L. monocytogenes in the lowest. Differences in contamination levels between game species and between meats distributed as chilled or frozen products were not significant. These results might be included in quantitative exposure assessments. Copyright © 2011 Elsevier Ltd. All rights reserved.

Validation of a near infrared microscopy method for the detection of animal products in feedingstuffs: results of a collaborative study.

PubMed

Boix, A; Fernández Pierna, J A; von Holst, C; Baeten, V

2012-01-01

The performance characteristics of a near infrared microscopy (NIRM) method, when applied to the detection of animal products in feedingstuffs, were determined via a collaborative study. The method delivers qualitative results in terms of the presence or absence of animal particles in feed and differentiates animal from vegetable feed ingredients on the basis of the evaluation of near infrared spectra obtained from individual particles present in the sample. The specificity ranged from 86% to 100%. The limit of detection obtained on the analysis of the sediment fraction, prepared as for the European official method, was 0.1% processed animal proteins (PAPs) in feed, since all laboratories correctly identified the positive samples. This limit has to be increased up to 2% for the analysis of samples which are not sedimented. The required sensitivity for the official control is therefore achieved in the analysis of the sediment fraction of the samples where the method can be applied for the detection of the presence of animal meal. Criteria for the classification of samples, when fewer than five spectra are found, as being of animal origin needs to be set up in order to harmonise the approach taken by the laboratories when applying NIRM for the detection of the presence of animal meal in feed.

[The host community of a child with food allergies: the personalized care project (PCP)].

PubMed

Rancé, F

2010-12-01

The personalized care project (PCP) can manage allergic emergencies that may occur during school hours. Other objectives are to facilitate academic achievement, social and professional integration of children and adolescents with chronic illness such as food allergy, by promoting education through certain changes. The PCP is derived from official files including Circular N(o) 2003-135 of September 8 and the inter-ministerial circular of 25 June 2001. The family must request a protocol with the host school principal or school head. Then, the doctor of Education organizes the drafting of the document based on information provided by the physician (or allergist). Copyright © 2010 Elsevier Masson SAS. All rights reserved.

Salivary cortisol and immunoglobulin A responses to simulated and official Jiu-Jitsu matches.

PubMed

Moreira, Alexandre; Franchini, Emerson; de Freitas, Camila Gobo; Schultz de Arruda, Ademir F; de Moura, Nivaldo Ribeiro; Costa, Eduardo Caldas; Aoki, Marcelo Saldanha

2012-08-01

The aim of this study was to compare the salivary cortisol (sC) and the salivary immunoglobulin A (sIgA) responses to simulated and official Brazilian Jiu-Jitsu (BJJ) matches. Saliva samples were collected from 9 male BJJ athletes before (pre) and after (post) 2 simulated matches (SMs) and 2 official matches (OMs) performed during 2 different competitions. Salivary cortisol and sIgA concentrations (absolute concentration of sIgA [sIgAabs] and the secretion rate of sIgA [sIgArate]) were measured by an enzyme-linked immunosorbent assay. For sC, there was an effect of condition (SM vs. OM) (p < 0.05) and a time effect (pre and post) (p < 0.05). The sC was lower during SMs as compared with that during OMs and lower at premeasurement when compared with postmeasurement. No changes were observed for sIgA measurements. In summary, both SMs and official BJJ matches can increase sC levels. Moreover, the higher sC resting levels, observed before OMs, suggest that psychological factors associated with high physical-physiological demands from official BJJ competitions maximize stress hormone responses. In addition, the present findings suggest that the acute effect of BJJ matches on mucosal immunity is minimal, and it seems unlikely that changes in cortisol play a major role in the alterations in sIgA levels in response to BJJ matches. The findings of this study suggest that the use of sC can provide valuable information for coaches regarding athletes' responses to competition. In addition, psychological strategies should be implemented before events, to improve the manner in which BJJ athletes cope with the stress inherent to official matches.

Who sends the email? Using electronic surveys in violence research.

PubMed

Sutherland, Melissa A; Amar, Angela F; Laughon, Kathryn

2013-08-01

Students aged 16-24 years are at greatest risk for interpersonal violence and the resulting short and long-term health consequences. Electronic survey methodology is well suited for research related to interpersonal violence. Yet methodological questions remain about best practices in using electronic surveys. While researchers often indicate that potential participants receive multiple emails as reminders to complete the survey, little mention is made of the sender of the recruitment email. The purpose of this analysis is to describe the response rates from three violence-focused research studies when the recruitment emails are sent from a campus office, researcher or survey sampling firm. Three violence-focused studies were conducted about interpersonal violence among college students in the United States. Seven universities and a survey sampling firm were used to recruit potential participants to complete an electronic survey. The sender of the recruitment emails varied within and across the each of the studies depending on institutional review boards and university protocols. An overall response rate of 30% was noted for the 3 studies. Universities in which researcher-initiated recruitment emails were used had higher response rates compared to universities where campus officials sent the recruitment emails. Researchers found lower response rates to electronic surveys at Historically Black Colleges or Universities and that other methods were needed to improve response rates. The sender of recruitment emails for electronic surveys may be an important factor in response rates for violence-focused research. For researchers identification of best practices for survey methodology is needed to promote accurate disclosure and increase response rates.

The zoonotic potential of Mycobacterium avium spp. paratuberculosis: a systematic review.

PubMed

Waddell, Lisa A; Rajić, Andrijana; Sargeant, Jan; Harris, Janet; Amezcua, Rocio; Downey, Lindsay; Read, Susan; McEwen, Scott A

2008-01-01

The zoonotic potential of Mycobacterium avium ssp. paratuberculosis (MAP) has been debated for almost a century because of similarities between Johne's Disease (JD) in cattle and Crohn's disease (CD) in humans. Our objective was to evaluate scientific literature investigating the potential association between these two diseases (MAP and CD) and the presence of MAP in retail milk or dairy products using a qualitative systematic review. The search strategy included 19 bibliographic databases, 8 conference proceedings, reference lists of 15 articles and contacting 28 topic-related scientists. Two independent reviewers performed relevance screening, quality assessment and data extraction stages of the review. Seventy-five articles were included. Among 60 case-control studies that investigated the association between MAP and CD, 37 were of acceptable quality. Twenty-three studies reported significant positive associations, 23 reported non-significant associations, and 14 did not detect MAP in any sample. Different laboratory tests, test protocols, types of samples and source populations were used in these studies resulting in large variability among studies. Seven studies investigated the association between CD and JD, two challenge trials reported contradictory results, one cross-sectional study did not support the association, and four descriptive studies suggested that isolated MAP is often closely related to cattle isolates. MAP detection in raw and pasteurized milk was reported in several studies. Evidence for the zoonotic potential of MAP is not strong, but should not be ignored. Interdisciplinary collaboration among medical, veterinary and other public health officials may contribute to a better understanding of the potential routes of human exposure to MAP.

A Protocol for Collecting Human Cardiac Tissue for Research.

PubMed

Blair, Cheavar A; Haynes, Premi; Campbell, Stuart G; Chung, Charles; Mitov, Mihail I; Dennis, Donna; Bonnell, Mark R; Hoopes, Charles W; Guglin, Maya; Campbell, Kenneth S

2016-01-01

This manuscript describes a protocol at the University of Kentucky that allows a translational research team to collect human myocardium that can be used for biological research. We have gained a great deal of practical experience since we started this protocol in 2008, and we hope that other groups might be able to learn from our endeavors. To date, we have procured ~4000 samples from ~230 patients. The tissue that we collect comes from organ donors and from patients who are receiving a heart transplant or a ventricular assist device because they have heart failure. We begin our manuscript by describing the importance of human samples in cardiac research. Subsequently, we describe the process for obtaining consent from patients, the cost of running the protocol, and some of the issues and practical difficulties that we have encountered. We conclude with some suggestions for other researchers who may be considering starting a similar protocol.

A Protocol for Collecting Human Cardiac Tissue for Research

PubMed Central

Blair, Cheavar A.; Haynes, Premi; Campbell, Stuart G.; Chung, Charles; Mitov, Mihail I.; Dennis, Donna; Bonnell, Mark R.; Hoopes, Charles W.; Guglin, Maya; Campbell, Kenneth S.

2016-01-01

This manuscript describes a protocol at the University of Kentucky that allows a translational research team to collect human myocardium that can be used for biological research. We have gained a great deal of practical experience since we started this protocol in 2008, and we hope that other groups might be able to learn from our endeavors. To date, we have procured ~4000 samples from ~230 patients. The tissue that we collect comes from organ donors and from patients who are receiving a heart transplant or a ventricular assist device because they have heart failure. We begin our manuscript by describing the importance of human samples in cardiac research. Subsequently, we describe the process for obtaining consent from patients, the cost of running the protocol, and some of the issues and practical difficulties that we have encountered. We conclude with some suggestions for other researchers who may be considering starting a similar protocol. PMID:28042604

A Mobile Satellite Experiment (MSAT-X) network definition

NASA Technical Reports Server (NTRS)

Wang, Charles C.; Yan, Tsun-Yee

1990-01-01

The network architecture development of the Mobile Satellite Experiment (MSAT-X) project for the past few years is described. The results and findings of the network research activities carried out under the MSAT-X project are summarized. A framework is presented upon which the Mobile Satellite Systems (MSSs) operator can design a commercial network. A sample network configuration and its capability are also included under the projected scenario. The Communication Interconnection aspect of the MSAT-X network is discussed. In the MSAT-X network structure two basic protocols are presented: the channel access protocol, and the link connection protocol. The error-control techniques used in the MSAT-X project and the packet structure are also discussed. A description of two testbeds developed for experimentally simulating the channel access protocol and link control protocol, respectively, is presented. A sample network configuration and some future network activities of the MSAT-X project are also presented.

76 FR 19975 - Proposed Information Collection; Comment Request; Survey of Building and Zoning Permit Systems

Federal Register 2010, 2011, 2012, 2013, 2014

2011-04-11

... local building permit officials needed for updating the universe of permit-issuing places. The questions... issued. The universe of permit-issuing places is the sampling frame for the Building Permits Survey (BPS...

Mars Sample Quarantine Protocol Workshop

NASA Technical Reports Server (NTRS)

DeVincenzi, Donald L. (Editor); Bagby, John (Editor); Race, Margaret (Editor); Rummel, John (Editor)

1999-01-01

The Mars Sample Quarantine Protocol (QP) Workshop was convened to deal with three specific aspects of the initial handling of a returned Mars sample: 1) biocontainment, to prevent uncontrolled release of sample material into the terrestrial environment; 2) life detection, to examine the sample for evidence of live organisms; and 3) biohazard testing, to determine if the sample poses any threat to terrestrial life forms and the Earth's biosphere. During the first part of the Workshop, several tutorials were presented on topics related to the workshop in order to give all participants a common basis in the technical areas necessary to achieve the objectives of the Workshop.

Adaptive Peer Sampling with Newscast

NASA Astrophysics Data System (ADS)

Tölgyesi, Norbert; Jelasity, Márk

The peer sampling service is a middleware service that provides random samples from a large decentralized network to support gossip-based applications such as multicast, data aggregation and overlay topology management. Lightweight gossip-based implementations of the peer sampling service have been shown to provide good quality random sampling while also being extremely robust to many failure scenarios, including node churn and catastrophic failure. We identify two problems with these approaches. The first problem is related to message drop failures: if a node experiences a higher-than-average message drop rate then the probability of sampling this node in the network will decrease. The second problem is that the application layer at different nodes might request random samples at very different rates which can result in very poor random sampling especially at nodes with high request rates. We propose solutions for both problems. We focus on Newscast, a robust implementation of the peer sampling service. Our solution is based on simple extensions of the protocol and an adaptive self-control mechanism for its parameters, namely—without involving failure detectors—nodes passively monitor local protocol events using them as feedback for a local control loop for self-tuning the protocol parameters. The proposed solution is evaluated by simulation experiments.

An efficacious oral health care protocol for immunocompromised patients.

PubMed

Solomon, C S; Shaikh, A B; Arendorf, T M

1995-01-01

A twice-weekly oral and perioral examination was provided to 120 patients receiving antineoplastic therapy. Sixty patients were monitored while following the traditional hospital oral care protocol (chlorhexidine, hydrogen peroxide, sodium bicarbonate, thymol glycol, benzocaine mouthrinse, and nystatin). The mouth care protocol was then changed (experimental protocol = chlorhexidine, benzocaine lozenges, amphotericin B lozenges), and patients were monitored until the sample size matched that of the hospital mouth care regime. There was a statistically significant reduction in oral complications upon introduction and maintenance of the experimental protocol.

PROTOCOL FOR EXAMINATION OF THE INNER CAN CLOSURE WELD REGION FOR 3013 DE CONTAINERS

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

Mickalonis, J.

2014-09-16

The protocol for the examination of the inner can closure weld region (ICCWR) for 3013 DE containers is presented within this report. The protocol includes sectioning of the inner can lid section, documenting the surface condition, measuring corrosion parameters, and storing of samples. This protocol may change as the investigation develops since findings may necessitate additional steps be taken. Details of the previous analyses, which formed the basis for this protocol, are also presented.

On fixed-area plot sampling for downed coarse woody debris

Treesearch

Jeffrey H. Gove; Paul C. Van Deusen

2011-01-01

The use of fixed-area plots for sampling down coarse woody debris is reviewed. A set of clearly defined protocols for two previously described methods is established and a new method, which we call the 'sausage' method, is developed. All methods (protocols) are shown to be unbiased for volume estimation, but not necessarily for estimation of population...

U.S.-MEXICO BORDER PROGRAM ARIZONA BORDER STUDY--STANDARD OPERATING PROCEDURE FOR LABORATORY ANALYSIS OF HAIR SAMPLES FOR MERCURY (RTI-L-1.0)

EPA Science Inventory

The purpose of this protocol is to provide guidelines for the analysis of hair samples for total mercury by cold vapor atomic fluorescence (CVAFS) spectrometry. This protocol describes the methodology and all other analytical aspects involved in the analysis. Keywords: hair; s...

Sampling and measurement protocols for long-term silvicultural studies on the Penobscot Experimental Forest

Treesearch

Justin D. Waskiewicz; Laura S. Kenefic; Nicole S. Rogers; Joshua J. Puhlick; John C. Brissette; Richard J. Dionne

2015-01-01

The U.S. Forest Service, Northern Research Station has been conducting research on the silviculture of northern conifers on the Penobscot Experimental Forest (PEF) in Maine since 1950. Formal study plans provide guidance and specifications for the experimental treatments, but documentation is also needed to ensure consistency in data collection and sampling protocols....

Toxoplasma Gondii and Pre-treatment Protocols for Polymerase Chain Reaction Analysis of Milk Samples: A Field Trial in Sheep from Southern Italy.

PubMed

Vismarra, Alice; Barilli, Elena; Miceli, Maura; Mangia, Carlo; Bacci, Cristina; Brindani, Franco; Kramer, Laura

2017-01-24

Toxoplasmosis is a zoonotic disease caused by the protozoan Toxoplasma gondii. Ingestion of raw milk has been suggested as a risk for transmission to humans. Here the authors evaluated pre-treatment protocols for DNA extraction on T. gondii tachyzoite-spiked sheep milk with the aim of identifying the method that resulted in the most rapid and reliable polymerase chain reaction (PCR) positivity. This protocol was then used to analyse milk samples from sheep of three different farms in Southern Italy, including real time PCR for DNA quantification and PCR-restriction fragment length polymorphism for genotyping. The pre-treatment protocol using ethylenediaminetetraacetic acid and Tris-HCl to remove casein gave the best results in the least amount of time compared to the others on spiked milk samples. One sample of 21 collected from sheep farms was positive on one-step PCR, real time PCR and resulted in a Type I genotype at one locus (SAG3). Milk usually contains a low number of tachyzoites and this could be a limiting factor for molecular identification. Our preliminary data has evaluated a rapid, cost-effective and sensitive protocol to treat milk before DNA extraction. The results of the present study also confirm the possibility of T. gondii transmission through consumption of raw milk and its unpasteurised derivatives.

A simplified field protocol for genetic sampling of birds using buccal swabs

USGS Publications Warehouse

Vilstrup, Julia T.; Mullins, Thomas D.; Miller, Mark P.; McDearman, Will; Walters, Jeffrey R.; Haig, Susan M.

2018-01-01

DNA sampling is an essential prerequisite for conducting population genetic studies. For many years, blood sampling has been the preferred method for obtaining DNA in birds because of their nucleated red blood cells. Nonetheless, use of buccal swabs has been gaining favor because they are less invasive yet still yield adequate amounts of DNA for amplifying mitochondrial and nuclear markers; however, buccal swab protocols often include steps (e.g., extended air-drying and storage under frozen conditions) not easily adapted to field settings. Furthermore, commercial extraction kits and swabs for buccal sampling can be expensive for large population studies. We therefore developed an efficient, cost-effective, and field-friendly protocol for sampling wild birds after comparing DNA yield among 3 inexpensive buccal swab types (2 with foam tips and 1 with a cotton tip). Extraction and amplification success was high (100% and 97.2% respectively) using inexpensive generic swabs. We found foam-tipped swabs provided higher DNA yields than cotton-tipped swabs. We further determined that omitting a drying step and storing swabs in Longmire buffer increased efficiency in the field while still yielding sufficient amounts of DNA for detailed population genetic studies using mitochondrial and nuclear markers. This new field protocol allows time- and cost-effective DNA sampling of juveniles or small-bodied birds for which drawing blood may cause excessive stress to birds and technicians alike.

Robowell: An automated process for monitoring ground water quality using established sampling protocols

USGS Publications Warehouse

Granato, G.E.; Smith, K.P.

1999-01-01

Robowell is an automated process for monitoring selected ground water quality properties and constituents by pumping a well or multilevel sampler. Robowell was developed and tested to provide a cost-effective monitoring system that meets protocols expected for manual sampling. The process uses commercially available electronics, instrumentation, and hardware, so it can be configured to monitor ground water quality using the equipment, purge protocol, and monitoring well design most appropriate for the monitoring site and the contaminants of interest. A Robowell prototype was installed on a sewage treatment plant infiltration bed that overlies a well-studied unconfined sand and gravel aquifer at the Massachusetts Military Reservation, Cape Cod, Massachusetts, during a time when two distinct plumes of constituents were released. The prototype was operated from May 10 to November 13, 1996, and quality-assurance/quality-control measurements demonstrated that the data obtained by the automated method was equivalent to data obtained by manual sampling methods using the same sampling protocols. Water level, specific conductance, pH, water temperature, dissolved oxygen, and dissolved ammonium were monitored by the prototype as the wells were purged according to U.S Geological Survey (USGS) ground water sampling protocols. Remote access to the data record, via phone modem communications, indicated the arrival of each plume over a few days and the subsequent geochemical reactions over the following weeks. Real-time availability of the monitoring record provided the information needed to initiate manual sampling efforts in response to changes in measured ground water quality, which proved the method and characterized the screened portion of the plume in detail through time. The methods and the case study described are presented to document the process for future use.

Intercomparison of thermal-optical method with different temperature protocols: Implications from source samples and solvent extraction

NASA Astrophysics Data System (ADS)

Cheng, Yuan; Duan, Feng-kui; He, Ke-bin; Du, Zhen-yu; Zheng, Mei; Ma, Yong-liang

2012-12-01

Three temperature protocols with different peak inert mode temperature (Tpeak-inert) were compared based on source and ambient samples (both untreated and extracted using a mixture of hexane, methylene chloride, and acetone) collected in Beijing, China. The ratio of EC580 (elemental carbon measured by the protocol with a Tpeak-inert of 580 °C; similar hereinafter) to EC850 could be as high as 4.8 for biomass smoke samples whereas the ratio was about 1.0 for diesel and gasoline exhaust samples. The EC580 to EC850 ratio averaged 1.95 ± 0.89 and 1.13 ± 0.20 for the untreated and extracted ambient samples, whereas the EC580 to EC650 ratio of ambient samples was 1.22 ± 0.10 and 1.20 ± 0.12 before and after extraction. It was suggested that there are two competing mechanisms for the effects of Tpeak-inert on the EC results such that when Tpeak-inert is increased, one mechanism tends to decrease EC by increasing the amount of charring whereas the other tends to increase EC through promoting more charring to evolve before native EC. Results from this study showed that EC does not always decrease when increasing the peak inert mode temperature. Moreover, reducing the charring amount could improve the protocols agreement on EC measurements, whereas temperature protocol would not influence the EC results if no charring is formed. This study also demonstrated the benefits of allowing for the OC and EC split occurring in the inert mode when a high Tpeak-inert is used (e.g., 850 °C).

Thermal/optical methods for elemental carbon quantification in soils and urban dusts: equivalence of different analysis protocols.

PubMed

Han, Yongming; Chen, Antony; Cao, Junji; Fung, Kochy; Ho, Fai; Yan, Beizhan; Zhan, Changlin; Liu, Suixin; Wei, Chong; An, Zhisheng

2013-01-01

Quantifying elemental carbon (EC) content in geological samples is challenging due to interferences of crustal, salt, and organic material. Thermal/optical analysis, combined with acid pretreatment, represents a feasible approach. However, the consistency of various thermal/optical analysis protocols for this type of samples has never been examined. In this study, urban street dust and soil samples from Baoji, China were pretreated with acids and analyzed with four thermal/optical protocols to investigate how analytical conditions and optical correction affect EC measurement. The EC values measured with reflectance correction (ECR) were found always higher and less sensitive to temperature program than the EC values measured with transmittance correction (ECT). A high-temperature method with extended heating times (STN120) showed the highest ECT/ECR ratio (0.86) while a low-temperature protocol (IMPROVE-550), with heating time adjusted for sample loading, showed the lowest (0.53). STN ECT was higher than IMPROVE ECT, in contrast to results from aerosol samples. A higher peak inert-mode temperature and extended heating times can elevate ECT/ECR ratios for pretreated geological samples by promoting pyrolyzed organic carbon (PyOC) removal over EC under trace levels of oxygen. Considering that PyOC within filter increases ECR while decreases ECT from the actual EC levels, simultaneous ECR and ECT measurements would constrain the range of EC loading and provide information on method performance. Further testing with standard reference materials of common environmental matrices supports the findings. Char and soot fractions of EC can be further separated using the IMPROVE protocol. The char/soot ratio was lower in street dusts (2.2 on average) than in soils (5.2 on average), most likely reflecting motor vehicle emissions. The soot concentrations agreed with EC from CTO-375, a pure thermal method.

An optimised protocol for molecular identification of Eimeria from chickens.

PubMed

Kumar, Saroj; Garg, Rajat; Moftah, Abdalgader; Clark, Emily L; Macdonald, Sarah E; Chaudhry, Abdul S; Sparagano, Olivier; Banerjee, Partha S; Kundu, Krishnendu; Tomley, Fiona M; Blake, Damer P

2014-01-17

Molecular approaches supporting identification of Eimeria parasites infecting chickens have been available for more than 20 years, although they have largely failed to replace traditional measures such as microscopy and pathology. Limitations of microscopy-led diagnostics, including a requirement for specialist parasitological expertise and low sample throughput, are yet to be outweighed by the difficulties associated with accessing genomic DNA from environmental Eimeria samples. A key step towards the use of Eimeria species-specific PCR as a sensitive and reproducible discriminatory tool for use in the field is the production of a standardised protocol that includes sample collection and DNA template preparation, as well as primer selection from the numerous PCR assays now published. Such a protocol will facilitate development of valuable epidemiological datasets which may be easily compared between studies and laboratories. The outcome of an optimisation process undertaken in laboratories in India and the UK is described here, identifying four steps. First, samples were collected into a 2% (w/v) potassium dichromate solution. Second, oocysts were enriched by flotation in saturated saline. Third, genomic DNA was extracted using a QIAamp DNA Stool mini kit protocol including a mechanical homogenisation step. Finally, nested PCR was carried out using previously published primers targeting the internal transcribed spacer region 1 (ITS-1). Alternative methods tested included sample processing in the presence of faecal material, DNA extraction using a traditional phenol/chloroform protocol, the use of SCAR multiplex PCR (one tube and two tube versions) and speciation using the morphometric tool COCCIMORPH for the first time with field samples. Copyright © 2013 Dirk Vulpius The Authors. Published by Elsevier B.V. All rights reserved.

Pilot studies for the North American Soil Geochemical Landscapes Project - Site selection, sampling protocols, analytical methods, and quality control protocols

USGS Publications Warehouse

Smith, D.B.; Woodruff, L.G.; O'Leary, R. M.; Cannon, W.F.; Garrett, R.G.; Kilburn, J.E.; Goldhaber, M.B.

2009-01-01

In 2004, the US Geological Survey (USGS) and the Geological Survey of Canada sampled and chemically analyzed soils along two transects across Canada and the USA in preparation for a planned soil geochemical survey of North America. This effort was a pilot study to test and refine sampling protocols, analytical methods, quality control protocols, and field logistics for the continental survey. A total of 220 sample sites were selected at approximately 40-km intervals along the two transects. The ideal sampling protocol at each site called for a sample from a depth of 0-5 cm and a composite of each of the O, A, and C horizons. The <2-mm fraction of each sample was analyzed for Al, Ca, Fe, K, Mg, Na, S, Ti, Ag, As, Ba, Be, Bi, Cd, Ce, Co, Cr, Cs, Cu, Ga, In, La, Li, Mn, Mo, Nb, Ni, P, Pb, Rb, Sb, Sc, Sn, Sr, Te, Th, Tl, U, V, W, Y, and Zn by inductively coupled plasma-mass spectrometry and inductively coupled plasma-atomic emission spectrometry following a near-total digestion in a mixture of HCl, HNO3, HClO4, and HF. Separate methods were used for Hg, Se, total C, and carbonate-C on this same size fraction. Only Ag, In, and Te had a large percentage of concentrations below the detection limit. Quality control (QC) of the analyses was monitored at three levels: the laboratory performing the analysis, the USGS QC officer, and the principal investigator for the study. This level of review resulted in an average of one QC sample for every 20 field samples, which proved to be minimally adequate for such a large-scale survey. Additional QC samples should be added to monitor within-batch quality to the extent that no more than 10 samples are analyzed between a QC sample. Only Cr (77%), Y (82%), and Sb (80%) fell outside the acceptable limits of accuracy (% recovery between 85 and 115%) because of likely residence in mineral phases resistant to the acid digestion. A separate sample of 0-5-cm material was collected at each site for determination of organic compounds. A subset of 73 of these samples was analyzed for a suite of 19 organochlorine pesticides by gas chromatography. Only three of these samples had detectable pesticide concentrations. A separate sample of A-horizon soil was collected for microbial characterization by phospholipid fatty acid analysis (PLFA), soil enzyme assays, and determination of selected human and agricultural pathogens. Collection, preservation and analysis of samples for both organic compounds and microbial characterization add a great degree of complication to the sampling and preservation protocols and a significant increase to the cost for a continental-scale survey. Both these issues must be considered carefully prior to adopting these parameters as part of the soil geochemical survey of North America.

Soil sampling and analytical strategies for mapping fallout in nuclear emergencies based on the Fukushima Dai-ichi Nuclear Power Plant accident.

PubMed

Onda, Yuichi; Kato, Hiroaki; Hoshi, Masaharu; Takahashi, Yoshio; Nguyen, Minh-Long

2015-01-01

The Fukushima Dai-ichi Nuclear Power Plant (FDNPP) accident resulted in extensive radioactive contamination of the environment via deposited radionuclides such as radiocesium and (131)I. Evaluating the extent and level of environmental contamination is critical to protecting citizens in affected areas and to planning decontamination efforts. However, a standardized soil sampling protocol is needed in such emergencies to facilitate the collection of large, tractable samples for measuring gamma-emitting radionuclides. In this study, we developed an emergency soil sampling protocol based on preliminary sampling from the FDNPP accident-affected area. We also present the results of a preliminary experiment aimed to evaluate the influence of various procedures (e.g., mixing, number of samples) on measured radioactivity. Results show that sample mixing strongly affects measured radioactivity in soil samples. Furthermore, for homogenization, shaking the plastic sample container at least 150 times or disaggregating soil by hand-rolling in a disposable plastic bag is required. Finally, we determined that five soil samples within a 3 m × 3-m area are the minimum number required for reducing measurement uncertainty in the emergency soil sampling protocol proposed here. Copyright © 2014 Elsevier Ltd. All rights reserved.

