Home-based versus clinic-based specimen collection in the management of Chlamydia trachomatis and Neisseria gonorrhoeae infections.

PubMed

Fajardo-Bernal, Luisa; Aponte-Gonzalez, Johanna; Vigil, Patrick; Angel-Müller, Edith; Rincon, Carlos; Gaitán, Hernando G; Low, Nicola

2015-09-29

Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG) are the most frequent causes of bacterial sexually transmitted infections (STIs). Management strategies that reduce losses in the clinical pathway from infection to cure might improve STI control and reduce complications resulting from lack of, or inadequate, treatment. To assess the effectiveness and safety of home-based specimen collection as part of the management strategy for Chlamydia trachomatis and Neisseria gonorrhoeae infections compared with clinic-based specimen collection in sexually-active people. We searched the Cochrane Sexually Transmitted Infections Group Specialized Register, the Cochrane Central Register of Controlled Trials (CENTRAL), MEDLINE, EMBASE and LILACS on 27 May 2015, together with the World Health Organization International Clinical Trials Registry (ICTRP) and ClinicalTrials.gov. We also handsearched conference proceedings, contacted trial authors and reviewed the reference lists of retrieved studies. Randomized controlled trials (RCTs) of home-based compared with clinic-based specimen collection in the management of C. trachomatis and N. gonorrhoeae infections. Three review authors independently assessed trials for inclusion, extracted data and assessed risk of bias. We contacted study authors for additional information. We resolved any disagreements through consensus. We used standard methodological procedures recommended by Cochrane. The primary outcome was index case management, defined as the number of participants tested, diagnosed and treated, if test positive. Ten trials involving 10,479 participants were included. There was inconclusive evidence of an effect on the proportion of participants with index case management (defined as individuals tested, diagnosed and treated for CT or NG, or both) in the group with home-based (45/778, 5.8%) compared with clinic-based (51/788, 6.5%) specimen collection (risk ratio (RR) 0.88, 95% confidence interval (CI) 0.60 to 1.29; 3 trials, I² = 0%, 1566 participants, moderate quality). Harms of home-based specimen collection were not evaluated in any trial. All 10 trials compared the proportions of individuals tested. The results for the proportion of participants completing testing had high heterogeneity (I² = 100%) and were not pooled. We could not combine data from individual studies looking at the number of participants tested because the proportions varied widely across the studies, ranging from 30% to 96% in home group and 6% to 97% in clinic group (low-quality evidence). The number of participants with positive test was lower in the home-based specimen collection group (240/2074, 11.6%) compared with the clinic-based group (179/967, 18.5%) (RR 0.72, 95% CI 0.61 to 0.86; 9 trials, I² = 0%, 3041 participants, moderate quality). Home-based specimen collection could result in similar levels of index case management for CT or NG infection when compared with clinic-based specimen collection. Increases in the proportion of individuals tested as a result of home-based, compared with clinic-based, specimen collection are offset by a lower proportion of positive results. The harms of home-based specimen collection compared with clinic-based specimen collection have not been evaluated. Future RCTs to assess the effectiveness of home-based specimen collection should be designed to measure biological outcomes of STI case management, such as proportion of participants with negative tests for the relevant STI at follow-up.

Lost in translation or deliberate falsification? Genetic analyses reveal erroneous museum data for historic penguin specimens.

PubMed

Boessenkool, Sanne; Star, Bastiaan; Scofield, R Paul; Seddon, Philip J; Waters, Jonathan M

2010-04-07

Historic museum specimens are increasingly used to answer a wide variety of questions in scientific research. Nevertheless, the scientific value of these specimens depends on the authenticity of the data associated with them. Here we use individual-based genetic analyses to demonstrate erroneous locality information for archive specimens from the late nineteenth century. Specifically, using 10 microsatellite markers, we analysed 350 contemporary and 43 historic yellow-eyed penguin (Megadyptes antipodes) specimens from New Zealand's South Island and sub-Antarctic regions. Factorial correspondence analysis and an assignment test strongly suggest that eight of the historic specimens purportedly of sub-Antarctic origin were in fact collected from the South Island. Interestingly, all eight specimens were obtained by the same collector, and all are currently held in the same museum collection. Further inspection of the specimen labels and evaluation of sub-Antarctic voyages did not reveal whether the erroneous data are caused by incorrect labelling or whether deliberate falsification was at play. This study highlights a promising extension to the well-known applications of assignment tests in molecular ecology, which can complement methods that are currently being applied for error detection in specimen data. Our results also serve as a warning to all who use archive specimens to invest time in the verification of collection information.

Efficiently Maintaining a National Resource of Historical and Contemporary Biological Collections: The NHLBI Biorepository Model.

PubMed

Shea, Katheryn E; Wagner, Elizabeth L; Marchesani, Leah; Meagher, Kevin; Giffen, Carol

2017-02-01

Reducing costs by improving storage efficiency has been a focus of the National Heart, Lung, and Blood Institute (NHLBI) Biologic Specimen Repository (Biorepository) and Biologic Specimen and Data Repositories Information Coordinating Center (BioLINCC) programs for several years. Study specimen profiles were compiled using the BioLINCC collection catalog. Cost assessments and calculations on the return on investments to consolidate or reduce a collection, were developed and implemented. Over the course of 8 months, the NHLBI Biorepository evaluated 35 collections that consisted of 1.8 million biospecimens. A total of 23 collections were selected for consolidation, with a total of 1.2 million specimens located in 21,355 storage boxes. The consolidation resulted in a savings of 4055 boxes of various sizes and 10.2 mechanical freezers (∼275 cubic feet) worth of space. As storage costs in a biorepository increase over time, the development and use of information technology tools to assess the potential advantage and feasiblity of vial consolidation can reduce maintenance expenses.

Evaluation of the role of the cyclooxygenase signaling pathway during inflammation in skin and muscle tissues of ball pythons (Python regius).

PubMed

Sadler, Ryan A; Schumacher, Juergen P; Rathore, Kusum; Newkirk, Kim M; Cole, Grayson; Seibert, Rachel; Cekanova, Maria

2016-05-01

OBJECTIVE To determine degrees of production of cyclooxygenase (COX)-1 and -2 and other mediators of inflammation in noninflamed and inflamed skin and muscle tissues in ball pythons (Python regius). ANIMALS 6 healthy adult male ball pythons. PROCEDURES Biopsy specimens of noninflamed skin and muscle tissue were collected from anesthetized snakes on day 0. A 2-cm skin and muscle incision was then made 5 cm distal to the biopsy sites with a CO2 laser to induce inflammation. On day 7, biopsy specimens of skin and muscle tissues were collected from the incision sites. Inflamed and noninflamed tissue specimens were evaluated for production of COX-1, COX-2, phosphorylated protein kinase B (AKT), total AKT, nuclear factor κ-light-chain-enhancer of activated B cells, phosphorylated extracellular receptor kinases (ERKs) 1 and 2, and total ERK proteins by western blot analysis. Histologic evaluation was performed on H&E-stained tissue sections. RESULTS All biopsy specimens of inflamed skin and muscle tissues had higher histologic inflammation scores than did specimens of noninflamed tissue. Inflamed skin specimens had significantly greater production of COX-1 and phosphorylated ERK than did noninflamed skin specimens. Inflamed muscle specimens had significantly greater production of phosphorylated ERK and phosphorylated AKT, significantly lower production of COX-1, and no difference in production of COX-2, compared with production in noninflamed muscle specimens. CONCLUSIONS AND CLINICAL RELEVANCE Production of COX-1, but not COX-2, was significantly greater in inflamed versus noninflamed skin specimens from ball pythons. Additional research into the reptilian COX signaling pathway is warranted.

An electronic specimen collection protocol schema (eSCPS). Document architecture for specimen management and the exchange of specimen collection protocols between biobanking information systems.

PubMed

Eminaga, O; Semjonow, A; Oezguer, E; Herden, J; Akbarov, I; Tok, A; Engelmann, U; Wille, S

2014-01-01

The integrity of collection protocols in biobanking is essential for a high-quality sample preparation process. However, there is not currently a well-defined universal method for integrating collection protocols in the biobanking information system (BIMS). Therefore, an electronic schema of the collection protocol that is based on Extensible Markup Language (XML) is required to maintain the integrity and enable the exchange of collection protocols. The development and implementation of an electronic specimen collection protocol schema (eSCPS) was performed at two institutions (Muenster and Cologne) in three stages. First, we analyzed the infrastructure that was already established at both the biorepository and the hospital information systems of these institutions and determined the requirements for the sufficient preparation of specimens and documentation. Second, we designed an eSCPS according to these requirements. Finally, a prospective study was conducted to implement and evaluate the novel schema in the current BIMS. We designed an eSCPS that provides all of the relevant information about collection protocols. Ten electronic collection protocols were generated using the supplementary Protocol Editor tool, and these protocols were successfully implemented in the existing BIMS. Moreover, an electronic list of collection protocols for the current studies being performed at each institution was included, new collection protocols were added, and the existing protocols were redesigned to be modifiable. The documentation time was significantly reduced after implementing the eSCPS (5 ± 2 min vs. 7 ± 3 min; p = 0.0002). The eSCPS improves the integrity and facilitates the exchange of specimen collection protocols in the existing open-source BIMS.

Rapid on-site evaluation of fine needle aspiration specimens by cytology scientists: a review of 3032 specimens.

PubMed

Shield, P W; Cosier, J; Ellerby, G; Gartrell, M; Papadimos, D

2014-10-01

To determine: (1) the accuracy of cytology scientists at assessing specimen adequacy by rapid on-site evaluation (ROSE) at fine needle aspiration (FNA) cytology collections; and (2) whether thyroid FNA with ROSE has lower inadequacy rates than non-attended FNAs. The ROSE of adequacy for 3032 specimens from 17 anatomical sites collected over a 20-month period was compared with the final report assessment of adequacy. ROSE was performed by 19 cytology scientists. The report profile for 1545 thyroid nodules with ROSE was compared with that for 1536 consecutive non-ROSE thyroid FNAs reported by the same cytopathologists during the study period. ROSE was adequate in 75% (2276/3032), inadequate in 12% (366/3032) and in 13% (390/3032) no opinion was rendered. Of the 2276 cases assessed as adequate by ROSE, 2268 (99.6%) were finally reported as adequate for assessment; eight specimens had adequacy downgraded on the final report. Fifty eight per cent of cases with a ROSE assessment of inadequate were reported as adequate (212/366), whereas 93% (363/390) with no opinion rendered were reported as adequate. The overall final report adequacy rate for the 3032 specimens was 94% (2843/3032). Confirmation of a ROSE of adequacy at reporting was uniformly high amongst the 19 scientists, ranging from 98% to 100%. The inadequacy rate for thyroid FNAs with ROSE (6%) was significantly (P < 0.0001) lower than for non-ROSE thyroid FNAs (17%). A significantly (P = 0.02) higher proportion of adequate ROSE thyroid specimens was reported with abnormalities, compared with non-ROSE thyroid collections. Cytology scientists are highly accurate at determining specimen adequacy at ROSE for a wide range of body sites. ROSE of thyroid FNAs can significantly reduce inadequate reports. © 2014 John Wiley & Sons Ltd.

Comparison of Test Results for Zika Virus RNA in Urine, Serum, and Saliva Specimens from Persons with Travel-Associated Zika Virus Disease - Florida, 2016.

PubMed

Bingham, Andrea M; Cone, Marshall; Mock, Valerie; Heberlein-Larson, Lea; Stanek, Danielle; Blackmore, Carina; Likos, Anna

2016-05-13

In May 2015, Zika virus was reported to be circulating in Brazil. This was the first identified introduction of the virus in the Region of the Americas. Since that time, Zika virus has rapidly spread throughout the region. As of April 20, 2016, the Florida Department of Health Bureau of Public Health Laboratories (BPHL) has tested specimens from 913 persons who met state criteria for Zika virus testing. Among these 913 persons, 91 met confirmed or probable Zika virus disease case criteria and all cases were travel-associated (1). On the basis of previous small case studies reporting real time reverse-transcription polymerase chain reaction (RT-PCR) detection of Zika virus RNA in urine, saliva, and semen (2-6), the Florida Department of Health collected multiple specimen types from persons with suspected Zika virus disease. Test results were evaluated by specimen type and number of days after symptom onset to determine the most sensitive and efficient testing algorithm for acute Zika virus disease. Urine specimens were collected from 70 patients with suspected Zika virus disease from zero to 20 days after symptom onset. Of these, 65 (93%) tested positive for Zika virus RNA by RT-PCR. Results for 95% (52/55) of urine specimens collected from persons within 5 days of symptom onset tested positive by RT-PCR; only 56% (31/55) of serum specimens collected on the same date tested positive by RT-PCR. Results for 82% (9/11) of urine specimens collected >5 days after symptom onset tested positive by RT-PCR; none of the RT-PCR tests for serum specimens were positive. No cases had results that were exclusively positive by RT-PCR testing of saliva. BPHL testing results suggest urine might be the preferred specimen type to identify acute Zika virus disease.

ETV Program Report: Coatings for Wastewater Collection ...

EPA Pesticide Factsheets

The Standard Cement Materials, Inc. Standard Epoxy Coating 4553™ (SEC 4553) epoxy coating used for wastewater collection system rehabilitation was evaluated by EPA’s Environmental Technology Verification Program under laboratory conditions at the Center for Innovative Grouting Material and Technology (CIGMAT) Laboratory at the University of Houston. Testing was conducted over a period of six months to evaluate the coating’s (1) chemical resistance and (2) bonding strength for infrastructure applications. For chemical resistance, coated concrete and clay bricks with holidays (holes created in the coating) were used to evaluate the chemical resistance of the coating/substrate bond under a corrosive environment. Twenty coated concrete (dry and wet) and 20 coated clay brick (dry and wet) specimens were exposed to DI water and sulfuric acid solution (pH=1), and the specimens were visually inspected and weight changes measured. Evaluation of the coating-to-substrate bonding strength was determined using two modified ASTM test methods – one to determine bond strength of the coating with two specimens sandwiched together using the coating, and the second to determine the bond strength by applying a tensile load to the coating applied to specimens of each substrate. Forty-eight bonding tests were performed over the six month evaluation. The tests resulted in the following conclusions about Standard Cement’s SEC 4553 coating: • After the six-month chemi

Bacteriological monitoring of water reservoirs in oxygen humidifiers: safety of prolonged and multipatient use of prefilled disposable oxygen humidifier bottles.

PubMed

Kobayashi, Nobuharu; Yamazaki, Tsutomu; Maesaki, Shigefumi

2006-03-01

Bacterial colony counts in water specimens from oxygen humidifiers that used reusable water reservoirs were compared with counts in water specimens from humidifiers that used prefilled disposable reservoir bottles to evaluate the effects of prolonged and multipatient use of humidifiers. Bacteria were detected after 1 week of operation in water specimens collected from many humidifiers with reusable reservoirs, but no bacteria were detected in water specimens from disposable bottles for up to 12 weeks during use of the humidifier by multiple patients.

Evaluation of the enterovirus laboratory surveillance system in Denmark, 2010 to 2013.

PubMed

Condell, Orla; Midgley, Sofie; Christiansen, Claus Bohn; Chen, Ming; Chen Nielsen, Xiaohui; Ellermann-Eriksen, Svend; Mølvadgaard, Mette; Schønning, Kristian; Vermedal Hoegh, Silje; Andersen, Peter Henrik; Voldstedlund, Marianne; Fischer, Thea Kølsen

2016-05-05

The primary aim of the Danish enterovirus (EV) surveillance system is to document absence of poliovirus infection. The conflict in Syria has left many children unvaccinated and movement from areas with polio cases to Europe calls for increased awareness to detect and respond to virus-transmission in a timely manner. We evaluate the national EV laboratory surveillance, to generate recommendations for system strengthening. The system was analysed for completeness of viral typing analysis and clinical information and timeliness of specimen collection, laboratory results and reporting of clinical information. Of 23,720 specimens screened, 2,202 (9.3%) were EV-positive. Submission of cerebrospinal fluid and faecal specimens from primary diagnostic laboratories was 79.5% complete (845/1,063), and varied by laboratory and patient age. EV genotypes were determined in 68.5% (979/1,430) of laboratory-confirmed cases, clinical information was available for 63.1% (903/1,430). Primary diagnostic results were available after a median of 1.4 days, typing results after 17 days, detailed clinical information after 33 days. The large number of samples typed demonstrated continued monitoring of EV-circulation in Denmark. The system could be strengthened by increasing the collection of supplementary faecal specimens, improving communication with primary diagnostic laboratories, adapting the laboratory typing methodology and collecting clinical information with electronic forms.

Medical microbiological analysis of Apollo-Soyuz test project crewmembers

NASA Technical Reports Server (NTRS)

Taylor, G. R.; Zaloguev, S. N.

1976-01-01

The procedures and results of the Microbial Exchange Experiment (AR-002) of the Apollo-Soyuz Test Project are described. Included in the discussion of procedural aspects are methods and materials, in-flight microbial specimen collection, and preliminary analysis of microbial specimens. Medically important microorganisms recovered from both Apollo and Soyuz crewmen are evaluated.

21 CFR 862.1675 - Blood specimen collection device.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Blood specimen collection device. 862.1675 Section... Systems § 862.1675 Blood specimen collection device. (a) Identification. A blood specimen collection device is a device intended for medical purposes to collect and to handle blood specimens and to separate...

21 CFR 862.1675 - Blood specimen collection device.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Blood specimen collection device. 862.1675 Section... Systems § 862.1675 Blood specimen collection device. (a) Identification. A blood specimen collection device is a device intended for medical purposes to collect and to handle blood specimens and to separate...

21 CFR 862.1675 - Blood specimen collection device.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Blood specimen collection device. 862.1675 Section... Systems § 862.1675 Blood specimen collection device. (a) Identification. A blood specimen collection device is a device intended for medical purposes to collect and to handle blood specimens and to separate...

21 CFR 862.1675 - Blood specimen collection device.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Blood specimen collection device. 862.1675 Section... Systems § 862.1675 Blood specimen collection device. (a) Identification. A blood specimen collection device is a device intended for medical purposes to collect and to handle blood specimens and to separate...

21 CFR 862.1675 - Blood specimen collection device.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Blood specimen collection device. 862.1675 Section... Systems § 862.1675 Blood specimen collection device. (a) Identification. A blood specimen collection device is a device intended for medical purposes to collect and to handle blood specimens and to separate...

Cytological Evaluation and REBA HPV-ID HPV Testing of Newly Developed Liquid-Based Cytology, EASYPREP: Comparison with SurePath.

PubMed

Lee, Youn Soo; Gong, Gyungyub; Sohn, Jin Hee; Ryu, Ki Sung; Lee, Jung Hun; Khang, Shin Kwang; Cho, Kyung-Ja; Kim, Yong-Man; Kang, Chang Suk

2013-06-01

The objective of this study was to evaluate a newly-developed EASYPREP liquid-based cytology method in cervicovaginal specimens and compare it with SurePath. Cervicovaginal specimens were prospectively collected from 1,000 patients with EASYPREP and SurePath. The specimens were first collected by brushing for SurePath and second for EASYPREP. The specimens of both methods were diagnosed according to the Bethesda System. Additionally, we performed to REBA HPV-ID genotyping and sequencing analysis for human papillomavirus (HPV) on 249 specimens. EASYPREP and SurePath showed even distribution of cells and were equal in cellularity and staining quality. The diagnostic agreement between the two methods was 96.5%. Based on the standard of SurePath, the sensitivity, specificity, positive predictive value, and negative predictive value of EASYPREP were 90.7%, 99.2%, 94.8%, and 98.5%, respectively. The positivity of REBA HPV-ID was 49.4% and 95.1% in normal and abnormal cytological samples, respectively. The result of REBA HPV-ID had high concordance with sequencing analysis. EASYPREP provided comparable results to SurePath in the diagnosis and staining quality of cytology examinations and in HPV testing with REBA HPV-ID. EASYPREP could be another LBC method choice for the cervicovaginal specimens. Additionally, REBA HPV-ID may be a useful method for HPV genotyping.

[Experimental study and clinical application of rapid diagnosis of systemic candida albicans infection in burns by polymerase chain reaction].

PubMed

Deng, G; Zhang, Y; Xiao, G

1995-09-01

For rapid diagnosis of systemic candidiasis, the polymerase chain reaction (PCR) was used to amplify a segment of Candida albican DNA coding for the cytochrome P450 L1 A1 in vitro. The technique provided unambiguous evidence of the presence of Candida albicans in as short as 8 hours with a detection threshold of 20 organisms. 200 blood and 120 urine specimens were collected from thirty rabbits with burn and candidiasis. Specimens of blood (n = 6), urine (n = 6), sputum (n = 7) and wound exudate (n = 7) were also collected from eight serious burn patients. PCR technique was used in all the specimens, and the result was compared with conventional fungus culture. It was shown that: (1) The positive detection rate of Candida by PCR was significantly higher than by culture for blood specimens (P < 0.01) and serial specimens of urine (P < 0.05) in infected burn animals. The clinical specimens showed the same results; (2) In evaluating diagnostic value of PCR for systemic Candida albicans infection, it was found that sensitivity, accuracy and negative prediction rate were superior to the conventional culture method. These results suggest that PCR technic may provide a rapid sensitive and specific means for the diagnosis of systemic Candida albicans infection. In addition, it may be helpful in the evaluation of therapeutic response or recurrence of infection.

Endoscopic ultrasound-guided fine-needle aspiration with liquid-based cytologic preparation in the diagnosis of primary pancreatic lymphoma.

PubMed

Rossi, Esther Diana; Larghi, Alberto; Verna, Elizabeth C; Martini, Maurizio; Galasso, Domenico; Carnuccio, Antonella; Larocca, Luigi Maria; Costamagna, Guido; Fadda, Guido

2010-11-01

The diagnosis subtyping of lymphoma on specimens collected by endoscopic ultrasound fine-needle aspiration (EUS-FNA) can be extremely difficult. When a cytopathologist is available for the on-site evaluation, the diagnosis may be achieved by applying flow cytometric techniques. We describe our experience with immunocytochemistry (ICC) and molecular biology studies applied on EUS-FNA specimens processed with a liquid-based cytologic (LBC) preparation for the diagnosis of primary pancreatic lymphoma (PPL). Three patients with a pancreatic mass underwent EUS-FNA. The collected specimens were processed with the ThinPrep method for the cytologic diagnosis and eventual additional investigations. A morphologic picture consistent with PPL was found on the LBC specimens of the 3 patients. Subsequent ICC and molecular biology studies for immunoglobulin heavy chain gene rearrangement established the diagnosis of pancreatic large B-cell non-Hodgkin lymphoma in 2 patients and a non-Hodgkin lymphoma with plasmoblastic/immunoblastic differentiation in the remaining one. An LBC preparation can be used to diagnose and subtype PPL by applying ICC and molecular biology techniques to specimens collected with EUS-FNA. This method can be an additional processing method for EUS-FNA specimens in centers where on-site cytopathologist expertise is not available.

Effectiveness of Preanalytic Practices on Contamination and Diagnostic Accuracy of Urine Cultures: a Laboratory Medicine Best Practices Systematic Review and Meta-analysis

PubMed Central

Franek, Jacob; Leibach, Elizabeth K.; Weissfeld, Alice S.; Kraft, Colleen S.; Sautter, Robert L.; Baselski, Vickie; Rodahl, Debra; Peterson, Edward J.; Cornish, Nancy E.

2015-01-01

SUMMARY Background. Urinary tract infection (UTI) in the United States is the most common bacterial infection, and urine cultures often make up the largest portion of workload for a hospital-based microbiology laboratory. Appropriately managing the factors affecting the preanalytic phase of urine culture contributes significantly to the generation of meaningful culture results that ultimately affect patient diagnosis and management. Urine culture contamination can be reduced with proper techniques for urine collection, preservation, storage, and transport, the major factors affecting the preanalytic phase of urine culture. Objectives. The purposes of this review were to identify and evaluate preanalytic practices associated with urine specimens and to assess their impact on the accuracy of urine culture microbiology. Specific practices included collection methods for men, women, and children; preservation of urine samples in boric acid solutions; and the effect of refrigeration on stored urine. Practice efficacy and effectiveness were measured by two parameters: reduction of urine culture contamination and increased accuracy of patient diagnosis. The CDC Laboratory Medicine Best Practices (LMBP) initiative's systematic review method for assessment of quality improvement (QI) practices was employed. Results were then translated into evidence-based practice guidelines. Search strategy. A search of three electronic bibliographic databases (PubMed, SCOPUS, and CINAHL), as well as hand searching of bibliographies from relevant information sources, for English-language articles published between 1965 and 2014 was conducted. Selection criteria. The search contained the following medical subject headings and key text words: urinary tract infections, UTI, urine/analysis, urine/microbiology, urinalysis, specimen handling, preservation, biological, preservation, boric acid, boric acid/borate, refrigeration, storage, time factors, transportation, transport time, time delay, time factor, timing, urine specimen collection, catheters, indwelling, urinary reservoirs, continent, urinary catheterization, intermittent urethral catheterization, clean voided, midstream, Foley, suprapubic, bacteriological techniques, and microbiological techniques. Main results. Both boric acid and refrigeration adequately preserved urine specimens prior to their processing for up to 24 h. Urine held at room temperature for more than 4 h showed overgrowth of both clinically significant and contaminating microorganisms. The overall strength of this body of evidence, however, was rated as low. For urine specimens collected from women, there was no difference in rates of contamination for midstream urine specimens collected with or without cleansing. The overall strength of this evidence was rated as high. The levels of diagnostic accuracy of midstream urine collection with or without cleansing were similar, although the overall strength of this evidence was rated as low. For urine specimens collected from men, there was a reduction in contamination in favor of midstream clean-catch over first-void specimen collection. The strength of this evidence was rated as high. Only one study compared midstream collection with cleansing to midstream collection without cleansing. Results showed no difference in contamination between the two methods of collection. However, imprecision was due largely to the small event size. The diagnostic accuracy of midstream urine collection from men compared to straight catheterization or suprapubic aspiration was high. However, the overall strength of this body of evidence was rated as low. For urine specimens collected from children and infants, the evidence comparing contamination rates for midstream urine collection with cleansing, midstream collection without cleansing, sterile urine bag collection, and diaper collection pointed to larger reductions in the odds of contamination in favor of midstream collection with cleansing over the other methods of collection. This body of evidence was rated as high. The accuracy of diagnosis of urinary tract infection from midstream clean-catch urine specimens, sterile urine bag specimens, or diaper specimens compared to straight catheterization or suprapubic aspiration was varied. Authors' conclusions. No recommendation for or against is made for delayed processing of urine stored at room temperature, refrigerated, or preserved in boric acid. This does not preclude the use of refrigeration or chemical preservatives in clinical practice. It does indicate, however, that more systematic studies evaluating the utility of these measures are needed. If noninvasive collection is being considered for women, midstream collection with cleansing is recommended, but no recommendation for or against is made for midstream collection without cleansing. If noninvasive collection is being considered for men, midstream collection with cleansing is recommended and collection of first-void urine is not recommended. No recommendation for or against is made for collection of midstream urine without cleansing. If noninvasive collection is being considered for children, midstream collection with cleansing is recommended and collection in sterile urine bags, from diapers, or midstream without cleansing is not recommended. Whether midstream collection with cleansing can be routinely used in place of catheterization or suprapubic aspiration is unclear. The data suggest that midstream collection with cleansing is accurate for the diagnosis of urinary tract infections in infants and children and has higher average accuracy than sterile urine bag collection (data for diaper collection were lacking); however, the overall strength of evidence was low, as multivariate modeling could not be performed, and thus no recommendation for or against can be made. PMID:26598386

Evaluation of coproexamination as a diagnostic test for avian botulism

USGS Publications Warehouse

Jensen, Wayne I.

1981-01-01

Fecal extracts and blood sera from 113 ducks showing clinical signs of botulism were examined for Clostridium botulinum type C toxin by means of the mouse toxicity test to evaluate coproexamination as a diagnostic procedure, as compared with demonstration of toxin in serum. When death of test mice unprotected with type specific antitoxin (while protected controls survived) was the criterion, 78.8% of the sera and 5.3% of the fecal extracts were positive. When characteristic signs of intoxication in the unprotected mice was included as evidence of toxin in the specimens, these percentages increased to 86.7 and 6.2, respectively.Fecal specimens were collected hourly for the first 6 h after peroral dosing of eight mallards (Anas platyrhynchos) with 1.0 LD50, of type C toxin and at 24, 48, and 72 h from birds surviving that long. From 2 to 4 toxin-positive specimens were passed by all eight ducks during the first 6 h, five specimens were positive at 24 h, and three were positive at 48 h. Only three specimens were collected at 72 h, all of which were negative. These findings suggest that attempts to detect toxin in the feces of wild ducks might have been more successful had the birds been captured earlier in the course of the disease.

Experimental evaluation of sand fly collection and storage methods for the isolation and molecular detection of Phlebotomus-borne viruses.

PubMed

Remoli, Maria Elena; Bongiorno, Gioia; Fortuna, Claudia; Marchi, Antonella; Bianchi, Riccardo; Khoury, Cristina; Ciufolini, Maria Grazia; Gramiccia, Marina

2015-11-09

Several viruses have been recently isolated from Mediterranean phlebotomine sand flies; some are known to cause human disease while some are new to science. To monitor the Phlebotomus-borne viruses spreading, field studies are in progress using different sand fly collection and storage methods. Two main sampling techniques consist of CDC light traps, an attraction method allowing collection of live insects in which the virus is presumed to be fairly preserved, and sticky traps, an interception method suitable to collect dead specimens in high numbers, with a risk for virus viability or integrity. Sand flies storage requires a "deep cold chain" or specimen preservation in ethanol. In the present study the influence of sand fly collection and storage methods on viral isolation and RNA detection performances was evaluated experimentally. Specimens of laboratory-reared Phlebotomus perniciosus were artificially fed with blood containing Toscana virus (family Bunyaviridae, genus Phlebovirus). Various collection and storage conditions of blood-fed females were evaluated to mimic field procedures using single and pool samples. Isolation on VERO cell cultures, quantitative Real time-Retro-transcriptase (RT)-PCR and Nested-RT-PCR were performed according to techniques commonly used in surveillance studies. Live engorged sand flies stored immediately at -80 °C were the most suitable sample for phlebovirus identification by both virus isolation and RNA detection. The viral isolation rate remained very high (26/28) for single dead engorged females frozen after 1 day, while it was moderate (10/30) for specimens collected by sticky traps maintained up to 3 days at room temperature and then stored frozen without ethanol. Opposed to viral isolation, molecular RNA detection kept very high on dead sand flies collected by sticky traps when left at room temperature up to 6 days post blood meal and then stored frozen in presence (88/95) or absence (87/88) of ethanol. Data were confirmed using sand fly pools. While the collection and storage methods investigated had not much impact on the ability to detect viral RNA by molecular methods, they affected the capacity to recover viable viruses. Consequently, sand fly collection and handling procedures should be established in advance depending on the goal of the surveillance studies.

Blood-collection device for trace and ultra-trace metal specimens evaluated.

PubMed

Moyer, T P; Mussmann, G V; Nixon, D E

1991-05-01

We evaluated the evacuated phlebotomy tube designed specifically for trace metal analysis by Sherwood Medical Co. Pools of human serum containing known concentrations of aluminum, arsenic, calcium, cadmium, copper, chromium, iron, lead, magnesium, manganese, mercury, selenium, and zinc were exposed to the tube and rubber stopper for defined periods ranging from 5 min to 24 h. Analysis for each element was performed in a randomized fashion under rigidly controlled conditions by use of standard electrothermal atomization atomic absorption spectroscopy, inductively coupled plasma atomic emission spectroscopy, and cold vapor atomic absorption spectrometry. In addition, for comparative purposes, we collected blood samples from normal volunteers by use of ultra-clean polystyrene phlebotomy syringes as well as standard evacuated phlebotomy tubes. We conclude that, except for lead, there was no significant contribution of any trace element studied from the evaluated tube and stopper to the serum. Because whole blood is the usual specimen for lead testing, the observation of a trace amount of lead in this tube designed for serum collection is trivial.

Restoration of an academic historical gross pathology collection-refreshed impact on current medical teaching?

PubMed

Eichhorn, Philip; Andraschke, Udo; Dross, Fritz; Geppert, Carol I; Hartmann, Arndt; Rau, Tilman T

2018-05-10

The declaration of Leiden pronounces the demand to conserve pathological-anatomical collections as cultural heritage. Likewise, the Institute of Pathology of the Friedrich-Alexander-University Erlangen-Nuremberg owns macroscopic pathological-anatomical specimens reaching back over 150 years. The purpose of this work is to examine the impact, meaning, and perception of such historical preparations during the current medical curriculum. Additionally, the experiences from the renovation process can be used as a template for other institutes. All preparations were documented, photographed, and catalogued in an electronic database. During a restoration period, a series of didactically suitable specimens were professionally restored. Hereby, the help of a special course of interested students was admitted. In a second step, the specimens were integrated into the regular teaching of students in macroscopic pathology. An evaluation was carried out on two student cohorts with and without historical specimens by means of a questionnaire with 23 items and two free text fields. In total, 1261 specimens were registered covering diseases from almost the complete human body with a strong representation of the cardiovascular, urinary, gastrointestinal, and central nervous systems. Hereby, exceptional rare and untreated cases with medical relevance could be found and stepwise implemented into the curriculum. The student evaluation positively addressed that the courses became livelier and interactive. Furthermore, a more comprehensive overview and a better understanding of the macroscopic pathology were appreciated. However, more self-study time with the specimen was demanded. The authenticity of historical specimens contrasts with the tendency to carry out virtual "online" didactic methods. The stereoscopic view on often untreated and, therefore, unbiased cases enhances a skill-oriented deeper understanding of diseases. In conclusion, historical specimens regain interest and even didactic value, especially in an era of declining autopsy rates.

Results of a pilot study using self-collected mid-turbinate nasal swabs for detection of influenza virus infection among pregnant women.

PubMed

Thompson, Mark G; Ferber, Jeannette R; Odouli, Roxana; David, Donna; Shifflett, Pat; Meece, Jennifer K; Naleway, Allison L; Bozeman, Sam; Spencer, Sarah M; Fry, Alicia M; Li, De-Kun

2015-05-01

We evaluated the feasibility of asking pregnant women to self-collect and ship respiratory specimens. In a preliminary laboratory study, we compared the RT-PCR cycle threshold (CT) values of influenza A and B viruses incubated at 4 storage temperatures (from 4 to 35°C) for 6 time periods (8, 24, 48, 72, and 168 hours and 30 days), resulting in 24 conditions that were compared to an aliquot tested after standard freezing (-20°C) (baseline condition). In a subsequent pilot study, during January-February, 2014, we delivered respiratory specimen collection kits to 53 pregnant women with a medically attended acute respiratory illness using three delivery methods. CT values were stable after storage at temperatures <27°C for up to 72 hours for influenza A viruses and 48 hours for influenza B viruses. Of 53 women who received kits during the pilot, 89% collected and shipped nasal swabs as requested. However, 30% (14/47) of the women took over 2 days to collect and ship their specimen. The human control gene, ribonuclease P (RNase P), was detected in 100% of nasal swab specimens. However, the mean CT values for RNase P (26.5, 95% confidence interval [CI] = 26.0-27.1) and for the 8 influenza A virus positives in our pilot (32.2, 95% CI = 28.9-35.5) were significantly higher than the CTs observed in our 2010-2012 study using staff-collected nasal pharyngeal swabs (P-values < 0.01). Self-collection of respiratory specimens is a promising research method, but further research is needed to quantify the sensitivity and specificity of the approach. © 2015 The Authors. Influenza and Other Respiratory Viruses Published by John Wiley & Sons Ltd.

Computer vision applied to herbarium specimens of German trees: testing the future utility of the millions of herbarium specimen images for automated identification.

PubMed

Unger, Jakob; Merhof, Dorit; Renner, Susanne

2016-11-16

Global Plants, a collaborative between JSTOR and some 300 herbaria, now contains about 2.48 million high-resolution images of plant specimens, a number that continues to grow, and collections that are digitizing their specimens at high resolution are allocating considerable recourses to the maintenance of computer hardware (e.g., servers) and to acquiring digital storage space. We here apply machine learning, specifically the training of a Support-Vector-Machine, to classify specimen images into categories, ideally at the species level, using the 26 most common tree species in Germany as a test case. We designed an analysis pipeline and classification system consisting of segmentation, normalization, feature extraction, and classification steps and evaluated the system in two test sets, one with 26 species, the other with 17, in each case using 10 images per species of plants collected between 1820 and 1995, which simulates the empirical situation that most named species are represented in herbaria and databases, such as JSTOR, by few specimens. We achieved 73.21% accuracy of species assignments in the larger test set, and 84.88% in the smaller test set. The results of this first application of a computer vision algorithm trained on images of herbarium specimens shows that despite the problem of overlapping leaves, leaf-architectural features can be used to categorize specimens to species with good accuracy. Computer vision is poised to play a significant role in future rapid identification at least for frequently collected genera or species in the European flora.

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

PubMed

Gros, Nataša

2013-05-01

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

Comparison of blood specimens from plain and gel vacuum blood collection tubes.

PubMed

Wiwanitkit, V

2001-05-01

This study was set in the Division of Laboratory Medicine, Chulalongkorn Hospital. All 2,000 blood specimens were randomly collected using evacuated blood collection by plain or gel vacuum tubes. After collection, each specimen was considered and judged using criteria of specimen rejection to determine how proper the specimen presentations were. All data were reviewed, collected and interpreted. It revealed that there were only 20 (1%) improper specimens and all were improper in quality. There was no significant difference between the ratio of improper specimens in both groups (P > 0.30). From this study, it revealed that efficacy of both types of vacuum tubes was not different. The new gel vacuum tube seems to be an effective tool in the evacuated blood collection system due to its advantage in reduction of time in specimen processing.

Thick Concrete Specimen Construction, Testing, and Preliminary Analysis

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

Clayton, Dwight A.; Hoegh, Kyle; Khazanovich, Lev

The purpose of the U.S. Department of Energy Office of Nuclear Energy’s Light Water Reactor Sustainability (LWRS) Program is to develop technologies and other solutions that can improve the reliability, sustain the safety, and extend the operating lifetimes of nuclear power plants (NPPs) beyond 60 years. Since many important safety structures in an NPP are constructed of concrete, inspection techniques must be developed and tested to evaluate the internal condition. In-service containment structures generally do not allow for the destructive measures necessary to validate the accuracy of these inspection techniques. This creates a need for comparative testing of the variousmore » nondestructive evaluation (NDE) measurement techniques on concrete specimens with known material properties, voids, internal microstructure flaws, and reinforcement locations. A preliminary report detailed some of the challenges associated with thick reinforced concrete sections and prioritized conceptual designs of specimens that could be fabricated to represent NPP concrete structures for using in NDE evaluation comparisons. This led to the construction of the concrete specimen presented in this report, which has sufficient reinforcement density and cross-sectional size to represent an NPP containment wall. Details on how a suitably thick concrete specimen was constructed are presented, including the construction materials, final nominal design schematic, as well as formwork and rigging required to safely meet the desired dimensions of the concrete structure. The report also details the type and methods of forming the concrete specimen as well as information on how the rebar and simulated defects were embedded. Details on how the resulting specimen was transported, safely anchored, and marked to allow access for systematic comparative NDE testing of defects in a representative NPP containment wall concrete specimen are also given. Data collection using the MIRA Ultrasonic NDE equipment and initial results are also presented along with a discussion of the preliminary findings. Comparative NDE of various defects in reinforced concrete specimens is a key component in identifying the most promising techniques and directing the research and development efforts needed to characterize concrete degradation in commercial NPPs. This requires access to the specimens for data collection using state-of-the-art technology. The construction of the specimen detailed in this report allows for an evaluation of how different NDE techniques may interact with the size and complexities of NPP concrete structures. These factors were taken into account when determining specimen size and features to ensure a realistic design. The lateral dimensions of the specimen were also chosen to mitigate unrealistic boundary effects that would not affect the results of field NPP concrete testing. Preliminary results show that, while the current methods are able to identify some of the deeper defects, improvements in data processing or hardware are necessary to be able to achieve the precision and reliability achieved in evaluating thinner and less heavily reinforced concrete structures.« less

SurePath Specimens Versus ThinPrep Specimen Types on the COBAS 4800 Platform: High-Risk HPV Status and Cytology Correlation in an Ethnically Diverse Bronx Population.

PubMed

Naeem, R C; Goldstein, D Y; Einstein, Mark H; Ramos Rivera, G; Schlesinger, K; Khader, S N; Suhrland, M; Fox, A S

2017-08-01

To compare the cytologic preparations of 130 cervical specimens (from women of various ethnicities at high risk for human papillomavirus [HPV] infection) using the SurePath (SP) collection system with specimens gathered using the ThinPrep (TP) system, as processed on the Cobas 4800 analyzer, to determine which collection method more accurately identifies HPV infection. In our prospective study, specimens were collected from 130 women of various ethnicities residing in or near Bronx County, NY. The SP-collected specimen was first processed for cytologic findings; if clinical HPV testing was requested on that specimen, it was tested using Hybrid Capture II (HC2) methodology. We tested the remnant SP-collected cell concentrate using the Cobas analyzer. Then, the TP-collected and SP-collected specimens were tested in the same run on that analyzer, and the results were compared. We also compared the results with the concurrent cytologic findings. The results were concordant for overall HR-HPV status in 93.8% of cases. Also, a statistically significant lower cycle threshold value was observed with Cobas testing of specimen concentrates tested via the BD SurePath Pap Test (P = .001), suggesting higher sensitivity compared with specimens tested via the ThinPrep Pap Test. Cobas 4800 HPV testing of SP-collected specimen concentrates yields comparable results to TP-collected specimen concentrates. Based on the limited data that we derived, SP collection may be a more favorable methodology than TP collection for HPV testing of individuals at high risk in our ethnically diverse, urban patient population. © American Society for Clinical Pathology, 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

Recommendations for clinical biomarker specimen preservation and stability assessments.

PubMed

Dakappagari, Naveen; Zhang, Hui; Stephen, Laurie; Amaravadi, Lakshmi; Khan, Masood U

2017-04-01

With the wide use of biomarkers to enable critical drug-development decisions, there is a growing concern from scientific community on the need for a 'standardized process' for ensuring biomarker specimen stability and hence, a strong desire to share best practices on preserving the integrity of biomarker specimens in clinical trials and the design of studies to evaluate analyte stability. By leveraging representative industry experience, we have attempted to provide an overview of critical aspects of biomarker specimen stability commonly encountered during clinical development, including: planning of clinical sample collection procedures, clinical site training, selection of sample preservation buffers, shipping logistics, fit-for-purpose stability assessments in the analytical laboratory and presentation of case studies covering widely utilized biomarker specimen types.

In vitro biomechanical evaluations of screw-bar-polymethylmethacrylate and pin-polymethylmethacrylate internal fixation implants used to stabilize the vertebral motion unit of the fourth and fifth cervical vertebrae in vertebral column specimens from dogs.

PubMed

Hicks, Daniel G; Pitts, Marvin J; Bagley, Rodney S; Vasavada, Anita; Chen, Annie V; Wininger, Fred A; Simon, Julianna C

2009-06-01

To determine the change in stiffness as evaluated by the dorsal bending moment of cervical vertebral specimens obtained from canine cadavers after internally stabilizing the vertebral motion unit (VMU) of C4 and C5 with a traditional pin-polymethylmethacrylate (PMMA) fixation implant or a novel screw-bar-PMMA fixation implant. 12 vertebral column specimens (C3 through C6) obtained from canine cadavers. A dorsal bending moment was applied to the vertebral specimens before and after fixation of the VMU of C4 and C5 by use of a traditional pin-PMMA implant or a novel screw-bar-PMMA implant. Biomechanical data were collected and compared within a specimen (unaltered vs treated) and between treatment groups. Additionally, implant placement was evaluated after biomechanical testing to screen for penetration of the transverse foramen or vertebral canal by the pins or screws. Treated vertebral specimens were significantly stiffer than unaltered specimens. There was no significant difference in stiffness between vertebral specimen groups after treatment. None of the screws in the novel screw-bar-PMMA implant group penetrated the transverse foramen or vertebral canal, whereas there was mild to severe penetration for 22 of 24 (92%) pins in the traditional pin-PMMA implant group. Both fixation treatments altered the biomechanical properties of the cervical vertebral specimens as evaluated by the dorsal bending moment. There was reduced incidence of penetration of the transverse foramen or vertebral canal with the novel screw-bar-PMMA implant, compared with the incidence for the traditional pin-PMMA implant.

10 CFR 26.115 - Collecting a urine specimen under direct observation.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 1 2014-01-01 2014-01-01 false Collecting a urine specimen under direct observation. 26.115 Section 26.115 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.115 Collecting a urine specimen under direct observation. (a) Procedures for...

10 CFR 26.115 - Collecting a urine specimen under direct observation.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 1 2013-01-01 2013-01-01 false Collecting a urine specimen under direct observation. 26.115 Section 26.115 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.115 Collecting a urine specimen under direct observation. (a) Procedures for...

10 CFR 26.115 - Collecting a urine specimen under direct observation.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 1 2012-01-01 2012-01-01 false Collecting a urine specimen under direct observation. 26.115 Section 26.115 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.115 Collecting a urine specimen under direct observation. (a) Procedures for...

10 CFR 26.115 - Collecting a urine specimen under direct observation.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false Collecting a urine specimen under direct observation. 26.115 Section 26.115 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.115 Collecting a urine specimen under direct observation. (a) Procedures for...

10 CFR 26.115 - Collecting a urine specimen under direct observation.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Collecting a urine specimen under direct observation. 26.115 Section 26.115 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.115 Collecting a urine specimen under direct observation. (a) Procedures for...

Evaluation of specimen preservatives for DNA analyses of bees

USGS Publications Warehouse

Frampton, M.; Droege, S.; Conrad, T.; Prager, S.; Richards, M.H.

2008-01-01

Large-scale insect collecting efforts that are facilitated by the use of pan traps result in large numbers of specimens being collected. Storage of these specimens can be problematic if space and equipment are limited. In this study, we investigated the effects of various preservatives (alcohol solutions and DMSO) on the amount and quality of DNA extracted from bees (specifically Halictidae, Apidae, and Andrenidae). In addition, we examined the amount and quality of DNA obtained from bee specimens killed and stored at -80 degrees C and from specimens stored for up to 24 years in ethanol. DNA quality was measured in terms of how well it could be PCR-amplified using a set of mitochondrial primers that are commonly used in insect molecular systematics. Overall the best methods of preservation were ultra-cold freezing and dimethyl sulfoxide, but these are both expensive and in the case of ultra-cold freezing, somewhat impractical for field entomologists. Additionally, dimethyl sulfoxide was shown to have adverse effects on morphological characters that are typically used for identification to the level of species. We therefore recommend that the best alternative is 95% ethanol, as it preserves bee specimens well for both morphological and molecular studies.

Characterization of specimens obtained by different sampling methods for evaluation of periodontal bacteria.

PubMed

Okada, Ayako; Sogabe, Kaoru; Takeuchi, Hiroaki; Okamoto, Masaaki; Nomura, Yoshiaki; Hanada, Nobuhiro

2017-12-27

Quantitative analysis of periodontal bacteria is considered useful for clinical diagnosis, evaluation and assessment of the risk of periodontal disease. The purpose of this study was to compare the effectiveness of sampling of saliva, supragingival and subgingival plaque for evaluation of periodontal bacteria. From each of 12 subjects, i) subgingival plaque was collected from the deepest pocket using a sterile paper point, ii) stimulated whole saliva was collected after chewing gum, and iii) supragingival plaque was collected using a tooth brush. These samples were sent to the medical examination laboratory for quantitative analysis of the counts of three periodontal bacterial species: Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia. The proportions of these bacteria in subgingival plaque were higher than those in saliva or supragingival plaque, but lower in subgingival plaque than in saliva or supragingival plaque. In several cases, periodontal bacteria were below the levels of detection in subgingival plaque. We concluded that samples taken from subgingival plaque may be more useful for evaluating the proportion of periodontal bacteria in deep pockets than is the case for other samples. Therefore, for evaluation of periodontal bacteria, clinicians should consider the characteristics of the specimens obtained using different sampling methods.

Guidelines for quality assurance and quality control of fish taxonomic data collected as part of the National Water-Quality Assessment Program

USGS Publications Warehouse

Walsh, Stephen Joseph; Meador, Michael R.