A Constrained and Versioned Data Model for TEAM Data

NASA Astrophysics Data System (ADS)

Andelman, S.; Baru, C.; Chandra, S.; Fegraus, E.; Lin, K.

2009-04-01

The objective of the Tropical Ecology Assessment and Monitoring Network (www.teamnetwork.org) is "To generate real time data for monitoring long-term trends in tropical biodiversity through a global network of TEAM sites (i.e. field stations in tropical forests), providing an early warning system on the status of biodiversity to effectively guide conservation action". To achieve this, the TEAM Network operates by collecting data via standardized protocols at TEAM Sites. The standardized TEAM protocols include the Climate, Vegetation and Terrestrial Vertebrate Protocols. Some sites also implement additional protocols. There are currently 7 TEAM Sites with plans to grow the network to 15 by June 30, 2009 and 50 TEAM Sites by the end of 2010. At each TEAM Site, data is gathered as defined by the protocols and according to a predefined sampling schedule. The TEAM data is organized and stored in a database based on the TEAM spatio-temporal data model. This data model is at the core of the TEAM Information System - it consumes and executes spatio-temporal queries, and analytical functions that are performed on TEAM data, and defines the object data types, relationships and operations that maintain database integrity. The TEAM data model contains object types including types for observation objects (e.g. bird, butterfly and trees), sampling unit, person, role, protocol, site and the relationship of these object types. Each observation data record is a set of attribute values of an observation object and is always associated with a sampling unit, an observation timestamp or time interval, a versioned protocol and data collectors. The operations on the TEAM data model can be classified as read operations, insert operations and update operations. Following are some typical operations: The operation get(site, protocol, [sampling unit block, sampling unit,] start time, end time) returns all data records using the specified protocol and collected at the specified site, block, sampling unit and time range. The operation insertSamplingUnit(sampling unit, site, protocol) saves a new sampling unit into the data model and links it with the site and protocol. The operation updateSampligUnit(sampling_unit_id, attribute, value) changes the attribute (e.g. latitude or longitude) of the sampling unit to the specified value. The operation insertData(observation record, site, protocol, sampling unit, timestamps, data collectors) saves a new observation record into the database and associates it with specified objects. The operation updateData(protocol, data_id, attribute, value) modifies the attribute of an existing observation record to the specified value. All the insert or update operations require: 1) authorization to ensure the user has necessary privileges to perform the operation; 2) timestamp validation to ensure the observation timestamps are in the designated time range specified in the sampling schedule; 3) data validation to check that the data records use correct taxonomy terms and data values. No authorization is performed for get operations, but under some specific condition, a username may be required for the purpose of authentication. Along with the validations above, the TEAM data model also supports human based data validation on observed data through the Data Review subsystem to ensure data quality. The data review is implemented by adding two attributes review_tag and review_comment to each observation data record. The attribute review_tag is used by a reviewer to specify the quality of data, and the attribute review_comment is for reviewers to give more information when a problem is identified. The review_tag attribute can be populated by either the system conducting QA/QC tests or by pre-specified scientific experts. The following is the review operation, which is actually a special case of the operation updateData: The operation updateReview(protocol, data_id, judgment, comment) sets the attribute review_tag and review_comment to the specified values. By systematically tracking every step, The TEAM data model can roll back to any previous state. This is achieved by introducing a historical data container for each editable object type. When the operation updateData is applied to an object to modify its attribute, the object will be tagged with the current timestamp and the name of the user who conducts the operation, the tagged object will then be moved into the historical data container, and finally a new object will be created with the new value for the specified attribute. The diagram illustrates the architecture of the TEAM data management system. A data collector can use the Data Ingestion subsystem to load new data records into the TEAM data model. The system establishes a first level of review (i.e. meets minimum data standards via QA/QC tests). Further review is done via experts and they can verify and provide their comments on data records through the Data Review subsystem. The data editor can then address data records based on the reviewer's comments. Users can use the Data Query and Download application to find data by sites, protocols and time ranges. The Data Query and Download system packages selected data with the data license and important metadata information into a single package and delivers it to the user.

Flow cytometry for enrichment and titration in massively parallel DNA sequencing

PubMed Central

Sandberg, Julia; Ståhl, Patrik L.; Ahmadian, Afshin; Bjursell, Magnus K.; Lundeberg, Joakim

2009-01-01

Massively parallel DNA sequencing is revolutionizing genomics research throughout the life sciences. However, the reagent costs and labor requirements in current sequencing protocols are still substantial, although improvements are continuously being made. Here, we demonstrate an effective alternative to existing sample titration protocols for the Roche/454 system using Fluorescence Activated Cell Sorting (FACS) technology to determine the optimal DNA-to-bead ratio prior to large-scale sequencing. Our method, which eliminates the need for the costly pilot sequencing of samples during titration is capable of rapidly providing accurate DNA-to-bead ratios that are not biased by the quantification and sedimentation steps included in current protocols. Moreover, we demonstrate that FACS sorting can be readily used to highly enrich fractions of beads carrying template DNA, with near total elimination of empty beads and no downstream sacrifice of DNA sequencing quality. Automated enrichment by FACS is a simple approach to obtain pure samples for bead-based sequencing systems, and offers an efficient, low-cost alternative to current enrichment protocols. PMID:19304748

Feasibility of Providing Safe Mouth Care and Collecting Oral and Fecal Microbiome Samples from Nursing Home Residents with Dysphagia: Proof of Concept Study.

PubMed

Jablonski, Rita A; Winstead, Vicki; Azuero, Andres; Ptacek, Travis; Jones-Townsend, Corteza; Byrd, Elizabeth; Geisinger, Maria L; Morrow, Casey

2017-09-01

Individuals with dysphagia who reside in nursing homes often receive inadequate mouth care and experience poor oral health. From a policy perspective, the combination of absent evidence-based mouth care protocols coupled with insufficient dental coverage create a pool of individuals at great risk for preventable infectious illnesses that contribute to high health care costs. The purpose of the current study was to determine (a) the safety of a mouth care protocol tailored for individuals with dysphagia residing in nursing homes without access to suction equipment, and (b) the feasibility of collecting oral and fecal samples for microbiota analyses. The mouth care protocol resulted in improved oral hygiene without aspiration, and oral and fecal samples were safely collected from participants. Policies supporting ongoing testing of evidence-based mouth care protocols for individuals with dysphagia are important to improve quality, demonstrate efficacy, and save health care costs. [Journal of Gerontological Nursing, 43(9), 9-15.]. Copyright 2017, SLACK Incorporated.

METHOD FOR MICRORNA ISOLATION FROM CLINICAL SERUM SAMPLES

PubMed Central

Li, Yu; Kowdley, Kris V.

2012-01-01

MicroRNAs are a group of intracellular non-coding RNA molecules that have been implicated in a variety of human diseases. Due to their high stability in blood, microRNAs released into circulation could be potentially utilized as non-invasive biomarkers for diagnosis or prognosis. Current microRNA isolation protocols are specifically designed for solid tissues and are impractical for biomarker development utilizing small-volume serum samples on a large scale. Thus, a protocol for microRNA isolation from serum is needed to accommodate these conditions in biomarker development. To establish such a protocol, we developed a simplified approach to normalize sample input by using single synthetic spike-in microRNA. We evaluated three commonly used commercial microRNA isolation kits for the best performance by comparing RNA quality and yield. The manufacturer’s protocol was further modified to improve the microRNA yield from 200 μL of human serum. MicroRNAs isolated from a large set of clinical serum samples were tested on the miRCURY LNA real-time PCR panel and confirmed to be suitable for high-throughput microRNA profiling. In conclusion, we have established a proven method for microRNA isolation from clinical serum samples suitable for microRNA biomarker development. PMID:22982505

Finite-key analysis for quantum key distribution with weak coherent pulses based on Bernoulli sampling

NASA Astrophysics Data System (ADS)

Kawakami, Shun; Sasaki, Toshihiko; Koashi, Masato

2017-07-01

An essential step in quantum key distribution is the estimation of parameters related to the leaked amount of information, which is usually done by sampling of the communication data. When the data size is finite, the final key rate depends on how the estimation process handles statistical fluctuations. Many of the present security analyses are based on the method with simple random sampling, where hypergeometric distribution or its known bounds are used for the estimation. Here we propose a concise method based on Bernoulli sampling, which is related to binomial distribution. Our method is suitable for the Bennett-Brassard 1984 (BB84) protocol with weak coherent pulses [C. H. Bennett and G. Brassard, Proceedings of the IEEE Conference on Computers, Systems and Signal Processing (IEEE, New York, 1984), Vol. 175], reducing the number of estimated parameters to achieve a higher key generation rate compared to the method with simple random sampling. We also apply the method to prove the security of the differential-quadrature-phase-shift (DQPS) protocol in the finite-key regime. The result indicates that the advantage of the DQPS protocol over the phase-encoding BB84 protocol in terms of the key rate, which was previously confirmed in the asymptotic regime, persists in the finite-key regime.

NIST-Traceable NMR Method to Determine Quantitative Weight Percentage Purity of Mustard (HD) Feedstock Samples

DTIC Science & Technology

2018-01-01

ECBC-TR-1506 NIST-TRACEABLE NMR METHOD TO DETERMINE QUANTITATIVE WEIGHT PERCENTAGE PURITY OF MUSTARD (HD) FEEDSTOCK SAMPLES David J...McGarvey RESEARCH AND TECHNOLOGY DIRECTORATE William R. Creasy LEIDOS, INC. Abingdon, MD 21009-1261 Theresa R. Connell EXCET, INC...be construed as an official Department of the Army position unless so designated by other authorizing documents. REPORT DOCUMENTATION PAGE

Maximizing Student Potential versus Building Community: An Exploration of Right-Wing Authoritarianism, Social Dominance Orientation, and Preferred Practice among Supporters of Gifted Education

ERIC Educational Resources Information Center

Cross, Jennifer Riedl; Cross, Tracy L.; Finch, Holmes

2010-01-01

Social dominance orientation (SDO), right-wing authoritarianism (RWA), and socially desirable responding were examined among a sample of self-identified supporters of gifted education (N = 341), 70% of whom had an official role in gifted education as researchers, teachers, or gifted-talented (G/T) trainers. The sample was primarily female, White,…

Biomarkers for pulmonary injury following deployment

DTIC Science & Technology

2013-10-01

construed as an official Department of the Army position, policy or decision unless so designated by other documentation. 2 REPORT DOCUMENTATION...cc x 3). BALF sample preparation for proteome analysis. Samples were thawed and desalted and concentrated with Amicon 3K MWCO spin filters (EMD...of the correlation heatmaps designate control and disease, respectively. Figure 2. PCA plot of BALF and urine datasets on left and right

A Comparison of Citizen and Leader Perceptions of Selected Quality of Life Indicators.

ERIC Educational Resources Information Center

Purohit, Sally R.; Clonts, Howard A.

A total enumeration of elected and appointed officials, a 30% sample of business firms in each of 3 counties, and a 2% sample of the household residents (N=a total of 800 respondents living in a 3-county rural area of Alabama) were surveyed for purposes of comparing the attitudes of leaders and citizens toward public services and economic…

Sustainability of knowledge translation interventions in healthcare decision-making: protocol for a scoping review.

PubMed

Tricco, Andrea C; Cogo, Elise; Ashoor, Huda; Perrier, Laure; McKibbon, K Ann; Grimshaw, Jeremy M; Straus, Sharon E

2013-05-14

Knowledge translation (KT also known as research utilisation, translational medicine and implementation science) is a dynamic and iterative process that includes the synthesis, dissemination, exchange and ethically sound application of knowledge to improve health. After the implementation of KT interventions, their impact on relevant outcomes should be monitored. The objectives of this scoping review are to: (1) conduct a systematic search of the literature to identify the impact on healthcare outcomes beyond 1 year, or beyond the termination of funding of the initiative of KT interventions targeting chronic disease management for end-users including patients, clinicians, public health officials, health services managers and policy-makers; (2) identify factors that influence sustainability of effective KT interventions; (3) identify how sustained change from KT interventions should be measured; and (4) develop a framework for assessing sustainability of KT interventions. Comprehensive searches of relevant electronic databases (eg, MEDLINE, EMBASE, Cochrane Central Register of Controlled Trials), websites of funding agencies and websites of healthcare provider organisations will be conducted to identify relevant material. We will include experimental, quasi-experimental and observational studies providing information on the sustainability of KT interventions targeting chronic disease management in adults and focusing on end-users including patients, clinicians, public health officials, health services managers and policy-makers. Two reviewers will pilot-test the screening criteria and data abstraction form. They will then screen all citations, full articles and abstract data in duplicate independently. The results of the scoping review will be synthesised descriptively and used to develop a framework to assess the sustainability of KT interventions. Our results will help inform end-users (ie, patients, clinicians, public health officials, health services managers and policy-makers) regarding the sustainability of KT interventions. Our dissemination plan includes publications, presentations, website posting and a stakeholder meeting.

A semi-nested real-time PCR method to detect low chimerism percentage in small quantity of hematopoietic stem cell transplant DNA samples.

PubMed

Aloisio, Michelangelo; Bortot, Barbara; Gandin, Ilaria; Severini, Giovanni Maria; Athanasakis, Emmanouil

2017-02-01

Chimerism status evaluation of post-allogeneic hematopoietic stem cell transplantation samples is essential to predict post-transplant relapse. The most commonly used technique capable of detecting small increments of chimerism is quantitative real-time PCR. Although this method is already used in several laboratories, previously described protocols often lack sensitivity and the amount of the DNA required for each chimerism analysis is too high. In the present study, we compared a novel semi-nested allele-specific real-time PCR (sNAS-qPCR) protocol with our in-house standard allele-specific real-time PCR (gAS-qPCR) protocol. We selected two genetic markers and analyzed technical parameters (slope, y-intercept, R2, and standard deviation) useful to determine the performances of the two protocols. The sNAS-qPCR protocol showed better sensitivity and precision. Moreover, the sNAS-qPCR protocol requires, as input, only 10 ng of DNA, which is at least 10-fold less than the gAS-qPCR protocols described in the literature. Finally, the proposed sNAS-qPCR protocol could prove very useful for performing chimerism analysis with a small amount of DNA, as in the case of blood cell subsets.

The UK Biobank sample handling and storage protocol for the collection, processing and archiving of human blood and urine.

PubMed

Elliott, Paul; Peakman, Tim C

2008-04-01

UK Biobank is a large prospective study in the UK to investigate the role of genetic factors, environmental exposures and lifestyle in the causes of major diseases of late and middle age. Extensive data and biological samples are being collected from 500,000 participants aged between 40 and 69 years. The biological samples that are collected and how they are processed and stored will have a major impact on the future scientific usefulness of the UK Biobank resource. The aim of the UK Biobank sample handling and storage protocol is to specify methods for the collection and storage of participant samples that give maximum scientific return within the available budget. Processing or storage methods that, as far as can be predicted, will preclude current or future assays have been avoided. The protocol was developed through a review of the literature on sample handling and processing, wide consultation within the academic community and peer review. Protocol development addressed which samples should be collected, how and when they should be processed and how the processed samples should be stored to ensure their long-term integrity. The recommended protocol was extensively tested in a series of validation studies. UK Biobank collects about 45 ml blood and 9 ml of urine with minimal local processing from each participant using the vacutainer system. A variety of preservatives, anti-coagulants and clot accelerators is used appropriate to the expected end use of the samples. Collection of other material (hair, nails, saliva and faeces) was also considered but rejected for the full cohort. Blood and urine samples from participants are transported overnight by commercial courier to a central laboratory where they are processed and aliquots of urine, plasma, serum, white cells and red cells stored in ultra-low temperature archives. Aliquots of whole blood are also stored for potential future production of immortalized cell lines. A standard panel of haematology assays is completed on whole blood from all participants, since such assays need to be conducted on fresh samples (whereas other assays can be done on stored samples). By the end of the recruitment phase, 15 million sample aliquots will be stored in two geographically separate archives: 9.5 million in a -80 degrees C automated archive and 5.5 million in a manual liquid nitrogen archive at -180 degrees C. Because of the size of the study and the numbers of samples obtained from participants, the protocol stipulates a highly automated approach for the processing and storage of samples. Implementation of the processes, technology, systems and facilities has followed best practices used in manufacturing industry to reduce project risk and to build in quality and robustness. The data produced from sample collection, processing and storage are highly complex and are managed by a commercially available LIMS system fully integrated with the entire process. The sample handling and storage protocol adopted by UK Biobank provides quality assured and validated methods that are feasible within the available funding and reflect the size and aims of the project. Experience from recruiting and processing the first 40,000 participants to the study demonstrates that the adopted methods and technologies are fit-for-purpose and robust.

7 CFR 800.60 - Deceptive actions and practices.

Code of Federal Regulations, 2010 CFR

2010-01-01

... Agriculture Regulations of the Department of Agriculture (Continued) GRAIN INSPECTION, PACKERS AND STOCKYARD ADMINISTRATION (FEDERAL GRAIN INSPECTION SERVICE), DEPARTMENT OF AGRICULTURE GENERAL REGULATIONS Grain Handling... official personnel, any action or practice, including the loading, weighing, handling, or sampling of grain...

A quarantine protocol for analysis of returned extraterrestrial samples

NASA Technical Reports Server (NTRS)

Bagby, J. R.; Sweet, H. C.; Devincenzi, D. L.

1983-01-01

A protocol is presented for the analysis at an earth-orbiting quarantine facility of return samples of extraterrestrial material that might contain (nonterrestrial) life forms. The protocol consists of a series of tests designed to determine whether the sample, conceptualized as a 1-kg sample of Martian soil, is free from nonterrestrial biologically active agents and so may safely be sent to a terrestrial containment facility, or it exhibits biological activity requiring further (second-order) testing outside the biosphere. The first-order testing procedure seeks to detect the presence of any replicating organisms or toxic substances through a series of experiments including gas sampling, analysis of radioactivity, stereomicroscopic inspection, chemical analysis, microscopic examination, the search for metabolic products under growth conditions, microbiologicl assays, and the challenge of cultured cells with any agents found or with the extraterrestrial material as is. Detailed plans for the second-order testing would be developed in response to the actual data received from primary testing.

A Field-Based Cleaning Protocol for Sampling Devices Used in Life-Detection Studies

NASA Astrophysics Data System (ADS)

Eigenbrode, Jennifer; Benning, Liane G.; Maule, Jake; Wainwright, Norm; Steele, Andrew; Amundsen, Hans E. F.

2009-06-01

Analytical approaches to extant and extinct life detection involve molecular detection often at trace levels. Thus, removal of biological materials and other organic molecules from the surfaces of devices used for sampling is essential for ascertaining meaningful results. Organic decontamination to levels consistent with null values on life-detection instruments is particularly challenging at remote field locations where Mars analog field investigations are carried out. Here, we present a seven-step, multi-reagent decontamination method that can be applied to sampling devices while in the field. In situ lipopolysaccharide detection via low-level endotoxin assays and molecular detection via gas chromatography-mass spectrometry were used to test the effectiveness of the decontamination protocol for sampling of glacial ice with a coring device and for sampling of sediments with a rover scoop during deployment at Arctic Mars-analog sites in Svalbard, Norway. Our results indicate that the protocols and detection technique sufficiently remove and detect low levels of molecular constituents necessary for life-detection tests.

A field-based cleaning protocol for sampling devices used in life-detection studies.

PubMed

Eigenbrode, Jennifer; Benning, Liane G; Maule, Jake; Wainwright, Norm; Steele, Andrew; Amundsen, Hans E F

2009-06-01

Analytical approaches to extant and extinct life detection involve molecular detection often at trace levels. Thus, removal of biological materials and other organic molecules from the surfaces of devices used for sampling is essential for ascertaining meaningful results. Organic decontamination to levels consistent with null values on life-detection instruments is particularly challenging at remote field locations where Mars analog field investigations are carried out. Here, we present a seven-step, multi-reagent decontamination method that can be applied to sampling devices while in the field. In situ lipopolysaccharide detection via low-level endotoxin assays and molecular detection via gas chromatography-mass spectrometry were used to test the effectiveness of the decontamination protocol for sampling of glacial ice with a coring device and for sampling of sediments with a rover scoop during deployment at Arctic Mars-analog sites in Svalbard, Norway. Our results indicate that the protocols and detection technique sufficiently remove and detect low levels of molecular constituents necessary for life-detection tests.

Counting at low concentrations: the statistical challenges of verifying ballast water discharge standards

USGS Publications Warehouse

Frazier, Melanie; Miller, A. Whitman; Lee, Henry; Reusser, Deborah A.

2013-01-01

Discharge from the ballast tanks of ships is one of the primary vectors of nonindigenous species in marine environments. To mitigate this environmental and economic threat, international, national, and state entities are establishing regulations to limit the concentration of living organisms that may be discharged from the ballast tanks of ships. The proposed discharge standards have ranged from zero detectable organisms to 3. If standard sampling methods are used, verifying whether ballast discharge complies with these stringent standards will be challenging due to the inherent stochasticity of sampling. Furthermore, at low concentrations, very large volumes of water must be sampled to find enough organisms to accurately estimate concentration. Despite these challenges, adequate sampling protocols comprise a critical aspect of establishing standards because they help define the actual risk level associated with a standard. A standard that appears very stringent may be effectively lax if it is paired with an inadequate sampling protocol. We describe some of the statistical issues associated with sampling at low concentrations to help regulators understand the uncertainties of sampling as well as to inform the development of sampling protocols that ensure discharge standards are adequately implemented.

[The role of German official medicines control laboratories in combating counterfeit medicines].

PubMed

Wiegard, Andrea; Heuermann, Matthias

2017-11-01

An official medicines control laboratory (OMCL) provides an important contribution to combat counterfeit and illegal medicines. The OMCL supports the competent authorities in controlling the quality of authorised medicinal products in the legal supply chain. For detecting counterfeit medicines in the legal supply chain, a risk-based approach in choice of products is conducted. Furthermore, the OMCL analyses suspicious medicines from the illegal supply chain for any other authority. The chemical analysis of a suspicious sample is needed to identify such a sample as a counterfeit medicine. The analytical results are fundamental for the evaluation of the legal status of the product and for the assessment of it's inherent hazard to public health. The global market of illegal medicines is rapidly changing. Therefore a good national and international working liaison and co-operation between laboratories and authorities is obligatory to protect public health. The OMCL provides important knowledge of new trends in counterfeit and illegal medicines. Hence, it is an essential part in surveillance of medicinal products. The efficient networking enables prompt official interventions. Thus, risks for the public health by substandard medicines were reduced. Beside the chemical analysis, the OMCL can help to raise public awareness about counterfeit and illegal medicines. In Germany, the risk of counterfeit medicines reaching patients through the legal supply chain is still low, but the possibility cannot be ignored.

Fertility Adaptation of Child Migrants to Canada

PubMed Central

Adsera, Alicia; Ferrer, Ana

2013-01-01

This study analyzes the fertility behavior of immigrant women arriving to Canada before age 19 using the 20 per cent sample of the Canadian Census from 1991 through 2006. Findings show that fertility increases with age at immigration, and is particularly high for those immigrating in their late teens. This pattern prevails regardless of the country of origin or whether the mother tongue of the migrant is an official language in Canada or not. We do not find a ‘critical age’ at which the behavior of migrants with and without official mother tongue start to diverge by more, even though the fertility of migrants without official mother tongue is always higher on average. Formal education matters as the fertility of immigrants who arrived to Canada before adulthood and graduated from college is similar to that of their native peers regardless of their age of arrival. However, the fertility of those with less than tertiary education increasingly diverges with age at migration from similarly educated Canadians. PMID:23800074

The relationship of mental illness to targeted contact behavior toward state government agencies and officials.

PubMed

Scalora, Mario J; Baumgartner, Jerome V; Plank, Gary L

2003-01-01

Research in the burgeoning field of threat assessment has illuminated the importance of mental illness factors when considering risk of targeted violence-particularly related to government agencies and officials. The authors analyzed 127 cases investigated by a state law enforcement agency regarding threatening or other contacts toward public officials or state agency employees prompting security intervention. Univariate and discriminant analysis indicated that mentally ill subjects were significantly more likely to engage in more contacts as well as to make specific demands during such contacts. Mentally ill subjects were also more likely to articulate help-seeking concerns and employ religious themes, as opposed to using insulting, degrading, or ominous language toward the target or issuing complaints regarding policy issues. Contrary to other research, the mentally ill subjects within this sample were not significantly more likely to engage in approach behavior, a threshold for higher risk of violence. Implications for threat assessment activity are discussed. Copyright 2003 John Wiley & Sons, Ltd.

Efficient Genome-Wide Sequencing and Low-Coverage Pedigree Analysis from Noninvasively Collected Samples

PubMed Central

Snyder-Mackler, Noah; Majoros, William H.; Yuan, Michael L.; Shaver, Amanda O.; Gordon, Jacob B.; Kopp, Gisela H.; Schlebusch, Stephen A.; Wall, Jeffrey D.; Alberts, Susan C.; Mukherjee, Sayan; Zhou, Xiang; Tung, Jenny

2016-01-01

Research on the genetics of natural populations was revolutionized in the 1990s by methods for genotyping noninvasively collected samples. However, these methods have remained largely unchanged for the past 20 years and lag far behind the genomics era. To close this gap, here we report an optimized laboratory protocol for genome-wide capture of endogenous DNA from noninvasively collected samples, coupled with a novel computational approach to reconstruct pedigree links from the resulting low-coverage data. We validated both methods using fecal samples from 62 wild baboons, including 48 from an independently constructed extended pedigree. We enriched fecal-derived DNA samples up to 40-fold for endogenous baboon DNA and reconstructed near-perfect pedigree relationships even with extremely low-coverage sequencing. We anticipate that these methods will be broadly applicable to the many research systems for which only noninvasive samples are available. The lab protocol and software (“WHODAD”) are freely available at www.tung-lab.org/protocols-and-software.html and www.xzlab.org/software.html, respectively. PMID:27098910

Session RPE and salivary immune-endocrine responses to simulated and official basketball matches in elite young male athletes.

PubMed

Moreira, A; Crewther, B; Freitas, C G; Arruda, A F S; Costa, E C; Aoki, M S

2012-12-01

The present study compared the ratings of perceived exertion (RPE) and immune-endocrine (IgA and cortisol) responses to simulated training matches (TM) and official matches (OM) in elite young male basketball players (N.=10). Saliva samples were collected from each player before and after three TM and two OM and subsequently tested for cortisol and IgA concentrations by immunoassay. The perceived intensity of each match was rated using a RPE scale (CR-10). The training match and official match data were pooled to provide an aggregate value for each setting. The session RPE scores from the OM were significantly (P<0.05) greater than the simulated TM. Pre- and postcortisol concentrations assessed during the OM were also found to be significantly higher than the TM (P<0.05). No significant changes in salivary IgA concentrations were observed across either the simulated or official match settings. In summary, the OM induced greater RPE and salivary cortisol responses than the simulated TM, probably due to the additional stressors associated with real competition. The data also suggests that acute changes in cortisol concentrations do not play a role in the regulation of salivary IgA under the current testing conditions.

Preventing disease transmission by deceased tissue donors by testing blood for viral nucleic acid.

PubMed

Strong, D Michael; Nelson, Karen; Pierce, Marge; Stramer, Susan L

2005-01-01

Nucleic acid testing (NAT) has reduced the risk of transmitting infectious disease through blood transfusion. Currently NAT for HIV-1 and HCV are FDA licensed and performed by nearly all blood collection facilities, but HBV NAT is performed under an investigational study protocol. Residual risk estimates indicate that NAT could potentially reduce disease transmission through transplanted tissue. However, tissue donor samples obtained post-mortem have the potential to produce an invalid NAT result due to inhibition of amplification reactions by hemolysis and other factors. The studies reported here summarize the development of protocols to allow NAT of deceased donor samples with reduced rates of invalid results. Using these protocols, inventories from two tissue centers were tested with greater than 99% of samples producing a valid test result.

Geochemical and mineralogical data for soils of the conterminous United States

USGS Publications Warehouse

Smith, David B.; Cannon, William F.; Woodruff, Laurel G.; Solano, Federico; Kilburn, James E.; Fey, David L.

2013-01-01

In 2007, the U.S. Geological Survey initiated a low-density (1 site per 1,600 square kilometers, 4,857 sites) geochemical and mineralogical survey of soils of the conterminous United States as part of the North American Soil Geochemical Landscapes Project. Sampling and analytical protocols were developed at a workshop in 2003, and pilot studies were conducted from 2004 to 2007 to test and refine these recommended protocols. The final sampling protocol for the national-scale survey included, at each site, a sample from a depth of 0 to 5 centimeters, a composite of the soil A horizon, and a deeper sample from the soil C horizon or, if the top of the C horizon was at a depth greater than 1 meter, from a depth of approximately 80–100 centimeters. The <2-millimeter fraction of each sample was analyzed for a suite of 45 major and trace elements by methods that yield the total or near-total elemental content. The major mineralogical components in the samples from the soil A and C horizons were determined by a quantitative X-ray diffraction method using Rietveld refinement. Sampling in the conterminous United States was completed in 2010, with chemical and mineralogical analyses completed in May 2013. The resulting dataset provides an estimate of the abundance and spatial distribution of chemical elements and minerals in soils of the conterminous United States and represents a baseline for soil geochemistry and mineralogy against which future changes may be recognized and quantified. This report (1) describes the sampling, sample preparation, and analytical methods used; (2) gives details of the quality control protocols used to monitor the quality of chemical and mineralogical analyses over approximately six years; and (3) makes available the soil geochemical and mineralogical data in downloadable tables.

PROFILE: Environmental Impact Assessment Under the National Environmental Policy Act and the Protocol on Environmental Protection to the Antarctic Treaty.

PubMed

Ensminger; McCold; Webb

1999-07-01

/ Antarctica has been set aside by the international community for protection as a natural reserve and a place for scientific research. Through the Antarctic Treaty of 1961, the signing nations agreed to cooperate in protecting the antarctic environment, in conducting scientific studies, and in abstaining from the exercise of territorial claims. The 1991 signing of the Protocol on Environmental Protection to the Antarctic Treaty (Protocol) by representatives of the 26 nations comprising the Antarctic Treaty Consultative Parties (Parties) significantly strengthened environmental protection measures for the continent. The Protocol required ratification by each of the governments individually prior to official implementation. The US government ratified the Protocol by passage of the Antarctic Science, Tourism, and Conservation Act of 1997. Japan completed the process by ratifying the Protocol on December 15, 1997. US government actions undertaken in Antarctica are subject to the requirements of both the Protocol and the US National Environmental Policy Act (NEPA). There are differences in the scope and intent of the Protocol and NEPA; however, both require environmental impact assessment (EIA) as part of the planning process for proposed actions that have the potential for environmental impacts. In this paper we describe the two instruments and highlight key similarities and differences with particular attention to EIA. Through this comparison of the EIA requirements of NEPA and the Protocol, we show how the requirements of each can be used in concert to provide enhanced environmental protection for the antarctic environment. NEPA applies only to actions of the US government; therefore, because NEPA includes certain desirable attributes that have been refined and clarified through numerous court cases, and because the Protocol is just entering implementation internationally, some recommendations are made for strengthening the procedural requirements of the Protocol for activities undertaken by all Parties in Antarctica. The Protocol gives clear and strong guidance for protection of specific, valued antarctic environmental resources including intrinsic wilderness and aesthetic values, and the value of Antarctica as an area for scientific research. That guidance requires a higher standard of environmental protection for Antarctica than is required in other parts of the world. This paper shows that taken together NEPA and the Protocol call for closer examination of proposed actions and a more rigorous consideration of environmental impacts than either would alone. Three areas are identified where the EIA provisions of the Protocol could be strengthened to improve its effectiveness. First, the thresholds defined by the Protocol need to be clarified. Specifically, the meanings of the terms "minor" and "transitory" are not clear in the context of the Protocol. The use of "or" in the phrase "minor or transitory" further confuses the meaning. Second, cumulative impact assessment is called for by the Protocol but is not defined. A clear definition could reduce the chance that cumulative impacts would be given inadequate consideration. Finally, the public has limited opportunities to comment on or influence the preparation of initial or comprehensive environmental evaluations. Experience has shown that public input to environmental documents has a considerable influence on agency decision making and the quality of EIA that agencies perform.KEY WORDS: Environment; Impact assessment; Antarctica; NEPA; Protocol; Antarctic Treatyhttp://link.springer-ny.com/link/service/journals/00267/bibs/24n1p13.html

Storage quality-of-service in cloud-based scientific environments: a standardization approach

NASA Astrophysics Data System (ADS)

Millar, Paul; Fuhrmann, Patrick; Hardt, Marcus; Ertl, Benjamin; Brzezniak, Maciej

2017-10-01

When preparing the Data Management Plan for larger scientific endeavors, PIs have to balance between the most appropriate qualities of storage space along the line of the planned data life-cycle, its price and the available funding. Storage properties can be the media type, implicitly determining access latency and durability of stored data, the number and locality of replicas, as well as available access protocols or authentication mechanisms. Negotiations between the scientific community and the responsible infrastructures generally happen upfront, where the amount of storage space, media types, like: disk, tape and SSD and the foreseeable data life-cycles are negotiated. With the introduction of cloud management platforms, both in computing and storage, resources can be brokered to achieve the best price per unit of a given quality. However, in order to allow the platform orchestrator to programmatically negotiate the most appropriate resources, a standard vocabulary for different properties of resources and a commonly agreed protocol to communicate those, has to be available. In order to agree on a basic vocabulary for storage space properties, the storage infrastructure group in INDIGO-DataCloud together with INDIGO-associated and external scientific groups, created a working group under the umbrella of the Research Data Alliance (RDA). As communication protocol, to query and negotiate storage qualities, the Cloud Data Management Interface (CDMI) has been selected. Necessary extensions to CDMI are defined in regular meetings between INDIGO and the Storage Network Industry Association (SNIA). Furthermore, INDIGO is contributing to the SNIA CDMI reference implementation as the basis for interfacing the various storage systems in INDIGO to the agreed protocol and to provide an official Open-Source skeleton for systems not being maintained by INDIGO partners.

7 CFR 29.133 - Identification number.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 2 2013-01-01 2013-01-01 false Identification number. 29.133 Section 29.133... REGULATIONS TOBACCO INSPECTION Regulations Miscellaneous § 29.133 Identification number. The Director may require the use of official identification numbers in connection with tobacco certificated or sampled...

7 CFR 29.133 - Identification number.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 2 2010-01-01 2010-01-01 false Identification number. 29.133 Section 29.133... REGULATIONS TOBACCO INSPECTION Regulations Miscellaneous § 29.133 Identification number. The Director may require the use of official identification numbers in connection with tobacco certificated or sampled...

7 CFR 29.133 - Identification number.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 2 2012-01-01 2012-01-01 false Identification number. 29.133 Section 29.133... REGULATIONS TOBACCO INSPECTION Regulations Miscellaneous § 29.133 Identification number. The Director may require the use of official identification numbers in connection with tobacco certificated or sampled...

7 CFR 29.133 - Identification number.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 2 2014-01-01 2014-01-01 false Identification number. 29.133 Section 29.133... REGULATIONS TOBACCO INSPECTION Regulations Miscellaneous § 29.133 Identification number. The Director may require the use of official identification numbers in connection with tobacco certificated or sampled...

7 CFR 29.133 - Identification number.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 2 2011-01-01 2011-01-01 false Identification number. 29.133 Section 29.133... REGULATIONS TOBACCO INSPECTION Regulations Miscellaneous § 29.133 Identification number. The Director may require the use of official identification numbers in connection with tobacco certificated or sampled...

78 FR 18560 - Submission for OMB Review; Comment Request

Federal Register 2010, 2011, 2012, 2013, 2014

2013-03-27

... approved collection for forms C-700, Private Construction Projects; C-700 (R), Multi-family Residential... private companies or individuals, private multi-family residential buildings, and on building projects... sample basis from federal, state and local agency officials, owners of private nonresidential projects...

Anti-malarial drug quality in Lagos and Accra - a comparison of various quality assessments

PubMed Central

2010-01-01

Background Two major cities in West Africa, Accra, the capital of Ghana, and Lagos, the largest city of Nigeria, have significant problems with substandard pharmaceuticals. Both have actively combated the problem in recent years, particularly by screening products on the market using the Global Pharma Health Fund e.V. Minilab® protocol. Random sampling of medicines from the two cities at least twice over the past 30 months allows a tentative assessment of whether improvements in drug quality have occurred. Since intelligence provided by investigators indicates that some counterfeit producers may be adapting products to pass Minilab tests, the results are compared with those from a Raman spectrometer and discrepancies are discussed. Methods Between mid-2007 and early-2010, samples of anti-malarial drugs were bought covertly from pharmacies in Lagos on three different occasions (October 2007, December 2008, February 2010), and from pharmacies in Accra on two different occasions (October 2007, February 2010). All samples were tested using the Minilab® protocol, which includes disintegration and active ingredient assays as well as visual inspection, and most samples were also tested by Raman spectrometry. Results In Lagos, the failure rate in the 2010 sampling fell to 29% of the 2007 finding using the Minilab® protocol, 53% using Raman spectrometry, and 46% using visual inspection. In Accra, the failure rate in the 2010 sampling fell to 54% of the 2007 finding using the Minilab® protocol, 72% using Raman spectrometry, and 90% using visual inspection. Conclusions The evidence presented shows that drug quality is probably improving in both cities, especially Lagos, since major reductions of failure rates over time occur with all means of assessment. Many more samples failed when examined by Raman spectrometry than by Minilab® protocol. The discrepancy is most likely caused by the two techniques measuring different aspects of the medication and hence the discrepancy may be the natural variation in these techniques. But other explanations are possible and are discussed. PMID:20537190

HEALTH-SCREENING PROTOCOLS FOR VINACEOUS AMAZONS (AMAZONA VINACEA) IN A REINTRODUCTION PROJECT.

PubMed

Saidenberg, André B S; Zuniga, Eveline; Melville, Priscilla A; Salaberry, Sandra; Benites, Nilson R

2015-12-01

Reintroduction is a growing field in the conservation of endangered species. The vinaceous Amazon parrot (Amazona vinacea) is extinct in several areas, and a project to release confiscated individuals to their former range is currently underway. The objective of this study was to evaluate and improve the selection and treatment of individual release candidates by detecting possible pathogen carriers using samples taken before and during release. As part of prerelease health protocols, samples were obtained from 29 parrots on three different occasions while in captivity and once after their release. Samples were screened for paramyxovirus type 1, avian influenza, poxvirus, coronavirus, psittacine herpesvirus 1, Chlamydia psittaci , enteropathogenic Escherichia coli (EPEC), Salmonella spp., and endoparasites. The majority of samples returned negative results, with the exception of two individuals that tested positive for C. psittaci in the first sampling and for Ascaridia spp. in the second pooled sampling. Treatments for C. psittaci and endoparasites were administered prior to release, and negative results were obtained in subsequent exams. The number of positive results for E. coli (non-EPEC) decreased during the rehabilitation period. Adequate quarantine procedures and health examinations greatly minimize disease risks. The protocols employed in this study resulted in acceptable health status in accordance with current environmental legislation in Brazil. Additionally, protocols allowed informed decisions to release candidates, minimized risks, and favored the selection of healthy individuals, thereby contributing to the recovery of this species. It is important to determine appropriate minimum health-screening protocols when advanced diagnostics may not be available or high costs make the tests prohibitive in countries where confiscations occur. We hypothesize that a minimum panel of tests of pooled samples can serve as an alternative approach that minimizes costs and overall workload and supports projects intended to restore and promote flagship species and hamper their illegal trade.

Human immunodeficiency virus bDNA assay for pediatric cases.

PubMed

Avila, M M; Liberatore, D; Martínez Peralta, L; Biglione, M; Libonatti, O; Coll Cárdenas, P; Hodara, V L

2000-01-01

Techniques to quantify plasma HIV-1 RNA viral load (VL) are commercially available, and they are adequate for monitoring adults infected by HIV and treated with antiretroviral drugs. Little experience on HIV VL has been reported in pediatric cases. In Argentina, the evaluation of several assays for VL in pediatrics are now being considered. To evaluate the pediatric protocol for bDNA assay in HIV-infected children, 25 samples from HIV-infected children (according to CDC criteria for pediatric AIDS) were analyzed by using Quantiplex HIV RNA 2.0 Assay (Chiron Corporation) following the manufacturer's recommendations in a protocol that uses 50 microliters of patient's plasma (sensitivity: 10,000 copies/ml). When HIV-RNA was not detected, samples were run with the 1 ml standard bDNA protocol (sensitivity: 500 HIV-RNA c/ml). Nine samples belonged to infants under 12 months of age (group A) and 16 were over 12 months (group B). All infants under one year of age had high HIV-RNA copies in plasma. VL ranged from 30,800 to 2,560,000 RNA copies/ml (median = 362,000 c/ml) for group A and < 10,000 to 554,600 c/ml (median = < 10,000) for group B. Only 25% of children in group B had detectable HIV-RNA. By using the standard test of quantification, none of the patients had non detectable HIV-RNA, ranging between 950 and 226,200 c/ml for group B (median = 23,300 RNA c/ml). The suggested pediatric protocol could be useful in children under 12 months of age, but 1 ml standard protocol must be used for older children. Samples with undetectable results from children under one year of age should be repeated using the standard protocol.

Bayesian adaptive survey protocols for resource management

USGS Publications Warehouse

Halstead, Brian J.; Wylie, Glenn D.; Coates, Peter S.; Casazza, Michael L.

2011-01-01

Transparency in resource management decisions requires a proper accounting of uncertainty at multiple stages of the decision-making process. As information becomes available, periodic review and updating of resource management protocols reduces uncertainty and improves management decisions. One of the most basic steps to mitigating anthropogenic effects on populations is determining if a population of a species occurs in an area that will be affected by human activity. Species are rarely detected with certainty, however, and falsely declaring a species absent can cause improper conservation decisions or even extirpation of populations. We propose a method to design survey protocols for imperfectly detected species that accounts for multiple sources of uncertainty in the detection process, is capable of quantitatively incorporating expert opinion into the decision-making process, allows periodic updates to the protocol, and permits resource managers to weigh the severity of consequences if the species is falsely declared absent. We developed our method using the giant gartersnake (Thamnophis gigas), a threatened species precinctive to the Central Valley of California, as a case study. Survey date was negatively related to the probability of detecting the giant gartersnake, and water temperature was positively related to the probability of detecting the giant gartersnake at a sampled location. Reporting sampling effort, timing and duration of surveys, and water temperatures would allow resource managers to evaluate the probability that the giant gartersnake occurs at sampled sites where it is not detected. This information would also allow periodic updates and quantitative evaluation of changes to the giant gartersnake survey protocol. Because it naturally allows multiple sources of information and is predicated upon the idea of updating information, Bayesian analysis is well-suited to solving the problem of developing efficient sampling protocols for species of conservation concern.

Immunizations, neonatal hyperbilirubinemia and animal-induced injuries.

PubMed

Bennett, Sean R; Brennan, Beth; Bernstein, Henry H

2007-08-01

To report recent research findings and new recommendations on immunizations, neonatal hyperbilirubinemia, and animal-induced injuries. Vaccines against rotavirus and human papilloma virus have entered clinical use. Varicella outbreaks among previously vaccinated children have prompted the recommendation for a two-dose varicella vaccine series. Broader coverage for influenza vaccination is now recommended in the US and Canada. Diagnosis and treatment of neonatal hyperbilirubinemia uses population and hour-based norms for total serum bilirubin and assessment of risk factors. Delayed cord clamping is not apparently a risk factor for jaundice but warrants more study. Universal predischarge screening shows promise but is not yet officially recommended. New treatments for hyperbilirubinemia are being evaluated. Dogs are the chief cause of animal bites in children and the largest reservoir for rabies worldwide. In North America and Europe, cats and wild animals cause most human rabies. Postexposure prophylaxis should follow region-appropriate guidelines. New vaccines are available against rotavirus and human papilloma virus. Changes have been made to official immunization recommendations. Appropriate vaccine use can reduce the pediatric disease burden further. Hyperbilirubinemia is the subject of ongoing study, which may lead to improved diagnosis and treatment protocols and reduce the incidence of acute bilirubin encephalopathy. The best tool for rabies prevention after an animal bite is prompt postexposure prophylaxis.

Transition of gastroenterological patients from paediatric to adult care: A position statement by the Italian Societies of Gastroenterology.

PubMed

Elli, Luca; Maieron, Roberto; Martelossi, Stefano; Guariso, Graziella; Buscarini, Elisabetta; Conte, Dario; di Giulio, Emilio; Staiano, Annamaria; Barp, Jacopo; Bassotti, Gabrio; Bianco, Maria Antonia; Buri, Luigi; Carrara, Maurizio; Ghidini, Benedetta; Giannini, Olivia; Knafelz, Daniela; Miele, Erasmo; Peralta, Sergio; Riccio, Elisabetta; Tomba, Carolina; Zilli, Maurizio; Guadagnini, Tiziana

2015-09-01

In 2013, four Italian Gastroenterological Societies (the Italian Society of Paediatric Gastroenterology, Hepatology and Nutrition, the Italian Society of Hospital Gastroenterologists and Endoscopists, the Italian Society of Endoscopy, and the Italian Society of Gastroenterology) formed a joint panel of experts with the aim of preparing an official statement on transition medicine in Gastroenterology. The transition of adolescents from paediatric to adult care is a crucial moment in managing chronic diseases such as celiac disease, inflammatory bowel disease, liver disease and liver transplantation. Improved medical treatment and availability of new drugs and surgical techniques have improved the prognosis of many paediatric disorders, prolonging survival, thus making the transition to adulthood possible and necessary. An inappropriate transition or the incomplete transmission of data from the paediatrician to the adult Gastroenterologist can dramatically decrease compliance to treatment and prognosis of a young patient, particularly in the case of severe disorders. For these reasons, the Italian gastroenterological societies decided to develop an official shared transition protocol. The resulting document discusses the factors influencing the transition process and highlights the main points to accomplish to optimize compliance and prognosis of gastroenterological patients during the difficult transition from childhood to adolescence and adulthood. Copyright © 2015 Editrice Gastroenterologica Italiana S.r.l. Published by Elsevier Ltd. All rights reserved.

HSRP and HSRP Partner Analytical Methods and Protocols

EPA Pesticide Factsheets

HSRP has worked with various partners to develop and test analytical methods and protocols for use by laboratories charged with analyzing environmental and/or buildling material samples following contamination incident.

Protocols for the analytical characterization of therapeutic monoclonal antibodies. II - Enzymatic and chemical sample preparation.

PubMed

Bobaly, Balazs; D'Atri, Valentina; Goyon, Alexandre; Colas, Olivier; Beck, Alain; Fekete, Szabolcs; Guillarme, Davy

2017-08-15

The analytical characterization of therapeutic monoclonal antibodies and related proteins usually incorporates various sample preparation methodologies. Indeed, quantitative and qualitative information can be enhanced by simplifying the sample, thanks to the removal of sources of heterogeneity (e.g. N-glycans) and/or by decreasing the molecular size of the tested protein by enzymatic or chemical fragmentation. These approaches make the sample more suitable for chromatographic and mass spectrometric analysis. Structural elucidation and quality control (QC) analysis of biopharmaceutics are usually performed at intact, subunit and peptide levels. In this paper, general sample preparation approaches used to attain peptide, subunit and glycan level analysis are overviewed. Protocols are described to perform tryptic proteolysis, IdeS and papain digestion, reduction as well as deglycosylation by PNGase F and EndoS2 enzymes. Both historical and modern sample preparation methods were compared and evaluated using rituximab and trastuzumab, two reference therapeutic mAb products approved by Food and Drug Administration (FDA) and European Medicines Agency (EMA). The described protocols may help analysts to develop sample preparation methods in the field of therapeutic protein analysis. Copyright © 2017 Elsevier B.V. All rights reserved.

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

PubMed Central

Lever, Mark A.; Torti, Andrea; Eickenbusch, Philip; Michaud, Alexander B.; Šantl-Temkiv, Tina; Jørgensen, Bo Barker

2015-01-01

A method for the extraction of nucleic acids from a wide range of environmental samples was developed. This method consists of several modules, which can be individually modified to maximize yields in extractions of DNA and RNA or separations of DNA pools. Modules were designed based on elaborate tests, in which permutations of all nucleic acid extraction steps were compared. The final modular protocol is suitable for extractions from igneous rock, air, water, and sediments. Sediments range from high-biomass, organic rich coastal samples to samples from the most oligotrophic region of the world's oceans and the deepest borehole ever studied by scientific ocean drilling. Extraction yields of DNA and RNA are higher than with widely used commercial kits, indicating an advantage to optimizing extraction procedures to match specific sample characteristics. The ability to separate soluble extracellular DNA pools without cell lysis from intracellular and particle-complexed DNA pools may enable new insights into the cycling and preservation of DNA in environmental samples in the future. A general protocol is outlined, along with recommendations for optimizing this general protocol for specific sample types and research goals. PMID:26042110

Modification of the BAX Salmonella test kit to include a hot start functionality (modification of AOAC Official Method 2003.09).

PubMed

Wallace, F Morgan; DiCosimo, Deana; Farnum, Andrew; Tice, George; Andaloro, Bridget; Davis, Eugene; Burns, Frank R

2011-01-01

In 2010, the BAX System PCR assay for Salmonella was modified to include a hot start functionality designed to keep the reaction enzyme inactive until PCR begins. To validate the assay's Official Methods of Analysis status to include this procedure modification, an evaluation was conducted on four food types that were simultaneously analyzed with the BAX System and either the U.S. Food and Drug Administration's Bacteriological Analytical Manual or the U.S. Department of Agriculture-Food Safety and Inspection Service Microbiology Laboratory Guidebook reference method for detecting Salmonella. Identical performance between the BAX System method and the reference methods was observed. Additionally, lysates were analyzed using both the BAX System Classic and BAX System Q7 instruments with identical results using both platforms for all samples tested. Of the 100 samples analyzed, 34 samples were positive for both the BAX System and reference methods, and 66 samples were negative by both the BAX System and reference methods, demonstrating 100% correlation. No instrument platform variation was observed. Additional inclusivity and exclusivity testing using the modified test kit demonstrated the test kit to be 100% accurate in evaluation of test panels of 352 Salmonella strains and 46 non-Salmonella strains.

Influence of feed provisioning prior to digesta sampling on precaecal amino acid digestibility in broiler chickens.

PubMed

Siegert, Wolfgang; Ganzer, Christian; Kluth, Holger; Rodehutscord, Markus

2018-06-01

A regression approach was applied to determine the influence of feed provisioning prior to digesta sampling on precaecal (pc) amino acid (AA) digestibility in broiler chickens. Soybean meal was used as an example test ingredient. Five feed-provisioning protocols were investigated, four with restricted provision and one with ad libitum provision. When provision was restricted, feed was provided for 30 min after a withdrawal period of 12 h. Digesta were sampled 1, 2, 4 and 6 h after feeding commenced. A diet containing 300 g maize starch/kg was prepared. Half or all the maize starch was replaced with soybean meal in two other diets. Average pc digestibility of all determined AA in the soybean meal was 86% for the 4 and 6-h protocols and 66% and 60% for the 2 and 1-h protocols, respectively. Average pc AA digestibility of soybean meal was 76% for ad libitum feed provision. Feed provisioning also influenced the determined variance. Variance in digestibility ranked in magnitude 1 h > ad libitum > 2 h > 6 h > 4 h for all AA. Owing to the considerable influence of feed-provisioning protocols found in this study, comparisons of pc AA digestibility between studies applying different protocols prior to digesta sampling must be treated with caution. Digestibility experiments aimed at providing estimates for practical feed formulation should use feed-provisioning procedures similar to those used in practice.

Sampling forest regeneration across northern U.S. forests: filling a void in regeneration model input

Treesearch

William H. McWilliams; Charles D. Canham; Randall S. Morin; Katherine Johnson; Paul Roth; James A. Westfall

2012-01-01

The Forest Inventory and Analysis Program of the Northern Research Station (NRS-FIA) has implemented new Advance Tree Seedling Regeneration (ATSR) protocols that include measurements of seedlings down to 2 inches in height. The addition of ATSR protocols is part of an evaluation of NRS-FIA Phase 3 indicator variables to increase sampling intensity from 1/96,000 acres...

Diverse Protocols for Correlative Super-Resolution Fluorescence Imaging and Electron Microscopy of Cells and Tissue

DTIC Science & Technology

2016-05-25

tissue is critical to biology. Many factors determine optimal experimental design, including attainable localization precision, ultrastructural...both imaging modalities. Examples include: weak tissue preservation protocols resulting in poor ultrastructure, e.g. mitochondrial cristae membranes...tension effects during sample drying that may result in artifacts44. Samples dried in the presence of polyvinyl alcohol do not have the haziness

Evaluation of two immunomagnetic separation techniques for the detection and recovery of E. coli O157:H7 from finished composts

USDA-ARS?s Scientific Manuscript database

Two rapid immunomagnetic separation (IMS) protocols were evaluated to recover 1-2 log CFU/g inoculated E. coli O157:H7 from 30 different commercial, finished compost samples. Both protocols detected E. coli O157:H7 in compost samples; PCR techniques required the removal of inhibitors to reduce poss...

Bioindicators in the MIDUS National Study: Protocol, Measures, Sample, and Comparative Context

PubMed Central

Love, Gayle Dienberg; Seeman, Teresa E.; Weinstein, Maxine; Ryff, Carol D.

2010-01-01

Objectives MIDUS is a national study of health and aging among individuals aged 25 to 74 at baseline(1995/96). Longitudinal survey assessments (2004/05), were followed by biological assessments on a subsample aged 35–85. To facilitate public use, we describe the protocol, measures, and sample. Methods Respondents traveled to clinics for a two-day data collection protocol that included fasting blood specimens, 12-hour urine specimen, medical history, physical exam, bone densitometry, a laboratory challenge (heart rate variability, blood pressure, respiration, salivary cortisol). Results Response rates for the biological protocol (N = 1,255) were 39.3%, or 43.1% (adjusting for those who could not be located or contacted). Reasons for non-participation were travel, family obligations, and being too busy. Respondents were comparable to the recruitment pool on most demographic characteristics and health assessments. Discussion Strengths of the protocol vis-à-vis other similar studies include opportunities to link biological factors with diverse content from other MIDUS projects. PMID:20876364

Quality assurance of the university medical education, hospital services and traditional pharmaceutical products of the Bhutanese So-wa-rig-pa health care system.