1998-01-01

Fish community structure is characterized by the U.S. Geological Survey's National Water-Quality Assessment (NAWQA) Program as part of a perennial, multidisciplinary approach to evaluating the physical, chemical, and biological conditions of the Nation's water resources. The objective of quality assurance and quality control of fish taxonomic data that are collected as part of the NAWQA Program is to establish uniform guidelines and protocols for the identification, processing, and archiving of fish specimens to ensure that accurate and reliable data are collected. Study unit biologists, collaborating with regional biologists and fish taxonomic specialists, prepare a pre-sampling study plan that includes a preliminary faunal list and identification of an ichthyological curation center for receiving preserved fish specimens. Problematic taxonomic issues and protected taxa also are identified in the study plan, and collecting permits are obtained in advance of sampling activities. Taxonomic specialists are selected to identify fish specimens in the field and to assist in determining what fish specimens should be sacrificed, fixed, and preserved for laboratory identification, independent taxonomic verification, and long-term storage in reference or voucher collections. Quantitative and qualitative sampling of fishes follows standard methods previously established for the NAWQA Program. Common ichthyological techniques are used to process samples in the field and prepare fish specimens to be returned to the laboratory or sent to an institutional repository. Taxonomic identifications are reported by using a standardized list of scientific names that provides nomenclatural consistency and uniformity across study units.

Specimen plastic containers used to store expressed breast milk in neonatal care units: a case of precautionary principle.

PubMed

Blouin, Mélissa; Coulombe, Martin; Rhainds, Marc

2014-05-09

Breast milk is the only milk that meets both the nutritional and immunitary needs of infants. Since breastfeeding is widely promoted, public health measures to preserve the nutritional qualities of expressed breast milk (EBM) should be applied in hospital care settings. The Health Technology Assessment Unit (HTAU) of the Centre hospitalier universitaire de Québec was requested by the Neonatal Care Unit to assess the acceptability of a plastic specimen container, designed to harvest tissues and body fluids, for storing collected EBM. An evidence-based public health perspective approach was taken to evaluate the safety of the specimen container. The HTAU recommended that plastic specimen containers no longer be used for storing EBM and that other options should be evaluated for neonatal care units. These recommendations are in accordance with the public health precaution principle and with legal considerations.

Cytomorphological identification of advanced pulmonary adenocarcinoma harboring KRAS mutation in lymph node fine-needle aspiration specimens: Comparative investigation of adenocarcinoma with KRAS and EGFR mutations.

PubMed

Song, Dae Hyun; Lee, Boram; Shin, Yooju; Choi, In Ho; Ha, Sang Yun; Lee, Jae Jun; Hong, Min Eui; Choi, Yoon-La; Han, Joungho; Um, Sang-Won

2015-07-01

Kirsten rat sarcoma 2 viral oncogene homolog (KRAS) mutation in pulmonary adenocarcinoma is clinically important due to its association with resistance to EGFR inhibitors and poor prognosis. To our knowledge, there has not been a comparative study focusing on cytological nuclear features of pulmonary adenocarcinoma harboring KRAS mutation (KRAS-AD). Hence, we compared the cytomorphology of metastatic KRAS-AD and EGFR-positive adenocarcinoma (EGFR-AD) in aspiration specimens from lymph nodes. Forty lymph node aspiration specimens from forty KRAS-AD patients were collected at Samsung Medical Center (Seoul, Korea) from 2009 to 2013. As a control group, 40 EBUS-FNA lymph node specimens from 20 EGFR-AD patients were collected. EGFR-AD specimens were evaluated at Samsung Medical Center (Seoul, Korea) from 2012 to 2013. All 80 specimens were histologically confirmed to metastatic adenocarcinoma. Two pathologists performed a blinded review of all specimens. Compared with EGFR-AD, KRAS-AD exhibited more severe nuclear pleomorphism (P < 0.001), coarse chromatin (P = 0.001), cherry-red nucleoli (P < 0.001) and naked tumor cells (P = 0.002) with necrotic (P < 0.001) and neutrophilic (P = 0.008) background. Our study provides the first demonstration of cytomorphologic differentiation between metastatic KRAS-AD and metastatic EGFR-AD in lymph node aspiration specimens. © 2014 Wiley Periodicals, Inc.

10 CFR 26.89 - Preparing to collect specimens for testing.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 1 2014-01-01 2014-01-01 false Preparing to collect specimens for testing. 26.89 Section 26.89 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.89 Preparing to collect specimens for testing. (a) When an individual has been notified of a...

10 CFR 26.83 - Specimens to be collected.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 1 2012-01-01 2012-01-01 false Specimens to be collected. 26.83 Section 26.83 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.83 Specimens to be collected. Except as permitted under § 26.31(d)(5), licensees and other entities who are...

10 CFR 26.89 - Preparing to collect specimens for testing.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 1 2012-01-01 2012-01-01 false Preparing to collect specimens for testing. 26.89 Section 26.89 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.89 Preparing to collect specimens for testing. (a) When an individual has been notified of a...

10 CFR 26.107 - Collecting a urine specimen.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 1 2013-01-01 2013-01-01 false Collecting a urine specimen. 26.107 Section 26.107 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.107 Collecting a urine specimen. (a) The collector shall direct the donor to go into the room or stall used for...

10 CFR 26.83 - Specimens to be collected.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 1 2014-01-01 2014-01-01 false Specimens to be collected. 26.83 Section 26.83 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.83 Specimens to be collected. Except as permitted under § 26.31(d)(5), licensees and other entities who are...

10 CFR 26.107 - Collecting a urine specimen.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 1 2012-01-01 2012-01-01 false Collecting a urine specimen. 26.107 Section 26.107 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.107 Collecting a urine specimen. (a) The collector shall direct the donor to go into the room or stall used for...

10 CFR 26.83 - Specimens to be collected.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 1 2013-01-01 2013-01-01 false Specimens to be collected. 26.83 Section 26.83 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.83 Specimens to be collected. Except as permitted under § 26.31(d)(5), licensees and other entities who are...

10 CFR 26.89 - Preparing to collect specimens for testing.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 1 2013-01-01 2013-01-01 false Preparing to collect specimens for testing. 26.89 Section 26.89 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.89 Preparing to collect specimens for testing. (a) When an individual has been notified of a...

10 CFR 26.107 - Collecting a urine specimen.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 1 2014-01-01 2014-01-01 false Collecting a urine specimen. 26.107 Section 26.107 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.107 Collecting a urine specimen. (a) The collector shall direct the donor to go into the room or stall used for...

10 CFR 26.89 - Preparing to collect specimens for testing.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Preparing to collect specimens for testing. 26.89 Section 26.89 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.89 Preparing to collect specimens for testing. (a) When an individual has been notified of a...

10 CFR 26.107 - Collecting a urine specimen.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Collecting a urine specimen. 26.107 Section 26.107 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.107 Collecting a urine specimen. (a) The collector shall direct the donor to go into the room or stall used for...

10 CFR 26.107 - Collecting a urine specimen.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false Collecting a urine specimen. 26.107 Section 26.107 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.107 Collecting a urine specimen. (a) The collector shall direct the donor to go into the room or stall used for...

10 CFR 26.83 - Specimens to be collected.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false Specimens to be collected. 26.83 Section 26.83 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.83 Specimens to be collected. Except as permitted under § 26.31(d)(5), licensees and other entities who are...

10 CFR 26.83 - Specimens to be collected.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Specimens to be collected. 26.83 Section 26.83 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.83 Specimens to be collected. Except as permitted under § 26.31(d)(5), licensees and other entities who are...

10 CFR 26.89 - Preparing to collect specimens for testing.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false Preparing to collect specimens for testing. 26.89 Section 26.89 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.89 Preparing to collect specimens for testing. (a) When an individual has been notified of a...

Improved sensitivity of vaginal self-collection and high-risk human papillomavirus testing.

PubMed

Belinson, Jerome L; Du, Hui; Yang, Bin; Wu, Ruifang; Belinson, Suzanne E; Qu, Xinfeng; Pretorius, Robert G; Yi, Xin; Castle, Philip E

2012-04-15

Self-collected vaginal specimens tested for high-risk human papillomavirus (HR-HPV) have been shown to be less sensitive for the detection of cervical intraepithelial neoplasia or cancer (≥CIN 3) than physician-collected endocervical specimens. To increase the sensitivity of self-collected specimens, we studied a self-sampling device designed to obtain a larger specimen from the upper vagina (POI/NIH self-sampler) and a more sensitive polymerase chain reaction (PCR)-based HR-HPV assay. Women (10,000) were screened with cervical cytology and HR-HPV testing of vaginal self-collected and endocervical physician-collected specimens. Women were randomly assigned to use either a novel self-collection device (POI/NIH self-sampler) or conical-shaped brush (Qiagen). The self-collected and clinician-collected specimens were assayed by Cervista (Hologic) and the research only PCR-based matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF). Women with any abnormal screening test underwent colposcopy and biopsy. Women (8,556), mean age of 38.9, had complete data; 1.6% had ≥ CIN 3. For either HR-HPV assay, the sensitivity was similar for the two self-collection devices. Tested with Cervista, the sensitivity for ≥CIN 3 of self-collected specimens was 70.9% and for endocervical specimens was 95.0% (p = 0.0001). Tested with MALDI-TOF, the sensitivity for ≥CIN 3 of self-collected specimens was 94.3% and for endocervical specimens was also 94.3% (p = 1.0). A self-collected sample using a PCR-based assay with the capability of very high throughput has similar sensitivity as a direct endocervical specimen obtained by a physician. Large population-based screening "events" in low-resource settings could be achieved by promoting self-collection and centralized high-throughput, low-cost testing by PCR-based MALDI-TOF. Copyright © 2011 UICC.

Evaluation of the Becton-Dickinson rapid serum tube: does it provide a suitable alternative to lithium heparin plasma tubes?

PubMed

Dimeski, Goce; Masci, Paul P; Trabi, Manuela; Lavin, Martin F; de Jersey, John

2010-05-01

Obtaining a suitable specimen for analysis in a timely manner is pivotal in clinical chemistry service provision. Serum is recognized as the preferred specimen for most assays, but because of time constraints for completion of clotting and an increasing number of patients on anti-coagulant therapy, latent clotting or no clotting is an outcome which can lead to errors and delay in delivery of critical results. Although lithium heparin plasma has unique problems, it has become an alternative in hospital-based laboratories. The Becton-Dickinson (BD) rapid serum tube (RST) was evaluated in a hospital environment using a total of 53 participants, both healthy and anticoagulated, for 31 analytes against BD PST II and BD SST II tubes measured with Beckman DxC800 and DxI800 analyzers. Most results from the RST tube were comparable with those from the SST II tube. Potassium results were closer to the PST II plasma concentrations. Incomplete and latent clotting was encountered in the RST specimens from participants (cardiac and dialysis) who had received a total of >7000 units of heparin [activated partial thromboplastin time (APTT) >150 s], warfarin/heparin combination, and specimens from cardiac surgery patients who had received a total of >25,000 units of heparin (APTT >200 s) at the time of collection of specimens. The RST tube provides a suitable alternative to lithium heparin plasma tubes for most patients in a hospital environment. However, latent clotting continued to occur in specimens collected from participants who had received high concentrations of anticoagulants.

Multicenter Evaluation of BD Max Enteric Parasite Real-Time PCR Assay for Detection of Giardia duodenalis, Cryptosporidium hominis, Cryptosporidium parvum, and Entamoeba histolytica

PubMed Central

Relich, R. F.; Doyle, L.; Espina, N.; Fuller, D.; Karchmer, T.; Lainesse, A.; Mortensen, J. E.; Pancholi, P.; Veros, W.; Harrington, S. M.

2016-01-01

Common causes of chronic diarrhea among travelers worldwide include protozoan parasites. The majority of parasitic infections are caused by Giardia duodenalis, Entamoeba histolytica, Cryptosporidium parvum, and Cryptosporidium hominis. Similarly, these species cause the majority of parasitic diarrhea acquired in the United States. Detection of parasites by gold standard microscopic methods is time-consuming and requires considerable expertise; enzyme immunoassays and direct fluorescent-antibody (DFA) stains have lowered hands-on time for testing, but improvements in sensitivity and technical time may be possible with a PCR assay. We performed a clinical evaluation of a multiplex PCR panel, the enteric parasite panel (EPP), for the detection of these common parasites using the BD Max instrument, which performs automated extraction and amplification. A total of 2,495 compliant specimens were enrolled, including 2,104 (84%) specimens collected prospectively and 391 (16%) specimens collected retrospectively. Approximately equal numbers were received in 10% formalin (1,273 specimens) and unpreserved (1,222 specimens). The results from the EPP were compared to those from alternate PCR and bidirectional sequencing (APCR), as well as DFA (G. duodenalis and C. parvum or C. hominis) or trichrome stain (E. histolytica). The sensitivity and specificity for prospective and retrospective specimens combined were 98.2% and 99.5% for G. duodenalis, 95.5% and 99.6 for C. parvum or C. hominis, and 100% and 100% for E. histolytica, respectively. The performance of the FDA-approved BD Max EPP compared well to the reference methods and may be an appropriate substitute for microscopic examination or immunoassays. PMID:27535690

Assessment of Breast Specimens With or Without Calcifications in Diagnosing Malignant and Atypia for Mammographic Breast Microcalcifications Without Mass: A STARD-Compliant Diagnostic Accuracy Article.

PubMed

Cheung, Yun-Chung; Juan, Yu-Hsiang; Ueng, Shir-Hwa; Lo, Yung-Feng; Huang, Pei-Chin; Lin, Yu-Ching; Chen, Shin-Cheh

2015-10-01

Presence of microcalcifications within the specimens frequently signifies a successful attempt of stereotactic vacuum-assisted breast biopsy (VABB) in obtaining a pathologic diagnosis of the breast microcalcifications. In this study, the authors aimed to assess and compare the accuracy and consistency of calcified or noncalcified specimens obtained from same sites of sampling on isolated microcalcifications without mass in diagnosing high-risk and malignant lesions. To the best of our knowledge, an individual case-based prospective comparison has not been reported.With the approval from institutional review board of our hospital (Chang Gung Memorial Hospital), the authors retrospectively reviewed all clinical cases of stereotactic VABBs on isolated breast microcalcifications without mass from our database. The authors included those having either surgery performed or had clinical follow-up of at least 3 years for analysis. All the obtained specimens with or without calcification were identified using specimen radiographs and separately submitted for pathologic evaluation. The concordance of diagnosis was assessed for both atypia and malignant lesions.A total of 390 stereotactic VABB procedures (1206 calcified and 1456 noncalcified specimens) were collected and reviewed. The consistent rates between calcified and noncalcified specimens were low for atypia and malignant microcalcifications (44.44% in flat epithelial atypia, 46.51% in atypical ductal hyperplasia, 55.73% in ductal carcinoma in situ, and 71.42% in invasive ductal carcinoma). The discordance in VABB diagnoses indicated that 41.33% of malignant lesions would be misdiagnosed by noncalcified specimens. Furthermore, calcified specimens showed higher diagnostic accuracy of breast cancer as compared with the noncalcified specimens (91.54 % versus 69.49%, respectively). The evaluation of both noncalcified specimens and calcified specimens did not show improvement of diagnostic accuracy as compared with evaluating calcified specimens alone (91.54% versus 91.54%, respectively).The high prevalence of diagnostic discordance between the calcified and noncalcified specimens indicated the higher value of calcified specimens in diagnosing atypia and malignant microcalcifications. Noncalcified specimens did not provide additional diagnostic benefit from this study. The separation of calcified and noncalcified specimens may facilitate more focused interpretation from pathologists among the large number of specimens.

A new HPLC-DAD-MS/MS method for the simultaneous determination of major compounds in the crude extract of Lychnophora salicifolia Mart. (Brazilian arnicão) leaves: application to chemical variability evaluation.

PubMed

Gouvea, Dayana Rubio; Meloni, Fernando; Ribeiro, Arthur de Barros Bello; Lopes, João Luis Callegari; Lopes, Norberto Peporine

2012-10-20

Lychnophora salicifolia Mart., which occurs in the Brazilian Cerrado in the states of Bahia and Minas Gerais as well as in the southeast of the state of Goiás, is the most widely distributed and also the most polymorphic species of the genus. This plant is popularly known to have anti-inflammatory and analgesic activities. In this work, we have studied the variation in terms of polar metabolites of ninety-three Lychnophora salicifolia Mart. specimens collected from different regions of the Brazilian Cerrado. Identification of the constituents of this mixture was carried out by analysis of the UV spectra and MS data after chromatographic separation. Twenty substances were identified, including chlorogenic acid derivatives, a flavonoid C-glucoside, and other sesquiterpenes. The analytical method was validated, and the reliability and credibility of the results was ensured for the purposes of this study. The concentration range required for analysis of content variability within the analyzed group of specimens was covered with appropriate values of limits of detection and quantitation, as well as satisfactory precision and recovery. A quantitative variability was observed among specimens collected from the same location, but on average they were similar from a chemical viewpoint. In relation to the study involving specimens from different locations, there were both qualitative and quantitative differences among plants collected from different regions of Brazil. Statistical analysis revealed that there is a correlation between geographical localization and polar metabolites profile for specimens collected from different locations. This is evidence that the pattern of metabolites concentration depends on the geographical distribution of the specimens. Copyright © 2012 Elsevier B.V. All rights reserved.

A new concept and a comprehensive evaluation of SYSMEX UF-1000i  flow cytometer to identify culture-negative urine specimens in patients with UTI.

PubMed

Monsen, T; Ryden, P

2017-09-01

Urinary tract infections (UTIs) are among the most common bacterial infections in men and urine culture is gold standard for diagnosis. Considering the high prevalence of culture-negative specimens, any method that identifies such specimens is of interest. The aim was to evaluate a new screening concept for flow cytometry analysis (FCA). The outcomes were evaluated against urine culture, uropathogen species and three conventional screening methods. A prospective, consecutive study examined 1,312 urine specimens, collected during January and February 2012. The specimens were analyzed using the Sysmex UF1000i FCA. Based on the FCA data culture negative specimens were identified in a new model by use of linear discriminant analysis (FCA-LDA). In total 1,312 patients were included. In- and outpatients represented 19.6% and 79.4%, respectively; 68.3% of the specimens originated from women. Of the 610 culture-positive specimens, Escherichia coli represented 64%, enterococci 8% and Klebsiella spp. 7%. Screening with FCA-LDA at 95% sensitivity identified 42% (552/1312) as culture negative specimens when UTI was defined according to European guidelines. The proposed screening method was either superior or similar in comparison to the three conventional screening methods. In conclusion, the proposed/suggested and new FCA-LDA screening method was superior or similar to three conventional screening methods. We recommend the proposed screening method to be used in clinic to exclude culture negative specimens, to reduce workload, costs and the turnaround time. In addition, the FCA data may add information that enhance handling and support diagnosis of patients with suspected UTI pending urine culture [corrected].

Factors influencing the time between onset of illness and specimen collection in the diagnosis of non-pregnancy associated listeriosis in England and Wales.

PubMed

Awofisayo-Okuyelu, Adedoyin; Verlander, Neville Q; Amar, Corinne; Elson, Richard; Grant, Kathie; Harris, John

2016-06-24

Listeriosis is an opportunistic bacterial infection caused by Listeria monocytogenes and predominantly affects people who are immunocompromised. Due to its severity and the population at risk, prompt clinical diagnosis and treatment of listeriosis is essential. A major step to making a clinical diagnosis is the collection of the appropriate specimen(s) for testing. This study explores factors that may influence the time between onset of illness and collection of specimen in order to inform clinical policy and develop necessary interventions. Enhanced surveillance data on non-pregnancy associated listeriosis in England and Wales between 2004 and 2013 were collected and analysed. The difference in days between onset of symptoms and collection of specimen was calculated and factors influencing the time difference were identified using a gamma regression model. The median number of days between onset of symptoms and collection of specimen was two days with 27.1 % of cases reporting one day between onset of symptoms and collection of specimen and 18.8 % of cases reporting more than seven days before collection of specimen. The median number of days between onset of symptoms and collection of specimen was shorter for cases infected with Listeria monocytogenes serogroup 1/2b (one day) and cases with an underlying condition (one day) compared with cases infected with serotype 4 (two days) and cases without underlying conditions (two days). Our study has shown that Listeria monocytogenes serotype and the presence of an underlying condition may influence the time between onset of symptoms and collection of specimen.

Ultrasonic Evaluation and Imaging

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

Crawford, Susan L.; Anderson, Michael T.; Diaz, Aaron A.

2015-10-01

Ultrasonic evaluation of materials for material characterization and flaw detection is as simple as manually moving a single-element probe across a speci-men and looking at an oscilloscope display in real time or as complex as automatically (under computer control) scanning a phased-array probe across a specimen and collecting encoded data for immediate or off-line data analyses. The reliability of the results in the second technique is greatly increased because of a higher density of measurements per scanned area and measurements that can be more precisely related to the specimen geometry. This chapter will briefly discuss applications of the collection ofmore » spatially encoded data and focus primarily on the off-line analyses in the form of data imaging. Pacific Northwest National Laboratory (PNNL) has been involved with as-sessing and advancing the reliability of inservice inspections of nuclear power plant components for over 35 years. Modern ultrasonic imaging techniques such as the synthetic aperture focusing technique (SAFT), phased-array (PA) technolo-gy and sound field mapping have undergone considerable improvements to effec-tively assess and better understand material constraints.« less

Evaluation of a commercial ligase chain reaction assay for the diagnosis of pulmonary and extra-pulmonary tuberculosis.

PubMed

Viveiros, M; Pinheiro, S; Moreira, P; Pacheco, T; Brum, L

1999-06-01

Egas Moniz Hospital, Lisbon, Portugal. To evaluate the Ligase Chain Reaction (LCx) Mycobacterium tuberculosis Assay for the direct detection of M. tuberculosis complex in respiratory specimens after smear observation, and its suitability for non-respiratory clinical specimens. Analysis of 156 specimens collected from 123 patients with pulmonary tuberculosis and/or extrapulmonary involvement. Among 93 pulmonary secretions and 63 extra-pulmonary samples and after resolution of discrepancies based on clinical and laboratory findings, two pulmonary samples from a patient with a diagnosis of sarcoidosis, four samples of cerebrospinal and one of seminal fluid were considered as false positives. Two tissue biopsy samples, one pericardial effusion and one pulmonary secretion from patients strongly suspected of having tuberculosis were considered as false negatives for the assay, without inhibition of amplification. All specimens yielding M. avium on culture were LCx negative. The LCx Mycobacterium tuberculosis Assay was found to be useful for the rapid identification of M. tuberculosis complex in all types of specimens. It revealed a high specificity both in pulmonary and extrapulmonary products, and a sensitivity of 97% for the pulmonary secretions and of 75% for the extra-pulmonary specimens, independently of the bacilloscopy results.

Frequency of Nucleic Acid Amplification Test Positivity Among Men Who Have Sex With Men Returning for a Test-of-Cure Visit 7 to 30 Days After Treatment of Laboratory-Confirmed Neisseria gonorrhoeae Infection at 2 Public Sexual Health Clinics, New York City, 2013 to 2016.

PubMed

Okah, Ebiere; Westheimer, Emily F; Jamison, Kelly; Schillinger, Julia A

2018-03-01

The Centers for Disease Control and Prevention 2015 Sexually Transmitted Disease Treatment Guidelines recommend that clinicians consider cephalosporin treatment failure in patients who deny interval sexual exposure and are nucleic acid amplification test (NAAT) positive for Neisseria gonorrhoeae (NG) at least 7 days after adequate treatment. We evaluate the real-world implications of the interval the Centers for Disease Control and Prevention recommends for a NAAT test-of-cure (TOC), by ascertaining the frequency of NG NAAT positivity at different anatomic sites among men who have sex with men (MSM) at TOC 7 to 30 days after treatment. We analyzed data from the medical records of MSM with laboratory-confirmed NG who were presumptively treated for NG during the period from June 2013 to April 2016 and returned for a TOC visit within 30 days. Data examined included symptoms, site of NG specimen collection, treatment regimen, follow-up testing, and intervening sexual activity. There were 1027 NG-positive specimens obtained from 763 MSM patients at 889 presumptive treatment visits. Of these, 44% (337/763) MSM returned for 1 or more TOC visits, and 413 specimens were collected a median of 10 days after presumptive treatment. Three percent (14/413) of specimens collected were NG NAAT positive at TOC a median of 13 days after treatment: 5% (12/256) of urethral specimens, 1% (1/147) of anorectal specimens (P = 0.037, urethral vs. anorectal), and 10% (1/10) of oropharyngeal specimens (P = 0.40, urethral vs. oropharyngeal). A small percent of patients were NG NAAT positive at TOC. Compared with anorectal specimens, urethral specimens were more frequently still positive at TOC. A large proportion of MSM will return for a TOC visit as part of standard clinical care.

Additions to the reptile fauna of Paraguay with notes on a small herpetological collection from Amambay

USGS Publications Warehouse

McDiarmid, Roy W.; Foster, Mercedes S.