PubMed

Wangchuk, Phurpa; Tashi, ᅟ

2016-08-12

The Bhutanese So-wa-rig-pa medicine (BSM) was integrated with the allopathic (modern) health care system in 1967. Ever since the health care integration policy was implemented, the BSM has gone through many phases of quality improvement and changes including the establishment of one university-based institute, 58 hospitals and Basic Health Units (BHU)-based health care services, and one traditional medicine factory. The BSM provides primary health care services to more than 20-30 % of patients who visit hospitals and BHU on a daily basis. However, there has been no study covering the quality assurance system of BSM. Our paper addresses this information gap. This study was an observational ethnographic study supported by phenomenological understanding and content analysis of the data. The information was triangulated through consultation with the BSM practitioners (discussion (N = 8)) and personalized in-depth question-answer sessions using electronic protocols (N = 5). These participants comprised BSM educationists, clinical physicians, researchers, production and the quality assurance staff who were selected using convenience and purposive sampling method. The relevant So-wa-rig-pa information and literature were obtained from the government policy documents, official websites, scientific papers and the traditional medical texts. This study is enhanced by our practical observations and first-hand experience with BSM while working as the researchers at the Ministry of Health in Bhutan. In addition, the information in this paper is crosschecked and authenticated by five So-wa-rig-pa practitioners of Bhutan. The study highlights the following: a) The BSM receives both the government and people's support, b) The quality assurance system have been developed by integrating the traditional empirical knowledge and modern scientific protocols, c) There exist three administrative and functional organizations responsible for providing the quality BSM health care services in Bhutan, d) Extensive standard treatment guidelines and Quality documentation system exist for BSM as required by the regulatory bodies in Bhutan. The paper also recommends appropriate future directions for BSM. The BSM plays significant role in the primary health care system of the country. Consequently, the quality, safety and efficacy of BSM has been given priority by the Bhutan government. Many scientific protocols were integrated with the traditional quality approaches and further scientific studies are still required to improve its quality.

Protocol for Detection of Bacillus anthracis in Environmental Samples

EPA Pesticide Factsheets

This pProtocol Method describes proceduresintended for the analyses of swabs, wipes, Sponge-Sticks, vacuum socks and filters, air filters, drinking water, and decontamination waste water for Bacillus anthracis spores.

Cryopreservation of human whole blood allows immunophenotyping by flow cytometry up to 30days after cell isolation.

PubMed

Paredes, R Madelaine; Tadaki, Douglas K; Sooter, Amanda; Gamboni, Fabia; Sheppard, Forest

2018-01-01

Immunophenotyping of whole blood (WB) by flow cytometry (FC) is used clinically to assess a patient's immune status and also in biomedical research. Current protocols recommend storage of immunolabeled samples at 4°C with FC analysis to be completed within seven days. This data acquisition window can be extended to up to one year post-labeling, but this requires cryopreservation of the samples at ultra-low temperatures (≤-80°C or in liquid nitrogen). In this study we optimized a standardized cryopreservation protocol to enable preservation of immunolabeled, human WB samples at -20°C for FC and tested its effectiveness after 0, 5, 15 or 30days. Analysis of stored samples shows that this protocol effectively preserves immunolabeled WB samples and that the duration of storage has no effect on morphology, viability or frequency of WB cell subpopulations, and that the intensity of fluorescent signal from labeled extracellular markers is fully preserved for at least 15days, and up to 30days for some markers. We demonstrate that using this protocol, we are able to differentiate resting versus activated WB cells as demonstrated by detection of significantly increased expression of CD11b by myeloid cells in WB samples pretreated with LPS (100μg/mL for 12h). Finally, we show that this method allows for labeling and detection of the intracellular cytokine (IL-8) up to 30days following cryopreservation from myeloid cells, in previously labeled and cryopreserved WB samples. Copyright © 2017 Elsevier B.V. All rights reserved.

Evaluating Protocols for Porcine Faecal Microbiome Recollection, Storage and DNA Extraction: from the Farm to the Lab.

PubMed

Muiños-Bühl, Anixa; González-Recio, Oscar; Muñoz, María; Óvilo, Cristina; García-Casco, Juan; Fernández, Ana I

2018-06-01

There is a growing interest in understanding the role of the gut microbiome on productive and meat quality-related traits in livestock species in order to develop new useful tools for improving pig production systems and industry. Faecal samples are analysed as a proxy of gut microbiota and here the selection of suitable protocols for faecal sampling and DNA isolation is a critical first step in order to obtain reliable results, even more to compare results obtained from different studies. The aim of the current study was to establish in a cost-effective way, using automated ribosomal intergenic spacer analysis technique, a protocol for porcine faecal sampling and storage at farm and slaughterhouse and to determine the most efficient microbiota DNA isolation kit among those most widely used. Operational Taxonomic Unit profiles were compared from Iberian pig faecal samples collected from rectum or ground, stored with liquid N 2 , room temperature or RNAlater, and processed with QIAamp DNA Stool (Qiagen), PowerFecal DNA Isolation (Mobio) or SpeedTools Tissue DNA extraction (Biotools) commercial kits. The results, focused on prokaryote sampling, based on DNA yield and quality, OTU number and Sørensen similarity Indexes, indicate that the recommended protocol for porcine faecal microbiome sampling at farm should include: the collection from porcine rectum to avoid contamination; the storage in liquid N 2 or even at room temperature, but not in RNAlater; and the isolation of microbiota DNA using PowerFecal DNA Isolation kit. These conditions provide more reliable DNA samples for further microbiome analysis.

Robust Sub-nanomolar Library Preparation for High Throughput Next Generation Sequencing.

PubMed

Wu, Wells W; Phue, Je-Nie; Lee, Chun-Ting; Lin, Changyi; Xu, Lai; Wang, Rong; Zhang, Yaqin; Shen, Rong-Fong

2018-05-04

Current library preparation protocols for Illumina HiSeq and MiSeq DNA sequencers require ≥2 nM initial library for subsequent loading of denatured cDNA onto flow cells. Such amounts are not always attainable from samples having a relatively low DNA or RNA input; or those for which a limited number of PCR amplification cycles is preferred (less PCR bias and/or more even coverage). A well-tested sub-nanomolar library preparation protocol for Illumina sequencers has however not been reported. The aim of this study is to provide a much needed working protocol for sub-nanomolar libraries to achieve outcomes as informative as those obtained with the higher library input (≥ 2 nM) recommended by Illumina's protocols. Extensive studies were conducted to validate a robust sub-nanomolar (initial library of 100 pM) protocol using PhiX DNA (as a control), genomic DNA (Bordetella bronchiseptica and microbial mock community B for 16S rRNA gene sequencing), messenger RNA, microRNA, and other small noncoding RNA samples. The utility of our protocol was further explored for PhiX library concentrations as low as 25 pM, which generated only slightly fewer than 50% of the reads achieved under the standard Illumina protocol starting with > 2 nM. A sub-nanomolar library preparation protocol (100 pM) could generate next generation sequencing (NGS) results as robust as the standard Illumina protocol. Following the sub-nanomolar protocol, libraries with initial concentrations as low as 25 pM could also be sequenced to yield satisfactory and reproducible sequencing results.

Porcelain surface conditioning protocols and shear bond strength of orthodontic brackets.

PubMed

Lestrade, Ashley M; Ballard, Richard W; Xu, Xiaoming; Yu, Qingzhao; Kee, Edwin L; Armbruster, Paul C

2016-05-01

The objective of the present study was to determine which of six bonding protocols yielded a clinically acceptable shear bond strength (SBS) of metal orthodontic brackets to CAD/CAM lithium disilicate porcelain restorations. A secondary aim was to determine which bonding protocol produced the least surface damage at debond. Sixty lithium disilicate samples were fabricated to replicate the facial surface of a mandibular first molar using a CEREC CAD/CAM machine. The samples were split into six test groups, each of which received different mechanical/chemical pretreatment protocols to roughen the porcelain surface prior to bonding a molar orthodontic attachment. Shear bond strength testing was conducted using an Instron machine. The mean, maximum, minimal, and standard deviation SBS values for each sample group including an enamel control were calculated. A t-test was used to evaluate the statistical significance between the groups. No significant differences were found in SBS values, with the exception of surface roughening with a green stone prior to HFA and silane treatment. This protocol yielded slightly higher bond strength which was statistically significant. Chemical treatment alone with HFA/silane yielded SBS values within an acceptable clinical range to withstand forces applied by orthodontic treatment and potentially eliminates the need to mechanically roughen the ceramic surface.

KSC-03PD-2453

NASA Technical Reports Server (NTRS)

2003-01-01

KENNEDY SPACE CENTER, FLA. Key officials are poised to cut the ribbon officially dedicating the new Security gates on Kennedy Parkway (Gate 2) and NASA Parkway (Gate 3). From left are Wally Schroeder, with Jones, Edmunds & Associates; Bobby Porter, with Oneida Construction; Daniel Tweed, NASA project manager; Jim Kennedy, Center director; and William Sample, SGS deputy program manager. The new gates were activated Aug. 1, allowing the general public to have access to the new Space Commerce Way, which will provide access to the Research Park and KSC Visitor Complex, and providing an alternate route for the general public between Titusville and Merritt Island that is accessible 24 hours a day. The gates are staffed 24 hours daily.

Coordinated Response to Reports of Possible Anthrax Contamination, Idaho, 2001

PubMed Central

Hudson, Richard; Barnes, Shana; Hahn, Christine

2002-01-01

In 2001, the intentional release of anthrax spores in the eastern United States increased concern about exposure to anthrax nationwide, and residents of Idaho sought assistance. Response from state and local agencies was required, increasing the strain on epidemiologists, laboratorians, and communications personnel. In late 2001, Idaho’s public health communications system handled 133 calls about suspicious powders. For each call, a multiagency bridge call was established, and participants (public health officials, epidemiologists, police, Federal Bureau of Investigation personnel, hazardous materials officials, and others) determined which samples would be tested by the state public health laboratory. A triage system for calls helped relieve the burden on public safety and health systems. PMID:12396922

Reasonable Forecasts

ERIC Educational Resources Information Center

Taylor, Kelley R.

2010-01-01

This article presents a sample legal battle that illustrates school officials' "reasonable forecasts" of substantial disruption in the school environment. In 2006, two students from a Texas high school came to school carrying purses decorated with images of the Confederate flag. The school district has a zero-tolerance policy for…

Institute of Education Science Findings from Interviews with Education Policymakers.

ERIC Educational Resources Information Center

Huang, Gary; Reiser, Mindy; Parker, Albert; Muniec, Judith; Salvucci, Sameena

This reports presents interview findings with education policymakers on various aspects of educational research. The sampling contained the following groups: superintendents and other local education officials; chief state school officers; state higher education executive officers; state legislators; governors' educational policy advisors;…

Picosecond beam monitor

DOEpatents

Schutt, D.W.; Beck, G.O.

1974-01-01

The current in the beam of a particle accelerator is monitored with picosecond resolution by causing the beam to impinge upon the center conductor of a coaxial line, generating a pulse of electromagnetic energy in response thereto. This pulse is detected by means such as a sampling oscilloscope. (Official Gazette)

Multicenter evaluation of a new closed system drug-transfer device in reducing surface contamination by antineoplastic hazardous drugs.

PubMed

Bartel, Sylvia B; Tyler, Timothy G; Power, Luci A

2018-02-15

Results of a study to evaluate the effectiveness of a recently introduced closed system drug-transfer device (CSTD) in reducing surface contamination during compounding and simulated administration of antineoplastic hazardous drugs (AHDs) are reported. Wipe samples were collected from 6 predetermined surfaces in compounding and infusion areas of 13 U.S. cancer centers to establish preexisting levels of surface contamination by 2 marker AHDs (cyclophosphamide and fluorouracil). Stainless steel templates were placed over the 6 previously sampled surfaces, and the marker drugs were compounded and infused per a specific protocol using all components of the CSTD. Wipe samples were collected from the templates after completion of tasks and analyzed for both marker AHDs. Aggregated results of wipe sampling to detect preexisting contamination at the 13 study sites showed that overall, 66.7% of samples (104 of 156) had detectable levels of at least 1 marker AHD; subsequent testing after CSTD use per protocol found a sample contamination rate of 5.8% (9 of 156 samples). In the administration areas alone, the rate of preexisting contamination was 78% (61 of 78 samples); with use of the CSTD protocol, the contamination rate was 2.6%. Twenty-six participants rated the CSTD for ease of use, with 100% indicating that they were satisfied or extremely satisfied. A study involving a rigorous protocol and 13 cancer centers across the United States demonstrated that the CSTD reduced surface contamination by cyclophosphamide and fluorouracil during compounding and simulated administration. Participants reported that the CSTD was easy to use. Copyright © 2018 by the American Society of Health-System Pharmacists, Inc. All rights reserved.

The use of FTA cards for preserving unfixed cytological material for high-throughput molecular analysis.

PubMed

Saieg, Mauro Ajaj; Geddie, William R; Boerner, Scott L; Liu, Ni; Tsao, Ming; Zhang, Tong; Kamel-Reid, Suzanne; da Cunha Santos, Gilda

2012-06-25

Novel high-throughput molecular technologies have made the collection and storage of cells and small tissue specimens a critical issue. The FTA card provides an alternative to cryopreservation for biobanking fresh unfixed cells. The current study compared the quality and integrity of the DNA obtained from 2 types of FTA cards (Classic and Elute) using 2 different extraction protocols ("Classic" and "Elute") and assessed the feasibility of performing multiplex mutational screening using fine-needle aspiration (FNA) biopsy samples. Residual material from 42 FNA biopsies was collected in the cards (21 Classic and 21 Elute cards). DNA was extracted using the Classic protocol for Classic cards and both protocols for Elute cards. Polymerase chain reaction for p53 (1.5 kilobase) and CARD11 (500 base pair) was performed to assess DNA integrity. Successful p53 amplification was achieved in 95.2% of the samples from the Classic cards and in 80.9% of the samples from the Elute cards using the Classic protocol and 28.5% using the Elute protocol (P = .001). All samples (both cards) could be amplified for CARD11. There was no significant difference in the DNA concentration or 260/280 purity ratio when the 2 types of cards were compared. Five samples were also successfully analyzed by multiplex MassARRAY spectrometry, with a mutation in KRAS found in 1 case. High molecular weight DNA was extracted from the cards in sufficient amounts and quality to perform high-throughput multiplex mutation assays. The results of the current study also suggest that FTA Classic cards preserve better DNA integrity for molecular applications compared with the FTA Elute cards. Copyright © 2012 American Cancer Society.

Integration of GC-MSD and ER-Calux® assay into a single protocol for determining steroid estrogens in environmental samples.

PubMed

Avberšek, Miha; Žegura, Bojana; Filipič, Metka; Heath, Ester

2011-11-01

There are many published studies that use either chemical or biological methods to investigate steroid estrogens in the aquatic environment, but rarer are those that combine both. In this study, gas chromatography with mass selective detection (GC-MSD) and the ER-Calux(®) estrogenicity assay were integrated into a single protocol for simultaneous determination of natural (estrone--E1, 17β-estradiol--E2, estriol--E3) and synthetic (17α-ethinylestradiol--EE2) steroid estrogens concentrations and the total estrogenic potential of environmental samples. For integration purposes, several solvents were investigated and the commonly used dimethyl sulphoxide (DMSO) in the ER-Calux(®) assay was replaced by ethyl acetate, which is more compatible with gas chromatography and enables the same sample to be analysed by both GC-MSD and the ER-Calux(®) assay. The integrated protocol was initially tested using a standard mixture of estrogens. The results for pure standards showed that the estrogenicity calculated on the basis of GC-MSD and the ER-Calux(®) assay exhibited good correlation (r(2)=0.96; α=0.94). The result remained the same when spiked waste water extracts were tested (r(2)=0.92, α=1.02). When applied to real waste water influent and effluent samples the results proved (r(2)=0.93; α=0.99) the applicability of the protocol. The main advantages of this newly developed protocol are simple sample handling for both methods, and reduced material consumption and labour. In addition, it can be applied as either a complete or sequential analysis where the ER-Calux(®) assay is used as a pre-screening method prior to the chemical analysis. Copyright © 2011 Elsevier B.V. All rights reserved.

Embedding and Chemical Reactivation of Green Fluorescent Protein in the Whole Mouse Brain for Optical Micro-Imaging

PubMed Central

Gang, Yadong; Zhou, Hongfu; Jia, Yao; Liu, Ling; Liu, Xiuli; Rao, Gong; Li, Longhui; Wang, Xiaojun; Lv, Xiaohua; Xiong, Hanqing; Yang, Zhongqin; Luo, Qingming; Gong, Hui; Zeng, Shaoqun

2017-01-01

Resin embedding has been widely applied to fixing biological tissues for sectioning and imaging, but has long been regarded as incompatible with green fluorescent protein (GFP) labeled sample because it reduces fluorescence. Recently, it has been reported that resin-embedded GFP-labeled brain tissue can be imaged with high resolution. In this protocol, we describe an optimized protocol for resin embedding and chemical reactivation of fluorescent protein labeled mouse brain, we have used mice as experiment model, but the protocol should be applied to other species. This method involves whole brain embedding and chemical reactivation of the fluorescent signal in resin-embedded tissue. The whole brain embedding process takes a total of 7 days. The duration of chemical reactivation is ~2 min for penetrating 4 μm below the surface in the resin-embedded brain. This protocol provides an efficient way to prepare fluorescent protein labeled sample for high-resolution optical imaging. This kind of sample was demonstrated to be imaged by various optical micro-imaging methods. Fine structures labeled with GFP across a whole brain can be detected. PMID:28352214

Optimization of scat detection methods for a social ungulate, the wild pig, and experimental evaluation of factors affecting detection of scat

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

Keiter, David A.; Cunningham, Fred L.; Rhodes, Jr., Olin E.

Collection of scat samples is common in wildlife research, particularly for genetic capture-mark-recapture applications. Due to high degradation rates of genetic material in scat, large numbers of samples must be collected to generate robust estimates. Optimization of sampling approaches to account for taxa-specific patterns of scat deposition is, therefore, necessary to ensure sufficient sample collection. While scat collection methods have been widely studied in carnivores, research to maximize scat collection and noninvasive sampling efficiency for social ungulates is lacking. Further, environmental factors or scat morphology may influence detection of scat by observers. We contrasted performance of novel radial search protocolsmore » with existing adaptive cluster sampling protocols to quantify differences in observed amounts of wild pig ( Sus scrofa) scat. We also evaluated the effects of environmental (percentage of vegetative ground cover and occurrence of rain immediately prior to sampling) and scat characteristics (fecal pellet size and number) on the detectability of scat by observers. We found that 15- and 20-m radial search protocols resulted in greater numbers of scats encountered than the previously used adaptive cluster sampling approach across habitat types, and that fecal pellet size, number of fecal pellets, percent vegetative ground cover, and recent rain events were significant predictors of scat detection. Our results suggest that use of a fixed-width radial search protocol may increase the number of scats detected for wild pigs, or other social ungulates, allowing more robust estimation of population metrics using noninvasive genetic sampling methods. Further, as fecal pellet size affected scat detection, juvenile or smaller-sized animals may be less detectable than adult or large animals, which could introduce bias into abundance estimates. In conclusion, knowledge of relationships between environmental variables and scat detection may allow researchers to optimize sampling protocols to maximize utility of noninvasive sampling for wild pigs and other social ungulates.« less

Optimization of scat detection methods for a social ungulate, the wild pig, and experimental evaluation of factors affecting detection of scat

DOE PAGES

Keiter, David A.; Cunningham, Fred L.; Rhodes, Jr., Olin E.; ...

2016-05-25

Collection of scat samples is common in wildlife research, particularly for genetic capture-mark-recapture applications. Due to high degradation rates of genetic material in scat, large numbers of samples must be collected to generate robust estimates. Optimization of sampling approaches to account for taxa-specific patterns of scat deposition is, therefore, necessary to ensure sufficient sample collection. While scat collection methods have been widely studied in carnivores, research to maximize scat collection and noninvasive sampling efficiency for social ungulates is lacking. Further, environmental factors or scat morphology may influence detection of scat by observers. We contrasted performance of novel radial search protocolsmore » with existing adaptive cluster sampling protocols to quantify differences in observed amounts of wild pig ( Sus scrofa) scat. We also evaluated the effects of environmental (percentage of vegetative ground cover and occurrence of rain immediately prior to sampling) and scat characteristics (fecal pellet size and number) on the detectability of scat by observers. We found that 15- and 20-m radial search protocols resulted in greater numbers of scats encountered than the previously used adaptive cluster sampling approach across habitat types, and that fecal pellet size, number of fecal pellets, percent vegetative ground cover, and recent rain events were significant predictors of scat detection. Our results suggest that use of a fixed-width radial search protocol may increase the number of scats detected for wild pigs, or other social ungulates, allowing more robust estimation of population metrics using noninvasive genetic sampling methods. Further, as fecal pellet size affected scat detection, juvenile or smaller-sized animals may be less detectable than adult or large animals, which could introduce bias into abundance estimates. In conclusion, knowledge of relationships between environmental variables and scat detection may allow researchers to optimize sampling protocols to maximize utility of noninvasive sampling for wild pigs and other social ungulates.« less

Bacterial and fungal DNA extraction from blood samples: automated protocols.

PubMed

Lorenz, Michael G; Disqué, Claudia; Mühl, Helge

2015-01-01

Automation in DNA isolation is a necessity for routine practice employing molecular diagnosis of infectious agents. To this end, the development of automated systems for the molecular diagnosis of microorganisms directly in blood samples is at its beginning. Important characteristics of systems demanded for routine use include high recovery of microbial DNA, DNA-free containment for the reduction of DNA contamination from exogenous sources, DNA-free reagents and consumables, ideally a walkaway system, and economical pricing of the equipment and consumables. Such full automation of DNA extraction evaluated and in use for sepsis diagnostics is yet not available. Here, we present protocols for the semiautomated isolation of microbial DNA from blood culture and low- and high-volume blood samples. The protocols include a manual pretreatment step followed by automated extraction and purification of microbial DNA.

Transient partial permeabilization with saponin enables cellular barcoding prior to surface marker staining1

PubMed Central

Behbehani, Gregory K.; Thom, Colin; Zunder, Eli R.; Finck, Rachel; Gaudilliere, Brice; Fragiadakis, Gabriela K.; Fantl, Wendy J.; Nolan, Garry P.

2015-01-01

Fluorescent cellular barcoding and mass-tag cellular barcoding are cytometric methods that enable high sample throughput, minimize inter-sample variation, and reduce reagent consumption. Previously employed barcoding protocols require that barcoding be performed after surface marker staining, complicating combining the technique with measurement of alcohol-sensitive surface epitopes. This report describes a method of barcoding fixed cells after a transient partial permeabilization with 0.02% saponin that results in efficient and consistent barcode staining with fluorescent or mass-tagged reagents while preserving surface marker staining. This approach simplifies barcoding protocols and allows direct comparison of surface marker staining of multiple samples without concern for variations in the antibody cocktail volume, antigen-antibody ratio, or machine sensitivity. Using this protocol, cellular barcoding can be used to reliably detect subtle differences in surface marker expression. PMID:25274027

Effect of laser and air abrasion pretreatment on the microleakage of a fissure sealant applied with conventional and self etch adhesives.

PubMed

Tirali, R E; Celik, C; Arhun, N; Berk, G; Cehreli, S B

2013-01-01

The purpose of this study was to investigate the effects of different pretreatment protocols along with different bonding agents on the microleakage of a fissure sealant material. A total of 144 freshly extracted noncarious human third molars were used The teeth were randomly assigned into three groups with respect to the pretreatment protocol employed: A. Air Abrasion B. Er,Cr:YSGG laser C. No pretreatment (Control). In each group specimens were further subjected to one of the following procedures before application of the sealant: 1. %36 Phosphoric acid-etch (AE) (DeTrey Conditioner 36/Denstply, UK) 2.AE+Prime&Bond NT (Dentsply, UK) 3. Clearfil S3 Bond (Kuraray, Japan) 4. Clearfil SE Bond (Kuraray, Japan). All teeth were sealed with the same fissure sealant material (Conseal F/SDI, Australia). Sealed teeth were further subjected to thermocycling, dye penetration test, sectioning and quantitative image analysis. Statistical evaluation of the microleakage data was performed with two way independent ANOVA and multiple comparisons test at p = 0.05. For qualitative evaluation 2 samples from each group were examined under Scanning Electron Microscopy. Microleakage was affected by both the type of pretreatment and the subsequent bonding protocols employed (p < 0.05). Overall, the highest (Mean = 0.36 mm) and lowest (Mean = 0.06 mm) microleakage values were observed in samples with unpretreated enamel sealed by S3+Conseal F and samples with laser pretreated enamel sealed by Acid Etch+Prime&-Bond+Conseal F protocols, respectively (p < 0.05). In the acid-etch group samples pretreated with laser yielded in slightly lower microleakage scores when compared with unpretreated samples and samples pretreated with air abrasion but the statistical significance was not important (p = 0,179). Similarly, when bonding agent is applied following acid-etching procedure, microleakage scores were not affected from pretreatment protocol (p = 0,615) (intact enamel/laser or air-abrasion). For both all-in one and two step self etch adhesive systems, unpretreated samples demonstrated the highest microleakage scores. For the groups in which bonding agent was utilized, pretreatments did not effected microleakage. Both the tested pretreatment protocols and adhesive procedures had different effects on the sealing properties of Conseal F in permanent tooth enamel.

A reference model for scientific information interchange

NASA Technical Reports Server (NTRS)

Reich, Lou; Sawyer, Don; Davis, Randy

1993-01-01

This paper presents an overview of an Information Interchange Reference Model (IIRM) currently being developed by individuals participating in the Consultative Committee for Space Data Systems (CCSDS) Panel 2, the Planetary Data Systems (PDS), and the Committee on Earth Observing Satellites (CEOS). This is an ongoing research activity and is not an official position by these bodies. This reference model provides a framework for describing and assessing current and proposed methodologies for information interchange within and among the space agencies. It is hoped that this model will improve interoperability between the various methodologies. As such, this model attempts to address key information interchange issues as seen by the producers and users of space-related data and to put them into a coherent framework. Information is understood as the knowledge (e.g., the scientific content) represented by data. Therefore, concern is not primarily on mechanisms for transferring data from user to user (e.g., compact disk read-only memory (CD-ROM), wide-area networks, optical tape, and so forth) but on how information is encoded as data and how the information content is maintained with minimal loss or distortion during transmittal. The model assumes open systems, which means that the protocols or methods used should be fully described and the descriptions publicly available. Ideally these protocols are promoted by recognized standards organizations using processes that permit involvement by those most likely to be affected, thereby enhancing the protocol's stability and the likelihood of wide support.

A method for estimating the relative degree of saponification of xanthophyll sources and feedstuffs.

PubMed

Fletcher, D L

2006-05-01

Saponification of xanthophyll esters in various feed sources has been shown to improve pigmentation efficiency in broiler skin and egg yolks. Three trials were conducted to evaluate a rapid liquid chromatography procedure for estimating the relative degree of xanthophyll saponification using samples of yellow corn, corn gluten meal, alfalfa, and 6 commercially available marigold meal concentrates. In each trial, samples were extracted using a modification of the 1984 Association of Official Analytical Chemists hot saponification procedure with and without the addition of KOH. A comparison of the chromatography results was used to estimate percent saponification of the original sample by dividing the nonsaponified extraction values by the saponified extraction values. A comparison of the percent saponified xanthophylls for each product (mg/kg) was: yellow corn, 101; corn gluten meal, 78; alfalfa, 97.9; and marigold concentrates A through F, 99.8, 4.6, 99.0, 95.6, 96.8, and 6.6, respectively. These results indicate that a modification of the 1984 Association of Official Analytical Chemists procedure and liquid column chromatography can be used to quickly verify saponification and can be used to estimate the relative degree of saponification of an unknown xanthophyll source.