1987-01-01

Specimens in a small collections of reptiles and amphibians from Parque Nacional Cerro Cora, Departamento Amambay, Paraguay are reported. Included are the first records of Bachia bresslaui, Phrynops gibbus, and Ololygon fuscomarginata for that country. Brief notes on morphology, distribution, and natural history of species collected are included. The systematic status of Phrynops tuberculatus vanderhaegei is evaluated.

Agreement for HPV genotyping detection between self-collected specimens on a FTA cartridge and clinician-collected specimens

PubMed Central

Guan, YaoYao; Gravitt, Patti E.; Howard, Roslyn; Eby, Yolanda J.; Wang, Shaoming; Li, Belinda; Feng, Changyan; Qiao, You-Lin; Castle, Philip E.

2016-01-01

The current method of transporting self-collected cervicovaginal specimen for HPV DNA testing relies on liquid based medium, which is challenging and expensive to transport. A novel, dry storage and transportation device, Whatman indicating FTA™ Elute Cartridge, avoids some of the pitfalls of liquid-based medium. This method has been shown to be comparable to liquid-based collection medium, but relative performance of self-collected (SC) and clinician-collected (CC) samples onto FTA cards has not been reported. The objective of this study is to compare the analytic performance of self- and clinician-collected samples onto FTA cartridges for the detection of carcinogenic HPV using Linear Array. There was a 91% agreement, 69% positive agreement, and kappa of 0.75 between the clinician-collected and self-collected specimens for detection of any carcinogenic HPV genotype. When the HPV results were categorized hierarchically according to cervical cancer risk, there was no difference in the distribution of the HPV results for the clinician- and self-collected specimens (p = 0.7). This study concludes that FTA elute cartridge is a promising method of specimen transport for cervical cancer screening programs considering using self-collected specimen and HPV testing. Larger studies with clinical endpoints are now needed to assess the clinical performance. PMID:23370404

National Mesothelioma Virtual Bank: A Platform for Collaborative Research and Mesothelioma Biobanking Resource to Support Translational Research

PubMed Central

Parwani, Anil V.; Melamed, Jonathan; Flores, Raja; Pennathur, Arjun; Valdivieso, Federico; Whelan, Nancy B.; Landreneau, Rodeny; Luketich, James; Feldman, Michael; Pass, Harvey I.; Becich, Michael J.

2013-01-01

The National Mesothelioma Virtual Bank (NMVB), developed six years ago, gathers clinically annotated human mesothelioma specimens for basic and clinical science research. During this period, this resource has greatly increased its collection of specimens by expanding the number of contributing academic health centers including New York University, University of Pennsylvania, University of Pittsburgh Medical Center, and Mount Sinai School of Medicine. Marketing efforts at both national and international annual conferences increase awareness and availability of the mesothelioma specimens at no cost to approved investigators, who query the web-based NMVB database for cumulative and appropriate patient clinicopathological information on the specimens. The data disclosure and specimen distribution protocols are tightly regulated to maintain compliance with participating institutions' IRB and regulatory committee reviews. The NMVB currently has over 1120 annotated cases available for researchers, including paraffin embedded tissues, fresh frozen tissue, tissue microarrays (TMA), blood samples, and genomic DNA. In addition, the resource offers expertise and assistance for collaborative research. Furthermore, in the last six years, the resource has provided hundreds of specimens to the research community. The investigators can request specimens and/or data by submitting a Letter of Intent (LOI) that is evaluated by NMVB research evaluation panel (REP). PMID:26316942

National Mesothelioma Virtual Bank: A Platform for Collaborative Research and Mesothelioma Biobanking Resource to Support Translational Research.

PubMed

Amin, Waqas; Parwani, Anil V; Melamed, Jonathan; Flores, Raja; Pennathur, Arjun; Valdivieso, Federico; Whelan, Nancy B; Landreneau, Rodeny; Luketich, James; Feldman, Michael; Pass, Harvey I; Becich, Michael J

2013-01-01

The National Mesothelioma Virtual Bank (NMVB), developed six years ago, gathers clinically annotated human mesothelioma specimens for basic and clinical science research. During this period, this resource has greatly increased its collection of specimens by expanding the number of contributing academic health centers including New York University, University of Pennsylvania, University of Pittsburgh Medical Center, and Mount Sinai School of Medicine. Marketing efforts at both national and international annual conferences increase awareness and availability of the mesothelioma specimens at no cost to approved investigators, who query the web-based NMVB database for cumulative and appropriate patient clinicopathological information on the specimens. The data disclosure and specimen distribution protocols are tightly regulated to maintain compliance with participating institutions' IRB and regulatory committee reviews. The NMVB currently has over 1120 annotated cases available for researchers, including paraffin embedded tissues, fresh frozen tissue, tissue microarrays (TMA), blood samples, and genomic DNA. In addition, the resource offers expertise and assistance for collaborative research. Furthermore, in the last six years, the resource has provided hundreds of specimens to the research community. The investigators can request specimens and/or data by submitting a Letter of Intent (LOI) that is evaluated by NMVB research evaluation panel (REP).

Standardization of Clinical Assessment and Sample Collection Across All PERCH Study Sites

PubMed Central

Prosperi, Christine; Baggett, Henry C.; Brooks, W. Abdullah; Deloria Knoll, Maria; Hammitt, Laura L.; Howie, Stephen R. C.; Kotloff, Karen L.; Levine, Orin S.; Madhi, Shabir A.; Murdoch, David R.; O’Brien, Katherine L.; Thea, Donald M.; Awori, Juliet O.; Bunthi, Charatdao; DeLuca, Andrea N.; Driscoll, Amanda J.; Ebruke, Bernard E.; Goswami, Doli; Hidgon, Melissa M.; Karron, Ruth A.; Kazungu, Sidi; Kourouma, Nana; Mackenzie, Grant; Moore, David P.; Mudau, Azwifari; Mwale, Magdalene; Nahar, Kamrun; Park, Daniel E.; Piralam, Barameht; Seidenberg, Phil; Sylla, Mamadou; Feikin, Daniel R.; Scott, J. Anthony G.; O’Brien, Katherine L.; Levine, Orin S.; Knoll, Maria Deloria; Feikin, Daniel R.; DeLuca, Andrea N.; Driscoll, Amanda J.; Fancourt, Nicholas; Fu, Wei; Hammitt, Laura L.; Higdon, Melissa M.; Kagucia, E. Wangeci; Karron, Ruth A.; Li, Mengying; Park, Daniel E.; Prosperi, Christine; Wu, Zhenke; Zeger, Scott L.; Watson, Nora L.; Crawley, Jane; Murdoch, David R.; Brooks, W. Abdullah; Endtz, Hubert P.; Zaman, Khalequ; Goswami, Doli; Hossain, Lokman; Jahan, Yasmin; Ashraf, Hasan; Howie, Stephen R. C.; Ebruke, Bernard E.; Antonio, Martin; McLellan, Jessica; Machuka, Eunice; Shamsul, Arifin; Zaman, Syed M.A.; Mackenzie, Grant; Scott, J. Anthony G.; Awori, Juliet O.; Morpeth, Susan C.; Kamau, Alice; Kazungu, Sidi; Kotloff, Karen L.; Tapia, Milagritos D.; Sow, Samba O.; Sylla, Mamadou; Tamboura, Boubou; Onwuchekwa, Uma; Kourouma, Nana; Toure, Aliou; Madhi, Shabir A.; Moore, David P.; Adrian, Peter V.; Baillie, Vicky L.; Kuwanda, Locadiah; Mudau, Azwifarwi; Groome, Michelle J.; Baggett, Henry C.; Thamthitiwat, Somsak; Maloney, Susan A.; Bunthi, Charatdao; Rhodes, Julia; Sawatwong, Pongpun; Akarasewi, Pasakorn; Thea, Donald M.; Mwananyanda, Lawrence; Chipeta, James; Seidenberg, Phil; Mwansa, James; wa Somwe, Somwe; Kwenda, Geoffrey

2017-01-01

Abstract Background. Variable adherence to standardized case definitions, clinical procedures, specimen collection techniques, and laboratory methods has complicated the interpretation of previous multicenter pneumonia etiology studies. To circumvent these problems, a program of clinical standardization was embedded in the Pneumonia Etiology Research for Child Health (PERCH) study. Methods. Between March 2011 and August 2013, standardized training on the PERCH case definition, clinical procedures, and collection of laboratory specimens was delivered to 331 clinical staff at 9 study sites in 7 countries (The Gambia, Kenya, Mali, South Africa, Zambia, Thailand, and Bangladesh), through 32 on-site courses and a training website. Staff competency was assessed throughout 24 months of enrollment with multiple-choice question (MCQ) examinations, a video quiz, and checklist evaluations of practical skills. Results. MCQ evaluation was confined to 158 clinical staff members who enrolled PERCH cases and controls, with scores obtained for >86% of eligible staff at each time-point. Median scores after baseline training were ≥80%, and improved by 10 percentage points with refresher training, with no significant intersite differences. Percentage agreement with the clinical trainer on the presence or absence of clinical signs on video clips was high (≥89%), with interobserver concordance being substantial to high (AC1 statistic, 0.62–0.82) for 5 of 6 signs assessed. Staff attained median scores of >90% in checklist evaluations of practical skills. Conclusions. Satisfactory clinical standardization was achieved within and across all PERCH sites, providing reassurance that any etiological or clinical differences observed across the study sites are true differences, and not attributable to differences in application of the clinical case definition, interpretation of clinical signs, or in techniques used for clinical measurements or specimen collection. PMID:28575355

Evaluation to determine the caries remineralization potential of three dentifrices: An in vitro study

PubMed Central

Balakrishnan, Arun; Jonathan, R; Benin, P; Kuumar, Arvind

2013-01-01

Aim: The aim of this study was to evaluate the remineralizing potential of three different remineralizing agents (GC tooth Mousse, Clinpro tooth crθme and SHY-NM) on demineralized tooth surfaces using micro CT and microhardness. Materials and Methods: Forty five freshly extracted mandibular premolars were collected and enamel specimens were prepared. The samples were assigned to three groups with fifteen specimens in each group. The specimens were then demineralized using McInne's demineralizing solution in two cycles. After that, remineralization was carried out in two cycles for 30 days using Casein phosphopeptide - Amorphous calcium phosphate (CPP - ACP), 0.21% sodium fluoride - Tricalcium phosphate (f-TCP) and Calcium Sodium Phosphosilicate (CSP) containing tooth pastes for groups I, II, III respectively. The specimens were evaluated for Linear attenuation co-efficient using micro CT (Scanco™) and Vicker's Micro Hardness (Schimadzu™) testing at different time periods. The results were tabulated and statistically analysed. Results: It was observed that all the three remineralizing agents used in the study significantly increased the Linear Attenuation Co-efficient and Vicker's hardness number values of the enamel specimens following 15 days and 30 days application. Conclusion: CPP – ACP showed the better remineralizing potential than the other two agents and there was no statistical significant difference between f-TCP and CSP groups. PMID:23956545

Clinical evaluation of high-risk HPV detection on self-samples using the indicating FTA-elute solid-carrier cartridge.

PubMed

Geraets, D T; van Baars, R; Alonso, I; Ordi, J; Torné, A; Melchers, W J G; Meijer, C J L M; Quint, W G V

2013-06-01

High-risk human papillomavirus (hrHPV) testing in cervical screening is usually performed on physician-taken cervical smears in liquid-based medium. However, solid-state specimen carriers allow easy, non-hazardous storage and transportation and might be suitable for self-collection by non-responders in screening and in low-resource settings. We evaluated the adequacy of self-collected cervicovaginal (c/v) samples using a Viba-brush stored on an Indicating FTA-elute cartridge (FTA-based self-sampling) for hrHPV testing in women referred to a gynecology clinic due to an abnormal smear. 182 women accepted to self-collect a c/v sample. After self-sampling, a physician obtained a conventional liquid-based cervical smear. Finally, women were examined by colposcopy and a biopsy was taken when clinically indicated. Self-samples required only simple DNA elution, and DNA was extracted from physician-obtained samples. Both samples were tested for 14 hrHPVs by GP5+/6+-EIA-LQ Test and SPF(10)-DEIA-LiPA(25). Both assays detected significantly more hrHPV in physician-collected specimens than in self-collected samples (75.3% and 67.6% by SPF(10); 63.3% and 53.3% by GP5+/6+, respectively). The combination of physician-collected specimen and GP5+/6+ testing demonstrated the optimal balance in sensitivity (98.0%) and specificity (48.1%) for CIN2+ detection in this referral population. A test system of FTA-based self-collection and SPF(10) hrHPV detection approached this sensitivity (95.9%) and specificity (42.9%). These results show that the clinical performance of hrHPV detection is determined by both the sample collection system and the test method. FTA-based self-collection with SPF(10) testing might be valuable when a liquid-based medium cannot be used, but requires further investigation in screening populations. Copyright © 2013 Elsevier B.V. All rights reserved.

Issues in collecting, processing and storing human tissues and associated information to support biomedical research.

PubMed

Grizzle, William E; Bell, Walter C; Sexton, Katherine C

2010-01-01

The availability of human tissues to support biomedical research is critical to advance translational research focused on identifying and characterizing approaches to individualized (personalized) medical care. Providing such tissues relies on three acceptable models - a tissue banking model, a prospective collection model and a combination of these two models. An unacceptable model is the "catch as catch can" model in which tissues are collected, processed and stored without goals or a plan or without standard operating procedures, i.e., portions of tissues are collected as available and processed and stored when time permits. In the tissue banking model, aliquots of tissues are collected according to SOPs. Usually specific sizes and types of tissues are collected and processed (e.g., 0.1 gm of breast cancer frozen in OCT). Using the banking model, tissues may be collected that may not be used and/or do not meet specific needs of investigators; however, at the time of an investigator request, tissues are readily available as is clinical information including clinical outcomes. In the model of prospective collection, tissues are collected based upon investigator requests including specific requirements of investigators. For example, the investigator may request that two 0.15 gm matching aliquots of breast cancer be minced while fresh, put in RPMI media with and without fetal calf serum, cooled to 4°C and shipped to the investigator on wet ice. Thus, the tissues collected prospectively meet investigator needs, all collected specimens are utilized and storage of specimens is minimized; however, investigators must wait until specimens are collected, and if needed, for clinical outcome. The operation of any tissue repository requires well trained and dedicated personnel. A quality assurance program is required which provides quality control information on the diagnosis of a specimen that is matched specifically to the specimen provided to an investigator instead of an overall diagnosis of the specimen via a surgical pathology report. This is necessary because a specific specimen may not match the diagnosis of the case due to many factors such as necrosis, unsuspected tumor invasion of apparently normal tissue, and areas of fibrosis which are mistaken grossly for tumor. Aliquots for quality control (QC) may or may not be collected at the time of collection and in some cases, QC may not occur until specimens are distributed to investigators. In establishing a tumor repository, multiple issues need to be considered. These include the available resources, long term support, space and equipment. The needs of the potential users need to be identified as to the types of tissues and services needed and the annotation expected. Other specific issues to be considered include collection of specimens potentially infected with blood borne pathogens (e.g., hepatitis B), charge back mechanisms, informatics needs and support, and investigator requirements (e.g., recognition of repository contributions in publications). In general, the repository should not perform the research of the investigators, but should provide the infrastructure necessary to support the research of the investigator. Thus, the goals of the repository must be established. Similarly, ethical and regulatory issues must be evaluated. In general, tissue repositories need ethical (e.g., IRB) and privacy (e.g., HIPAA) review. Also, safety issues need to be considered as well as how biohazards will be addressed by investigator-users. Considerations involving the transfer of specimens to other organization usually require a material transfer agreement (MTA). A MTA should address biohazards as well as indemnification. Thus, many issues must be considered and addressed in order to establish and operate successfully a biorepository.

43 CFR 15.9 - Collection of scientific specimens.

Code of Federal Regulations, 2012 CFR

2012-10-01

... 43 Public Lands: Interior 1 2012-10-01 2011-10-01 true Collection of scientific specimens. 15.9 Section 15.9 Public Lands: Interior Office of the Secretary of the Interior KEY LARGO CORAL REEF PRESERVE § 15.9 Collection of scientific specimens. Collection of natural objects and marine life for...

43 CFR 15.9 - Collection of scientific specimens.

Code of Federal Regulations, 2013 CFR

2013-10-01

... 43 Public Lands: Interior 1 2013-10-01 2013-10-01 false Collection of scientific specimens. 15.9 Section 15.9 Public Lands: Interior Office of the Secretary of the Interior KEY LARGO CORAL REEF PRESERVE § 15.9 Collection of scientific specimens. Collection of natural objects and marine life for...

43 CFR 15.9 - Collection of scientific specimens.

Code of Federal Regulations, 2014 CFR

2014-10-01

... 43 Public Lands: Interior 1 2014-10-01 2014-10-01 false Collection of scientific specimens. 15.9 Section 15.9 Public Lands: Interior Office of the Secretary of the Interior KEY LARGO CORAL REEF PRESERVE § 15.9 Collection of scientific specimens. Collection of natural objects and marine life for...

43 CFR 15.9 - Collection of scientific specimens.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 43 Public Lands: Interior 1 2010-10-01 2010-10-01 false Collection of scientific specimens. 15.9 Section 15.9 Public Lands: Interior Office of the Secretary of the Interior KEY LARGO CORAL REEF PRESERVE § 15.9 Collection of scientific specimens. Collection of natural objects and marine life for...

43 CFR 15.9 - Collection of scientific specimens.

Code of Federal Regulations, 2011 CFR

2011-10-01

... 43 Public Lands: Interior 1 2011-10-01 2011-10-01 false Collection of scientific specimens. 15.9 Section 15.9 Public Lands: Interior Office of the Secretary of the Interior KEY LARGO CORAL REEF PRESERVE § 15.9 Collection of scientific specimens. Collection of natural objects and marine life for...

Bringing together raptor collections in Europe for contaminant research and monitoring in relation to chemicals regulations.

PubMed

Movalli, Paola; Dekker, René; Koschorreck, Jan; Treu, Gabriele

2017-11-01

Raptors are good sentinels of environmental contamination and there is good capability for raptor biomonitoring in Europe. Raptor biomonitoring can benefit from natural history museums (NHMs), environmental specimen banks (ESBs) and other collections (e.g. specialist raptor specimen collections). Europe's NHMs, ESBs and other collections hold large numbers of raptor specimens and samples, covering long periods of time. These collections are potentially a valuable resource for contaminant studies over time and space. There are strong needs to monitor contaminants in the environment to support EU and national chemical management. However, data on raptor specimens in NHMs, ESBs and other collections are dispersed, few are digitised, and they are thus not easy to access. Specimen coverage is patchy in terms of species, space and time. Contaminant research with raptors would be facilitated by creating a framework to link relevant collections, digitising all collections, developing a searchable meta-database covering all existing collections, making them more visible and accessible for contaminant research. This would also help identify gaps in coverage and stimulate specimen collection to fill gaps in support of prioritised contaminant monitoring. Collections can further support raptor biomonitoring by making samples available for analysis on request.

Agreement for HPV genotyping detection between self-collected specimens on a FTA cartridge and clinician-collected specimens.

PubMed

Guan, Yaoyao; Gravitt, Patti E; Howard, Roslyn; Eby, Yolanda J; Wang, Shaoming; Li, Belinda; Feng, Changyan; Qiao, You-Lin; Castle, Philip E

2013-04-01

The current method of transporting self-collected cervicovaginal specimen for HPV DNA testing relies on liquid based medium, which is challenging and expensive to transport. A novel, dry storage and transportation device, Whatman indicating FTA™ Elute Cartridge, avoids some of the pitfalls of liquid-based medium. This method has been shown to be comparable to liquid-based collection medium, but relative performance of self-collected (SC) and clinician-collected (CC) samples onto FTA cards has not been reported. The objective of this study is to compare the analytic performance of self- and clinician-collected samples onto FTA cartridges for the detection of carcinogenic HPV using Linear Array. There was a 91% agreement, 69% positive agreement, and kappa of 0.75 between the clinician-collected and self-collected specimens for detection of any carcinogenic HPV genotype. When the HPV results were categorized hierarchically according to cervical cancer risk, there was no difference in the distribution of the HPV results for the clinician- and self-collected specimens (p=0.7). This study concludes that FTA elute cartridge is a promising method of specimen transport for cervical cancer screening programs considering using self-collected specimen and HPV testing. Larger studies with clinical endpoints are now needed to assess the clinical performance. Copyright © 2012 Elsevier B.V. All rights reserved.

iCollections - Digitising the British and Irish Butterflies in the Natural History Museum, London.

PubMed

Paterson, Gordon; Albuquerque, Sara; Blagoderov, Vladimir; Brooks, Stephen; Cafferty, Steve; Cane, Elisa; Carter, Victoria; Chainey, John; Crowther, Robyn; Douglas, Lyndsey; Durant, Joanna; Duffell, Liz; Hine, Adrian; Honey, Martin; Huertas, Blanca; Howard, Theresa; Huxley, Rob; Kitching, Ian; Ledger, Sophie; McLaughlin, Caitlin; Martin, Geoff; Mazzetta, Gerardo; Penn, Malcolm; Perera, Jasmin; Sadka, Mike; Scialabba, Elisabetta; Self, Angela; Siebert, Darrell J; Sleep, Chris; Toloni, Flavia; Wing, Peter

2016-01-01

The Natural History Museum, London (NHMUK) has embarked on an ambitious programme to digitise its collections . The first phase of this programme has been to undertake a series of pilot projects that will develop the necessary workflows and infrastructure development needed to support mass digitisation of very large scientific collections. This paper presents the results of one of the pilot projects - iCollections. This project digitised all the lepidopteran specimens usually considered as butterflies, 181,545 specimens representing 89 species from the British Isles and Ireland. The data digitised includes, species name, georeferenced location, collector and collection date - the what, where, who and when of specimen data. In addition, a digital image of each specimen was taken. This paper explains the way the data were obtained and the background to the collections which made up the project. Specimen-level data associated with British and Irish butterfly specimens have not been available before and the iCollections project has released this valuable resource through the NHM data portal.

49 CFR 40.49 - What materials are used to collect urine specimens?

Code of Federal Regulations, 2012 CFR

2012-10-01

... 49 Transportation 1 2012-10-01 2012-10-01 false What materials are used to collect urine specimens? 40.49 Section 40.49 Transportation Office of the Secretary of Transportation PROCEDURES FOR... in DOT Urine Collections § 40.49 What materials are used to collect urine specimens? For each DOT...

49 CFR 40.49 - What materials are used to collect urine specimens?

Code of Federal Regulations, 2014 CFR

2014-10-01

... 49 Transportation 1 2014-10-01 2014-10-01 false What materials are used to collect urine specimens? 40.49 Section 40.49 Transportation Office of the Secretary of Transportation PROCEDURES FOR... in DOT Urine Collections § 40.49 What materials are used to collect urine specimens? For each DOT...

49 CFR 40.49 - What materials are used to collect urine specimens?

Code of Federal Regulations, 2013 CFR

2013-10-01

... 49 Transportation 1 2013-10-01 2013-10-01 false What materials are used to collect urine specimens? 40.49 Section 40.49 Transportation Office of the Secretary of Transportation PROCEDURES FOR... in DOT Urine Collections § 40.49 What materials are used to collect urine specimens? For each DOT...

49 CFR 40.49 - What materials are used to collect urine specimens?

Code of Federal Regulations, 2011 CFR

2011-10-01

... 49 Transportation 1 2011-10-01 2011-10-01 false What materials are used to collect urine specimens? 40.49 Section 40.49 Transportation Office of the Secretary of Transportation PROCEDURES FOR... in DOT Urine Collections § 40.49 What materials are used to collect urine specimens? For each DOT...

49 CFR 40.49 - What materials are used to collect urine specimens?

Code of Federal Regulations, 2010 CFR

2010-10-01

... 49 Transportation 1 2010-10-01 2010-10-01 false What materials are used to collect urine specimens? 40.49 Section 40.49 Transportation Office of the Secretary of Transportation PROCEDURES FOR... in DOT Urine Collections § 40.49 What materials are used to collect urine specimens? For each DOT...

49 CFR 40.31 - Who may collect urine specimens for DOT drug testing?

Code of Federal Regulations, 2014 CFR

2014-10-01

... TRANSPORTATION WORKPLACE DRUG AND ALCOHOL TESTING PROGRAMS Urine Collection Personnel § 40.31 Who may collect urine specimens for DOT drug testing? (a) Collectors meeting the requirements of this subpart are the only persons authorized to collect urine specimens for DOT drug testing. (b) A collector must meet...

49 CFR 40.31 - Who may collect urine specimens for DOT drug testing?

Code of Federal Regulations, 2010 CFR

2010-10-01

... TRANSPORTATION WORKPLACE DRUG AND ALCOHOL TESTING PROGRAMS Urine Collection Personnel § 40.31 Who may collect urine specimens for DOT drug testing? (a) Collectors meeting the requirements of this subpart are the only persons authorized to collect urine specimens for DOT drug testing. (b) A collector must meet...

49 CFR 40.31 - Who may collect urine specimens for DOT drug testing?

Code of Federal Regulations, 2012 CFR

2012-10-01

... TRANSPORTATION WORKPLACE DRUG AND ALCOHOL TESTING PROGRAMS Urine Collection Personnel § 40.31 Who may collect urine specimens for DOT drug testing? (a) Collectors meeting the requirements of this subpart are the only persons authorized to collect urine specimens for DOT drug testing. (b) A collector must meet...

49 CFR 40.31 - Who may collect urine specimens for DOT drug testing?

Code of Federal Regulations, 2011 CFR

2011-10-01

... TRANSPORTATION WORKPLACE DRUG AND ALCOHOL TESTING PROGRAMS Urine Collection Personnel § 40.31 Who may collect urine specimens for DOT drug testing? (a) Collectors meeting the requirements of this subpart are the only persons authorized to collect urine specimens for DOT drug testing. (b) A collector must meet...

49 CFR 40.31 - Who may collect urine specimens for DOT drug testing?

Code of Federal Regulations, 2013 CFR

2013-10-01

... TRANSPORTATION WORKPLACE DRUG AND ALCOHOL TESTING PROGRAMS Urine Collection Personnel § 40.31 Who may collect urine specimens for DOT drug testing? (a) Collectors meeting the requirements of this subpart are the only persons authorized to collect urine specimens for DOT drug testing. (b) A collector must meet...

The type specimen of Anoura geoffroyi lasiopyga (Chiroptera: Phyllostomidae)

USGS Publications Warehouse

Arroyo-Cabrales, Joaquin; Gardner, A.L.

2003-01-01

In 1868, Wilhelm Peters described Glossonycteris lasiopyga, based on a specimen provided by Henri de Saussure and collected in Mexico. The type specimen was presumed to be among those housed in the collections of the Zoologisches Museum of the Humboldt Universitat in Berlin, Germany. Our study of one of Saussure?s specimens from Mexico, discovered in the collections of the Museum d?Histoire Naturelle, Geneva, Switzerland, demonstrates that it and not one of the Berlin specimens is the holotype.

DNA Extraction Method Affects the Detection of a Fungal Pathogen in Formalin-Fixed Specimens Using qPCR.

PubMed

Adams, Andrea J; LaBonte, John P; Ball, Morgan L; Richards-Hrdlicka, Kathryn L; Toothman, Mary H; Briggs, Cheryl J

2015-01-01

Museum collections provide indispensable repositories for obtaining information about the historical presence of disease in wildlife populations. The pathogenic amphibian chytrid fungus Batrachochytrium dendrobatidis (Bd) has played a significant role in global amphibian declines, and examining preserved specimens for Bd can improve our understanding of its emergence and spread. Quantitative PCR (qPCR) enables Bd detection with minimal disturbance to amphibian skin and is significantly more sensitive to detecting Bd than histology; therefore, developing effective qPCR methodologies for detecting Bd DNA in formalin-fixed specimens can provide an efficient and effective approach to examining historical Bd emergence and prevalence. Techniques for detecting Bd in museum specimens have not been evaluated for their effectiveness in control specimens that mimic the conditions of animals most likely to be encountered in museums, including those with low pathogen loads. We used American bullfrogs (Lithobates catesbeianus) of known infection status to evaluate the success of qPCR to detect Bd in formalin-fixed specimens after three years of ethanol storage. Our objectives were to compare the most commonly used DNA extraction method for Bd (PrepMan, PM) to Macherey-Nagel DNA FFPE (MN), test optimizations for Bd detection with PM, and provide recommendations for maximizing Bd detection. We found that successful detection is relatively high (80-90%) when Bd loads before formalin fixation are high, regardless of the extraction method used; however, at lower infection levels, detection probabilities were significantly reduced. The MN DNA extraction method increased Bd detection by as much as 50% at moderate infection levels. Our results indicate that, for animals characterized by lower pathogen loads (i.e., those most commonly encountered in museum collections), current methods may underestimate the proportion of Bd-infected amphibians. Those extracting DNA from archived museum specimens should ensure that the techniques they are using are known to provide high-quality throughput DNA for later analysis.

The Hemiptera (Insecta) of Canada: Constructing a Reference Library of DNA Barcodes

PubMed Central

Gwiazdowski, Rodger A.; Foottit, Robert G.; Maw, H. Eric L.; Hebert, Paul D. N.

2015-01-01

DNA barcode reference libraries linked to voucher specimens create new opportunities for high-throughput identification and taxonomic re-evaluations. This study provides a DNA barcode library for about 45% of the recognized species of Canadian Hemiptera, and the publically available R workflow used for its generation. The current library is based on the analysis of 20,851 specimens including 1849 species belonging to 628 genera and 64 families. These individuals were assigned to 1867 Barcode Index Numbers (BINs), sequence clusters that often coincide with species recognized through prior taxonomy. Museum collections were a key source for identified specimens, but we also employed high-throughput collection methods that generated large numbers of unidentified specimens. Many of these specimens represented novel BINs that were subsequently identified by taxonomists, adding barcode coverage for additional species. Our analyses based on both approaches includes 94 species not listed in the most recent Canadian checklist, representing a potential 3% increase in the fauna. We discuss the development of our workflow in the context of prior DNA barcode library construction projects, emphasizing the importance of delineating a set of reference specimens to aid investigations in cases of nomenclatural and DNA barcode discordance. The identification for each specimen in the reference set can be annotated on the Barcode of Life Data System (BOLD), allowing experts to highlight questionable identifications; annotations can be added by any registered user of BOLD, and instructions for this are provided. PMID:25923328

Virtual Specimens

NASA Astrophysics Data System (ADS)

de Paor, D. G.

2009-12-01

Virtual Field Trips have been around almost as long as the Worldwide Web itself yet virtual explorers do not generally return to their desktops with folders full of virtual hand specimens. Collection of real specimens on fields trips for later analysis in the lab (or at least in the pub) has been an important part of classical field geoscience education and research for generations but concern for the landscape and for preservation of key outcrops from wanton destruction has lead to many restrictions. One of the author’s favorite outcrops was recently vandalized presumably by a geologist who felt the need to bash some of the world’s most spectacular buckle folds with a rock sledge. It is not surprising, therefore, that geologists sometimes leave fragile localities out of field trip itineraries. Once analyzed, most specimens repose in drawers or bins, never to be seen again. Some end up in teaching collections but recent pedagogical research shows that undergraduate students have difficulty relating specimens both to their collection location and ultimate provenance in the lithosphere. Virtual specimens can be created using 3D modeling software and imported into virtual globes such as Google Earth (GE) where, they may be linked to virtual field trip stops or restored to their source localities on the paleo-globe. Sensitive localities may be protected by placemark approximation. The GE application program interface (API) has a distinct advantage over the stand-alone GE application when it comes to viewing and manipulating virtual specimens. When instances of the virtual globe are embedded in web pages using the GE plug-in, Collada models of specimens can be manipulated with javascript controls residing in the enclosing HTML, permitting specimens to be magnified, rotated in 3D, and sliced. Associated analytical data may be linked into javascript and localities for comparison at various points on the globe referenced by ‘fetching’ KML. Virtual specimens open up new possibilities for distance learning, where design of effective lab exercises has long been an issue, and they permit independent evaluation of published field research by reviewers who do not have access to the physical field area. Although their creation can be labor intensive, the benefits of virtual specimens for education and research are potentially great. Interactive 3D Specimen of Sierra Granodiorite at Outcrop Location

LED Fluorescence Microscopy for the Diagnosis of Pulmonary Tuberculosis: A Multi-Country Cross-Sectional Evaluation

PubMed Central

Cuevas, Luis Eduardo; Al-Sonboli, Najla; Lawson, Lovett; Yassin, Mohammed Ahmed; Arbide, Isabel; Al-Aghbari, Nasher; Bahadur Sherchand, Jeevan; Al-Absi, Amin; Emenyonu, Emmanuel Nnamdi; Merid, Yared; Okobi, Mosis Ifenyi; Onuoha, Juliana Olubunmi; Aschalew, Melkamsew; Aseffa, Abraham; Harper, Greg; Anderson de Cuevas, Rachel Mary; Theobald, Sally Jane; Nathanson, Carl-Michael; Joly, Jean; Faragher, Brian; Squire, Stephen Bertel; Ramsay, Andrew

2011-01-01

Background The diagnosis of tuberculosis (TB) in resource-limited settings relies on Ziehl-Neelsen (ZN) smear microscopy. LED fluorescence microscopy (LED-FM) has many potential advantages over ZN smear microscopy, but requires evaluation in the field. The aim of this study was to assess the sensitivity/specificity of LED-FM for the diagnosis of pulmonary TB and whether its performance varies with the timing of specimen collection. Methods and Findings Adults with cough ≥2 wk were enrolled consecutively in Ethiopia, Nepal, Nigeria, and Yemen. Sputum specimens were examined by ZN smear microscopy and LED-FM and compared with culture as the reference standard. Specimens were collected using a spot-morning-spot (SMS) or spot-spot-morning (SSM) scheme to explore whether the collection of the first two smears at the health care facility (i.e., “on the spot”) the first day of consultation followed by a morning sample the next day (SSM) would identify similar numbers of smear-positive patients as smears collected via the SMS scheme (i.e., one on-the-spot-smear the first day, followed by a morning specimen collected at home and a second on-the-spot sample the second day). In total, 529 (21.6%) culture-positive and 1,826 (74.6%) culture-negative patients were enrolled, of which 1,156 (49%) submitted SSM specimens and 1,199 (51%) submitted SMS specimens. Single LED-FM smears had higher sensitivity but lower specificity than single ZN smears. Using two LED-FM or two ZN smears per patient was 72.8% (385/529, 95% CI 68.8%–76.5%) and 65.8% (348/529, 95% CI 61.6%–69.8%) sensitive (p<0.001) and 90.9% (1,660/1,826, 95% CI 89.5%–92.2%) and 98% (1,790/1,826, 95% CI 97.3%–98.6%) specific (p<0.001). Using three LED-FM or three ZN smears per patient was 77% (408/529, 95% CI 73.3%–80.6%) and 70.5% (373/529, 95% CI 66.4%–74.4%, p<0.001) sensitive and 88.1% (95% CI 86.5%–89.6%) and 96.5% (95% CI 96.8%–98.2%, p<0.001) specific. The sensitivity/specificity of ZN smear microscopy and LED-FM did not vary between SMS and SSM. Conclusions LED-FM had higher sensitivity but, in this study, lower specificity than ZN smear microscopy for diagnosis of pulmonary TB. Performance was independent of the scheme used for collecting specimens. The introduction of LED-FM needs to be accompanied by appropriate training, quality management, and monitoring of performance in the field. Trial Registration Current Controlled Trials ISRCTN53339491 Please see later in the article for the Editors' Summary PMID:21765809

Can Diopatra neapolitana (Annelida: Onuphidae) regenerate body damage caused by bait digging or predation?

NASA Astrophysics Data System (ADS)

Pires, A.; Freitas, R.; Quintino, V.; Rodrigues, A. M.

2012-09-01

The regenerative ability of Diopatra neapolitana was evaluated under laboratory conditions following nine experimental amputation levels: before the beginning of the branchiae (chaetiger 3 or 4), in the branchial region, at chaetigers 10, 15, 20, 25, 30, 35 and 40 and after the branchiae, at chaetigers 45-55. Specimens amputated at the 20th chaetiger were not able to regenerate and did not survive. The posterior portion of the specimens amputated up to chaetiger 15, regenerated the anterior part but the anterior ends were unable to survive. The anterior end of the specimens amputated at and beyond the 25th chaetiger regenerated the posterior part but the posterior ends were not able to regenerate an anterior part. Percent survival was directly related to the number of branchial segments left in the regenerating specimen and reached 100% only when the specimens were amputated beyond the branchial region. These results indicate that the species has regenerative ability and should survive the loss of a few anterior chaetigers, namely caused by predation. However, the results also indicate that bait digging could impair the survival of the posterior part remaining in the tube, as usually more than 20 chaetigers are harvested by bait collectors. Regarding field-collected specimens, D. neapolitana was found regenerating a mean of 9.0 ± 2.51 chaetigers, and Diopatra marocensis 7.5 ± 1.93 chaetigers, at the anterior end. The higher percentage of field-collected specimens showing regeneration of the anterior end belonged to D. marocensis. Only very few specimens, for both species, were found regenerating the posterior part of the body.

Rapid detection of fungal keratitis with DNA-stabilizing FTA filter paper.

PubMed

Menassa, Nardine; Bosshard, Philipp P; Kaufmann, Claude; Grimm, Christian; Auffarth, Gerd U; Thiel, Michael A

2010-04-01

Purpose. Polymerase chain reaction (PCR) is increasingly important for the rapid detection of fungal keratitis. However, techniques of specimen collection and DNA extraction before PCR may interfere with test sensitivity. The purpose of this study was to investigate the use of DNA-stabilizing FTA filter paper (Indicating FTA filter paper; Whatman International, Ltd., Maidstone, UK) for specimen collection without DNA extraction in a single-step, nonnested PCR for fungal keratitis. Methods. Specimens were collected from ocular surfaces with FTA filter discs, which automatically lyse collected cells and stabilize nucleic acids. Filter discs were directly used in single-step PCR reactions to detect fungal DNA. Test sensitivity was evaluated with serial dilutions of Candida albicans, Fusarium oxysporum, and Aspergillus fumigatus cultures. Test specificity was analyzed by comparing 196 and 155 healthy individuals from Switzerland and Egypt, respectively, with 15 patients with a diagnosis of microbial keratitis. Results. PCR with filter discs detected 3 C. albicans, 25 F. oxysporum, and 125 A. fumigatus organisms. In healthy volunteers, fungal PCR was positive in 1.0% and 8.4% of eyes from Switzerland and Egypt, respectively. Fungal PCR remained negative in 10 cases of culture-proven bacterial keratitis, became positive in 4 cases of fungal keratitis, but missed 1 case of culture-proven A. fumigatus keratitis. Conclusions. FTA filter paper for specimen collection together with direct PCR is a promising method of detecting fungal keratitis. The analytical sensitivity is high without the need for a semi-nested or nested second PCR, the clinical specificity is 91.7% to 99.0%, and the method is rapid and inexpensive.

Benthic macrofauna data for San Francisco Bay, California, September 1986

USGS Publications Warehouse

Schemel, Laurence E.; Thompson, J.K.; Harmon, J.G.; Yost, B.T.

1995-01-01

Benthic macrofauna were collected during September 1986 to evaluate locations for long-term monitoring stations as part of the U.S. Geological Survey Regional Effects Monitoring Program in San Francisco Bay, California. Three to ten replicate samples were collected with a modified Van Veen sampler (0.05 m2 area) at ten locations. One box core sample (0.06 m2 area) was collected at seven to the ten locations. Six of the box core samples were split into an upper 10 cm sample and a deeper sample before analysis. Macrofauna specimens were identified to the lowest possible taxon, usually genus and species, then counted. An average of 88 percent of the benthic macrofauna specimens were identified to the species level. The fraction identified varied among stations from 54 to 98 percent. Nematodes and oligochaetes accounted for most of the unidentified specimens. Relative to the total number of species identified in five replicates at each location, an average of 90 percent of the species were collected with three replicates. In general, species with high to moderate abundances were present in all replicates, and species collected only after three or more replicates averaged less than one specimen per replicate. Results from the box cores showed that the dominant species were most abundant in the upper 10 cm, the depth of sediment that can be adequately sampled with a modified Van Veen sampler. On the basis of the number of species and their abundances at each location, seven of the ten locations were selected for sampling in the regular program, which began in March 1987.

Ichthyological collection of the Museu Oceanográfico D. Carlos I.

PubMed

Silva, Ana Serra; Groz, Maria Pitta; Leandro, Paula; Assis, Carlos A; Figueira, Rui

2018-01-01

The collection of the Museu Oceanográfico D. Carlos I is a historical specimen, instrument, and document collection that has been housed at the Aquário Vasco da Gama since 1935. The collection is largely the result of several scientific campaigns conducted by Dom Carlos de Bragança between 1896 and 1907. Specifically, the ichthyological collection consists of 675 surviving catalogue records of specimens caught, acquired or offered to D. Carlos I between 1892 to 1907, and includes the type specimen for Odontaspis nasutus Bragança, 1904 (junior synonym of Mitsukurina owstoni Jordan, 1898), along with several specimens of deep sea species. All specimens were captured in coastal Portuguese waters, and were preserved in alcohol, formalin, or mounted.

Systematic evaluation of serum and plasma collection on the endogenous metabolome.

PubMed

Zhou, Zhi; Chen, Yanhua; He, Jiuming; Xu, Jing; Zhang, Ruiping; Mao, Yan; Abliz, Zeper

2017-02-01

In metabolomics research, the use of different blood collection methods may influence endogenous metabolites. Ultra HPLC coupled with MS/MS was applied together with multivariate statistics to investigate metabolomics differences in serum and plasma samples handled by different anticoagulants. A total of 135 known representative metabolites were assessed for comprehensive evaluation of the effects of anticoagulants. Exogenous factors, including separation gel ingredients from the serum collection tubes and the anticoagulants, affected mass spectrometer detection. Heparin plasma yielded the best detection of different functional groups and is therefore the optimal blood specimen for metabolomics research, followed by potassium oxalate plasma.

Data on introduced plants in Zimbabwe: Floristic changes and patterns of collection based on historical herbarium records.

PubMed

Maroyi, Alfred

2017-12-01

National herbaria with significant historical plant collections are critical to tracking floristic changes and patterns, which include the introduction and spread of non-native plant species. To explore the importance of herbarium specimen data in understanding floristic changes in Zimbabwe, the plant collections housed by the National Herbarium (SRGH) in Harare, Zimbabwe were utilized with historical specimens dating back to 1870. A list of naturalised plant taxa and collection data were compiled. A total of 2916 plant specimens were recorded, comprising of 401 taxa, 237 genera and 76 plant families. Twenty eight specimens (1.0%) were collected between 1870 and 1908, prior to the establishment of the National Herbarium in 1909 and 123 specimens (4.2%) were collected in the first 25 years of the establishment of the institute (1909-1934). Intensive collection of herbarium specimens of casual, naturalised and invasive alien plant species occurred between 1950 and 1970. This data demonstrates the utility of plant species data housed in the National Herbaria and how such data can be used to map floristic changes and patterns.

On specimen killing in the era of conservation crisis - A quantitative case for modernizing taxonomy and biodiversity inventories.

PubMed

Waeber, Patrick O; Gardner, Charlie J; Lourenço, Wilson R; Wilmé, Lucienne

2017-01-01

For centuries taxonomy has relied on dead animal specimens, a practice that persists today despite the emergence of innovative biodiversity assessment methods. Taxonomists and conservationists are engaged in vigorous discussions over the necessity of killing animals for specimen sampling, but quantitative data on taxonomic trends and specimen sampling over time, which could inform these debates, are lacking. We interrogated a long-term research database documenting 2,723 land vertebrate and 419 invertebrate taxa from Madagascar, and their associated specimens conserved in the major natural history museums. We further compared specimen collection and species description rates for the birds, mammals and scorpions over the last two centuries, to identify trends and links to taxon descriptions. We located 15,364 specimens documenting endemic mammals and 11,666 specimens documenting endemic birds collected between 1820 and 2010. Most specimens were collected at the time of the Mission Zoologique Franco-Anglo-Américaine (MZFAA) in the 1930s and during the last two decades, with major differences according to the groups considered. The small mammal and bat collections date primarily from recent years, and are paralleled by the description of new species. Lemur specimens were collected during the MZFAA but the descriptions of new taxa are recent, with the type series limited to non-killed specimens. Bird specimens, particularly of non-passerines, are mainly from the time of the MZFAA. The passerines have also been intensely collected during the last two decades; the new material has been used to solve the phylogeny of the groups and only two new endemic taxa of passerine birds have been described over the last two decades. Our data show that specimen collection has been critical for advancing our understanding of the taxonomy of Madagascar's biodiversity at the onset of zoological work in Madagascar, but less so in recent decades. It is crucial to look for alternatives to avoid killing animals in the name of documenting life, and encourage all efforts to share the information attached to historical and recent collections held in natural history museums. In times of conservation crisis and the advancement in digital technologies and open source sharing, it seems obsolete to kill animals in well-known taxonomic groups for the sake of enriching natural history collections around the world.

U-series ages of solitary corals from the California coast by mass spectrometry

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

Stein, M.; Wasserburg, G.J.; Chen, J.H.

1991-12-01

The purpose of this study is to evaluate the feasibility of dating fossil solitary corals from Pleistocene marine strandlines outside tropical latitudes using the recently developed high sensitivity, high-precision U-series technique based on thermal-ionization mass-spectrometry (TIMS). The TIMS technique is much more efficient than conventional {alpha} spectrometry and, as a result, multiple samples of an individual coral skeleton, or different specimens from the same bed can be analyzed. Detached and well-rounded fossil specimens of the solitary coral Balanophyllia elegans were collected from relict littoral deposits on emergent marine terraces along the California coast at Cayucos terrace, Shell Beach terrace, Nestormore » terrace, San Diego, Bird Rock terrace, San Diego. Attached living specimens were collected from the intertidal zone on the modern terrace at Moss Beach. The calculated initial {sup 234}U activities in the fossil specimens of Balanophyllia elegans are higher than the {sup 234}U activity in modern seawater or in the modern specimen. The higher initial activities could possibly reflect the influx of {sup 234}U-enriched continental water into Pleistocene coastal waters, or it could reflect the influx of {sup 234}U-enriched continental water into Pleistocene coastal waters, or it could reflect minor diagenetic alteration, a persistent and fundamental problem in dating all corals.« less

Preliminary buprenorphine sublingual tablet pharmacokinetic data in plasma, oral fluid and sweat during treatment of opioid-dependent pregnant women

PubMed Central

Concheiro, Marta; Jones, Hendreé E.; Johnson, Rolley E.; Choo, Robin; Huestis, Marilyn A.

2011-01-01

Background Buprenorphine is currently under investigation as a pharmacotherapy to treat pregnant women for opioid dependence. This research evaluates buprenorphine (BUP), norbuprenophine (NBUP), buprenorphine-glucuronide (BUP-Gluc) and norbuprenorphine-glucuronide (NBUP-Gluc) pharmacokinetics after high dose (14–20 mg) BUP sublingual tablet administration in three opioid-dependent pregnant women. Methods Oral fluid and sweat specimens were collected in addition to plasma specimens for 24 h during gestation weeks 28 or 29 and 34, and 2 months after delivery. Tmax was not affected by pregnancy; however, BUP and NBUP Cmax and AUC0–24h tended to be lower during pregnancy compared to postpartum levels. Results Statistically significant but weak positive correlations were found for BUP plasma and OF concentrations, and BUP/NBUP ratios in plasma and OF. Conclusion Statistically significant negative correlations were observed for times of specimen collection and BUP and NBUP OF/plasma ratios. BUP-Gluc and NBUP-Gluc were detected in only 5% of OF specimens. In sweat, BUP and NBUP were detected in only 4 of 25 (12 or 24 h) specimens in low concentrations (<2.4 ng/patch). These preliminary data describe BUP and metabolite pharmacokinetics in pregnant women and suggest that, like methadone, upward dose adjustments may be needed with advancing gestation. PMID:21860340

Design of a high-temperature experiment for evaluating advanced structural materials

NASA Technical Reports Server (NTRS)

Mockler, Theodore T.; Castro-Cedeno, Mario; Gladden, Herbert J.; Kaufman, Albert

1992-01-01

This report describes the design of an experiment for evaluating monolithic and composite material specimens in a high-temperature environment and subject to big thermal gradients. The material specimens will be exposed to aerothermal loads that correspond to thermally similar engine operating conditions. Materials evaluated in this study were monolithic nickel alloys and silicon carbide. In addition, composites such as tungsten/copper were evaluated. A facility to provide the test environment has been assembled in the Engine Research Building at the Lewis Research Center. The test section of the facility will permit both regular and Schlieren photography, thermal imaging, and laser Doppler anemometry. The test environment will be products of hydrogen-air combustion at temperatures from about 1200 F to as high as 4000 F. The test chamber pressure will vary up to 60 psia, and the free-stream flow velocity can reach Mach 0.9. The data collected will be used to validate thermal and stress analysis models of the specimen. This process of modeling, testing, and validation is expected to yield enhancements to existing analysis tools and techniques.