In-house validation study of the DuPont Qualicon BAX system Q7 instrument with the BAX system PCR Assay for Salmonella (modification of AOAC Official Method 2003.09 and AOAC Research Institute Performance-Tested Method 100201).

PubMed

Tice, George; Andaloro, Bridget; White, H Kirk; Bolton, Lance; Wang, Siqun; Davis, Eugene; Wallace, Morgan

2009-01-01

In 2006, DuPont Qualicon introduced the BAX system Q7 instrument for use with its assays. To demonstrate the equivalence of the new and old instruments, a validation study was conducted using the BAX system PCR Assay for Salmonella, AOAC Official Method 2003.09, on three food types. The foods were simultaneously analyzed with the BAX system Q7 instrument and either the U.S. Food and Drug Administration Bacteriological Analytical Manual or the U.S. Department of Agriculture-Food Safety and Inspection Service Microbiology Laboratory Guidebook reference method for detecting Salmonella. Comparable performance between the BAX system and the reference methods was observed. Of the 75 paired samples analyzed, 39 samples were positive by both the BAX system and reference methods, and 36 samples were negative by both the BAX system and reference methods, demonstrating 100% correlation. Inclusivity and exclusivity for the BAX system Q7 instrument were also established by testing 50 Salmonella strains and 20 non-Salmonella isolates. All Salmonella strains returned positive results, and all non-Salmonella isolates returned a negative response.

Evaluation of DNA extraction protocols for Brucella abortus pcr detection in aborted fetuses or calves born from cows experimentally infected with strain 2308

PubMed Central

Matrone, M.; Keid, L.B.; Rocha, V.C.M.; Vejarano, M.P.; Ikuta, C.Y.; Rodriguez, C.A.R.; Ferreira, F.; Dias, R.A.; Ferreira Neto, J.S

2009-01-01

The objective of the present study was to improve the detection of B. abortus by PCR in organs of aborted fetuses from infected cows, an important mechanism to find infected herds on the eradication phase of the program. So, different DNA extraction protocols were compared, focusing the PCR detection of B. abortus in clinical samples collected from aborted fetuses or calves born from cows challenged with the 2308 B. abortus strain. Therefore, two gold standard groups were built based on classical bacteriology, formed from: 32 lungs (17 positives), 26 spleens (11 positives), 23 livers (8 positives) and 22 bronchial lymph nodes (7 positives). All samples were submitted to three DNA extraction protocols, followed by the same amplification process with the primers B4 and B5. From the accumulated results for organ, the proportion of positives for the lungs was higher than the livers (p=0.04) or bronchial lymph nodes (p=0.004) and equal to the spleens (p=0.18). From the accumulated results for DNA extraction protocol, the proportion of positives for the Boom protocol was bigger than the PK (p< 0.0001) and GT (p=0.0004). There was no difference between the PK and GT protocols (p=0.5). Some positive samples from the classical bacteriology were negative to the PCR and vice-versa. Therefore, the best strategy for B. abortus detection in the organs of aborted fetuses or calves born from infected cows is the use, in parallel, of isolation by classical bacteriology and the PCR, with the DNA extraction performed by the Boom protocol. PMID:24031391

A fast and mild decellularization protocol for obtaining extracellular matrix.

PubMed

Mirzarafie, Ariana; Grainger, Rhian K; Thomas, Ben; Bains, William; Ustok, Fatma I; Lowe, Chris R

2014-04-01

Degradation of extracellular matrix (ECM) function with age is a major cause of loss of tissue function with age that we would wish to reverse. Tissue engineering to provide replacement tissue requires an ECM-mimicking scaffold for cell organization. The standard protocols for achieving this take 10 days and include steps that may change the protein structure of the ECM. Here we describe a much shorter protocol for decellularizing chicken muscle, skin, and tendon samples that achieves the same efficiency as the original protocol without protein cross-link interference. Our protocol can be completed in 72 hr.

Evaluating optimal therapy robustness by virtual expansion of a sample population, with a case study in cancer immunotherapy

PubMed Central

Barish, Syndi; Ochs, Michael F.; Sontag, Eduardo D.; Gevertz, Jana L.

2017-01-01

Cancer is a highly heterogeneous disease, exhibiting spatial and temporal variations that pose challenges for designing robust therapies. Here, we propose the VEPART (Virtual Expansion of Populations for Analyzing Robustness of Therapies) technique as a platform that integrates experimental data, mathematical modeling, and statistical analyses for identifying robust optimal treatment protocols. VEPART begins with time course experimental data for a sample population, and a mathematical model fit to aggregate data from that sample population. Using nonparametric statistics, the sample population is amplified and used to create a large number of virtual populations. At the final step of VEPART, robustness is assessed by identifying and analyzing the optimal therapy (perhaps restricted to a set of clinically realizable protocols) across each virtual population. As proof of concept, we have applied the VEPART method to study the robustness of treatment response in a mouse model of melanoma subject to treatment with immunostimulatory oncolytic viruses and dendritic cell vaccines. Our analysis (i) showed that every scheduling variant of the experimentally used treatment protocol is fragile (nonrobust) and (ii) discovered an alternative region of dosing space (lower oncolytic virus dose, higher dendritic cell dose) for which a robust optimal protocol exists. PMID:28716945

Relative Importance of Different Water Categories as Sources of N-Nitrosamine Precursors.

PubMed

Zeng, Teng; Glover, Caitlin M; Marti, Erica J; Woods-Chabane, Gwen C; Karanfil, Tanju; Mitch, William A; Dickenson, Eric R V

2016-12-20

A comparison of loadings of N-nitrosamines and their precursors from different source water categories is needed to design effective source water blending strategies. Previous research using Formation Potential (FP) chloramination protocols (high dose and prolonged contact times) raised concerns about precursor loadings from various source water categories, but differences in the protocols employed rendered comparisons difficult. In this study, we applied Uniform Formation Condition (UFC) chloramination and ozonation protocols mimicking typical disinfection practice to compare loadings of ambient specific and total N-nitrosamines as well as chloramine-reactive and ozone-reactive precursors in 47 samples, including 6 pristine headwaters, 16 eutrophic waters, 4 agricultural runoff samples, 9 stormwater runoff samples, and 12 municipal wastewater effluents. N-Nitrosodimethylamine (NDMA) formation from UFC and FP chloramination protocols did not correlate, with NDMA FP often being significant in samples where no NDMA formed under UFC conditions. N-Nitrosamines and their precursors were negligible in pristine headwaters. Conventional, and to a lesser degree, nutrient removal wastewater effluents were the dominant source of NDMA and its chloramine- and ozone-reactive precursors. While wastewater effluents were dominant sources of TONO and their precursors, algal blooms, and to a lesser degree agricultural or stormwater runoff, could be important where they affect a major fraction of the water supply.

Avoiding artefacts during electron microscopy of silver nanomaterials exposed to biological environments

PubMed Central

Goode, Angela E.; Skepper, Jeremy N.; Thorley, Andrew J.; Seiffert, Joanna M.; Chung, K. Fan; Tetley, Teresa D.; Shaffer, Milo S. P.; Ryan, Mary P.

2015-01-01

Electron microscopy has been applied widely to study the interaction of nanomaterials with proteins, cells and tissues at nanometre scale. Biological material is most commonly embedded in thermoset resins to make it compatible with the high vacuum in the electron microscope. Room temperature sample preparation protocols developed over decades provide contrast by staining cell organelles, and aim to preserve the native cell structure. However, the effect of these complex protocols on the nanomaterials in the system is seldom considered. Any artefacts generated during sample preparation may ultimately interfere with the accurate prediction of the stability and reactivity of the nanomaterials. As a case study, we review steps in the room temperature preparation of cells exposed to silver nanomaterials (AgNMs) for transmission electron microscopy imaging and analysis. In particular, embedding and staining protocols, which can alter the physicochemical properties of AgNMs and introduce artefacts thereby leading to a misinterpretation of silver bioreactivity, are scrutinised. Recommendations are given for the application of cryogenic sample preparation protocols, which simultaneously fix both particles and diffusible ions. By being aware of the advantages and limitations of different sample preparation methods, compromises or selection of different correlative techniques can be made to draw more accurate conclusions about the data. PMID:25606708

Analytical platform for metabolome analysis of microbial cells using methyl chloroformate derivatization followed by gas chromatography-mass spectrometry.

PubMed

Smart, Kathleen F; Aggio, Raphael B M; Van Houtte, Jeremy R; Villas-Bôas, Silas G

2010-09-01

This protocol describes an analytical platform for the analysis of intra- and extracellular metabolites of microbial cells (yeast, filamentous fungi and bacteria) using gas chromatography-mass spectrometry (GC-MS). The protocol is subdivided into sampling, sample preparation, chemical derivatization of metabolites, GC-MS analysis and data processing and analysis. This protocol uses two robust quenching methods for microbial cultures, the first of which, cold glycerol-saline quenching, causes reduced leakage of intracellular metabolites, thus allowing a more reliable separation of intra- and extracellular metabolites with simultaneous stopping of cell metabolism. The second, fast filtration, is specifically designed for quenching filamentous micro-organisms. These sampling techniques are combined with an easy sample-preparation procedure and a fast chemical derivatization reaction using methyl chloroformate. This reaction takes place at room temperature, in aqueous medium, and is less prone to matrix effect compared with other derivatizations. This protocol takes an average of 10 d to complete and enables the simultaneous analysis of hundreds of metabolites from the central carbon metabolism (amino and nonamino organic acids, phosphorylated organic acids and fatty acid intermediates) using an in-house MS library and a data analysis pipeline consisting of two free software programs (Automated Mass Deconvolution and Identification System (AMDIS) and R).

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues.

PubMed

Corces, M Ryan; Trevino, Alexandro E; Hamilton, Emily G; Greenside, Peyton G; Sinnott-Armstrong, Nicholas A; Vesuna, Sam; Satpathy, Ansuman T; Rubin, Adam J; Montine, Kathleen S; Wu, Beijing; Kathiria, Arwa; Cho, Seung Woo; Mumbach, Maxwell R; Carter, Ava C; Kasowski, Maya; Orloff, Lisa A; Risca, Viviana I; Kundaje, Anshul; Khavari, Paul A; Montine, Thomas J; Greenleaf, William J; Chang, Howard Y

2017-10-01

We present Omni-ATAC, an improved ATAC-seq protocol for chromatin accessibility profiling that works across multiple applications with substantial improvement of signal-to-background ratio and information content. The Omni-ATAC protocol generates chromatin accessibility profiles from archival frozen tissue samples and 50-μm sections, revealing the activities of disease-associated DNA elements in distinct human brain structures. The Omni-ATAC protocol enables the interrogation of personal regulomes in tissue context and translational studies.

A Data Scheduling and Management Infrastructure for the TEAM Network

NASA Astrophysics Data System (ADS)

Andelman, S.; Baru, C.; Chandra, S.; Fegraus, E.; Lin, K.; Unwin, R.

2009-04-01

The objective of the Tropical Ecology Assessment and Monitoring Network (www.teamnetwork.org) is "To generate real time data for monitoring long-term trends in tropical biodiversity through a global network of TEAM sites (i.e. field stations in tropical forests), providing an early warning system on the status of biodiversity to effectively guide conservation action". To achieve this, the TEAM Network operates by collecting data via standardized protocols at TEAM Sites. The standardized TEAM protocols include the Climate, Vegetation and Terrestrial Vertebrate Protocols. Some sites also implement additional protocols. There are currently 7 TEAM Sites with plans to grow the network to 15 by June 30, 2009 and 50 TEAM Sites by the end of 2010. Climate Protocol The Climate Protocol entails the collection of climate data via meteorological stations located at the TEAM Sites. This includes information such as precipitation, temperature, wind direction and strength and various solar radiation measurements. Vegetation Protocol The Vegetation Protocol collects standardized information on tropical forest trees and lianas. A TEAM Site will have between 6-9 1ha plots where trees and lianas larger than a pre-specified size are mapped, identified and measured. This results in each TEAM Site repeatedly measuring between 3000-5000 trees annually. Terrestrial Vertebrate Protocol The Terrestrial Vertebrate Protocol collects standardized information on mid-sized tropical forest fauna (i.e. birds and mammals). This information is collected via camera traps (i.e. digital cameras with motion sensors housed in weather proof casings). The images taken by the camera trap are reviewed to identify what species are captured in the image by the camera trap. The image and the interpretation of what is in the image are the data for the Terrestrial Vertebrate Protocol. The amount of data collected through the TEAM protocols provides a significant yet exciting IT challenge. The TEAM Network is currently partnering with the San Diego Super Computer Center to build the data management infrastructure. Data collected from the three core protocols as well as others are currently made available through the TEAM Network portal, which provides the content management framework, the data scheduling and management framework, an administrative framework to implement and manage TEAM sites, collaborative tools and a number of tools and applications utilizing Google Map and Google Earth products. A critical element of the TEAM Network data management infrastructure is to make the data publicly available in as close to real-time as possible (the TEAM Network Data Use Policy: http://www.teamnetwork.org/en/data/policy). This requires two essential tasks to be accomplished, 1) A data collection schedule has to be planned, proposed and approved for a given TEAM site. This is a challenging process since TEAM sites are geographically distributed across the tropics and hence have different seasons where they schedule field sampling for the different TEAM protocols. Capturing this information and ensuring that TEAM sites follow the outlined legal contract is key to the data collection process and 2) A stream-lined and efficient information management system to ensure data collected from the field meet the minimum data standards (i.e. are of the highest scientific quality) and are securely transferred, archived, processed and be rapidly made publicaly available, as a finished consumable product via the TEAM Network portal. The TEAM Network is achieving these goals by implementing an end-to-end framework consisting of the Sampling Scheduler application and the Data Management Framework. Sampling Scheduler The Sampling Scheduler is a project management, calendar based portal application that will allow scientists at a TEAM site to schedule field sampling for each of the TEAM protocols implemented at that site. The sampling scheduler addresses the specific requirements established in the TEAM protocols with the logistical scheduling needs of each TEAM Site. For example, each TEAM protocol defines when data must be collected (e.g. time of day, number of times per year, during which seasons, etc) as well as where data must be collected (from which sampling units, which trees, etc). Each TEAM Site has a limited number of resources and must create plans that will both satisfy the requirements of the protocols as well as be logistically feasible for their TEAM Site. With 15 TEAM Sites (and many more coming soon) the schedules of each TEAM Site must be communicated to the Network Office to ensure data are being collected as scheduled and to address the many problems when working in difficult environments like Tropical Forests. The Sampling Schedule provides built-in proposal and approval functionality to ensure that the TEAM Sites are and the Network office are in sync as well as provides the capability to modify schedules when needed. The Data Management Framework The Data Management framework is a three-tier data ingestion, edit and review application for protocols defined in the TEAM network. The data ingestion framework provides online web forms for field personnel to submit and edit data collected at TEAM Sites. These web forms will be accessible from the TEAM content management site. Once the data is securely uploaded, cured, processed and approved, it will be made publicly available for consumption by the scientific community. The Data Management framework, when combined with the Sampling Scheduler provides a closed loop Data Scheduling and Management infrastructure. All information starting from data collection plan, tools to input, modify and curate data, review and run QA/QC tests, as well as verify data are collected as planed are included. Finally, TEAM Network data are available for download via the Data Query and Download Application. This application utilizes a Google Maps custom interface to search, visualize, and download TEAM Network data. References • TEAM Network, http://www.teamnetwork.org • Center for Applied Biodiversity Science, Conservation International. http://science.conservation.org/portal/server.pt • TEAM Data Query and Download Application, http://www.teamnetwork.org/en/data/query

Juvenile hypothyroidism among two populations exposed to radioiodine.

PubMed Central

Goldsmith, J R; Grossman, C M; Morton, W E; Nussbaum, R H; Kordysh, E A; Quastel, M R; Sobel, R B; Nussbaum, F D

1999-01-01

We found an epidemic of juvenile hypothyroidism among a population of self-defined "downwinders" living near the Hanford nuclear facility located in southeast Washington State. The episode followed massive releases of 131I. Self-reported data on 60 cases of juvenile hypothyroidism (<20 years of age) among a group of 801 Hanford downwinders are presented, as well as data concerning the thyroid status of approximately 160,000 children exposed to radioiodine before 10 years of age as a result of the 26 April 1986 Chernobyl explosion in the former Soviet Union. These children were residents of five regions near Chernobyl. They were examined by standardized screening protocols over a period of 5 years from 1991 to 1996. They are a well-defined group of 10 samples. Fifty-six cases of hypothyroidism were found among boys and 92 among girls. Body burdens of 137Cs have been correlated with hypothyroidism prevalence rates. On the other hand, the group of juvenile (<20 years of age) Hanford downwinders is not a representative sample. Most of the 77 cases of juvenile hypothyroidism in the Hanford group were diagnosed from 1945 to 1970. However, the ratio of reported cases to the county population under 20 years of age is roughly correlated with officially estimated mean levels of cumulative thyroid 131I uptake in these counties, providing evidence that juvenile hypothyroidism was associated with radioiodine exposures. Because even subtle hypothyroidism may be of clinical significance in childhood and can be treated, it may be useful to screen for the condition in populations exposed to radioiodine fallout. Although radiation exposure is associated with hypothyroidism, its excess among fallout-exposed children has not been previously quantified. Images Figure 1 Figure 2 Figure 3 Figure 4 Figure 5 Figure 6 PMID:10090710

Analyzing pathways from childhood maltreatment to internalizing symptoms and disorders in children and adolescents (AMIS): a study protocol.

PubMed

White, Lars O; Klein, Annette M; Kirschbaum, Clemens; Kurz-Adam, Maria; Uhr, Manfred; Müller-Myhsok, Bertram; Hoffmann, Katrin; Sierau, Susan; Michel, Andrea; Stalder, Tobias; Horlich, Jenny; Keil, Jan; Andreas, Anna; Resch, Leonhard; Binser, Martin J; Costa, Anna; Giourges, Elena; Neudecker, Eva; Wolf, Christiane; Scheuer, Sandra; Ising, Marcus; von Klitzing, Kai

2015-06-10

Effective interventions for maltreated children are impeded by gaps in our knowledge of the etiopathogenic mechanisms leading from maltreatment to mental disorders. Although some studies have already identified individual risk factors, there is a lack of large-scale multilevel research on how psychosocial, neurobiological, and genetic factors act in concert to modulate risk of internalizing psychopathology in childhood following maltreatment. To help close this gap, we aim to delineate gender-specific pathways from maltreatment to psychological disorder/resilience. To this end, we examine the interplay of specific maltreatment characteristics and psychological, endocrine, metabolomic, and (epi-)genomic stress response patterns as well as cognitive-emotional/social processes as determinants of developmental outcome. Specifically, we will explore endocrine, metabolomic, and epigenetic mechanisms leading from maltreatment to a higher risk of depression and anxiety disorders. Four large samples amounting to a total of N = 920 children aged 4-16 years will be assessed: Two cohorts with prior internalizing psychopathology and controls will be checked for maltreatment and two cohorts with substantiated maltreatment will be checked for internalizing (and externalizing) psychopathology. We will apply a multi-source (interview, questionnaires, official records), multi-informant strategy (parents, children, teachers) to assess maltreatment characteristics (e.g., subtypes, developmental timing, chronicity) and psychopathological symptoms, supplemented with multiple measurements of risk and protective factors and cutting-edge laboratory analyses of endocrine, steroid metabolomic and epigenetic factors. As previous assessments in the two largest samples are already available, longitudinal data will be generated within the three year study period. Our results will lay the empirical foundation for (a) detection of early biopsychosocial markers, (b) development of screening measures, and (c) multisystem-oriented interventions in the wake of maltreatment.

The National Riparian Core Protocol: A riparian vegetation monitoring protocol for wadeable streams of the conterminous United States

Treesearch

David M. Merritt; Mary E. Manning; Nate Hough-Snee

2017-01-01

Riparian areas are hotspots of biological diversity that may serve as high quality habitat for fish and wildlife. The National Riparian Core Protocol (NRCP) provides tools and methods to assist natural resource professionals in sampling riparian vegetation and physical characteristics along wadeable streams. Guidance is provided for collecting basic information on...

Evaluation of cleaning and disinfection performance of automatic washer disinfectors machines in programs presenting different cycle times and temperatures.

PubMed

Bergo, Maria do Carmo Noronha Cominato

2006-01-01

Thermal washer-disinfectors represent a technology that brought about great advantages such as, establishment of protocols, standard operating procedures, reduction in occupational risk of a biological and environmental nature. The efficacy of the cleaning and disinfection obtained by automatic washer disinfectors machines in running programs with different times and temperatures determined by the different official agencies was validated according to recommendations from ISO Standards 15883-1/1999 and HTM2030 (NHS Estates, 1997) for the determining of the Minimum Lethality and DAL both theoretically and through the use with thermocouples. In order to determine the cleaning efficacy, the Soil Test, Biotrace Pro-tect and the Protein Test Kit were used. The procedure to verify the CFU count of viable microorganisms was performed before and after the thermal disinfection. This article shows that the results are in compliance with the ISO and HTM Standards. The validation steps confirmed the high efficacy level of the Medical Washer-Disinfectors. This protocol enabled the evaluation of the procedure based on evidence supported by scientific research, aiming at the support of the Supply Center multi-professional personnel with information and the possibility of developing further research.

A study of zero tolerance policies in schools: a multi-integrated systems approach to improve outcomes for adolescents.

PubMed

Teske, Steven C

2011-05-01

School officials throughout the United States have adopted zero tolerance policies to address student discipline, resulting in an increase in out-of-school suspensions and expulsions. The introduction of police on school campuses also increased the referral of students to the juvenile courts. Although school personnel generally view zero tolerance policies as a constructive measure, this approach denies recent research on adolescent brain development that mischief is a foreseeable derivative of adolescence. A case study method examined one juvenile court's innovative multi-integrated systems approach related to the adverse trends associated with zero tolerance policies. A multi-disciplinary protocol resulted in more effective youth assessments that reduced out-of-school suspensions and school referrals; increased graduation rates by 20%; and decreased delinquent felony rates by nearly 50%. The resulting protocol changed how the system responds to disruptive students by significantly reducing out-of-school suspensions and school referrals, and putting into place alternatives as well as providing community resources to address the underlying causes of the behavior. A multi-systems approach that targets the reasons for disruptive behavior improves student educational and behavioral outcomes. © 2011 Wiley Periodicals, Inc.

Establishing a successful coronary CT angiography program in the emergency department: official writing of the Fellow and Resident Leaders of the Society of Cardiovascular Computed Tomography (FiRST).

PubMed

Maroules, Christopher D; Blaha, Michael J; El-Haddad, Mohamed A; Ferencik, Maros; Cury, Ricardo C

2013-01-01

Coronary CT angiography is an effective, evidence-based strategy for evaluating acute chest pain in the emergency department for patients at low-to-intermediate risk of acute coronary syndrome. Recent multicenter trials have reported that coronary CT angiography is safe, reduces time to diagnosis, facilitates discharge, and may lower overall cost compared with routine care. Herein, we provide a 10-step approach for establishing a successful coronary CT angiography program in the emergency department. The importance of strategic planning and multidisciplinary collaboration is emphasized. Patient selection and preparation guidelines for coronary CT angiography are reviewed with straightforward protocols that can be adapted and modified to clinical sites, depending on available cardiac imaging capabilities. Technical parameters and patient-specific modifications are also highlighted to maximize the likelihood of diagnostic quality examinations. Practical suggestions for quality control, process monitoring, and standardized reporting are reviewed. Finally, the role of a "triple rule-out" protocol is featured in the context of acute chest pain evaluation in the emergency department. Copyright © 2013 Society of Cardiovascular Computed Tomography. Published by Elsevier Inc. All rights reserved.

The Common Alerting Protocol (CAP) adaption in National Early Warning Alerting Systems of China

NASA Astrophysics Data System (ADS)

Li, Chao

2017-04-01

The Common Alerting Protocol (CAP) [1] is an XML-based data format for exchanging public warnings and emergencies between alerting technologies. In China, from local communities to entire nations, there was a patchwork of specialized hazard public alerting systems. And each system was often designed just for certain emergency situations and for certain communications media. Application took place in the NEWAS (National Early Warning Alerting Systems) [2]project where CAP serves as central message to integrate all kind of hazard situations, including the natural calamity, accident disaster, public health emergency , social safety etc. Officially operated on May 2015, NEWAS now has completed docking work with 14 departments including civil administration, safety supervision, forestry, land, water conservancy, earthquake, traffic, meteorology, agriculture, tourism, food and drug supervision, public security and oceanic administration. Thus, several items in CAP has been modified, redefined and extended according to the various grading standards and publishing strategies, as well as the characteristics of Chinese Geocoding. NEWAS successfully delivers information to end users through 4 levels (i.e. State, province, prefecture and county) structure and by various means. [1] CAP, http://www.oasis-emergency.org/cap [2] http://www.12379.cn/

Plant and metagenomic DNA extraction of mucilaginous seeds.

PubMed

Ramos, Simone N M; Salazar, Marcela M; Pereira, Gonçalo A G; Efraim, Priscilla

2014-01-01

The pulp surrounding the seeds of some fruits is rich in mucilage, carbohydrates, etc. Some seeds are rich in proteins and polyphenols. Fruit seeds, like cacao (Theobroma cacao) and cupuassu (Theobroma grandiflorum), are subjected to fermentation to develop flavor. During fermentation, ethanol is produced [2-6]. All of these compounds are considered as interfering substances that hinder the DNA extraction [4-8]. Protocols commonly used in the DNA extraction in samples of plant origin were used, but without success. Thus, a protocol for DNA samples under different conditions that can be used for similar samples was developed and applied with success. The protocol initially described for RNA samples by Zeng et al. [9] and with changes proposed by Provost et al. [5] was adapted for extracting DNA samples from those described. However, several modifications have been proposed:•Samples were initially washed with petroleum ether for fat phase removal.•RNAse was added to the extraction buffer, while spermidin was removed.•Additional steps of extraction with 5 M NaCl, saturated NaCl and CTAB (10%) were included and precipitation was carried out with isopropanol, followed by washing with ethanol.

Plant and metagenomic DNA extraction of mucilaginous seeds

PubMed Central

Ramos, Simone N.M.; Salazar, Marcela M.; Pereira, Gonçalo A.G.; Efraim, Priscilla

2014-01-01

The pulp surrounding the seeds of some fruits is rich in mucilage, carbohydrates, etc. Some seeds are rich in proteins and polyphenols. Fruit seeds, like cacao (Theobroma cacao) and cupuassu (Theobroma grandiflorum), are subjected to fermentation to develop flavor. During fermentation, ethanol is produced [2–6]. All of these compounds are considered as interfering substances that hinder the DNA extraction [4–8]. Protocols commonly used in the DNA extraction in samples of plant origin were used, but without success. Thus, a protocol for DNA samples under different conditions that can be used for similar samples was developed and applied with success. The protocol initially described for RNA samples by Zeng et al. [9] and with changes proposed by Provost et al. [5] was adapted for extracting DNA samples from those described. However, several modifications have been proposed:•Samples were initially washed with petroleum ether for fat phase removal.•RNAse was added to the extraction buffer, while spermidin was removed.•Additional steps of extraction with 5 M NaCl, saturated NaCl and CTAB (10%) were included and precipitation was carried out with isopropanol, followed by washing with ethanol. PMID:26150956

Asbestos Analysis: What School Officials Should Know.

ERIC Educational Resources Information Center

Harris, Bonnie Lee

1984-01-01

Transmission electron microscopy and scanning electron microscopy are used to detect asbestos by analyzing filters from air tests. The modes of operation and types of samples examined by each are explained. Circumstances that a school board should consider when deciding whether to use these methods are discussed. (MLF)

Prospective Analyses of Childhood Factors and Antisocial Behavior for Students with High-Incidence Disabilities

ERIC Educational Resources Information Center

Chen, Chin-Chih; Symons, Frank J.; Reynolds, Arthur J.

2011-01-01

This prospective longitudinal study investigated the association between childhood factors (individual, family, and school characteristics) and later antisocial behavior (official juvenile delinquency and adult crime) for students identified with high-incidence disabilities (i.e., learning disabilities, emotional disturbance). The sample consisted…

TECHNICAL MANUAL: A SURVEY OF EQUIPMENT AND METHODS FOR PARTICULATE SAMPLING IN INDUSTRIAL PROCESS STREAMS

EPA Science Inventory

The manual lists and describes the instruments and techniques that are available for measuring the concentration or size distribution of particles suspended in process streams. The standard, official, well established methods are described as well as some experimental methods and...

GY SAMPLING THEORY IN ENVIRONMENTAL STUDIES 1: ASSESSING SOIL SPLITTING PROTOCOLS

EPA Science Inventory

Five soil sample splitting methods (riffle splitting, paper cone riffle splitting, fractional shoveling, coning and quartering, and grab sampling) were evaluated with synthetic samples to verify Pierre Gy sampling theory expectations. Individually prepared samples consisting of l...

Rapid whole-brain resting-state fMRI at 3 T: Efficiency-optimized three-dimensional EPI versus repetition time-matched simultaneous-multi-slice EPI.

PubMed

Stirnberg, Rüdiger; Huijbers, Willem; Brenner, Daniel; Poser, Benedikt A; Breteler, Monique; Stöcker, Tony

2017-12-01

State-of-the-art simultaneous-multi-slice (SMS-)EPI and 3D-EPI share several properties that benefit functional MRI acquisition. Both sequences employ equivalent parallel imaging undersampling with controlled aliasing to achieve high temporal sampling rates. As a volumetric imaging sequence, 3D-EPI offers additional means of acceleration complementary to 2D-CAIPIRINHA sampling, such as fast water excitation and elliptical sampling. We performed an application-oriented comparison between a tailored, six-fold CAIPIRINHA-accelerated 3D-EPI protocol at 530 ms temporal and 2.4 mm isotropic spatial resolution and an SMS-EPI protocol with identical spatial and temporal resolution for whole-brain resting-state fMRI at 3 T. The latter required eight-fold slice acceleration to compensate for the lack of elliptical sampling and fast water excitation. Both sequences used vendor-supplied on-line image reconstruction. We acquired test/retest resting-state fMRI scans in ten volunteers, with simultaneous acquisition of cardiac and respiration data, subsequently used for optional physiological noise removal (nuisance regression). We found that the 3D-EPI protocol has significantly increased temporal signal-to-noise ratio throughout the brain as compared to the SMS-EPI protocol, especially when employing motion and nuisance regression. Both sequence types reliably identified known functional networks with stronger functional connectivity values for the 3D-EPI protocol. We conclude that the more time-efficient 3D-EPI primarily benefits from reduced parallel imaging noise due to a higher, actual k-space sampling density compared to SMS-EPI. The resultant BOLD sensitivity increase makes 3D-EPI a valuable alternative to SMS-EPI for whole-brain fMRI at 3 T, with voxel sizes well below 3 mm isotropic and sampling rates high enough to separate dominant cardiac signals from BOLD signals in the frequency domain. Copyright © 2017 Elsevier Inc. All rights reserved.

Thermal/Optical Methods for Elemental Carbon Quantification in Soils and Urban Dusts: Equivalence of Different Analysis Protocols

PubMed Central

Han, Yongming; Chen, Antony; Cao, Junji; Fung, Kochy; Ho, Fai; Yan, Beizhan; Zhan, Changlin; Liu, Suixin; Wei, Chong; An, Zhisheng

2013-01-01

Quantifying elemental carbon (EC) content in geological samples is challenging due to interferences of crustal, salt, and organic material. Thermal/optical analysis, combined with acid pretreatment, represents a feasible approach. However, the consistency of various thermal/optical analysis protocols for this type of samples has never been examined. In this study, urban street dust and soil samples from Baoji, China were pretreated with acids and analyzed with four thermal/optical protocols to investigate how analytical conditions and optical correction affect EC measurement. The EC values measured with reflectance correction (ECR) were found always higher and less sensitive to temperature program than the EC values measured with transmittance correction (ECT). A high-temperature method with extended heating times (STN120) showed the highest ECT/ECR ratio (0.86) while a low-temperature protocol (IMPROVE-550), with heating time adjusted for sample loading, showed the lowest (0.53). STN ECT was higher than IMPROVE ECT, in contrast to results from aerosol samples. A higher peak inert-mode temperature and extended heating times can elevate ECT/ECR ratios for pretreated geological samples by promoting pyrolyzed organic carbon (PyOC) removal over EC under trace levels of oxygen. Considering that PyOC within filter increases ECR while decreases ECT from the actual EC levels, simultaneous ECR and ECT measurements would constrain the range of EC loading and provide information on method performance. Further testing with standard reference materials of common environmental matrices supports the findings. Char and soot fractions of EC can be further separated using the IMPROVE protocol. The char/soot ratio was lower in street dusts (2.2 on average) than in soils (5.2 on average), most likely reflecting motor vehicle emissions. The soot concentrations agreed with EC from CTO-375, a pure thermal method. PMID:24358286

Brucella abortus surveillance of cattle in Fiji, Papua New Guinea, Vanuatu, the Solomon Islands and a case for active disease surveillance as a training tool.

PubMed

Tukana, Andrew; Hedlefs, Robert; Gummow, Bruce

2016-10-01

There have been no surveys of the cattle population for brucellosis in the Pacific Island Countries and Territories (PICTs) for more than 15 years. This study used disease surveillance as a capacity building training tool and to examine some of the constraints that impede surveillance in PICTs. The study also developed and implemented a series of surveys for detecting antibodies to B. abortus in cattle in Fiji, Papua New Guinea, Vanuatu and the Solomon Islands contributing to OIE requirements. The findings indicated lack of funds, lack of technical capacity, shortage of veterinarians, high turnover of in-country officials and lack of awareness on the impacts of animal diseases on public health that were constraining active disease surveillance. During the development and implementation of the surveys, constraints highlighted were outdated census data on farm numbers and cattle population, lack of funds for mobilisation of officials to carry out the surveys, lack of equipment for collecting and processing samples, lack of staff knowledge on blood sampling, geographical difficulties and security in accessing farms. Some of the reasons why these were constraints are discussed with likely solutions presented. The detection surveys had the objectives of building capacity for the country officials and demonstrating freedom from brucellosis in cattle for PNG, Vanuatu and the Solomon Islands. PNG, Vanuatu and the Solomon Islands all demonstrated freedom from bovine brucellosis in the areas surveyed using the indirect ELISA test. Fiji had an outbreak of brucellosis, and the objective was to determine its distribution and prevalence on untested farms. The Muaniweni district surveyed during the training had a 95 % confidence interval for true prevalence between 1.66 and 5.45 %. The study showed that active disease surveillance could be used as a tool for training officials thus, improves surveillance capacity in resource poor countries.

Resource allocation in public health practice: a national survey of local public health officials.

PubMed

Baum, Nancy M; DesRoches, Catherine; Campbell, Eric G; Goold, Susan Dorr

2011-01-01

The purpose of this study was to gain an empirical understanding of the types of allocation decisions local health officials (LHOs) make and the factors that influence those allocation decisions. We conducted a national survey of LHOs in the United States in 2008 to 2009. The sample was stratified by the size of the population served by the department. We merged our data with data from the 2008 National Association of County and City Health Officials Profile survey. Descriptive statistics were generated using weighted data. Our final sample size was 608 respondents, with an average of 10 years experience. The LHOs reported little shifting of resources among population groups but greater capacity to redirect staffing time. Less than half of LHOs reported using economic analyses or conducting needs assessments when setting priorities. Having sole provider status in a community strongly influenced LHOs' allocation decisions. In addition, the effectiveness of activities, previous budget allocations, and input from boards of health were influential factors in allocation decisions. Public expectations were moderately to very influential, but direct public input had a low impact on allocation decisions. Survey findings provide a clearer understanding of how LHOs fulfill their obligations as stewards of public health resources and ensure effective activities and access to needed services. It may be useful to assess the value of more structured allocation methods (eg, decision frameworks) in the allocation process. Expanding opportunities for public engagement in priority setting may also be valuable for difficult allocation decisions.

Improvement of AOAC Official Method 984.27 for the determination of nine nutritional elements in food products by Inductively coupled plasma-atomic emission spectroscopy after microwave digestion: single-laboratory validation and ring trial.

PubMed

Poitevin, Eric; Nicolas, Marine; Graveleau, Laetitia; Richoz, Janique; Andrey, Daniel; Monard, Florence

2009-01-01

A single-laboratory validation (SLV) and a ring trial (RT) were undertaken to determine nine nutritional elements in food products by inductively coupled plasma-atomic emission spectroscopy in order to improve and update AOAC Official Method 984.27. The improvements involved optimized microwave digestion, selected analytical lines, internal standardization, and ion buffering. Simultaneous determination of nine elements (calcium, copper, iron, potassium, magnesium, manganese, sodium, phosphorus, and zinc) was made in food products. Sample digestion was performed through wet digestion of food samples by microwave technology with either closed or open vessel systems. Validation was performed to characterize the method for selectivity, sensitivity, linearity, accuracy, precision, recovery, ruggedness, and uncertainty. The robustness and efficiency of this method was proved through a successful internal RT using experienced food industry laboratories. Performance characteristics are reported for 13 certified and in-house reference materials, populating the AOAC triangle food sectors, which fulfilled AOAC criteria and recommendations for accuracy (trueness, recovery, and z-scores) and precision (repeatability and reproducibility RSD and HorRat values) regarding SLV and RT. This multielemental method is cost-efficient, time-saving, accurate, and fit-for-purpose according to ISO 17025 Norm and AOAC acceptability criteria, and is proposed as an improved version of AOAC Official Method 984.27 for fortified food products, including infant formula.

Field Geologic Observation and Sample Collection Strategies for Planetary Surface Exploration: Insights from the 2010 Desert RATS Geologist Crewmembers

NASA Technical Reports Server (NTRS)

Hurtado, Jose M., Jr.; Young, Kelsey; Bleacher, Jacob E.; Garry, W. Brent; Rice, James W., Jr.

2012-01-01

Observation is the primary role of all field geologists, and geologic observations put into an evolving conceptual context will be the most important data stream that will be relayed to Earth during a planetary exploration mission. Sample collection is also an important planetary field activity, and its success is closely tied to the quality of contextual observations. To test protocols for doing effective planetary geologic field- work, the Desert RATS(Research and Technology Studies) project deployed two prototype rovers for two weeks of simulated exploratory traverses in the San Francisco volcanic field of northern Arizona. The authors of this paper represent the geologist crew members who participated in the 2010 field test.We document the procedures adopted for Desert RATS 2010 and report on our experiences regarding these protocols. Careful consideration must be made of various issues that impact the interplay between field geologic observations and sample collection, including time management; strategies relatedtoduplicationofsamplesandobservations;logisticalconstraintson the volume and mass of samples and the volume/transfer of data collected; and paradigms for evaluation of mission success. We find that the 2010 field protocols brought to light important aspects of each of these issues, and we recommend best practices and modifications to training and operational protocols to address them. Underlying our recommendations is the recognition that the capacity of the crew to flexibly execute their activities is paramount. Careful design of mission parameters, especially field geologic protocols, is critical for enabling the crews to successfully meet their science objectives.

Tools and Technologies Needed for Conducting Planetary Field Geology While On EVA: Insights from the 2010 Desert RATS Geologist Crewmembers

NASA Technical Reports Server (NTRS)

Young, Kelsey; Hurtado, Jose M., Jr.; Bleacher, Jacob E.; Garry, W. Brent; Bleisath, Scott; Buffington, Jesse; Rice, James W., Jr.

2011-01-01

Observation is the primary role of all field geologists, and geologic observations put into an evolving conceptual context will be the most important data stream that will be relayed to Earth during a planetary exploration mission. Sample collection is also an important planetary field activity, and its success is closely tied to the quality of contextual observations. To test protocols for doing effective planetary geologic fieldwork, the Desert RATS (Research and Technology Studies) project deployed two prototype rovers for two weeks of simulated exploratory traverses in the San Francisco volcanic field of northern Arizona. The authors of this paper represent the geologist crewmembers who participated in the 2010 field test. We document the procedures adopted for Desert RATS 2010 and report on our experiences regarding these protocols. Careful consideration must be made of various issues that impact the interplay between field geologic observations and sample collection, including time management; strategies related to duplication of samples and observations; logistical constraints on the volume and mass of samples and the volume/transfer of data collected; and paradigms for evaluation of mission success. We find that the 2010 field protocols brought to light important aspects of each of these issues, and we recommend best practices and modifications to training and operational protocols to address them. Underlying our recommendations is the recognition that the capacity of the crew to "flexibly execute" their activities is paramount. Careful design of mission parameters, especially field geologic protocols, is critical for enabling the crews to successfully meet their science objectives.

Identification of forensic samples by using an infrared-based automatic DNA sequencer.

PubMed

Ricci, Ugo; Sani, Ilaria; Klintschar, Michael; Cerri, Nicoletta; De Ferrari, Francesco; Giovannucci Uzielli, Maria Luisa

2003-06-01

We have recently introduced a new protocol for analyzing all core loci of the Federal Bureau of Investigation's (FBI) Combined DNA Index System (CODIS) with an infrared (IR) automatic DNA sequencer (LI-COR 4200). The amplicons were labeled with forward oligonucleotide primers, covalently linked to a new infrared fluorescent molecule (IRDye 800). The alleles were displayed as familiar autoradiogram-like images with real-time detection. This protocol was employed for paternity testing, population studies, and identification of degraded forensic samples. We extensively analyzed some simulated forensic samples and mixed stains (blood, semen, saliva, bones, and fixed archival embedded tissues), comparing the results with donor samples. Sensitivity studies were also performed for the four multiplex systems. Our results show the efficiency, reliability, and accuracy of the IR system for the analysis of forensic samples. We also compared the efficiency of the multiplex protocol with ultraviolet (UV) technology. Paternity tests, undegraded DNA samples, and real forensic samples were analyzed with this approach based on IR technology and with UV-based automatic sequencers in combination with commercially-available kits. The comparability of the results with the widespread UV methods suggests that it is possible to exchange data between laboratories using the same core group of markers but different primer sets and detection methods.

Establishment and optimization of NMR-based cell metabonomics study protocols for neonatal Sprague-Dawley rat cardiomyocytes.

PubMed

Zhang, Ming; Sun, Bo; Zhang, Qi; Gao, Rong; Liu, Qiao; Dong, Fangting; Fang, Haiqin; Peng, Shuangqing; Li, Famei; Yan, Xianzhong

2017-01-15

A quenching, harvesting, and extraction protocol was optimized for cardiomyocytes NMR metabonomics analysis in this study. Trypsin treatment and direct scraping cells in acetonitrile were compared for sample harvesting. The results showed trypsin treatment cause normalized concentration increasing of phosphocholine and metabolites leakage, since the trypsin-induced membrane broken and long term harvesting procedures. Then the intracellular metabolite extraction efficiency of methanol and acetonitrile were compared. As a result, washing twice with phosphate buffer, direct scraping cells and extracting with acetonitrile were chosen to prepare cardiomyocytes extracts samples for metabonomics studies. This optimized protocol is rapid, effective, and exhibits greater metabolite retention. Copyright © 2016 Elsevier Inc. All rights reserved.

Utility of a fecal real-time PCR protocol for detection of Mycobacterium bovis infection in African buffalo (Syncerus caffer).

PubMed

Roug, Annette; Geoghegan, Claire; Wellington, Elizabeth; Miller, Woutrina A; Travis, Emma; Porter, David; Cooper, David; Clifford, Deana L; Mazet, Jonna A K; Parsons, Sven

2014-01-01

A real-time PCR protocol for detecting Mycobacterium bovis in feces was evaluated in bovine tuberculosis-infected African buffalo (Syncerus caffer). Fecal samples spiked with 1.42 × 10(3) cells of M. bovis culture/g and Bacille Calmette-Guérin standards with 1.58 × 10(1) genome copies/well were positive by real-time PCR but all field samples were negative.

Use of Compound-Specific Stable Isotope Analysis to Distinguish Between Vapor Intrusion and Indoor Sources of VOCs - CSIA Protocol for Vapor Intrusion Investigations

DTIC Science & Technology

2014-07-01

Analyzer TCE Trichloroethene USEPA U.S. Environmental Protection Agency V- PDB Vienna - Pee Dee Belemnite V-SMOW Vienna – Standard Mean Ocean Water ... PDB ) for carbon, Standard Mean Ocean Chloride (SMOC) for chlorine, and Vienna-Standard Mean Ocean Water (V-SMOW) for hydrogen. CSIA Protocol for...7 3.3 INDOOR AIR SAMPLING LOCATIONS ............................................................ 8 3.4 COLLECTION OF WATER SAMPLES

An Investigation of Community Attitudes Toward Blast Noise: Complaint Survey Protocol

DTIC Science & Technology

2010-10-11

increase complaints (Hume et al., 2003a). If an individual is already stressed by other non-noise factors, the source noise many be more annoying than...protocol (lab staffing, sampling and locating records, callback schedules) focused on completing the data collection for any given noise event within...relationship (e.g., increased feelings of importance of the installation tend to be associated with decreased annoyance). Due to the limited sample size only

Laboratory procedures to generate viral metagenomes.

PubMed

Thurber, Rebecca V; Haynes, Matthew; Breitbart, Mya; Wegley, Linda; Rohwer, Forest

2009-01-01

This collection of laboratory protocols describes the steps to collect viruses from various samples with the specific aim of generating viral metagenome sequence libraries (viromes). Viral metagenomics, the study of uncultured viral nucleic acid sequences from different biomes, relies on several concentration, purification, extraction, sequencing and heuristic bioinformatic methods. No single technique can provide an all-inclusive approach, and therefore the protocols presented here will be discussed in terms of hypothetical projects. However, care must be taken to individualize each step depending on the source and type of viral-particles. This protocol is a description of the processes we have successfully used to: (i) concentrate viral particles from various types of samples, (ii) eliminate contaminating cells and free nucleic acids and (iii) extract, amplify and purify viral nucleic acids. Overall, a sample can be processed to isolate viral nucleic acids suitable for high-throughput sequencing in approximately 1 week.

Survival of emerald ash borer in chips

Treesearch

Deborah G. McCullough; Therese M. Poland; David L. Cappaert

2005-01-01

The ability of emerald ash borer (EAB), Agrilus planipennis Fairmaire, to survive following chipping or grinding of infested ash trees remains a critical question for regulatory officials. In October 2002, we felled eight infested ash trees and sampled sections of the trunk and large branches from each tree to estimate EAB density.

"Interactive Whole Class Teaching" in the National Literacy Strategy.

ERIC Educational Resources Information Center

Hardman, Frank; Smith, Fay; Wall, Kate

2003-01-01

Presents findings of extensive investigation (n=70) into interactive and discourse styles of a nationally representative sample of primary teachers. Explores impact of official endorsement of interactive whole class teaching in the teaching of England's National Literacy Strategy to examine whether it is promoting pupils' higher interaction and…

Poverty among Elderly in India

ERIC Educational Resources Information Center

Srivastava, Akanksha; Mohanty, Sanjay K.

2012-01-01

Using consumption expenditure data of the National Sample Survey 2004-2005, this paper estimates the size of elderly poor and tests the hypotheses that elderly households are not economically better-off compared to non-elderly households in India. Poverty estimates are derived under three scenarios--by applying the official cut-off point of the…

Your Official Job-Application Checklist

ERIC Educational Resources Information Center

Perlmutter, David D.

2012-01-01

For the novice, the logistical challenges of an academic job search can be exasperating, especially when dozens of applications are involved. Getting things right (providing the correct materials, from CV to sample syllabi, in the style and form most sought by a particular search committee) and submitting the application on time (via sometimes…

Disregarding Graduated Treatment: Why Transfer Aggravates Recidivism

ERIC Educational Resources Information Center

Johnson, Kristin; Lanza-Kaduce, Lonn; Woolard, Jennifer

2011-01-01

These data merge correctional histories with official state and courthouse information for a sample of teenage offenders, some of whom had been transferred to the adult system. Previous research indicated that transfer aggravates recidivism after the age of 18. The correctional data allow the examination of the relationship between sanctions and…

7 CFR 75.48 - Identification number.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 7 Agriculture 3 2014-01-01 2014-01-01 false Identification number. 75.48 Section 75.48 Agriculture... number. The Director may require the use of official identification numbers in connection with seed certificated or sampled under the Act. When identification numbers are required, they shall be specified by the...

7 CFR 75.48 - Identification number.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 7 Agriculture 3 2013-01-01 2013-01-01 false Identification number. 75.48 Section 75.48 Agriculture... number. The Director may require the use of official identification numbers in connection with seed certificated or sampled under the Act. When identification numbers are required, they shall be specified by the...

7 CFR 75.48 - Identification number.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 7 Agriculture 3 2010-01-01 2010-01-01 false Identification number. 75.48 Section 75.48 Agriculture... number. The Director may require the use of official identification numbers in connection with seed certificated or sampled under the Act. When identification numbers are required, they shall be specified by the...

7 CFR 75.48 - Identification number.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 7 Agriculture 3 2012-01-01 2012-01-01 false Identification number. 75.48 Section 75.48 Agriculture... number. The Director may require the use of official identification numbers in connection with seed certificated or sampled under the Act. When identification numbers are required, they shall be specified by the...

7 CFR 75.48 - Identification number.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 7 Agriculture 3 2011-01-01 2011-01-01 false Identification number. 75.48 Section 75.48 Agriculture... number. The Director may require the use of official identification numbers in connection with seed certificated or sampled under the Act. When identification numbers are required, they shall be specified by the...

50 CFR 216.74 - Cooperation with Federal officials.

Code of Federal Regulations, 2011 CFR

2011-10-01

... research on the Pribilof Islands who may need assistance in recording tag or other data and collecting tissue or other fur seal samples for research purposes. In addition, Pribilovians who take fur seals for... Pribilof Islands who are responsible for compiling the following information on a daily basis: (a) The...

50 CFR 216.74 - Cooperation with Federal officials.

Code of Federal Regulations, 2010 CFR

2010-10-01

... research on the Pribilof Islands who may need assistance in recording tag or other data and collecting tissue or other fur seal samples for research purposes. In addition, Pribilovians who take fur seals for... Pribilof Islands who are responsible for compiling the following information on a daily basis: (a) The...

Estuarine water quality in parks of the Northeast Coastal and Barrier Network: Development and early implementation of vital signs estuarine nutrient-enrichment monitoring, 2003-06

USGS Publications Warehouse

Kopp, Blaine S.; Nielsen, Martha; Glisic, Dejan; Neckles, Hilary A.

2009-01-01

This report documents results of pilot tests of a protocol for monitoring estuarine nutrient enrichment for the Vital Signs Monitoring Program of the National Park Service Northeast Coastal and Barrier Network. Data collected from four parks during protocol development in 2003-06 are presented: Gateway National Recreation Area, Colonial National Historic Park, Fire Island National Seashore, and Assateague Island National Seashore. The monitoring approach incorporates several spatial and temporal designs to address questions at a hierarchy of scales. Indicators of estuarine response to nutrient enrichment were sampled using a probability design within park estuaries during a late-summer index period. Monitoring variables consisted of dissolved-oxygen concentration, chlorophyll a concentration, water temperature, salinity, attenuation of downwelling photosynthetically available radiation (PAR), and turbidity. The statistical sampling design allowed the condition of unsampled locations to be inferred from the distribution of data from a set of randomly positioned "probability" stations. A subset of sampling stations was sampled repeatedly during the index period, and stations were not rerandomized in subsequent years. These "trend stations" allowed us to examine temporal variability within the index period, and to improve the sensitivity of the monitoring protocol to detecting change through time. Additionally, one index site in each park was equipped for continuous monitoring throughout the index period. Thus, the protocol includes elements of probabilistic and targeted spatial sampling, and the temporal intensity ranges from snapshot assessments to continuous monitoring.

[Care-Dependency in Parkinson's Disease: More Frequent than Assumed?].

PubMed

Riedel, O

2015-06-01

Parkinson's disease (PD) increases the risk of care-dependency (CDP). While motor functions worsen continuously, the assignment of patients to CDP occurs categorically. It is unknown how many patients are already sufficiently severely impaired to be categorised as CDP yet do not have an officially acknowledged level of CDP. A random sample of 1,449 PD outpatients was clinically characterised by office-based neurologists, including impairments of activities of daily living (ADL with the Unified Parkinson's Disease Rating scale (UPDRS subscale II) as well as regarding the presence of dementia according to DSM-IV criteria and the Mini-Mental State Exam (MMSE). Depression was screened for with the Montgomery-Asberg Depression Rating Scale (MADRS). For each patient the officially acknowledged level of CDP was documented; for patients without official CDP level, the clinician appraised whether the patient was care-dependent anyhow. 266 patients (18.3%) were officially acknowledged as care-dependent, while n=121 patients (8.5%) were not, yet were appraised to be care-dependent according to the clinician. Compared to non-CDP patients, they differed on every measure considered. Compared to patients with an official CDP, their PD duration was significantly shorter (6.0 vs. 8.0 years, p<0.01) and they were less severely impaired in ADL (13.3 vs. 15.5, p<0.01). They did not differ regarding the rates of dementia (52.9 vs. 44.9%, p=0.203) or depression according to the MADRS (13.1 vs. 13.1, p=0.989). ADL impairments are the most important predictor for CDP while dementia and depression are not considered despite the impairments that are additionally caused by them. © Georg Thieme Verlag KG Stuttgart · New York.

Planetary protection on international waters: An onboard protocol for capsule retrieval and biosafety control in sample return mission

NASA Astrophysics Data System (ADS)

Takano, Yoshinori; Yano, Hajime; Sekine, Yasuhito; Funase, Ryu; Takai, Ken

2014-04-01

Planetary protection has been recognized as one of the most important issues in sample return missions that may host certain living forms and biotic signatures in a returned sample. This paper proposes an initiative of sample capsule retrieval and onboard biosafety protocol in international waters for future biological and organic constituent missions to bring samples from possible habitable bodies in the solar system. We suggest the advantages of international waters being outside of national jurisdiction and active regions of human and traffic affairs on the condition that we accept the Outer Space Treaty. The scheme of onboard biological quarantine definitely reduces the potential risk of back-contamination of extraterrestrial materials to the Earth.

Provable classically intractable sampling with measurement-based computation in constant time

NASA Astrophysics Data System (ADS)

Sanders, Stephen; Miller, Jacob; Miyake, Akimasa

We present a constant-time measurement-based quantum computation (MQC) protocol to perform a classically intractable sampling problem. We sample from the output probability distribution of a subclass of the instantaneous quantum polynomial time circuits introduced by Bremner, Montanaro and Shepherd. In contrast with the usual circuit model, our MQC implementation includes additional randomness due to byproduct operators associated with the computation. Despite this additional randomness we show that our sampling task cannot be efficiently simulated by a classical computer. We extend previous results to verify the quantum supremacy of our sampling protocol efficiently using only single-qubit Pauli measurements. Center for Quantum Information and Control, Department of Physics and Astronomy, University of New Mexico, Albuquerque, NM 87131, USA.

A rapid and efficient SDS-based RNA isolation protocol from different tissues of coffee.