49 CFR 40.63 - What steps does the collector take in the collection process before the employee provides a urine...

Code of Federal Regulations, 2011 CFR

2011-10-01

... collection process before the employee provides a urine specimen? 40.63 Section 40.63 Transportation Office... PROGRAMS Urine Specimen Collections § 40.63 What steps does the collector take in the collection process before the employee provides a urine specimen? As the collector, you must take the following steps before...

49 CFR 40.63 - What steps does the collector take in the collection process before the employee provides a urine...

Code of Federal Regulations, 2013 CFR

2013-10-01

... collection process before the employee provides a urine specimen? 40.63 Section 40.63 Transportation Office... PROGRAMS Urine Specimen Collections § 40.63 What steps does the collector take in the collection process before the employee provides a urine specimen? As the collector, you must take the following steps before...

49 CFR 40.63 - What steps does the collector take in the collection process before the employee provides a urine...

Code of Federal Regulations, 2014 CFR

2014-10-01

... collection process before the employee provides a urine specimen? 40.63 Section 40.63 Transportation Office... PROGRAMS Urine Specimen Collections § 40.63 What steps does the collector take in the collection process before the employee provides a urine specimen? As the collector, you must take the following steps before...

49 CFR 40.63 - What steps does the collector take in the collection process before the employee provides a urine...

Code of Federal Regulations, 2012 CFR

2012-10-01

... collection process before the employee provides a urine specimen? 40.63 Section 40.63 Transportation Office... PROGRAMS Urine Specimen Collections § 40.63 What steps does the collector take in the collection process before the employee provides a urine specimen? As the collector, you must take the following steps before...

An evaluation of matching unknown writing inks with the United States International Ink Library.

PubMed

Laporte, Gerald M; Arredondo, Marlo D; McConnell, Tyra S; Stephens, Joseph C; Cantu, Antonio A; Shaffer, Douglas K

2006-05-01

Utilizing a database of standards for forensic casework is a valuable resource. Undoubtedly, as more standards (and corresponding information about the specimens) are collected, there is a greater certainty of identification when a questioned and a known item cannot be distinguished after a series of analyses. The United States Secret Service and the Internal Revenue Service National Forensic Laboratory jointly maintain the largest known forensic collection of writing inks in the world, which is comprised of over 8500 ink standards collected worldwide, dating back to the 1920s. This study was conducted to evaluate the reliability of matching arbitrarily purchased pens with known inks from a database. One hundred pens were randomly obtained from a variety of sources and their respective ink compositions were compared with standards. Eighty-five of the inks were determined to be suitable for comparison utilizing optical examinations and thin-layer chromatography. Three of the inks did not match any of the specimens on record; one of these inks was similar to an ink from an identical brand of pen that was in the database, but had a modified formulation.

10 CFR 707.12 - Specimen collection, handling and laboratory analysis for drug testing.

Code of Federal Regulations, 2011 CFR

2011-01-01

... drug testing. 707.12 Section 707.12 Energy DEPARTMENT OF ENERGY WORKPLACE SUBSTANCE ABUSE PROGRAMS AT DOE SITES Procedures § 707.12 Specimen collection, handling and laboratory analysis for drug testing... collection to final disposition of specimens, and testing laboratories shall use appropriate cutoff levels in...

10 CFR 707.12 - Specimen collection, handling and laboratory analysis for drug testing.

Code of Federal Regulations, 2010 CFR

2010-01-01

... drug testing. 707.12 Section 707.12 Energy DEPARTMENT OF ENERGY WORKPLACE SUBSTANCE ABUSE PROGRAMS AT DOE SITES Procedures § 707.12 Specimen collection, handling and laboratory analysis for drug testing... collection to final disposition of specimens, and testing laboratories shall use appropriate cutoff levels in...

10 CFR 707.12 - Specimen collection, handling and laboratory analysis for drug testing.

Code of Federal Regulations, 2014 CFR

2014-01-01

... drug testing. 707.12 Section 707.12 Energy DEPARTMENT OF ENERGY WORKPLACE SUBSTANCE ABUSE PROGRAMS AT DOE SITES Procedures § 707.12 Specimen collection, handling and laboratory analysis for drug testing... collection to final disposition of specimens, and testing laboratories shall use appropriate cutoff levels in...

10 CFR 707.12 - Specimen collection, handling and laboratory analysis for drug testing.

Code of Federal Regulations, 2012 CFR

2012-01-01

... drug testing. 707.12 Section 707.12 Energy DEPARTMENT OF ENERGY WORKPLACE SUBSTANCE ABUSE PROGRAMS AT DOE SITES Procedures § 707.12 Specimen collection, handling and laboratory analysis for drug testing... collection to final disposition of specimens, and testing laboratories shall use appropriate cutoff levels in...

10 CFR 707.12 - Specimen collection, handling and laboratory analysis for drug testing.

Code of Federal Regulations, 2013 CFR

2013-01-01

... drug testing. 707.12 Section 707.12 Energy DEPARTMENT OF ENERGY WORKPLACE SUBSTANCE ABUSE PROGRAMS AT DOE SITES Procedures § 707.12 Specimen collection, handling and laboratory analysis for drug testing... collection to final disposition of specimens, and testing laboratories shall use appropriate cutoff levels in...

Ichthyological collection of the Museu Oceanográfico D. Carlos I

PubMed Central

Silva, Ana Serra; Groz, Maria Pitta; Leandro, Paula; Assis, Carlos A.; Figueira, Rui

2018-01-01

Abstract The collection of the Museu Oceanográfico D. Carlos I is a historical specimen, instrument, and document collection that has been housed at the Aquário Vasco da Gama since 1935. The collection is largely the result of several scientific campaigns conducted by Dom Carlos de Bragança between 1896 and 1907. Specifically, the ichthyological collection consists of 675 surviving catalogue records of specimens caught, acquired or offered to D. Carlos I between 1892 to 1907, and includes the type specimen for Odontaspis nasutus Bragança, 1904 (junior synonym of Mitsukurina owstoni Jordan, 1898), along with several specimens of deep sea species. All specimens were captured in coastal Portuguese waters, and were preserved in alcohol, formalin, or mounted. PMID:29719477

Fixing Formalin: A Method to Recover Genomic-Scale DNA Sequence Data from Formalin-Fixed Museum Specimens Using High-Throughput Sequencing.

PubMed

Hykin, Sarah M; Bi, Ke; McGuire, Jimmy A

2015-01-01

For 150 years or more, specimens were routinely collected and deposited in natural history collections without preserving fresh tissue samples for genetic analysis. In the case of most herpetological specimens (i.e. amphibians and reptiles), attempts to extract and sequence DNA from formalin-fixed, ethanol-preserved specimens-particularly for use in phylogenetic analyses-has been laborious and largely ineffective due to the highly fragmented nature of the DNA. As a result, tens of thousands of specimens in herpetological collections have not been available for sequence-based phylogenetic studies. Massively parallel High-Throughput Sequencing methods and the associated bioinformatics, however, are particularly suited to recovering meaningful genetic markers from severely degraded/fragmented DNA sequences such as DNA damaged by formalin-fixation. In this study, we compared previously published DNA extraction methods on three tissue types subsampled from formalin-fixed specimens of Anolis carolinensis, followed by sequencing. Sufficient quality DNA was recovered from liver tissue, making this technique minimally destructive to museum specimens. Sequencing was only successful for the more recently collected specimen (collected ~30 ybp). We suspect this could be due either to the conditions of preservation and/or the amount of tissue used for extraction purposes. For the successfully sequenced sample, we found a high rate of base misincorporation. After rigorous trimming, we successfully mapped 27.93% of the cleaned reads to the reference genome, were able to reconstruct the complete mitochondrial genome, and recovered an accurate phylogenetic placement for our specimen. We conclude that the amount of DNA available, which can vary depending on specimen age and preservation conditions, will determine if sequencing will be successful. The technique described here will greatly improve the value of museum collections by making many formalin-fixed specimens available for genetic analysis.

Clinical evaluation and validation of laboratory methods for the diagnosis of Bordetella pertussis infection: Culture, polymerase chain reaction (PCR) and anti-pertussis toxin IgG serology (IgG-PT).

PubMed

Lee, Adria D; Cassiday, Pamela K; Pawloski, Lucia C; Tatti, Kathleen M; Martin, Monte D; Briere, Elizabeth C; Tondella, M Lucia; Martin, Stacey W

2018-01-01

The appropriate use of clinically accurate diagnostic tests is essential for the detection of pertussis, a poorly controlled vaccine-preventable disease. The purpose of this study was to estimate the sensitivity and specificity of different diagnostic criteria including culture, multi-target polymerase chain reaction (PCR), anti-pertussis toxin IgG (IgG-PT) serology, and the use of a clinical case definition. An additional objective was to describe the optimal timing of specimen collection for the various tests. Clinical specimens were collected from patients with cough illness at seven locations across the United States between 2007 and 2011. Nasopharyngeal and blood specimens were collected from each patient during the enrollment visit. Patients who had been coughing for ≤ 2 weeks were asked to return in 2-4 weeks for collection of a second, convalescent blood specimen. Sensitivity and specificity of each diagnostic test were estimated using three methods-pertussis culture as the "gold standard," composite reference standard analysis (CRS), and latent class analysis (LCA). Overall, 868 patients were enrolled and 13.6% were B. pertussis positive by at least one diagnostic test. In a sample of 545 participants with non-missing data on all four diagnostic criteria, culture was 64.0% sensitive, PCR was 90.6% sensitive, and both were 100% specific by LCA. CRS and LCA methods increased the sensitivity estimates for convalescent serology and the clinical case definition over the culture-based estimates. Culture and PCR were most sensitive when performed during the first two weeks of cough; serology was optimally sensitive after the second week of cough. Timing of specimen collection in relation to onset of illness should be considered when ordering diagnostic tests for pertussis. Consideration should be given to including IgG-PT serology as a confirmatory test in the Council of State and Territorial Epidemiologists (CSTE) case definition for pertussis.

Recovering data from historical collections: stratigraphic and spatial reconstruction of the outstanding carnivoran record from the Late Pleistocene Equi cave (Apuane Alps, Italy)

NASA Astrophysics Data System (ADS)

Ghezzo, Elena; Palchetti, Alessandro; Rook, Lorenzo

2014-07-01

Equi Terme is a hamlet located in northern Tuscany, in Apuan Alps regional Park. An outstanding fossil vertebrate collection housed in Florence is the result of excavations in the Equi cave and shelter during the period 1911-1919. This faunal assemblage (associated with Mousterian artefacts) may be correlated with the middle of MIS 3. All of the specimens recovered at Equi early in the last century were collected with attention to their stratigraphical positions. Detailed field annotation for nearly every specimen allowed us to organize them and attempt a stratigraphical and spatial reconstruction of the fossiliferous deposits. We present the results of the study of the spatial and stratigraphic distribution of the carnivoran species in the Equi cave and shelter, and re-evaluate the taphonomic agents of accumulation and the fossil distribution within the stratigraphic record. In particular, we evaluated the distribution of Panthera pardus, which, unusually for Europe, is abundant in the Equi cave assemblage. This analysis highlights the importance of the re-evaluation of historical collections and allows for future comparisons with data from more recent excavations at the Equi site. The analysis also provides an account of the distribution of carnivorans throughout the stratigraphic record. The constant presence and the predominance of leopards and wolves over lions and smaller carnivorans, allow for evaluations of their ethology and may be related to a short period of sediment accumulation.

Standard Specimen Reference Set: Pancreatic — EDRN Public Portal

Cancer.gov

The primary objective of the EDRN Pancreatic Cancer Working Group Proposal is to create a reference set consisting of well-characterized serum/plasma specimens to use as a resource for the development of biomarkers for the early detection of pancreatic adenocarcinoma. The testing of biomarkers on the same sample set permits direct comparison among them; thereby, allowing the development of a biomarker panel that can be evaluated in a future validation study. Additionally, the establishment of an infrastructure with core data elements and standardized operating procedures for specimen collection, processing and storage, will provide the necessary preparatory platform for larger validation studies when the appropriate marker/panel for pancreatic adenocarcinoma has been identified.

Establishment of a cervical cancer bio-bank for the Chinese population: from project-based sample collection to routine management.

PubMed

Yang, Ru; Li, Xiong; Zhou, Hang; Jia, Yao; Zhou, Jin; Huang, Kecheng; Tang, Fangxu; Hu, Ting; Shen, Jian; Chen, Zhilan; Wang, Shaoshuai; Sun, Haiying; Guo, Lili; Wang, Lin; Wang, Hui; Ma, Ding; Li, Shuang

2015-08-01

There is an increasing need for the establishment of a cervical cancer bio-bank that will facilitate both clinical and basic research. The cervical cancer bio-bank was first established in January 1999 and included two stages. First, a GWAS-based sample collection was conducted with special emphasis on the diagnosis and the retrieval of the corresponding bio-specimens, especially blood samples. Second, clinical data and their corresponding bio-specimens were routinely collected and handled. Notably, these bio-specimens also included samples from Wufeng Tujia Autonomous County, which has the highest incidence of cervical cancer in China. The specimens were collected from patients with cervical cancer and those with cervical intraepithelial neoplasia, while the control samples were collected from normal individuals. With special emphasis on clinical data and blood samples for the GWAS analysis, the collection of other bio-specimens was slow, and the pairing of specimens and clinical data was poor during the first stage. However, in the second stage, the pairing of the clinical data and its corresponding bio-specimens improved. At present, the samples procured and preserved in the bio-bank cover most regions of China and different ethnic groups for both the normal controls and cervical cancer patients of different pathological categories. This bio-bank of cervical cancer specimens from the Chinese population will greatly promote the studies of cervical cancer in China.

Review of forensically important entomological specimens collected from human cadavers in Malaysia (2005-2010).

PubMed

Kavitha, Rajagopal; Nazni, Wasi Ahmad; Tan, Tian Chye; Lee, Han Lim; Azirun, Mohd Sofian

2013-07-01

Forensic entomological specimens collected from human decedents during crime scene investigations in Malaysia in the past 6 years (2005-2010) are reviewed. A total of 80 cases were recorded and 93 specimens were collected. From these specimens, 10 species of cyclorrphagic flies were identified, consisting of Chrysomya rufifacies (Macquart) -38 specimens (40.86%), Chrysomya megacephala (Fabricius) -36 specimens (38.70%), Chrysomya villeneuvi (Patton) -2 specimens (2.15%), Chrysomya nigripes (Aubertin) -2 specimens (2.15%), Chrysomya pinguis (Walker) -1 specimen (1.08%), Hermetia illucens (Linnaeus) -1 specimen (1.08%), Hemipyrellia liguriens (Wiedemann) -5 specimens (5.37%), Synthesiomyia nudiseta (Wulp) -1 specimen (1.08%), Megaselia scalaris (Loew)-1 specimen (1.08%) and Sarcophaga ruficornis (Fabricius) -4 specimens (4.30%). In two specimens (2.15%), the maggots were not identifiable. Ch. megacephala and Ch. rufifacies were the commonest species found in human decedents from three different ecological habitats. S. nudiseta is an uncommon species found only on human cadavers from indoors. A total of 75 cases (93.75%) had a single fly infestation and 5 cases (6.25%) had double fly infestation. In conclusion, although large numbers of fly species were found on human decedents, the predominant species are still those of Chrysomya. Copyright © 2013 Elsevier Ltd and Faculty of Forensic and Legal Medicine. All rights reserved.

Specimen Collection and Submission Manual

DTIC Science & Technology

2016-06-01

immunoassays Specimen: tissue or bone marrow (100 mg); Whole EDTA blood or serum (0.5 ml) Nasopharyngeal or throat swab, dry or in transport medium; Sputum... Syndrome Coronavirus (MERS-CoV) – detection in clinical samples Methodology: molecular Specimen: If possible collect 3 specimen types (lower...guidelines-clinical-specimens.html) Shipping: ship cold on wet ice or ice packs. For delays exceeding 72 hours, ship frozen on dry ice. Turnaround: 1-2

Using Spot Biomarker Data to Inform Chronic Exposure and Health Risk

EPA Science Inventory

The U.S. NHANES and other health surveys frequently collect and analyze spot biological specimens to inform chemical exposures. These spot measurements can be compared to biomarker-based reference levels, such as “Biomonitoring Equivalents” (BEs), to evaluate health r...

A 3D photogrammetric reconstruction attempt of specimens of Badenian echinoids

NASA Astrophysics Data System (ADS)

Polonkai, Bálint; Raveloson, Andrea; Görög, Ágnes; Bodor, Emese; Székely, Balázs

2016-04-01

The rich echinoid fauna of the Badenian (Middle Miocene) from Budapest (Hungary) is well known for more than one hundred years. Along the road cuts and due to the construction of large buildings from 1960 to 2011, new Badenian outcrops with rich and well preserved echinoids were found in the city. Thus the main aim of this study was to revise historically collected echinoids (in the collection of Geological and Geophysical Institute of Hungary) from different parts of the city (Örs Vezér Square, Gyakorló Street, Rákos and District of Budafok-Tétény) and to classify the newly collected fossils, moreover to carry out the palaeoenvironmental reconstruction of the different localities. The specimens studied are from the Upper Badenian Leithakalk Formation Rákos Member, which consists of sandy limestone, calcareous loose sandstone with volcanic clast and/or calcarenite without terrigenous or volcanic clast. One of the most common echinoidea in the Badenian, the Parascutella gibbercula DE SERRES, 1829 is well known and researched in both morphological and taxonomic aspects. However there are some intraspecific morphological features that show sharp differences across the specimens: the adapical conical convexity is considerably different between several forms. The petalodium's length/width ratio is also different between many specimens. Other morphological characters for example peristomal and periproctal aperture and the food groove can also be different. These differences within this relatively small area could be determined by ecological conditions (such as substrate, palaeodepth), or can be related to taxonomical or pathological changes. For an appropriate comparison, quantification of these features is necessary. Photogrammetry is in general a useful and well-developed tool to reconstruct 3D surfaces of artefacts (e.g., in archaeology, cultural heritage, and also in palaeontology). In order to evaluate the differences found in P. gibbercula specimens various photogrammetric technologies have been used as our initial experiments showed that it could be a good tool to get three dimensional information about the collected fossils. This contribution discusses which photogrammetric techniques are adequate to study and compare the studied echinoid specimens. Our goal is to review modern techniques and current software solutions to model the fossils and also to study the resulting 3D point cloud. Different methods are evaluated and compared from taking the pictures (with different camera types and different target tables) through data processing, analyzing potential errors, resolution and accuracy for each one of them. Time- and cost-effectiveness of the software packages were also taken into account in order to render the images into 3D model effectively. Preliminary results show that 3D analysis using photogrammetrical method is a good tool to study the collected echinoid specimens showing more information than the classical morphometry studies, especially in the convex part of the studied fossils. Furthermore, the resulting 3D point clouds of different fossils make it possible to compare and maybe even quantify the differences across the specimens. Balázs Székely contributed as an Alexander von Humboldt Research Fellow.

Evaluation of Sampling Recommendations From the Influenza Virologic Surveillance Right Size Roadmap for Idaho.

PubMed

Rosenthal, Mariana; Anderson, Katey; Tengelsen, Leslie; Carter, Kris; Hahn, Christine; Ball, Christopher

2017-08-24

The Right Size Roadmap was developed by the Association of Public Health Laboratories and the Centers for Disease Control and Prevention to improve influenza virologic surveillance efficiency. Guidelines were provided to state health departments regarding representativeness and statistical estimates of specimen numbers needed for seasonal influenza situational awareness, rare or novel influenza virus detection, and rare or novel influenza virus investigation. The aim of this study was to compare Roadmap sampling recommendations with Idaho's influenza virologic surveillance to determine implementation feasibility. We calculated the proportion of medically attended influenza-like illness (MA-ILI) from Idaho's influenza-like illness surveillance among outpatients during October 2008 to May 2014, applied data to Roadmap-provided sample size calculators, and compared calculations with actual numbers of specimens tested for influenza by the Idaho Bureau of Laboratories (IBL). We assessed representativeness among patients' tested specimens to census estimates by age, sex, and health district residence. Among outpatients surveilled, Idaho's mean annual proportion of MA-ILI was 2.30% (20,834/905,818) during a 5-year period. Thus, according to Roadmap recommendations, Idaho needs to collect 128 specimens from MA-ILI patients/week for situational awareness, 1496 influenza-positive specimens/week for detection of a rare or novel influenza virus at 0.2% prevalence, and after detection, 478 specimens/week to confirm true prevalence is ≤2% of influenza-positive samples. The mean number of respiratory specimens Idaho tested for influenza/week, excluding the 2009-2010 influenza season, ranged from 6 to 24. Various influenza virus types and subtypes were collected and specimen submission sources were representative in terms of geographic distribution, patient age range and sex, and disease severity. Insufficient numbers of respiratory specimens are submitted to IBL for influenza laboratory testing. Increased specimen submission would facilitate meeting Roadmap sample size recommendations. ©Mariana Rosenthal, Katey Anderson, Leslie Tengelsen, Kris Carter, Christine Hahn, Christopher Ball. Originally published in JMIR Public Health and Surveillance (http://publichealth.jmir.org), 24.08.2017.

Evaluation of Sampling Recommendations From the Influenza Virologic Surveillance Right Size Roadmap for Idaho

PubMed Central

2017-01-01

Background The Right Size Roadmap was developed by the Association of Public Health Laboratories and the Centers for Disease Control and Prevention to improve influenza virologic surveillance efficiency. Guidelines were provided to state health departments regarding representativeness and statistical estimates of specimen numbers needed for seasonal influenza situational awareness, rare or novel influenza virus detection, and rare or novel influenza virus investigation. Objective The aim of this study was to compare Roadmap sampling recommendations with Idaho’s influenza virologic surveillance to determine implementation feasibility. Methods We calculated the proportion of medically attended influenza-like illness (MA-ILI) from Idaho’s influenza-like illness surveillance among outpatients during October 2008 to May 2014, applied data to Roadmap-provided sample size calculators, and compared calculations with actual numbers of specimens tested for influenza by the Idaho Bureau of Laboratories (IBL). We assessed representativeness among patients’ tested specimens to census estimates by age, sex, and health district residence. Results Among outpatients surveilled, Idaho’s mean annual proportion of MA-ILI was 2.30% (20,834/905,818) during a 5-year period. Thus, according to Roadmap recommendations, Idaho needs to collect 128 specimens from MA-ILI patients/week for situational awareness, 1496 influenza-positive specimens/week for detection of a rare or novel influenza virus at 0.2% prevalence, and after detection, 478 specimens/week to confirm true prevalence is ≤2% of influenza-positive samples. The mean number of respiratory specimens Idaho tested for influenza/week, excluding the 2009-2010 influenza season, ranged from 6 to 24. Various influenza virus types and subtypes were collected and specimen submission sources were representative in terms of geographic distribution, patient age range and sex, and disease severity. Conclusions Insufficient numbers of respiratory specimens are submitted to IBL for influenza laboratory testing. Increased specimen submission would facilitate meeting Roadmap sample size recommendations. PMID:28838883

Fixing Formalin: A Method to Recover Genomic-Scale DNA Sequence Data from Formalin-Fixed Museum Specimens Using High-Throughput Sequencing

PubMed Central

Hykin, Sarah M.; Bi, Ke; McGuire, Jimmy A.

2015-01-01

For 150 years or more, specimens were routinely collected and deposited in natural history collections without preserving fresh tissue samples for genetic analysis. In the case of most herpetological specimens (i.e. amphibians and reptiles), attempts to extract and sequence DNA from formalin-fixed, ethanol-preserved specimens—particularly for use in phylogenetic analyses—has been laborious and largely ineffective due to the highly fragmented nature of the DNA. As a result, tens of thousands of specimens in herpetological collections have not been available for sequence-based phylogenetic studies. Massively parallel High-Throughput Sequencing methods and the associated bioinformatics, however, are particularly suited to recovering meaningful genetic markers from severely degraded/fragmented DNA sequences such as DNA damaged by formalin-fixation. In this study, we compared previously published DNA extraction methods on three tissue types subsampled from formalin-fixed specimens of Anolis carolinensis, followed by sequencing. Sufficient quality DNA was recovered from liver tissue, making this technique minimally destructive to museum specimens. Sequencing was only successful for the more recently collected specimen (collected ~30 ybp). We suspect this could be due either to the conditions of preservation and/or the amount of tissue used for extraction purposes. For the successfully sequenced sample, we found a high rate of base misincorporation. After rigorous trimming, we successfully mapped 27.93% of the cleaned reads to the reference genome, were able to reconstruct the complete mitochondrial genome, and recovered an accurate phylogenetic placement for our specimen. We conclude that the amount of DNA available, which can vary depending on specimen age and preservation conditions, will determine if sequencing will be successful. The technique described here will greatly improve the value of museum collections by making many formalin-fixed specimens available for genetic analysis. PMID:26505622

Evaluation of the FTA carrier device for human papillomavirus testing in developing countries.