PubMed

Huded, Arun Kumar C; Jingade, Pavankumar; Mishra, Manoj Kumar

2018-03-01

Isolation of high-quality RNA from coffee is challenging because of high level of polysaccharides, polyphenols and other secondary metabolites. In the present study, a rapid and efficient RNA extraction protocol from different tissues of coffee was optimized. Sufficiently high quality and quantity (225.6-454.8 µg/g) of RNA was obtained by using the optimized protocol. The presence of two distinct bands of 28S rRNA and 18S rRNA in agarose gel proved the intactness of the RNA samples. The average spectrophotometric values of the isolated RNA ranged from 1.96 to 2.02 ( A 260/280 ) and 1.95 to 2.14 ( A 260/230 ), indicating the high quality of RNA devoid of polyphenols, polysaccharides and protein contamination. In the optimized protocol, addition of PVPP to the extraction buffer and a brief incubation of samples at 65 °C and subsequent purification with potassium acetate resulted in good-quality RNA isolation. The suitability of RNA for downstream processing was confirmed by PCR amplification with cytochrome c oxidase gene-specific primers. The amplification of a single 392 bp fragment using cDNA and 1.5 kb fragment using genomic DNA samples confirmed the absence of DNA contamination. The present protocol is rapid and yielded good quality and quantity of RNA suitable for functional genomics studies.

On-farm comparisons of different cleaning protocols in broiler houses.

PubMed

Luyckx, K Y; Van Weyenberg, S; Dewulf, J; Herman, L; Zoons, J; Vervaet, E; Heyndrickx, M; De Reu, K

2015-08-01

The present study evaluated the effectiveness of 4 cleaning protocols designed to reduce the bacteriological infection pressure on broiler farms and prevent food-borne zoonoses. Additionally, difficult to clean locations and possible sources of infection were identified. Cleaning and disinfection rounds were evaluated in 12 broiler houses on 5 farms through microbiological analyses and adenosine triphosphate hygiene monitoring. Samples were taken at 3 different times: before cleaning, after cleaning, and after disinfection. At each sampling time, swabs were taken from various locations for enumeration of the total aerobic flora and Enterococcus species pluralis ( SPP:). In addition, before cleaning and after disinfection, testing for Escherichia coli and Salmonella was carried out. Finally, adenosine triphosphate swabs and agar contact plates for total aerobic flora counts were taken after cleaning and disinfection, respectively. Total aerobic flora and Enterococcus spp. counts on the swab samples showed that cleaning protocols which were preceded by an overnight soaking with water caused a higher bacterial reduction compared to protocols without a preceding soaking step. Moreover, soaking of broiler houses leads to less water consumption and reduced working time during high pressure cleaning. No differences were found between protocols using cold or warm water during cleaning. Drinking cups, drain holes, and floor cracks were identified as critical locations for cleaning and disinfection in broiler houses. © 2015 Poultry Science Association Inc.

Collecting and Storing Blood Samples From Patients With Cancer

ClinicalTrials.gov

2011-12-08

Brain and Central Nervous System Tumors; Chronic Myeloproliferative Disorders; Leukemia; Lymphoma; Lymphoproliferative Disorder; Multiple Myeloma and Plasma Cell Neoplasm; Myelodysplastic Syndromes; Myelodysplastic/Myeloproliferative Neoplasms; Nonmalignant Neoplasm; Unspecified Adult Solid Tumor, Protocol Specific; Unspecified Childhood Solid Tumor, Protocol Specific

A universal TaqMan-based RT-PCR protocol for cost-efficient detection of small noncoding RNA.

PubMed

Jung, Ulrike; Jiang, Xiaoou; Kaufmann, Stefan H E; Patzel, Volker

2013-12-01

Several methods for the detection of RNA have been developed over time. For small RNA detection, a stem-loop reverse primer-based protocol relying on TaqMan RT-PCR has been described. This protocol requires an individual specific TaqMan probe for each target RNA and, hence, is highly cost-intensive for experiments with small sample sizes or large numbers of different samples. We describe a universal TaqMan-based probe protocol which can be used to detect any target sequence and demonstrate its applicability for the detection of endogenous as well as artificial eukaryotic and bacterial small RNAs. While the specific and the universal probe-based protocol showed the same sensitivity, the absolute sensitivity of detection was found to be more than 100-fold lower for both than previously reported. In subsequent experiments, we found previously unknown limitations intrinsic to the method affecting its feasibility in determination of mature template RISC incorporation as well as in multiplexing. Both protocols were equally specific in discriminating between correct and incorrect small RNA targets or between mature miRNA and its unprocessed RNA precursor, indicating the stem-loop RT-primer, but not the TaqMan probe, triggers target specificity. The presented universal TaqMan-based RT-PCR protocol represents a cost-efficient method for the detection of small RNAs.

A simplified and cost-effective enrichment protocol for the isolation of Campylobacter spp. from retail broiler meat without microaerobic incubation

PubMed Central

2011-01-01

Background To simplify the methodology for the isolation of Campylobacter spp. from retail broiler meat, we evaluated 108 samples (breasts and thighs) using an unpaired sample design. The enrichment broths were incubated under aerobic conditions (subsamples A) and for comparison under microaerobic conditions (subsamples M) as recommended by current reference protocols. Sensors were used to measure the dissolved oxygen (DO) in the broth and the percentage of oxygen (O2) in the head space of the bags used for enrichment. Campylobacter isolates were identified with multiplex PCR assays and typed using pulsed-field gel electrophoresis (PFGE). Ribosomal intergenic spacer analyses (RISA) and denaturing gradient gel electrophoresis (DGGE) were used to study the bacterial communities of subsamples M and A after 48 h enrichment. Results The number of Campylobacter positive subsamples were similar for A and M when all samples were combined (P = 0.81) and when samples were analyzed by product (breast: P = 0.75; thigh: P = 1.00). Oxygen sensors showed that DO values in the broth were around 6 ppm and O2 values in the head space were 14-16% throughout incubation. PFGE demonstrated high genomic similarity of isolates in the majority of the samples in which isolates were obtained from subsamples A and M. RISA and DGGE results showed a large variability in the bacterial populations that could be attributed to sample-to-sample variations and not enrichment conditions (aerobic or microaerobic). These data also suggested that current sampling protocols are not optimized to determine the true number of Campylobacter positive samples in retail boiler meat. Conclusions Decreased DO in enrichment broths is naturally achieved. This simplified, cost-effective enrichment protocol with aerobic incubation could be incorporated into reference methods for the isolation of Campylobacter spp. from retail broiler meat. PMID:21812946

Efficiency of Adaptive Temperature-Based Replica Exchange for Sampling Large-Scale Protein Conformational Transitions.

PubMed

Zhang, Weihong; Chen, Jianhan

2013-06-11

Temperature-based replica exchange (RE) is now considered a principal technique for enhanced sampling of protein conformations. It is also recognized that existence of sharp cooperative transitions (such as protein folding/unfolding) can lead to temperature exchange bottlenecks and significantly reduce the sampling efficiency. Here, we revisit two adaptive temperature-based RE protocols, namely, exchange equalization (EE) and current maximization (CM), that were previously examined using atomistic simulations (Lee and Olson, J. Chem. Physics2011, 134, 24111). Both protocols aim to overcome exchange bottlenecks by adaptively adjusting the simulation temperatures, either to achieve uniform exchange rates (in EE) or to maximize temperature diffusion (CM). By designing a realistic yet computationally tractable coarse-grained protein model, one can sample many reversible folding/unfolding transitions using conventional constant temperature molecular dynamics (MD), standard REMD, EE-REMD, and CM-REMD. This allows rigorous evaluation of the sampling efficiency, by directly comparing the rates of folding/unfolding transitions and convergence of various thermodynamic properties of interest. The results demonstrate that both EE and CM can indeed enhance temperature diffusion compared to standard RE, by ∼3- and over 10-fold, respectively. Surprisingly, the rates of reversible folding/unfolding transitions are similar in all three RE protocols. The convergence rates of several key thermodynamic properties, including the folding stability and various 1D and 2D free energy surfaces, are also similar. Therefore, the efficiency of RE protocols does not appear to be limited by temperature diffusion, but by the inherent rates of spontaneous large-scale conformational rearrangements. This is particularly true considering that virtually all RE simulations of proteins in practice involve exchange attempt frequencies (∼ps(-1)) that are several orders of magnitude faster than the slowest protein motions (∼μs(-1)). Our results also suggest that the efficiency of RE will not likely be improved by other protocols that aim to accelerate exchange or temperature diffusion. Instead, protocols with some types of guided tempering will likely be necessary to drive faster large-scale conformational transitions.

Investigation of differences between field and laboratory pH measurements of national atmospheric deposition program/national trends network precipitation samples

USGS Publications Warehouse

Latysh, N.; Gordon, J.

2004-01-01

A study was undertaken to investigate differences between laboratory and field pH measurements for precipitation samples collected from 135 weekly precipitation-monitoring sites in the National Trends Network from 12/30/1986 to 12/28/1999. Differences in pH between field and laboratory measurements occurred for 96% of samples collected during this time period. Differences between the two measurements were evaluated for precipitation samples collected before and after January 1994, when modifications to sample-handling protocol and elimination of the contaminating bucket o-ring used in sample shipment occurred. Median hydrogen-ion and pH differences between field and laboratory measurements declined from 3.9 ??eq L-1 or 0.10 pH units before the 1994 protocol change to 1.4 ??eq L-1 or 0.04 pH units after the 1994 protocol change. Hydrogen-ion differences between field and laboratory measurements had a high correlation with the sample pH determined in the field. The largest pH differences between the two measurements occurred for high-pH samples (>5.6), typical of precipitation collected in Western United States; however low- pH samples (<5.0) displayed the highest variability in hydrogen-ion differences between field and laboratory analyses. Properly screened field pH measurements are a useful alternative to laboratory pH values for trend analysis, particularly before 1994 when laboratory pH values were influenced by sample-collection equipment.

Psychopathy in women: Prediction of criminality and violence in UK and USA psychiatric patients resident in the community.

PubMed

Gray, Nicola S; Snowden, Robert J

2016-03-30

Psychopathy is an important clinical construct often used in the assessment and management of psychiatric patients and offenders. This, in part, is due to the strong association between psychopathy, crime, and particularly violent crime. However, there are few studies of these associations in women. These relationships were examined using information from two large databases. The Partnerships in Care database contains data from a sample of forensic psychiatric patients (154 women and 777 men) in the UK that were discharged from secure psychiatric units. Follow-up was via official conviction data within the next 2 years. The MacArthur study examined violence and aggression in a sample of civil psychiatric patients (367 women and 496 men) in the USA following discharge from an acute psychiatric hospital. Follow-up was via a mixture of self-report, informant report and official records. Psychopathy in both samples was measured via the PCL:SV prior to discharge. Psychopathy was a good predictor of target events for the women in both samples and for all time intervals used. No significant gender differences in the PCL:SV's predictive efficacy were found. The results provide a strong evidence-base for the use of psychopathy in women when considering future community behaviour and reoffending. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

Minerals and Trace Elements in Milk, Milk Products, Infant Formula, and Adult/Pediatric Nutritional Formula, ICP-MS Method: Collaborative Study, AOAC Final Action 2015.06, ISO/DIS 21424, IDF 243.

PubMed

Pacquette, Lawrence H; Thompson, Joseph J; Malaviole, I; Zywicki, R; Woltjes, F; Ding, Y; Mittal, A; Ikeuchi, Y; Sadipiralla, B; Kimura, S; Veltman, H; Miura, A

2018-03-01

AOAC Final Action Official MethodSM 2015.06 "Minerals and Trace Elements in Milk, Milk Products, Infant Formula and Adult/Pediatric Nutritional Formula, ICP-MS Method" was collaboratively studied. Note that "milk, milk products" has now been added to the title of the Final Action method because whole milk and several dairy ingredients were successfully incorporated into the collaborative study for the purpose of developing an International Organization for Standardization/International Dairy Federation standard (ISO/DIS 21424; in progress). The method determines sodium, magnesium, phosphorus, potassium, calcium, iron, manganese, zinc, copper, chromium, molybdenum, and selenium by inductively coupled plasma (ICP)-MS after microwave digestion. Ten laboratories participated in the study, and data from five different model ICP-MS units were represented. Thirteen products, five placebo products, and six dairy samples were tested as blind duplicates in this study, along with a standard reference material, for a total 50 samples. The overall repeatability and reproducibility for all samples met Standard Method Performance Requirements put forth by the AOAC Stakeholder Panel on Infant Formula and Adult Nutritionals, with a few exceptions. Comparisons are made to ICP-atomic emission data from a collaborative study of AOAC Official Method 2011.14 carried out concurrently on these same samples.

Modeling the Sensitivity of Field Surveys for Detection of Environmental DNA (eDNA)

PubMed Central

Schultz, Martin T.; Lance, Richard F.

2015-01-01

The environmental DNA (eDNA) method is the practice of collecting environmental samples and analyzing them for the presence of a genetic marker specific to a target species. Little is known about the sensitivity of the eDNA method. Sensitivity is the probability that the target marker will be detected if it is present in the water body. Methods and tools are needed to assess the sensitivity of sampling protocols, design eDNA surveys, and interpret survey results. In this study, the sensitivity of the eDNA method is modeled as a function of ambient target marker concentration. The model accounts for five steps of sample collection and analysis, including: 1) collection of a filtered water sample from the source; 2) extraction of DNA from the filter and isolation in a purified elution; 3) removal of aliquots from the elution for use in the polymerase chain reaction (PCR) assay; 4) PCR; and 5) genetic sequencing. The model is applicable to any target species. For demonstration purposes, the model is parameterized for bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix) assuming sampling protocols used in the Chicago Area Waterway System (CAWS). Simulation results show that eDNA surveys have a high false negative rate at low concentrations of the genetic marker. This is attributed to processing of water samples and division of the extraction elution in preparation for the PCR assay. Increases in field survey sensitivity can be achieved by increasing sample volume, sample number, and PCR replicates. Increasing sample volume yields the greatest increase in sensitivity. It is recommended that investigators estimate and communicate the sensitivity of eDNA surveys to help facilitate interpretation of eDNA survey results. In the absence of such information, it is difficult to evaluate the results of surveys in which no water samples test positive for the target marker. It is also recommended that invasive species managers articulate concentration-based sensitivity objectives for eDNA surveys. In the absence of such information, it is difficult to design appropriate sampling protocols. The model provides insights into how sampling protocols can be designed or modified to achieve these sensitivity objectives. PMID:26509674

Modeling the Sensitivity of Field Surveys for Detection of Environmental DNA (eDNA).

PubMed

Schultz, Martin T; Lance, Richard F

2015-01-01

The environmental DNA (eDNA) method is the practice of collecting environmental samples and analyzing them for the presence of a genetic marker specific to a target species. Little is known about the sensitivity of the eDNA method. Sensitivity is the probability that the target marker will be detected if it is present in the water body. Methods and tools are needed to assess the sensitivity of sampling protocols, design eDNA surveys, and interpret survey results. In this study, the sensitivity of the eDNA method is modeled as a function of ambient target marker concentration. The model accounts for five steps of sample collection and analysis, including: 1) collection of a filtered water sample from the source; 2) extraction of DNA from the filter and isolation in a purified elution; 3) removal of aliquots from the elution for use in the polymerase chain reaction (PCR) assay; 4) PCR; and 5) genetic sequencing. The model is applicable to any target species. For demonstration purposes, the model is parameterized for bighead carp (Hypophthalmichthys nobilis) and silver carp (H. molitrix) assuming sampling protocols used in the Chicago Area Waterway System (CAWS). Simulation results show that eDNA surveys have a high false negative rate at low concentrations of the genetic marker. This is attributed to processing of water samples and division of the extraction elution in preparation for the PCR assay. Increases in field survey sensitivity can be achieved by increasing sample volume, sample number, and PCR replicates. Increasing sample volume yields the greatest increase in sensitivity. It is recommended that investigators estimate and communicate the sensitivity of eDNA surveys to help facilitate interpretation of eDNA survey results. In the absence of such information, it is difficult to evaluate the results of surveys in which no water samples test positive for the target marker. It is also recommended that invasive species managers articulate concentration-based sensitivity objectives for eDNA surveys. In the absence of such information, it is difficult to design appropriate sampling protocols. The model provides insights into how sampling protocols can be designed or modified to achieve these sensitivity objectives.

[Sampling optimization for tropical invertebrates: an example using dung beetles (Coleoptera: Scarabaeinae) in Venezuela].

PubMed

Ferrer-Paris, José Rafael; Sánchez-Mercado, Ada; Rodríguez, Jon Paul

2013-03-01

The development of efficient sampling protocols is an essential prerequisite to evaluate and identify priority conservation areas. There are f ew protocols for fauna inventory and monitoring in wide geographical scales for the tropics, where the complexity of communities and high biodiversity levels, make the implementation of efficient protocols more difficult. We proposed here a simple strategy to optimize the capture of dung beetles, applied to sampling with baited traps and generalizable to other sampling methods. We analyzed data from eight transects sampled between 2006-2008 withthe aim to develop an uniform sampling design, that allows to confidently estimate species richness, abundance and composition at wide geographical scales. We examined four characteristics of any sampling design that affect the effectiveness of the sampling effort: the number of traps, sampling duration, type and proportion of bait, and spatial arrangement of the traps along transects. We used species accumulation curves, rank-abundance plots, indicator species analysis, and multivariate correlograms. We captured 40 337 individuals (115 species/morphospecies of 23 genera). Most species were attracted by both dung and carrion, but two thirds had greater relative abundance in traps baited with human dung. Different aspects of the sampling design influenced each diversity attribute in different ways. To obtain reliable richness estimates, the number of traps was the most important aspect. Accurate abundance estimates were obtained when the sampling period was increased, while the spatial arrangement of traps was determinant to capture the species composition pattern. An optimum sampling strategy for accurate estimates of richness, abundance and diversity should: (1) set 50-70 traps to maximize the number of species detected, (2) get samples during 48-72 hours and set trap groups along the transect to reliably estimate species abundance, (3) set traps in groups of at least 10 traps to suitably record the local species composition, and (4) separate trap groups by a distance greater than 5-10km to avoid spatial autocorrelation. For the evaluation of other sampling protocols we recommend to, first, identify the elements of sampling design that could affect the sampled effort (the number of traps, sampling duration, type and proportion of bait) and their spatial distribution (spatial arrangement of the traps) and then, to evaluate how they affect richness, abundance and species composition estimates.

Screening for plant viruses by next generation sequencing using a modified double strand RNA extraction protocol with an internal amplification control.

PubMed

Kesanakurti, Prasad; Belton, Mark; Saeed, Hanaa; Rast, Heidi; Boyes, Ian; Rott, Michael

2016-10-01

The majority of plant viruses contain RNA genomes. Detection of viral RNA genomes in infected plant material by next generation sequencing (NGS) is possible through the extraction and sequencing of total RNA, total RNA devoid of ribosomal RNA, small RNA interference (RNAi) molecules, or double stranded RNA (dsRNA). Plants do not typically produce high molecular weight dsRNA, therefore the presence of dsRNA makes it an attractive target for plant virus diagnostics. The sensitivity of NGS as a diagnostic method demands an effective dsRNA protocol that is both representative of the sample and minimizes sample cross contamination. We have developed a modified dsRNA extraction protocol that is more efficient compared to traditional protocols, requiring reduced amounts of starting material, that is less prone to sample cross contamination. This was accomplished by using bead based homogenization of plant material in closed, disposable 50ml tubes. To assess the quality of extraction, we also developed an internal control by designing a real-time (quantitative) PCR (qPCR) assay that targets endornaviruses present in Phaseolus vulgaris cultivar Black Turtle Soup (BTS). Crown Copyright © 2016. Published by Elsevier B.V. All rights reserved.

Novel multi-day sputum transport reagent works with routine tuberculosis tests and eliminates need for cold chain: Preliminary study of compatibility with the Xpert® MTB/RIF assay.

PubMed

Kelly-Cirino, Cassandra D; Curry, Patricia S; Marola, Jamie L; Helstrom, Niels K; Salfinger, Max

2016-11-01

OMNIgene®•SPUTUM (OM-S) is a sputum transport reagent designed to work with all tuberculosis diagnostics and eliminate the need for cold chain. The aim of this preliminary study was to assess the compatibility of OM-S-treated sputum with the Xpert® MTB/RIF assay. Fifty-five characterized sputa from the FIND TB Specimen Bank were used. Compatibility of OM-S was assessed for both Xpert sample preparation methods: H.1 protocol (sediment, n=25) and H.2 protocol (direct expectorate, n=30). All controls were prepared using the H.2 protocol. Results revealed 100% concordance of MTB/RIF results for all except the low-positive group in the H.1 study arm (n=10; 88% concordance). OM-S-treated sputa were successful in both protocols; if the Xpert buffer is not added during the H.2 procedure, sample viscosity may require repeat testing. Using OM-S could offer users flexibility in clinical testing algorithms. Larger compatibility studies are warranted, particularly with respect to MTB/RIF results for low-positive samples. Copyright © 2016 Elsevier Inc. All rights reserved.

Comparison of PCR methods for the detection of genetic variants of carp edema virus.

PubMed

Adamek, Mikolaj; Matras, Marek; Jung-Schroers, Verena; Teitge, Felix; Heling, Max; Bergmann, Sven M; Reichert, Michal; Way, Keith; Stone, David M; Steinhagen, Dieter

2017-09-20

The infection of common carp and its ornamental variety, koi, with the carp edema virus (CEV) is often associated with the occurrence of a clinical disease called 'koi sleepy disease'. The disease may lead to high mortality in both koi and common carp populations. To prevent further spread of the infection and the disease, a reliable detection method for this virus is required. However, the high genetic variability of the CEV p4a gene used for PCR-based diagnostics could be a serious obstacle for successful and reliable detection of virus infection in field samples. By analysing 39 field samples from different geographical origins obtained from koi and farmed carp and from all 3 genogroups of CEV, using several recently available PCR protocols, we investigated which of the protocols would allow the detection of CEV from all known genogroups present in samples from Central European carp or koi populations. The comparison of 5 different PCR protocols showed that the PCR assays (both end-point and quantitative) developed in the Centre for Environment, Fisheries and Aquaculture Science exhibited the highest analytical inclusivity and diagnostic sensitivity. Currently, this makes them the most suitable protocols for detecting viruses from all known CEV genogroups.

9 CFR 325.5 - Unmarked inspected product transported under official seal between official establishments for...

Code of Federal Regulations, 2010 CFR

2010-01-01

... under official seal between official establishments for further processing; certificate. 325.5 Section... CERTIFICATION TRANSPORTATION § 325.5 Unmarked inspected product transported under official seal between official... other means of conveyance which is sealed by a Program employee with an official seal of the Department...

Mars Sample Handling Protocol Workshop Series

NASA Technical Reports Server (NTRS)

Rummel, John D. (Editor); Race, Margaret S. (Editor); Acevedo, Sara (Technical Monitor)

2000-01-01

This document is the report resulting from the first workshop of the series on development of the criteria for a Mars sample handling protocol. Workshop 1 was held in Bethesda, Maryland on March 20-22, 2000. This report serves to document the proceedings of Workshop 1; it summarizes relevant background information, provides an overview of the deliberations to date, and helps frame issues that will need further attention or resolution in upcoming workshops. Specific recommendations are not part of this report.

Evaluation of a shortened QIAsymphony DNA extraction protocol for stool samples using a multiplex real-time PCR for the detection of enteric pathogens.

PubMed

van Zanten, E; Wisselink, G J; Stoll, S; Alvarez, R; Kooistra-Smid, A M D

2011-02-01

A shortened DNA extraction protocol for the QIAsymphony SP was evaluated by quantitative and qualitative comparison of real-time PCR results of 150 co-extracted stool samples. The average ∆Cycle threshold value for positive pathogenic targets was 0.28 Ct. A consensus of 96.91%, with a correlation coefficient of 0.9880 was recorded. Copyright © 2010 Elsevier B.V. All rights reserved.

Transmission electron microscopy artifacts in characterization of the nanomaterial-cell interactions.

PubMed

Leung, Yu Hang; Guo, Mu Yao; Ma, Angel P Y; Ng, Alan M C; Djurišić, Aleksandra B; Degger, Natalie; Leung, Frederick C C

2017-07-01

We investigated transmission electron microscopy artifacts obtained using standard sample preparation protocols applied to the investigation of Escherichia coli cells exposed to common nanomaterials, such as TiO 2 , Ag, ZnO, and MgO. While the common protocols for some nanomaterials result only in known issues of nanomaterial-independent generation of anomalous deposits due to fixation and staining, for others, there are reactions between the nanomaterial and chemicals used for post-fixation or staining. Only in the case of TiO 2 do we observe only the known issues of nanomaterial-independent generation of anomalous deposits due to exceptional chemical stability of this material. For the other three nanomaterials, different artifacts are observed. For each of those, we identify causes of the observed problems and suggest alternative sample preparation protocols to avoid artifacts arising from the sample preparation, which is essential for correct interpretation of the obtained images and drawing correct conclusions on cell-nanomaterial interactions. Finally, we propose modified sample preparation and characterization protocols for comprehensive and conclusive investigations of nanomaterial-cell interactions using electron microscopy and for obtaining clear and unambiguous revelation whether the nanomaterials studied penetrate the cells or accumulate at the cell membranes. In only the case of MgO and ZnO, the unambiguous presence of Zn and Mg could be observed inside the cells.

A two-step dilution tris-egg yolk extender containing Equex STM significantly improves sperm cryopreservation in the African wild dog (Lycaon pictus).

PubMed

Van den Berghe, Femke; Paris, Monique Christina Johanna; Briggs, Michael Brent; Farstad, Wenche Kristin; Paris, Damien Boyd Bertrand Paul

2018-02-01

Conservation management of endangered African wild dogs (AWD; Lycaon pictus) can benefit greatly from development of sperm freezing and artificial insemination. Previous freezing attempts yielded nearly 0% motile sperm within 2 h of thawing. In this study, two canine freezing protocols were tested: Protocol 1: a one-step dilution in TRIS-20% egg yolk containing 8% glycerol; and Protocol 2: a two-step dilution in TRIS-20% egg yolk containing a final extender concentration of 5% glycerol and 0.5% Equex STM, coupled with a TRIS-citrate-fructose thawing solution. Semen was collected by electroejaculation from n = 24 AWDs, of which eight ejaculates of sufficient quality (four good quality with initial sperm motility of 75.0 ± 4.4% and four poor quality; showing rapid decrease in sperm motility to 3.3 ± 3.3% prior to freezing) were frozen. For good quality samples, motility and sperm motility index persisted for up to 8 h for Protocol 2, and was higher between 2 and 6 h after thawing with a decrease from 4 h of incubation. Motility dropped to nearly 0% after 2 h incubation for Protocol 1. Viability was higher for Protocol 2 throughout the 8 h of incubation, with a decrease after 6 h, compared to 4 h for Protocol 1. Acrosome integrity was higher for Protocol 2 throughout post-thaw incubation, with a decrease after 2 h for both protocols. Protocols did not differ in normal sperm morphology or DNA integrity. Poor quality samples yielded similar results, except for acrosome integrity, which declined for Protocol 2. In conclusion, a two-step dilution in TRIS-egg yolk-glycerol extender containing Equex STM yields significantly improved post-thaw quality and longevity of AWD spermatozoa, making it suitable for sperm banking and artificial insemination initiatives. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

Sample of Second Grade Classroom Protocols from Special Study A of the Beginning Teacher Evaluation Study for the California Commission for Teacher Preparation and Licensing.

ERIC Educational Resources Information Center

Tikunoff, William J.; And Others

Second grade classroom protocols collected within this volume are examples of the protocols developed by the ethnographers associated with Special Study A: "An Ethnographic Study of the Forty Classrooms of the Beginning Teacher Evaluation Study." Twenty teachers at both the second and fifth grades were observed for one week by an…

Sample of Fifth Grade Classroom Protocols from Special Study A of the Beginning Teacher Evaluation Study for the California Commission for Teacher Preparation and Licensing.

ERIC Educational Resources Information Center

Tikunoff, William J.; And Others

Classroom protocols collected within this volume are examples of the protocols from grade 5 developed by the ethnographers associated with Special Study A: "An Ethnographic Study of the Forty Classrooms of the Beginning Teacher Evaluation Study." Twenty teachers at both the second and fifth grades were observed for one week by an…

Organizational principles of cloud storage to support collaborative biomedical research.

PubMed

Kanbar, Lara J; Shalish, Wissam; Robles-Rubio, Carlos A; Precup, Doina; Brown, Karen; Sant'Anna, Guilherme M; Kearney, Robert E

2015-08-01

This paper describes organizational guidelines and an anonymization protocol for the management of sensitive information in interdisciplinary, multi-institutional studies with multiple collaborators. This protocol is flexible, automated, and suitable for use in cloud-based projects as well as for publication of supplementary information in journal papers. A sample implementation of the anonymization protocol is illustrated for an ongoing study dealing with Automated Prediction of EXtubation readiness (APEX).

Protocol and standard operating procedures for common use in a worldwide multicenter study on reference values.

PubMed

Ozarda, Yesim; Ichihara, Kiyoshi; Barth, Julian H; Klee, George

2013-05-01

The reference intervals (RIs) given in laboratory reports have an important role in aiding clinicians in interpreting test results in reference to values of healthy populations. In this report, we present a proposed protocol and standard operating procedures (SOPs) for common use in conducting multicenter RI studies on a national or international scale. The protocols and consensus on their contents were refined through discussions in recent C-RIDL meetings. The protocol describes in detail (1) the scheme and organization of the study, (2) the target population, inclusion/exclusion criteria, ethnicity, and sample size, (3) health status questionnaire, (4) target analytes, (5) blood collection, (6) sample processing and storage, (7) assays, (8) cross-check testing, (9) ethics, (10) data analyses, and (11) reporting of results. In addition, the protocol proposes the common measurement of a panel of sera when no standard materials exist for harmonization of test results. It also describes the requirements of the central laboratory, including the method of cross-check testing between the central laboratory of each country and local laboratories. This protocol and the SOPs remain largely exploratory and may require a reevaluation from the practical point of view after their implementation in the ongoing worldwide study. The paper is mainly intended to be a basis for discussion in the scientific community.

Organic Contamination Baseline Study in NASA Johnson Space Center Astromaterials Curation Laboratories

NASA Technical Reports Server (NTRS)

Calaway, Michael J.; Allen, Carlton C.; Allton, Judith H.

2014-01-01

Future robotic and human spaceflight missions to the Moon, Mars, asteroids, and comets will require curating astromaterial samples with minimal inorganic and organic contamination to preserve the scientific integrity of each sample. 21st century sample return missions will focus on strict protocols for reducing organic contamination that have not been seen since the Apollo manned lunar landing program. To properly curate these materials, the Astromaterials Acquisition and Curation Office under the Astromaterial Research and Exploration Science Directorate at NASA Johnson Space Center houses and protects all extraterrestrial materials brought back to Earth that are controlled by the United States government. During fiscal year 2012, we conducted a year-long project to compile historical documentation and laboratory tests involving organic investigations at these facilities. In addition, we developed a plan to determine the current state of organic cleanliness in curation laboratories housing astromaterials. This was accomplished by focusing on current procedures and protocols for cleaning, sample handling, and storage. While the intention of this report is to give a comprehensive overview of the current state of organic cleanliness in JSC curation laboratories, it also provides a baseline for determining whether our cleaning procedures and sample handling protocols need to be adapted and/or augmented to meet the new requirements for future human spaceflight and robotic sample return missions.

Environmental policies, politics, and community risk perception: case study of community contamination in Casper, Wyoming.

PubMed

Tajik, Mansoureh; Gottlieb, Karen; Lowndes, Nita; Stewart, Gloria

2007-01-01

We identify and explain factors that affected a community's perception of risk due to extensive industrial contamination and people's distrust of government agencies regarding the environmental investigations. Intrinsic bounded case study methodology was used to conduct research about extensive environmental contaminations due to activities of an oil refinery in North Casper, Wyoming, and the citizens' response. Data were collected from multiple sources that included public testimonies, observations, public hearings and meetings minutes, newspaper articles, archived records obtained from federal and state environmental and health agencies, as well as industry records obtained through Freedom of Information Act (FOIA) requests. The overarching theme that emerged was lack of trust due to several critical events and factors such as no response or delay in response time to community concerns, lack of transparency, perceived cover up, vague and fragmented communication by government and state officials, perception of pro-industry stance, and perceived unfair treatment. People's perception of environmental risks and their willingness to accept official explanations and outcomes of environmental investigations are strongly affected by their direct experiences with government agencies and the evidence of influence the powerful industries exert over relevant investigations. The government cannot successfully address public and community concerns about environmental health impacts of contaminations and in turn the public perception of risk unless it adopts and implements policies, procedures, and protocols that are clear, timely, transparent, and free from industry influence.

A high-throughput microRNA expression profiling system.

PubMed

Guo, Yanwen; Mastriano, Stephen; Lu, Jun

2014-01-01

As small noncoding RNAs, microRNAs (miRNAs) regulate diverse biological functions, including physiological and pathological processes. The expression and deregulation of miRNA levels contain rich information with diagnostic and prognostic relevance and can reflect pharmacological responses. The increasing interest in miRNA-related research demands global miRNA expression profiling on large numbers of samples. We describe here a robust protocol that supports high-throughput sample labeling and detection on hundreds of samples simultaneously. This method employs 96-well-based miRNA capturing from total RNA samples and on-site biochemical reactions, coupled with bead-based detection in 96-well format for hundreds of miRNAs per sample. With low-cost, high-throughput, high detection specificity, and flexibility to profile both small and large numbers of samples, this protocol can be adapted in a wide range of laboratory settings.

Photonic-crystal fiber as a multifunctional optical sensor and sample collector.

PubMed

Konorov, Stanislav; Zheltikov, Aleksei; Scalora, Michael

2005-05-02

Two protocols of optical sensing realized with the same photonic-crystal fiber are compared. In the first protocol, diode-laser radiation is delivered to a sample through the central core of a dual-cladding photonic-crystal fiber with a diameter of a few micrometers, while the large-diameter fiber cladding serves to collect the fluorescent response from the sample and to guide it to a detector in the backward direction. In the second scheme, liquid sample is collected by a microcapillary array in the fiber cladding and is interrogated by laser radiation guided in the fiber modes. For sample fluids with refractive indices exceeding the refractive index of the fiber material, fluid channels in photonic-crystal fibers can guide laser light by total internal reflection, providing an 80% overlap of interrogating radiation with sample fluid.

Experimental aspect of solid-state nuclear magnetic resonance studies of biomaterials such as bones.

PubMed

Singh, Chandan; Rai, Ratan Kumar; Sinha, Neeraj

2013-01-01

Solid-state nuclear magnetic resonance (SSNMR) spectroscopy is increasingly becoming a popular technique to probe micro-structural details of biomaterial such as bone with pico-meter resolution. Due to high-resolution structural details probed by SSNMR methods, handling of bone samples and experimental protocol are very crucial aspects of study. We present here first report of the effect of various experimental protocols and handling methods of bone samples on measured SSNMR parameters. Various popular SSNMR experiments were performed on intact cortical bone sample collected from fresh animal, immediately after removal from animal systems, and results were compared with bone samples preserved in different conditions. We find that the best experimental conditions for SSNMR parameters of bones correspond to preservation at -20 °C and in 70% ethanol solution. Various other SSNMR parameters were compared corresponding to different experimental conditions. Our study has helped in finding best experimental protocol for SSNMR studies of bone. This study will be of further help in the application of SSNMR studies on large bone disease related animal model systems for statistically significant results. © 2013 Elsevier Inc. All rights reserved.

Estimating occupancy and abundance of stream amphibians using environmental DNA from filtered water samples

USGS Publications Warehouse

Pilliod, David S.; Goldberg, Caren S.; Arkle, Robert S.; Waits, Lisette P.

2013-01-01

Environmental DNA (eDNA) methods for detecting aquatic species are advancing rapidly, but with little evaluation of field protocols or precision of resulting estimates. We compared sampling results from traditional field methods with eDNA methods for two amphibians in 13 streams in central Idaho, USA. We also evaluated three water collection protocols and the influence of sampling location, time of day, and distance from animals on eDNA concentration in the water. We found no difference in detection or amount of eDNA among water collection protocols. eDNA methods had slightly higher detection rates than traditional field methods, particularly when species occurred at low densities. eDNA concentration was positively related to field-measured density, biomass, and proportion of transects occupied. Precision of eDNA-based abundance estimates increased with the amount of eDNA in the water and the number of replicate subsamples collected. eDNA concentration did not vary significantly with sample location in the stream, time of day, or distance downstream from animals. Our results further advance the implementation of eDNA methods for monitoring aquatic vertebrates in stream habitats.

Comprehensive Analysis of Transcription Dynamics from Brain Samples Following Behavioral Experience

PubMed Central

Turm, Hagit; Mukherjee, Diptendu; Haritan, Doron; Tahor, Maayan; Citri, Ami

2014-01-01

The encoding of experiences in the brain and the consolidation of long-term memories depend on gene transcription. Identifying the function of specific genes in encoding experience is one of the main objectives of molecular neuroscience. Furthermore, the functional association of defined genes with specific behaviors has implications for understanding the basis of neuropsychiatric disorders. Induction of robust transcription programs has been observed in the brains of mice following various behavioral manipulations. While some genetic elements are utilized recurrently following different behavioral manipulations and in different brain nuclei, transcriptional programs are overall unique to the inducing stimuli and the structure in which they are studied1,2. In this publication, a protocol is described for robust and comprehensive transcriptional profiling from brain nuclei of mice in response to behavioral manipulation. The protocol is demonstrated in the context of analysis of gene expression dynamics in the nucleus accumbens following acute cocaine experience. Subsequent to a defined in vivo experience, the target neural tissue is dissected; followed by RNA purification, reverse transcription and utilization of microfluidic arrays for comprehensive qPCR analysis of multiple target genes. This protocol is geared towards comprehensive analysis (addressing 50-500 genes) of limiting quantities of starting material, such as small brain samples or even single cells. The protocol is most advantageous for parallel analysis of multiple samples (e.g. single cells, dynamic analysis following pharmaceutical, viral or behavioral perturbations). However, the protocol could also serve for the characterization and quality assurance of samples prior to whole-genome studies by microarrays or RNAseq, as well as validation of data obtained from whole-genome studies. PMID:25225819

Establishment of a protocol for the gene expression analysis of laser microdissected rat kidney samples with affymetrix genechips

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

Stemmer, Kerstin; Ellinger-Ziegelbauer, Heidrun; Lotz, Kerstin

2006-11-15

Laser microdissection in conjunction with microarray technology allows selective isolation and analysis of specific cell populations, e.g., preneoplastic renal lesions. To date, only limited information is available on sample preparation and preservation techniques that result in both optimal histomorphological preservation of sections and high-quality RNA for microarray analysis. Furthermore, amplification of minute amounts of RNA from microdissected renal samples allowing analysis with genechips has only scantily been addressed to date. The objective of this study was therefore to establish a reliable and reproducible protocol for laser microdissection in conjunction with microarray technology using kidney tissue from Eker rats p.o. treatedmore » for 7 days and 6 months with 10 and 1 mg Aristolochic acid/kg bw, respectively. Kidney tissues were preserved in RNAlater or snap frozen. Cryosections were cut and stained with either H and E or cresyl violet for subsequent morphological and RNA quality assessment and laser microdissection. RNA quality was comparable in snap frozen and RNAlater-preserved samples, however, the histomorphological preservation of renal sections was much better following cryopreservation. Moreover, the different staining techniques in combination with sample processing time at room temperature can have an influence on RNA quality. Different RNA amplification protocols were shown to have an impact on gene expression profiles as demonstrated with Affymetrix Rat Genome 230{sub 2}.0 arrays. Considering all the parameters analyzed in this study, a protocol for RNA isolation from laser microdissected samples with subsequent Affymetrix chip hybridization was established that was also successfully applied to preneoplastic lesions laser microdissected from Aristolochic acid-treated rats.« less

MPLEx: a Robust and Universal Protocol for Single-Sample Integrative Proteomic, Metabolomic, and Lipidomic Analyses

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

Nakayasu, Ernesto S.; Nicora, Carrie D.; Sims, Amy C.

2016-05-03

ABSTRACT Integrative multi-omics analyses can empower more effective investigation and complete understanding of complex biological systems. Despite recent advances in a range of omics analyses, multi-omic measurements of the same sample are still challenging and current methods have not been well evaluated in terms of reproducibility and broad applicability. Here we adapted a solvent-based method, widely applied for extracting lipids and metabolites, to add proteomics to mass spectrometry-based multi-omics measurements. Themetabolite,protein, andlipidextraction (MPLEx) protocol proved to be robust and applicable to a diverse set of sample types, including cell cultures, microbial communities, and tissues. To illustrate the utility of thismore » protocol, an integrative multi-omics analysis was performed using a lung epithelial cell line infected with Middle East respiratory syndrome coronavirus, which showed the impact of this virus on the host glycolytic pathway and also suggested a role for lipids during infection. The MPLEx method is a simple, fast, and robust protocol that can be applied for integrative multi-omic measurements from diverse sample types (e.g., environmental,in vitro, and clinical). IMPORTANCEIn systems biology studies, the integration of multiple omics measurements (i.e., genomics, transcriptomics, proteomics, metabolomics, and lipidomics) has been shown to provide a more complete and informative view of biological pathways. Thus, the prospect of extracting different types of molecules (e.g., DNAs, RNAs, proteins, and metabolites) and performing multiple omics measurements on single samples is very attractive, but such studies are challenging due to the fact that the extraction conditions differ according to the molecule type. Here, we adapted an organic solvent-based extraction method that demonstrated broad applicability and robustness, which enabled comprehensive proteomics, metabolomics, and lipidomics analyses from the same sample.« less

Mars Sample Handling Protocol Workshop Series: Workshop 2a (Sterilization)

NASA Technical Reports Server (NTRS)

Rummel, John D. (Editor); Brunch, Carl W. (Editor); Setlow, Richard B. (Editor); DeVincenzi, Donald L. (Technical Monitor)

2001-01-01

The Space Studies Board of the National Research Council provided a series of recommendations to NASA on planetary protection requirements for future Mars sample return missions. One of the Board's key findings suggested, although current evidence of the martian surface suggests that life as we know it would not tolerate the planet's harsh environment, there remain 'plausible scenarios for extant microbial life on Mars.' Based on this conclusion, all samples returned from Mars should be considered potentially hazardous until it has been demonstrated that they are not. In response to the National Research Council's findings and recommendations, NASA has undertaken a series of workshops to address issues regarding NASA's proposed sample return missions. Work was previously undertaken at the Mars Sample Handling and Protocol Workshop 1 (March 2000) to formulate recommendations on effective methods for life detection and/or biohazard testing on returned samples. The NASA Planetary Protection Officer convened the Mars Sample Sterilization Workshop, the third in the Mars Sample Handling Protocol Workshop Series, on November 28-30, 2000 at the Holiday Inn Rosslyn Westpark, Arlington, Virginia. Because of the short timeframe between this Workshop and the second Workshop in the Series, which was convened in October 2000 in Bethesda, Maryland, they were developed in parallel, so the Sterilization Workshop and its report have therefore been designated as '2a'). The focus of Workshop 2a was to make recommendations for effective sterilization procedures for all phases of Mars sample return missions, and to answer the question of whether we can sterilize samples in such a way that the geological characteristics of the samples are not significantly altered.

Sample size requirements for estimating effective dose from computed tomography using solid-state metal-oxide-semiconductor field-effect transistor dosimetry

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

Trattner, Sigal; Cheng, Bin; Pieniazek, Radoslaw L.

2014-04-15

Purpose: Effective dose (ED) is a widely used metric for comparing ionizing radiation burden between different imaging modalities, scanners, and scan protocols. In computed tomography (CT), ED can be estimated by performing scans on an anthropomorphic phantom in which metal-oxide-semiconductor field-effect transistor (MOSFET) solid-state dosimeters have been placed to enable organ dose measurements. Here a statistical framework is established to determine the sample size (number of scans) needed for estimating ED to a desired precision and confidence, for a particular scanner and scan protocol, subject to practical limitations. Methods: The statistical scheme involves solving equations which minimize the sample sizemore » required for estimating ED to desired precision and confidence. It is subject to a constrained variation of the estimated ED and solved using the Lagrange multiplier method. The scheme incorporates measurement variation introduced both by MOSFET calibration, and by variation in MOSFET readings between repeated CT scans. Sample size requirements are illustrated on cardiac, chest, and abdomen–pelvis CT scans performed on a 320-row scanner and chest CT performed on a 16-row scanner. Results: Sample sizes for estimating ED vary considerably between scanners and protocols. Sample size increases as the required precision or confidence is higher and also as the anticipated ED is lower. For example, for a helical chest protocol, for 95% confidence and 5% precision for the ED, 30 measurements are required on the 320-row scanner and 11 on the 16-row scanner when the anticipated ED is 4 mSv; these sample sizes are 5 and 2, respectively, when the anticipated ED is 10 mSv. Conclusions: Applying the suggested scheme, it was found that even at modest sample sizes, it is feasible to estimate ED with high precision and a high degree of confidence. As CT technology develops enabling ED to be lowered, more MOSFET measurements are needed to estimate ED with the same precision and confidence.« less

Comparison of macroinvertebrate community structure between two riffle-based sampling protocols in Wyoming, Colorado, and Montana, 2000-2001

USGS Publications Warehouse

Peterson, David A.; Zumberge, Jeremy R.

2006-01-01

Samples of benthic macroinvertebrates were collected side-by-side from riffles at 12 stream sites in Wyoming, Colorado, and Montana during 2000-2001, following protocols established by the U.S. Geological Survey National Water-Quality Assessment (NAWQA) Program and the U.S. Environmental Protection Agency Environmental Monitoring and Assessment Program (EMAP). Samples from riffles were collected following NAWQA protocols, using a sampler with 425-micron net mesh-opening size from a total area of 1.25 m2 per sample in multiple riffles. Samples also were collected following EMAP protocols, using a sampler with 500-micron net mesh-opening size from a total area of 0.72 m2 per sample in multiple riffles. The taxonomic identification and enumeration of the samples followed procedures established for each program. Benthic macroinvertebrate community structure was compared between the data sets using individual metrics, a multimetric index, and multivariate analysis. Comparisons between the macroinvertebrate community structures were made after sequentially adjusting both data sets for: (1) ambiguous taxa, (2) taxonomic inconsistencies, and (3) differences in laboratory subsampling. After removal of ambiguous taxa, pair-wise differences in total taxa richness and Ephemeroptera taxa richness were statistically significant (p < 0.05). Differences between the data sets generally were not significant for richness of other taxa, tolerant taxa, semi-voltine taxa, functional feeding groups, diversity, and dominance. Sample scores calculated using the Wyoming Stream Integrity Index were not significantly different between the two data sets. After reconciling both data sets for taxonomic inconsistencies, total taxa richness and Ephemeroptera taxa richness remained significantly different between the data sets. After adjusting the data for differences in laboratory subsampling, the differences in taxa richness were no longer significant. Bray-Curtis similarity coefficients and non-metric multi-dimensional scaling were used to examine macroinvertebrate community structure. Similarity in community structure between sites was affected to a greater extent by taxa reconciliation than by adjustment for subsampling.

Sample size requirements for estimating effective dose from computed tomography using solid-state metal-oxide-semiconductor field-effect transistor dosimetry

PubMed Central

Trattner, Sigal; Cheng, Bin; Pieniazek, Radoslaw L.; Hoffmann, Udo; Douglas, Pamela S.; Einstein, Andrew J.

2014-01-01

Purpose: Effective dose (ED) is a widely used metric for comparing ionizing radiation burden between different imaging modalities, scanners, and scan protocols. In computed tomography (CT), ED can be estimated by performing scans on an anthropomorphic phantom in which metal-oxide-semiconductor field-effect transistor (MOSFET) solid-state dosimeters have been placed to enable organ dose measurements. Here a statistical framework is established to determine the sample size (number of scans) needed for estimating ED to a desired precision and confidence, for a particular scanner and scan protocol, subject to practical limitations. Methods: The statistical scheme involves solving equations which minimize the sample size required for estimating ED to desired precision and confidence. It is subject to a constrained variation of the estimated ED and solved using the Lagrange multiplier method. The scheme incorporates measurement variation introduced both by MOSFET calibration, and by variation in MOSFET readings between repeated CT scans. Sample size requirements are illustrated on cardiac, chest, and abdomen–pelvis CT scans performed on a 320-row scanner and chest CT performed on a 16-row scanner. Results: Sample sizes for estimating ED vary considerably between scanners and protocols. Sample size increases as the required precision or confidence is higher and also as the anticipated ED is lower. For example, for a helical chest protocol, for 95% confidence and 5% precision for the ED, 30 measurements are required on the 320-row scanner and 11 on the 16-row scanner when the anticipated ED is 4 mSv; these sample sizes are 5 and 2, respectively, when the anticipated ED is 10 mSv. Conclusions: Applying the suggested scheme, it was found that even at modest sample sizes, it is feasible to estimate ED with high precision and a high degree of confidence. As CT technology develops enabling ED to be lowered, more MOSFET measurements are needed to estimate ED with the same precision and confidence. PMID:24694150

Recovery of human DNA profiles from poached deer remains part 2: improved recovery protocol without the need for LCN analysis.

PubMed

Tobe, Shanan S; Bailey, Stuart; Govan, James; Welch, Lindsey A

2013-03-01

Although poaching is a common wildlife crime, the high and prohibitive cost of specialised animal testing means that many cases are left un-investigated. We previously described a novel approach to wildlife crime investigation that looked at the identification of human DNA on poached animal remains (Tobe, Govan and Welch, 2011). Human DNA was successfully isolated and amplified from simulated poaching incidents, however a low template protocol was required which made this method unsuitable for use in many laboratories. We now report on an optimised recovery and amplification protocol which removes the need for low template analysis. Samples from 10 deer (40 samples total - one from each leg) analysed in the original study were re-analysed in the current study with an additional 11 deer samples. Four samples analysed using Chelex did not show any results and a new method was devised whereby the available DNA was concentrated. By combining the DNA extracts from all tapings of the same deer remains followed by concentration, the recovered quantity of human DNA was found to be 29.5pg±43.2pg, 31× greater than the previous study. The use of the Investigator Decaplex SE (QIAGEN) STR kit provided better results in the form of more complete profiles than did the AmpFℓSTR® SGM Plus® kit at 30cycles (Applied Biosystems). Re-analysis of the samples from the initial study using the new, optimised protocol resulted in an average increase of 18% of recovered alleles. Over 17 samples, 71% of the samples analysed using the optimised protocol showed sufficient amplification for comparison to a reference profile and gave match probabilities ranging from 7.7690×10(-05) to 2.2706×10(-14). The removal of low template analysis means this optimised method provides evidence of high probative value and is suitable for immediate use in forensic laboratories. All methods and techniques used are standard and are compatible with current SOPs. As no high cost non-human DNA analysis is required the overall process is no more expensive than the investigation of other volume crime samples. The technique is suitable for immediate use in poaching incidents. Copyright © 2012 Forensic Science Society. Published by Elsevier Ireland Ltd. All rights reserved.

Quantification of trace elements and speciation of iron in atmospheric particulate matter

NASA Astrophysics Data System (ADS)

Upadhyay, Nabin

Trace metal species play important roles in atmospheric redox processes and in the generation of oxidants in cloud systems. The chemical impact of these elements on atmospheric and cloud chemistry is dependent on their occurrence, solubility and speciation. First, analytical protocols have been developed to determine trace elements in particulate matter samples collected for carbonaceous analysis. The validated novel protocols were applied to the determination of trace elements in particulate samples collected in the remote marine atmosphere and urban areas in Arizona to study air pollution issues. The second part of this work investigates on solubility and speciation in environmental samples. A detailed study on the impact of the nature and strength of buffer solutions on solubility and speciation of iron lead to a robust protocol, allowing for comparative measurements in matrices representative of cloud water conditions. Application of this protocol to samples from different environments showed low iron solubility (less than 1%) in dust-impacted events and higher solubility (5%) in anthropogenically impacted urban samples. In most cases, Fe(II) was the dominant oxidation state in the soluble fraction of iron. The analytical protocol was then applied to investigate iron processing by fogs. Field observations showed that only a small fraction (1%) of iron was scavenged by fog droplets for which each of the soluble and insoluble fraction were similar. A coarse time resolution limited detailed insights into redox cycling within fog system. Overall results suggested that the major iron species in the droplets was Fe(1I) (80% of soluble iron). Finally, the occurrence and sources of emerging organic pollutants in the urban atmosphere were investigated. Synthetic musk species are ubiquitous in the urban environment (less than 5 ng m-3) and investigations at wastewater treatment plants showed that wastewater aeration basins emit a substantial amount of these species to the atmosphere.

An intra-laboratory cultural and real-time PCR method comparison and evaluation for the detection of subclinical paratuberculosis in dairy herds.

PubMed

Heuvelink, Annet; Hassan, Abdulwahed Ahmed; van Weering, Hilmar; van Engelen, Erik; Bülte, Michael; Akineden, Ömer

2017-05-01

Mycobacterium avium subsp. paratuberculosis (MAP) is a vigorous microorganism which causes incurable chronic enteritis, Johne's disease (JD) in cattle. A target of control programmes for JD is to accurately detect MAP-infected cattle early to reduce disease transmission. The present study evaluated the efficacy of two different cultural procedures and a TaqMan real-time PCR assay for detection of subclinical paratuberculosis in dairy herds. Therefore, sixty-one faecal samples were collected from two Dutch dairy herds (n = 40 and n = 21, respectively) which were known to be MAP-ELISA positive. All individual samples were assessed using two different cultural protocols in two different laboratories. The first cultural protocol (first laboratory) included a decontamination step with 0.75% hexadecylpyridinium chloride (HPC) followed by inoculation on Herrold's egg yolk media (HEYM). The second protocol (second laboratory) comprised of a decontamination step using 4% NaOH and malachite green-oxalic acid followed by inoculation on two media, HEYM and in parallel on modified Löwenstein-Jensen media (mLJ). For the TaqMan real-time PCR assay, all faecal samples were tested in two different laboratories using TaqMan® MAP (Johne's) reagents (Life Technologies). The cultural procedures revealed positive reactions in 1.64% of the samples for cultivation protocol 1 and 6.56 and 8.20% of the samples for cultivation protocol 2, respectively. The results of the TaqMan real-time PCR performed in two different laboratories yielded 13.11 and 19.76% positive reaction. The kappa test showed proportional agreement 0.54 between the mLJ media (second laboratory) and TaqMan® real-time PCR method (second laboratory). In conclusion, the TaqMan real-time PCR could be a strongly useful and efficient assay for the detection of subclinical paratuberculosis in dairy cattle leading to an improvement in the efficiency of MAP control strategies.

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.

A Novel Protocol to Analyze Short- and Long-Chain Fatty Acids Using Nonaqueous Microchip Capillary Electrophoresis

NASA Technical Reports Server (NTRS)

Cable, M. L.; Stockton, A. M.; Mora, Maria F; Willis, P. A.

2013-01-01

We propose a new protocol to identify and quantify both short- and long-chain saturated fatty acids in samples of astrobiological interest using non-aqueous microchip capillary electrophoresis (micronNACE) with laser induced fluorescence (LIF).