PubMed

Gonzalez, Paula; Cortes, Bernal; Quint, Wim; Kreimer, Aimée R; Porras, Carolina; Rodríguez, Ana Cecilia; Jimenez, Silvia; Herrero, Rolando; Struijk, Linda; Hildesheim, Allan; Melchers, Willem

2012-12-01

Liquid-based methods for the collection, transportation, and storage of cervical cells are cumbersome and expensive and involve laborious DNA extraction. An FTA cartridge is a solid carrier device, easier to handle and allowing simple DNA elution for human papillomavirus (HPV) testing. HPV-DNA results from cervical specimens collected in PreservCyt medium (Hologic, Inc.) and the indicating FTA elute cartridge were compared in an area where transportation and storage may affect the performance of the test. Cervical cells from 319 young adult women enrolled in the Costa Rica Vaccine Trial were collected by a nurse using a Cervex brush (Roberts), which was placed on the FTA cartridge and subsequently rinsed in 20 ml of PreservCyt medium. Two 0.5-ml PreservCyt aliquots were frozen for HPV-PCR testing; the FTA cartridges were kept at room temperature. HPV-DNA detection and typing was performed using SPF(10) PCR/DEIA (DNA enzyme immunoassay detection of amplimers)/LiPA(25) system. The percent agreement, agreement among positives, and kappas were estimated. Positivity was higher for FTA compared to PreservCyt specimens (54.5% versus 45.8%, P < 0.001). For oncogenic types, the overall agreement was 0.92, the agreement between positives was 0.74, and the kappa was 0.79. For individual HPV types, the overall agreement ranged from 0.97 to 1.00. We did not observe reduced cytology adequacy when specimen collection for cytology was preceded by FTA collection for HPV testing. HPV-DNA detection from FTA cartridges is broadly comparable to detection from PC medium. The higher HPV detection observed for FTA-collected specimens should be explored further. FTA cartridges could provide a simpler and more cost-effective method for cervical cell collection, storage, and transportation for HPV-DNA detection in research settings in developing countries.

Evaluation of the FTA Carrier Device for Human Papillomavirus Testing in Developing Countries

PubMed Central

Cortes, Bernal; Quint, Wim; Kreimer, Aimée R.; Porras, Carolina; Rodríguez, Ana Cecilia; Jimenez, Silvia; Herrero, Rolando; Struijk, Linda; Hildesheim, Allan; Melchers, Willem

2012-01-01

Liquid-based methods for the collection, transportation, and storage of cervical cells are cumbersome and expensive and involve laborious DNA extraction. An FTA cartridge is a solid carrier device, easier to handle and allowing simple DNA elution for human papillomavirus (HPV) testing. HPV-DNA results from cervical specimens collected in PreservCyt medium (Hologic, Inc.) and the indicating FTA elute cartridge were compared in an area where transportation and storage may affect the performance of the test. Cervical cells from 319 young adult women enrolled in the Costa Rica Vaccine Trial were collected by a nurse using a Cervex brush (Roberts), which was placed on the FTA cartridge and subsequently rinsed in 20 ml of PreservCyt medium. Two 0.5-ml PreservCyt aliquots were frozen for HPV-PCR testing; the FTA cartridges were kept at room temperature. HPV-DNA detection and typing was performed using SPF10 PCR/DEIA (DNA enzyme immunoassay detection of amplimers)/LiPA25 system. The percent agreement, agreement among positives, and kappas were estimated. Positivity was higher for FTA compared to PreservCyt specimens (54.5% versus 45.8%, P < 0.001). For oncogenic types, the overall agreement was 0.92, the agreement between positives was 0.74, and the kappa was 0.79. For individual HPV types, the overall agreement ranged from 0.97 to 1.00. We did not observe reduced cytology adequacy when specimen collection for cytology was preceded by FTA collection for HPV testing. HPV-DNA detection from FTA cartridges is broadly comparable to detection from PC medium. The higher HPV detection observed for FTA-collected specimens should be explored further. FTA cartridges could provide a simpler and more cost-effective method for cervical cell collection, storage, and transportation for HPV-DNA detection in research settings in developing countries. PMID:22993174

Birds of Antioquia: Georeferenced database of specimens from the Colección de Ciencias Naturales del Museo Universitario de la Universidad de Antioquia (MUA).

PubMed

Rozo, Andrea Morales; Valencia, Fernando; Acosta, Alexis; Parra, Juan Luis

2014-01-01

The department of Antioquia, Colombia, lies in the northwestern corner of South America and provides a biogeographical link among divergent faunas, including Caribbean, Andean, Pacific and Amazonian. Information about the distribution of biodiversity in this area is of relevance for academic, practical and social purposes. This data paper describes the dataset containing all bird specimens deposited in the Colección de Ciencias Naturales del Museo Universitario de la Universidad de Antioquia (MUA). We curated all the information associated with the bird specimens, including the georeferences and taxonomy, and published the database through the Global Biodiversity Information Facility network. During this process we checked the species identification and existing georeferences and completed the information when possible. The collection holds 663 bird specimens collected between 1940 and 2011. Even though most specimens are from Antioquia (70%), the collection includes material from several other departments and one specimen from the United States. The collection holds specimens from three endemic and endangered species (Coeligena orina, Diglossa gloriossisima, and Hypopirrhus pyrohipogaster), and includes localities poorly represented in other collections. The information contained in the collection has been used for biodiversity modeling, conservation planning and management, and we expect to further facilitate these activities by making it publicly available.

List of type specimens deposited since 1998 in the United States Department of Agriculture Nematode Collection, Beltsville, Maryland

USDA-ARS?s Scientific Manuscript database

The United States Department of Agriculture Nematode Collection (USDANC) is one of the largest and most valuable in existence and includes millions of specimens housed in over 39,800 permanent slides and 9,300 vials. This Collection preserves type specimens of nematodes to serve as a reference for i...

Incidental non-benign gallbladder histopathology after cholecystectomy in an United Kingdom population: Need for routine histological analysis?

PubMed Central

Patel, Krashna; Dajani, Khaled; Iype, Satheesh; Chatzizacharias, Nikolaos A; Vickramarajah, Saranya; Singh, Prateush; Davies, Susan; Brais, Rebecca; Liau, Siong S; Harper, Simon; Jah, Asif; Praseedom, Raaj K; Huguet, Emmanuel L

2016-01-01

AIM To analyse the range of histopathology detected in the largest published United Kingdom series of cholecystectomy specimens and to evaluate the rational for selective histopathological analysis. METHODS Incidental gallbladder malignancy is rare in the United Kingdom with recent literature supporting selective histological assessment of gallbladders after routine cholecystectomy. All cholecystectomy gallbladder specimens examined by the histopathology department at our hospital during a five year period between March 2008 and March 2013 were retrospectively analysed. Further data was collected on all specimens demonstrating carcinoma, dysplasia and polypoid growths. RESULTS The study included 4027 patients. The majority (97%) of specimens exhibited gallstone or cholecystitis related disease. Polyps were demonstrated in 44 (1.09%), the majority of which were cholesterol based (41/44). Dysplasia, ranging from low to multifocal high-grade was demonstrated in 55 (1.37%). Incidental primary gallbladder adenocarcinoma was detected in 6 specimens (0.15%, 5 female and 1 male), and a single gallbladder revealed carcinoma in situ (0.02%). This large single centre study demonstrated a full range of gallbladder disease from cholecystectomy specimens, including more than 1% neoplastic histology and two cases of macroscopically occult gallbladder malignancies. CONCLUSION Routine histological evaluation of all elective and emergency cholecystectomies is justified in a United Kingdom population as selective analysis has potential to miss potentially curable life threatening pathology. PMID:27830040

Sputum, sex and scanty smears: new case definition may reduce sex disparities in smear-positive tuberculosis.

PubMed

Ramsay, A; Bonnet, M; Gagnidze, L; Githui, W; Varaine, F; Guérin, P J

2009-05-01

Urban clinic, Nairobi. To evaluate the impact of specimen quality and different smear-positive tuberculosis (TB) case (SPC) definitions on SPC detection by sex. Prospective study among TB suspects. A total of 695 patients were recruited: 644 produced > or =1 specimen for microscopy. The male/female sex ratio was 0.8. There were no significant differences in numbers of men and women submitting three specimens (274/314 vs. 339/380, P = 0.43). Significantly more men than women produced a set of three 'good' quality specimens (175/274 vs. 182/339, P = 0.01). Lowering thresholds for definitions to include scanty smears resulted in increases in SPC detection in both sexes; the increase was significantly higher for women. The revised World Health Organization (WHO) case definition was associated with the highest detection rates in women. When analysis was restricted only to patients submitting 'good' quality specimen sets, the difference in detection between sexes was on the threshold for significance (P = 0.05). Higher SPC notification rates in men are commonly reported by TB control programmes. The revised WHO SPC definition may reduce sex disparities in notification. This should be considered when evaluating other interventions aimed at reducing these. Further study is required on the effects of the human immuno-deficiency virus and instructed specimen collection on sex-specific impact of new SPC definition.

A Study to Determine the Incidence of Urinary Tract Infections in Infants and Children Ages 4 Months to 6 Years With Febrile Diarrhea.

PubMed

Nibhanipudi, Kumara V

2016-01-01

To determine the incidence of urinary tract infections (UTIs) in infants and children (4 months to 6 years of age) with febrile diarrhea, as outpatients. This was a prospective institutional review board-approved study. patients (between 4 months and 6 years of age) were enrolled in the study who presented to the pediatric emergency room with a complaint of fever (rectal temperature 101°F or more) and diarrhea (watery stools >3 in number). The patients were evaluated for state of hydration, and also urine samples were collected. For those children not toilet trained, urine specimens were collected by bladder catheterization, and for those children toilet trained, urine specimens were obtained by midstream collection method. The urine samples obtained were sent for analysis and culture. Eighty patients were enrolled in the study. The number of specimens obtained by clean catch midstream was 20, and by bladder catheterization was 60. None of the urine specimens obtained by both methods of collection grew any organism. There was no increased incidence of infections in male children whether circumcised (10/60) or uncircumcised (50/60). The mean temperature was 102.8°F (range = 101°F to 105°F). Using in silico online 2 × 2 χ(2) test by comparing both the positive and negative urine culture results, 2-tailed P value is <.0001. Our prospective randomized study concluded that there is no increased incidence of UTIs in infants and children (4 months to 6 years of age) with febrile diarrhea.

49 CFR 40.71 - How does the collector prepare the specimens?

Code of Federal Regulations, 2011 CFR

2011-10-01

... TRANSPORTATION WORKPLACE DRUG AND ALCOHOL TESTING PROGRAMS Urine Specimen Collections § 40.71 How does the... brings the urine specimen to you. You must take these steps in the presence of the employee. (1) Check... employee, must first pour at least 30 mL of urine from the collection container into one specimen bottle...

49 CFR 40.71 - How does the collector prepare the specimens?

Code of Federal Regulations, 2014 CFR

2014-10-01

... TRANSPORTATION WORKPLACE DRUG AND ALCOHOL TESTING PROGRAMS Urine Specimen Collections § 40.71 How does the... brings the urine specimen to you. You must take these steps in the presence of the employee. (1) Check... employee, must first pour at least 30 mL of urine from the collection container into one specimen bottle...

49 CFR 40.71 - How does the collector prepare the specimens?

Code of Federal Regulations, 2010 CFR

2010-10-01

... TRANSPORTATION WORKPLACE DRUG AND ALCOHOL TESTING PROGRAMS Urine Specimen Collections § 40.71 How does the... brings the urine specimen to you. You must take these steps in the presence of the employee. (1) Check... employee, must first pour at least 30 mL of urine from the collection container into one specimen bottle...

49 CFR 40.71 - How does the collector prepare the specimens?

Code of Federal Regulations, 2012 CFR

2012-10-01

... TRANSPORTATION WORKPLACE DRUG AND ALCOHOL TESTING PROGRAMS Urine Specimen Collections § 40.71 How does the... brings the urine specimen to you. You must take these steps in the presence of the employee. (1) Check... employee, must first pour at least 30 mL of urine from the collection container into one specimen bottle...

49 CFR 40.71 - How does the collector prepare the specimens?

Code of Federal Regulations, 2013 CFR

2013-10-01

... TRANSPORTATION WORKPLACE DRUG AND ALCOHOL TESTING PROGRAMS Urine Specimen Collections § 40.71 How does the... brings the urine specimen to you. You must take these steps in the presence of the employee. (1) Check... employee, must first pour at least 30 mL of urine from the collection container into one specimen bottle...

The Mineral Collection of the University of Michigan: its History and Future

NASA Astrophysics Data System (ADS)

Stefano, C. J.; Ewing, R. C.; Erwin, K.

2012-12-01

The mineral collection at the University of Michigan is among the oldest and finest in the Great Lakes region. The collection was created in 1838 with the purchase, under Douglass Houghton, one of the first professors at the University of Michigan, of 2,600 specimens, largely of European origin, from Baron Louis von Lederer of Vienna. This was one of the first major purchases by the Board of Regents. The collection was actively curated and continued to grow under the direction of Edward H. Kraus, one of the founders of the Mineralogical Society of America and the Chair of the then separate Department of Mineralogy. The collection is the repository for specimens collected by Douglass Houghton, as well as specimens collected during the first geological survey of Michigan. Specimens from Michigan's Keweenaw copper district are of exceptional quality, mainly due to the world-class specimens donated by then Regent L. L. Hubbard between 1917 and the mid-1920s. There is also a significant suite of fine Sicilian sulfur specimens collected during the Ph.D. research of Professor Walter F. Hunt. Other important suites include the Stuart H. Perry Meteorite collection, the Frederick S. Stearns gemstone collection, and a suite of Antarctic rock samples collected during the Byrd expedition in 1928-30. The collection also has a wide variety of worldwide specimens, mostly of reference quality, although there are several hundred excellent to world class pieces that do not fit into the core suites. Overall, the collection contains approximately 15,000 mineral specimens, about 1,000 meteorites, and several thousand gemstones and related materials. Although the collection continued to be an important part of the teaching and research efforts after the Departments of Mineralogy and Geology were merged in 1961, the collection was little used and without active curation through the latter half of the 20th Century. Recently, the University has initiated an inventory process prior to determining the fate of the Collection. The range of options are driven by the research needs of the Department, which have changed substantially in recent years, as well as the need for financial support and space in order to properly curate and preserve the collection. A major issue is how one weighs the historical, scientific and aesthetic value of such a collection against the mission and financial demands of the University.

NDE detectability of fatigue-type cracks in high-strength alloys: NDI reliability assessments

NASA Technical Reports Server (NTRS)

Christner, Brent K.; Long, Donald L.; Rummel, Ward D.

1988-01-01

This program was conducted to generate quantitative flaw detection capability data for the nondestructive evaluation (NDE) techniques typically practiced by aerospace contractors. Inconel 718 and Haynes 188 alloy test specimens containing fatigue flaws with a wide distribution of sizes were used to assess the flaw detection capabilities at a number of contractor and government facilities. During this program 85 inspection sequences were completed presenting a total of 20,994 fatigue cracks to 53 different inspectors. The inspection sequences completed included 78 liquid penetrant, 4 eddy current, and 3 ultrasonic evaluations. The results of the assessment inspections are presented and discussed. In generating the flaw detection capability data base, procedures for data collection, data analysis, and specimen care and maintenance were developed, demonstrated, and validated. The data collection procedures and methods that evolved during this program for the measurement of flaw detection capabilities and the effects of inspection variables on performance are discussed. The Inconel 718 and Haynes 188 test specimens that were used in conducting this program and the NDE assessment procedures that were demonstrated, provide NASA with the capability to accurately assess the flaw detection capabilities of specific inspection procedures being applied or proposed for use on current and future fracture control hardware program.

Characterisation of swabbing for virological analysis in the Spanish Influenza Sentinel Surveillance System during four influenza seasons in the period 2002-2006.

PubMed

Larrauri, A; de Mateo, S

2007-05-01

This study sought to characterise the swabbing pattern in the Spanish Influenza Sentinel Surveillance System (SISSS) and ascertain to what extent the system meets the guidelines currently being drafted by The European Influenza Surveillance Scheme (EISS). Data on seasons 2002/2003 to 2005/2006 were drawn from SISSS. The study analysed collection and dispatch of swab specimens for virological analysis by reference to variables relating to patient sex, age group, vaccination status, specimen collection period, period of influenza activity, time of swabbing and epidemiological season. SISSS adapts to EISS recommendations with respect to the specimen collection period and period of influenza activity, but there is a tendency to collect fewer specimens than recommended as the age of patients increases, and in the case of elderly patients (65 years and older), frequency of collection is clearly insufficient. Furthermore, sentinel physicians collect a higher percentage of specimens in cases where patients have received the influenza vaccine.

[Applying healthcare failure mode and effect analysis to improve the surgical specimen transportation process and rejection rate].

PubMed

Hu, Pao-Hsueh; Hu, Hsiao-Chen; Huang, Hui-Ju; Chao, Hui-Lin; Lei, Ei-Fang

2014-04-01

Because surgical pathology specimens are crucial to the diagnosis and treatment of disease, it is critical that they be collected and transported safely and securely. Due to recent near-miss events in our department, we used the healthcare failure model and effect analysis to identify 14 potential perils in the specimen collection and transportation process. Improvement and prevention strategies were developed accordingly to improve quality of care. Using health care failure mode and effect analysis (HFMEA) may improve the surgical specimen transportation process and reduce the rate of surgical specimen rejection. Rectify standard operating procedures for surgical pathology specimen collection and transportation. Create educational videos and posters. Rectify methods of specimen verification. Organize and create an online and instantaneous management system for specimen tracking and specimen rejection. Implementation of the new surgical specimen transportation process effectively eliminated the 14 identified potential perils. In addition, the specimen rejection fell from 0.86% to 0.03%. This project was applied to improve the specimen transportation process, enhance interdisciplinary cooperation, and improve the patient-centered healthcare system. The creation and implementation of an online information system significantly facilitates specimen tracking, hospital cost reductions, and patient safety improvements. The success in our department is currently being replicated across all departments in our hospital that transport specimens. Our experience and strategy may be applied to inter-hospital specimen transportation in the future.

Evaluation of Intraosseous Fluid as an Alternative Biological Specimen in Postmortem Toxicology.

PubMed

Rodda, Luke N; Volk, Justin A; Moffat, Ellen; Williams, Chinyere M; Lynch, Kara L; Wu, Alan H B

2018-04-01

The postmortem redistribution phenomenon is an important factor in the interpretation of blood drug concentrations as a cause or factor in death. Intraosseous fluid (IOF) may serve as an alternative matrix for drug testing. Intraosseous fluid was collected from the left and right tibias and humerus of 29 decedents using the Arrow EZ-IO Intraosseous Vascular Access System. Standard autopsy specimens including blood were also collected at the same time during autopsy. Blood and IOF specimens were screened by immunoassay for opioids, fentanyl analogs, oxycodone, methadone, cocaine, methamphetamine, amphetamines, phencyclidine, tricyclic antidepressants, benzodiazepines and cannabinoids, using commercially available enzyme-linked immunosorbent assay (ELISA) kits. Correlation between cardiac/central blood ELISA and IOF ELISA results was mostly 100% for drug targets. Further blood confirmation analysis was performed by gas chromatography mass spectrometry also showed comparable correlation to IOF screen results. There was no significant difference between the IOF sites or sides of the body. This novel study supports the use of IOF as an alternative postmortem specimen for toxicological investigations as a potentially less-compromised tissue in decomposed or traumatized bodies. Preliminary data is provided for the screening of common drugs of abuse in IOF that may show to be subject to alternative rates of postmortem redistribution than to that of other biological specimens in future studies that quantitate IOF drug concentrations.

Analysis of polyfluoroalkyl substances and bisphenol A in dried blood spots by liquid chromatography tandem mass spectrometry.

PubMed

Ma, Wanli; Kannan, Kurunthachalam; Wu, Qian; Bell, Erin M; Druschel, Charlotte M; Caggana, Michele; Aldous, Kenneth M

2013-05-01

Dried blood spots (DBS), collected as part of the newborn screening program (NSP) in the USA, is a valuable resource for studies on environmental chemical exposures and associated health outcomes in newborns. Nevertheless, determination of concentrations of environmental chemicals in DBS requires assays with great sensitivity, as the typical volume of blood available on a DBS with 16-mm diameter disc is approximately 50 μL. In this study, we developed a liquid-liquid extraction and high-performance liquid chromatography/tandem mass spectrometry method for the detection of perfluorooctanesulfonate (PFOS), perfluorooctanoate (PFOA), and bisphenol A (BPA) in DBS. The method was validated for accuracy, precision, and sensitivity, by spiking of target chemicals at different levels on Whatman 903 filter cards, which is used in the collection of DBS by the NSP. Contamination arising from collection, storage, and handling of DBS is an important issue to be considered in the analysis of trace levels of environmental chemicals in DBS. For the evaluation of the magnitude of background contamination, field blanks were prepared from unspotted portions of DBS filter cards collected by the NSP. The method was applied for the measurement of PFOS, PFOA, and BPA in 192 DBS specimens provided by NSP of New York State. PFOS and PFOA were detected in 100 % of the specimens analyzed. The concentrations of PFOS and PFOA measured in DBS were similar to those reported earlier in the whole blood samples of newborns. BPA was also found in 86 % of the specimens at concentrations ranging from 0.2 to 36 ng/mL (excluding two outliers). Further studies are needed to evaluate the sources of BPA exposures and health outcomes in newborns.

A technique for magnetic resonance imaging of equine cadaver specimens.

PubMed

Widmer, W R; Buckwalter, K A; Hill, M A; Fessler, J F; Ivancevich, S

1999-01-01

We tested an adaptation of a technique for performing magnetic resonance (MR) imaging of human cadaver limbs in the horse. The forelimbs from a normal horse were collected, frozen, and sealed with a paraffin-polymer combination prior to imaging with either a high- or midfield magnetic resonance scanner. Each forelimb was defrosted, scanned, and refrozen on two separate occasions. A five-point scale was used to evaluate the quality of each set of sagittal and transverse, T1-weighted images of each digit. There was no difference in image quality between first and second scans of either specimen (p > 0.05). We conclude that this technique allows investigators to bank tissue specimens for future magnetic resonance imaging without significant loss of image quality.

Assessment of the stability of DNA in specimens collected under conditions for drug testing-A pilot study.

PubMed

White, Robert M; Mitchell, John M; Hart, E Dale; Evans, Amy; Meaders, Meredith; Norsworthy, Sarah E; Hayes, Eugene D; Flegel, Ron; Maha, George C; Shaffer, Megan D; Hall, Erin M; Rogers, Kelley

2018-02-01

For forensic biological sample collections, the specimen donor is linked solidly to his or her specimen through a chain of custody (CoC) sometimes referenced as a chain of evidence. Rarely, a donor may deny that a urine or oral fluid (OF) specimen is his or her specimen even with a patent CoC. The goal of this pilot study was to determine the potential effects of short-term storage on the quality and quantity of DNA in both types of specimen under conditions that may be encountered with employment-related drug testing specimens. Fresh urine and freshly collected oral fluid all produced complete STR profiles. For the "pad" type OF collectors, acceptable DNA was extractable both from the buffer/preservative and the pad. Although fresh urine and OF produced complete STR profiles, partial profiles were obtained after storage for most samples. An exception was the DNA in the Quantisal OF collector, from which a complete profile was obtained for both freshly collected OF and stored OF. Copyright © 2017 Elsevier B.V. All rights reserved.

Mushroom Flora of Ulleung-gun and a Newly Recorded Bovista Species in the Republic of Korea

PubMed Central

Kim, Chang Sun; Jo, Jong Won; Kwag, Young-Nam; Sung, Gi-Ho; Lee, Sle-gee; Kim, Sang-Yong; Shin, Chang-Ho

2015-01-01

We conducted five times surveys, in June, September and October in 2012; June and September 2013, to catalog the mushroom flora in Ulleung-gun, Republic of Korea. More than 400 specimens were collected, and 317 of the specimens were successfully sequenced using the ribosomal DNA internal transcribed spacer barcode marker. We also surveyed the morphological characteristics of the sequenced specimens. The specimens were classified into 2 phyla, 7 classes, 21 orders, 59 families, 122 genera, and 221 species, and were deposited in the herbarium of Korea National Arboretum. Among the collected species, 72% were saprophytic, 25% were symbiotic, and 3% were parasitic. The most common order was Agaricales (189 specimens, 132 species), followed by Polyporales (47 specimens, 27 species), Russulales (31 specimens, 22 species), Boletales (10 specimens, 7 species), and so on. Herein, we also reported the first Bovista species in Korea, which was collected from Dokdo, the far-eastern island of Korea. PMID:26539040

A Comparative Study on the Role of Xpert MTB/RIF in Testing Different Types of Spinal Tuberculosis Tissue Specimens.

PubMed

Tang, Liang; Feng, Shiqing; Gao, Ruixiao; Han, Chenfu; Sun, Xiaochen; Bao, Yucheng; Zhang, Wenlong

2017-12-01

The aim of the present study was to compare the efficacy of the commercial Xpert Mycobacterium tuberculosis/rifampin (MTB/RIF) test for evaluating different types of spinal tuberculosis (TB) tissue specimens. Pus, granulation tissue, and caseous necrotic tissue specimens from 223 patients who were diagnosed with spinal TB and who underwent curettage were collected for bacterial culture and the Xpert MTB/RIF assay to calculate the positive rate. Bacterial culture and phenotypic drug sensitivity testing (pDST) were adopted as the gold standards to calculate the sensitivity and specificity of the Xpert bacterial detection and drug resistance (DR) test. The positive rate (68.61% ± 7.35%) from the Xpert MTB/RIF assays of spinal TB patients' tissue specimens was higher compared with bacterial culture (44.39% ± 6.51%, Z = 5.1642, p < 0.01), and the positive rates from Xpert MTB/RIF assays on the three types of specimens were all higher than those of bacterial culture, with statistically significant results for pus and granulation tissue specimens. The positive rates for pus using the two bacteriological tests were higher than those for granulation tissue but were not statistically significant. However, the positive rates obtained from granulation tissue were statistically significantly higher than those obtained from caseous necrotic tissue. With bacterial culture and pDST as the gold standards, the sensitivity of Xpert MTB/RIF assays for MTB was 96.97%, while the sensitivity and specificity of the DR test also remained relatively high. For efficient and accurate diagnosis of spinal TB and DR and timely provision of effective treatment, multiple specimens, especially the pus of spinal TB patients, should be collected for Xpert MTB/RIF assays.

Iberian Odonata distribution: data of the BOS Arthropod Collection (University of Oviedo, Spain)

PubMed Central

Torralba-Burrial, Antonio; Ocharan, Francisco J.

2013-01-01

Abstract Odonata are represented from the Iberian Peninsula by 79 species. However, there exists a significant gap in accessible knowledge about these species,especially regarding their distribution. This data paper describes the specimen-based Odonata data of the Arthropod Collection of the Department of Biología de Organismos y Sistemas (BOS), University of Oviedo, Spain. The specimens were mainly collected from the Iberian Peninsula (98.63% of the data records), especially the northern region. The earliest specimen deposited in the collection dates back to 1950, while the 1980’s and 2000’s are the best-represented time periods. Between 1950 and 2009, 16, 604 Odonata specimens were deposited and are documented in the dataset. Approximately 20% of the specimens belong to the families Coenagrionidae and Calopterygidae. Specimens include the holotype and paratypes of the Iberian subspecies Calopteryx haemorrhoidalis asturica Ocharan, 1983 and Sympetrum vulgatum ibericum Ocharan, 1985. The complete dataset is also provided in Darwin Core Archive format. PMID:23794917

Iberian Odonata distribution: data of the BOS Arthropod Collection (University of Oviedo, Spain).

PubMed

Torralba-Burrial, Antonio; Ocharan, Francisco J

2013-01-01

Odonata are represented from the Iberian Peninsula by 79 species. However, there exists a significant gap in accessible knowledge about these species,especially regarding their distribution. This data paper describes the specimen-based Odonata data of the Arthropod Collection of the Department of Biología de Organismos y Sistemas (BOS), University of Oviedo, Spain. The specimens were mainly collected from the Iberian Peninsula (98.63% of the data records), especially the northern region. The earliest specimen deposited in the collection dates back to 1950, while the 1980's and 2000's are the best-represented time periods. Between 1950 and 2009, 16, 604 Odonata specimens were deposited and are documented in the dataset. Approximately 20% of the specimens belong to the families Coenagrionidae and Calopterygidae. Specimens include the holotype and paratypes of the Iberian subspecies Calopteryx haemorrhoidalis asturica Ocharan, 1983 and Sympetrum vulgatum ibericum Ocharan, 1985. The complete dataset is also provided in Darwin Core Archive format.

Effect of the specimen length on ultrasonic P-wave velocity in some volcanic rocks and limestones

NASA Astrophysics Data System (ADS)

Karaman, Kadir; Kaya, Ayberk; Kesimal, Ayhan

2015-12-01

Ultrasonic P-wave velocity (UPV) is commonly used in different fields such as civil, mining, geotechnical, and rock engineering. One of the significant parameters which affect the UPV of rock materials is likely to be the length of test cores although it is not mentioned in the literature. In this study, in order to explore the influence of the specimen length on the UPV, rock samples were collected from eight different locations in Turkey. The NX-sized core specimens having different length of 50, 75, 100, 125, and 150 mm were prepared. Before the analyses, rocks were divided into two groups in terms of their geological origins such as volcanic and chemical sedimentary (limestone) rocks. The UPV tests were carried out under dry and saturated conditions for each 200 core specimens. By evaluating the test results, it was shown that the length of the specimens significantly affects the UPV values. Based on the regression analyses, a method was developed to determine the threshold specimen length of studied rocks. Fluctuations in UPVdry and UPVsat values were generally observed for cores smaller than the threshold specimen length. In this study, the threshold specimen length was determined as 79 mm for volcanic rocks and 109 mm for limestones.

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

PubMed

Ahmed, Hussain G; Tom, Murtada Am

2011-01-01

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

Collecting in collections: a PCR strategy and primer set for DNA barcoding of decades-old dried museum specimens.

PubMed

Mitchell, Andrew

2015-09-01

Natural history museums are vastly underutilized as a source of material for DNA analysis because of perceptions about the limitations of DNA degradation in older specimens. Despite very few exceptions, most DNA barcoding projects, which aim to obtain sequence data from all species, generally use specimens collected specifically for that purpose, instead of the wealth of identified material in museums, constrained by the lack of suitable PCR methods. Any techniques that extend the utility of museum specimens for DNA analysis therefore are highly valuable. This study first tested the effects of specimen age and PCR amplicon size on PCR success rates in pinned insect specimens, then developed a PCR primer set and amplification strategy allowing greatly increased utilization of older museum specimens for DNA barcoding. PCR success rates compare favourably with the few published studies utilizing similar aged specimens, and this new strategy has the advantage of being easily automated for high-throughput laboratory workflows. The strategy uses hemi-nested, degenerate, M13-tailed PCR primers to amplify two overlapping amplicons, using two PCRs per amplicon (i.e. four PCRs per DNA sample). Initial PCR products are reamplified using an internal primer and a M13 primer. Together the two PCR amplicons yield 559 bp of the COI gene from Coleoptera, Lepidoptera, Diptera, Hemiptera, Odonata and presumably also other insects. BARCODE standard-compliant data were recovered from 67% (56 of 84) of specimens up to 25 years old, and 51% (102 of 197) of specimens up to 55 years old. Given the time, cost and specialist expertise required for fieldwork and identification, 'collecting in collections' is a viable alternative allowing researchers to capitalize on the knowledge captured by curation work in decades past. © 2015 John Wiley & Sons Ltd.

Identification of phlebotomine sand flies using one MALDI-TOF MS reference database and two mass spectrometer systems.

PubMed

Mathis, Alexander; Depaquit, Jérôme; Dvořák, Vit; Tuten, Holly; Bañuls, Anne-Laure; Halada, Petr; Zapata, Sonia; Lehrter, Véronique; Hlavačková, Kristýna; Prudhomme, Jorian; Volf, Petr; Sereno, Denis; Kaufmann, Christian; Pflüger, Valentin; Schaffner, Francis

2015-05-10

Rapid, accurate and high-throughput identification of vector arthropods is of paramount importance in surveillance programmes that are becoming more common due to the changing geographic occurrence and extent of many arthropod-borne diseases. Protein profiling by MALDI-TOF mass spectrometry fulfils these requirements for identification, and reference databases have recently been established for several vector taxa, mostly with specimens from laboratory colonies. We established and validated a reference database containing 20 phlebotomine sand fly (Diptera: Psychodidae, Phlebotominae) species by using specimens from colonies or field-collections that had been stored for various periods of time. Identical biomarker mass patterns ('superspectra') were obtained with colony- or field-derived specimens of the same species. In the validation study, high quality spectra (i.e. more than 30 evaluable masses) were obtained with all fresh insects from colonies, and with 55/59 insects deep-frozen (liquid nitrogen/-80 °C) for up to 25 years. In contrast, only 36/52 specimens stored in ethanol could be identified. This resulted in an overall sensitivity of 87 % (140/161); specificity was 100 %. Duration of storage impaired data counts in the high mass range, and thus cluster analyses of closely related specimens might reflect their storage conditions rather than phenotypic distinctness. A major drawback of MALDI-TOF MS is the restricted availability of in-house databases and the fact that mass spectrometers from 2 companies (Bruker, Shimadzu) are widely being used. We have analysed fingerprints of phlebotomine sand flies obtained by automatic routine procedure on a Bruker instrument by using our database and the software established on a Shimadzu system. The sensitivity with 312 specimens from 8 sand fly species from laboratory colonies when evaluating only high quality spectra was 98.3 %; the specificity was 100 %. The corresponding diagnostic values with 55 field-collected specimens from 4 species were 94.7 % and 97.4 %, respectively. A centralized high-quality database (created by expert taxonomists and experienced users of mass spectrometers) that is easily amenable to customer-oriented identification services is a highly desirable resource. As shown in the present work, spectra obtained from different specimens with different instruments can be analysed using a centralized database, which should be available in the near future via an online platform in a cost-efficient manner.

[Soil mesofauna in differents systems of land use soil in Upper River Solimões, AM, Brazil].

PubMed

Morais, José W De; Oliveira, Viviane Dos S; Dambros, Cristian De S; Tapia-Coral, Sandra C; Acioli, Agno N S

2010-01-01

The mesofauna has an important function in the soil and it is represented mainly by Acari Oribatida and Collembola. We report the first data on the density and diversity of the soil mesofauna in Benjamin Constant, Amazonas State, Brazil. The following systems were evaluated: primary forest, secondary forest, agroforestry system, cultivated areas and pastures. A total of 101 samples were collected 100 m apart from each other and specimens were collected by using Berlese-Tullgren method. The highest density was registered in secondary forest (29,776 specimens.m-2). Acari Oribatida was the dominant group (7.072 specimens.m-2) in the pasture, suggesting that mites show higher capacity of adaptation to disturbed environments and/or due to the presence of gregarious species. The density of Collembola (5,632 specimens.m-2) was higher in secondary forest. Formicidae was the dominant group (27,824 specimens.m-2) and its highest density occurred in the secondary forest (12,336 specimens.m-2). Seven species and ten morphospecies of Isoptera and three species of Symphyla were identified. The highest density and diversity were found in secondary forest. One supposes that the low density of mesofauna found in all of the studied systems is being influenced by soil structure and composition as well as litter volume. For SUT, the composition of taxonomic groups in the cultivated areas is similar to the one found in primary forest, while the groups found in the agroforestry system are similar to those in the pasture, which may help to decide on land use strategies.

Clinical Evaluation of the Cepheid Xpert TV Assay for Detection of Trichomonas vaginalis with Prospectively Collected Specimens from Men and Women

PubMed Central

Gaydos, C. A.; Davis, T.; Marrazzo, J.; Furgerson, D.; Taylor, S. N.; Smith, B.; Bachmann, L. H.; Ackerman, R.; Spurrell, T.; Ferris, D.; Burnham, C.-A. D.; Reno, H.; Lebed, J.; Eisenberg, D.; Kerndt, P.; Philip, S.; Jordan, J.; Quigley, N.

2017-01-01

ABSTRACT Trichomoniasis is the most prevalent curable sexually transmitted disease (STD). It has been associated with preterm birth and the acquisition and transmission of HIV. Recently, nucleic acid amplification tests (NAAT) have been FDA cleared in the United States for detection of Trichomonas vaginalis in specimens from both women and men. This study reports the results of a multicenter study recently conducted using the Xpert TV (T. vaginalis) assay to test specimens from both men and women. On-demand results were available in as little as 40 min for positive specimens. A total of 1,867 women and 4,791 men were eligible for inclusion in the analysis. In women, the performance of the Xpert TV assay was compared to the patient infected status (PIS) derived from the results of InPouch TV broth culture and Aptima NAAT for T. vaginalis. The diagnostic sensitivities and specificities of the Xpert TV assay for the combined female specimens (urine samples, self-collected vaginal swabs, and endocervical swabs) ranged from 99.5 to 100% and 99.4 to 99.9%, respectively. For male urine samples, the diagnostic sensitivity and specificity were 97.2% and 99.9%, respectively, compared to PIS results derived from the results of broth culture for T. vaginalis and bidirectional gene sequencing of amplicons. Excellent performance characteristics were seen using both female and male specimens. The ease of using the Xpert TV assay should result in opportunities for enhanced screening for T. vaginalis in both men and women and, hopefully, improved control of this infection. PMID:29167292

MALACOLOGICAL INVESTIGATION OF THE FULLY OPERATIONAL NAM THEUN 2 HYDROELECTRIC DAM PROJECT IN KHAMMOUANE PROVINCE, CENTRAL LAO PDR.

PubMed

Sri-aroon, Pusadee; Chusongsang, Phiraphol; Chusongsang, Yupa; Limpanont, Yanin; Surinthwong, Pornpimol; Vongphayloth, Khamsing; Brey, Paul T

2015-09-01

We conducted a malacological investigation in four districts of the Nam Theun 2 (NT2) hydroelectric dam project area, Khammouane Province, central Lao PDR (Nakai, Gnommalath, Mahaxai and Xe Bang Fai), after the first and second years of full operation in March 2010 and November 2011 to determine health risks for humans. A total 10,863 snail specimens (10 families/23 species) from 57 sampling stations and 12,902 snail specimens (eight families/21 species) from 66 sampling stations were collected in 2010 and 2011, respectively. Neotricula aperta (gamma race), the intermediate host for Schistosoma mekongi, was found in large numbers (5,853 specimens) in 2010 in Nam Gnom (downstream) at Station 25 (Mueang Gnommalath: Gnommalath District) and in fewer numbers (170 specimens) at Station 26 (Ban Thathod: Gnommalath District). In 2011, significantly fewer numbers (434 specimens) of N. aperta were found at Station 25. No snails were found to be infected with S. mekongi; however, 3.6% and 0.45% of Bithynia (D.). s. goniomphalos specimens collected were found to be infected with Opisthorchis viverrini (human liver fluke) during 2010 and 2011, respectively. Pomacea canaliculata, the rice crop pest, the intermediate host of Angiostrongylus (Parastrongylus) cantonensis, was found in the greatest numbers during 2010 and 2011; the prevalence increased significantly from 1.3% in 2010 to 53.3% in 2011. We also found seasonal variation in snail populations in terms of abundance and diversity. The snail fauna and risk for transmission of parasitic diseases need to be monitored continuously to evaluate the long-term impact of the dam project.

Release of ICTP and CTX telopeptides from demineralized dentin matrices: Effect of time, mass and surface area.

PubMed

Turco, Gianluca; Cadenaro, Milena; Maravić, Tatjana; Frassetto, Andrea; Marsich, Eleonora; Mazzoni, Annalisa; Di Lenarda, Roberto; Tay, Franklin R; Pashley, David H; Breschi, Lorenzo

2018-03-01

The present study evaluated the influence of time, mass and surface area of demineralized dentin collagen matrices on telopeptides release. The hypotheses tested were that the rates of ICTP and CTX release by matrix bound endogenous proteases are 1) not time-dependent, 2) unrelated to specimen mass, 3) unrelated to specimen surface area. Non-carious human molars (N=24) were collected and randomly assigned to three groups. Dentin slabs with three different thicknesses: 0.37mm, 0.75mm, and 1.50mm were completely demineralized and stored in artificial saliva for one week. Collagen degradation was evaluated by sampling storage media for ICTP and CTX telopeptidases. Activity of MMPs in the aging medium was evaluated using fluorometric activity assay kit. A statistically significant (p<0.05) decrease in the release of both ICTP and CTX fragments over time was observed irrespective of the specimen thickness. When data were normalized by the specimen mass, no significant differences were observed. Releases of ICTP and CTX were significantly related to the aging time as a function of surface area for the first 12h. Total MMP activity, mainly related to MMP-2 and -9, decreased with time (p<0.05). Because the release of collagen fragments was influenced by specimen storage time and surface area, it is likely that cleaved collagen fragments closer to the specimen surface diffuse into the incubation medium; those further away from the exposed surface are still entrapped within the demineralized dentin matrix. Bound MMPs can only degrade the substrate within the limited zone of their molecular mobility. Copyright © 2017 The Academy of Dental Materials. Published by Elsevier Ltd. All rights reserved.

An evaluation of the use of serum 7-alpha-hydroxycholestenone as a diagnostic test of bile acid malabsorption causing watery diarrhea

PubMed Central

Brydon, W Gordon; Culbert, Pearl; Kingstone, Kathleen; Jarvie, Ann; Iacucci, Marietta; Tenhage, Merel; Ghosh, Subrata

2011-01-01

BACKGROUND: Bile acid malabsorption (BAM) is a recognized cause of watery diarrhea, often diagnosed empirically based on clinical response to cholestyramine. The radionuclide selenium-labelled homocholic acid-taurine whole body retention test is expensive, labour intensive and of limited availability. OBJECTIVE: To report on the clinical performance of serum 7-alpha-hydroxy-4-cholesten-3-one (7HCO) as a test of BAM in adult patients with unexplained diarrhea. METHODS: Patients with unexplained diarrhea were investigated over a three-year period. Final diagnosis was determined based on medical history and investigations, serum levels of 7HCO and response to cholestyramine. ROC analysis was used to determine the ideal upper reference range cut-off value to optimize sensitivity/specificity for BAM. Time of blood specimen collection was recorded to investigate possible variation in results throughout the working day. RESULTS: ROC analysis yielded a sensitivity/specificity of 90%/77% for type 1 BAM (ileal disease/resection) and 97%/74% for type 2 BAM (idiopathic) using 30 ng/mL as the upper limit of normal for serum 7HCO when compared with all other patients. Of 813 patients, 196 tested positive. Serum 7HCO levels were significantly higher in blood specimens that were collected between 12:00 and 13:00 (median 24 ng/mL) than in specimens collected between 09:00 and 10:00 (median 17 ng/mL) (P<0.05). CONCLUSION: Serum 7HCO testing is a simple, sensitive, noninvasive, inexpensive alternative to other more commonly used tests for BAM. Time of specimen collection, however, resulted in small but significant result variations and, although unlikely to have much impact on test value, it should ideally be standardized. PMID:21766092

Widespread presence of human-pathogenic E. bieneusi genotypes in chickens

USDA-ARS?s Scientific Manuscript database

A total of 151 fecal specimens from chickens were randomly collected from local markets in Uberlandia and Belo in the state of Minas Gerais, Brazil, to evaluate the presence of Enterocytozoon bieneusi by polymerase chain reaction (PCR). Enterocytozoon bieneusi was identified in 24 fecal samples (15....

Recommendations for Collection and Handling of Specimens From Group Breast Cancer Clinical Trials

PubMed Central

Leyland-Jones, Brian R.; Ambrosone, Christine B.; Bartlett, John; Ellis, Matthew J.C.; Enos, Rebecca A.; Raji, Adekunle; Pins, Michael R.; Zujewski, Jo Anne; Hewitt, Stephen M.; Forbes, John F.; Abramovitz, Mark; Braga, Sofia; Cardoso, Fatima; Harbeck, Nadia; Denkert, Carsten; Jewell, Scott D.

2008-01-01

Recommendations for specimen collection and handling have been developed for adoption across breast cancer clinical trials conducted by the Breast International Group (BIG)-sponsored Groups and the National Cancer Institute (NCI)-sponsored North American Cooperative Groups. These recommendations are meant to promote identifiable standards for specimen collection and handling within and across breast cancer trials, such that the variability in collection/handling practices that currently exists is minimized and specimen condition and quality are enhanced, thereby maximizing results from specimen-based diagnostic testing and research. Three working groups were formed from the Cooperative Group Banking Committee, BIG groups, and North American breast cancer cooperative groups to identify standards for collection and handling of (1) formalin-fixed, paraffin-embedded (FFPE) tissue; (2) blood and its components; and (3) fresh/frozen tissue from breast cancer trials. The working groups collected standard operating procedures from multiple group specimen banks, administered a survey on banking practices to those banks, and engaged in a series of discussions from 2005 to 2007. Their contributions were synthesized into this document, which focuses primarily on collection and handling of specimens to the point of shipment to the central bank, although also offers some guidance to central banks. Major recommendations include submission of an FFPE block, whole blood, and serial serum or plasma from breast cancer clinical trials, and use of one fixative and buffer type (10% neutral phosphate-buffered formalin, pH 7) for FFPE tissue across trials. Recommendations for proper handling and shipping were developed for blood, serum, plasma, FFPE, and fresh/frozen tissue. PMID:18955459

Clinical evaluation and validation of laboratory methods for the diagnosis of Bordetella pertussis infection: Culture, polymerase chain reaction (PCR) and anti-pertussis toxin IgG serology (IgG-PT)

PubMed Central

Cassiday, Pamela K.; Pawloski, Lucia C.; Tatti, Kathleen M.; Martin, Monte D.; Briere, Elizabeth C.; Tondella, M. Lucia; Martin, Stacey W.

2018-01-01

Introduction The appropriate use of clinically accurate diagnostic tests is essential for the detection of pertussis, a poorly controlled vaccine-preventable disease. The purpose of this study was to estimate the sensitivity and specificity of different diagnostic criteria including culture, multi-target polymerase chain reaction (PCR), anti-pertussis toxin IgG (IgG-PT) serology, and the use of a clinical case definition. An additional objective was to describe the optimal timing of specimen collection for the various tests. Methods Clinical specimens were collected from patients with cough illness at seven locations across the United States between 2007 and 2011. Nasopharyngeal and blood specimens were collected from each patient during the enrollment visit. Patients who had been coughing for ≤ 2 weeks were asked to return in 2–4 weeks for collection of a second, convalescent blood specimen. Sensitivity and specificity of each diagnostic test were estimated using three methods—pertussis culture as the “gold standard,” composite reference standard analysis (CRS), and latent class analysis (LCA). Results Overall, 868 patients were enrolled and 13.6% were B. pertussis positive by at least one diagnostic test. In a sample of 545 participants with non-missing data on all four diagnostic criteria, culture was 64.0% sensitive, PCR was 90.6% sensitive, and both were 100% specific by LCA. CRS and LCA methods increased the sensitivity estimates for convalescent serology and the clinical case definition over the culture-based estimates. Culture and PCR were most sensitive when performed during the first two weeks of cough; serology was optimally sensitive after the second week of cough. Conclusions Timing of specimen collection in relation to onset of illness should be considered when ordering diagnostic tests for pertussis. Consideration should be given to including IgG-PT serology as a confirmatory test in the Council of State and Territorial Epidemiologists (CSTE) case definition for pertussis. PMID:29652945

[Quality Management and Quality Specifications of Laboratory Tests in Clinical Studies--Challenges in Pre-Analytical Processes in Clinical Laboratories].

PubMed

Ishibashi, Midori

2015-01-01

The cost, speed, and quality are the three important factors recently indicated by the Ministry of Health, Labour and Welfare (MHLW) for the purpose of accelerating clinical studies. Based on this background, the importance of laboratory tests is increasing, especially in the evaluation of clinical study participants' entry and safety, and drug efficacy. To assure the quality of laboratory tests, providing high-quality laboratory tests is mandatory. For providing adequate quality assurance in laboratory tests, quality control in the three fields of pre-analytical, analytical, and post-analytical processes is extremely important. There are, however, no detailed written requirements concerning specimen collection, handling, preparation, storage, and shipping. Most laboratory tests for clinical studies are performed onsite in a local laboratory; however, a part of laboratory tests is done in offsite central laboratories after specimen shipping. As factors affecting laboratory tests, individual and inter-individual variations are well-known. Besides these factors, standardizing the factors of specimen collection, handling, preparation, storage, and shipping, may improve and maintain the high quality of clinical studies in general. Furthermore, the analytical method, units, and reference interval are also important factors. It is concluded that, to overcome the problems derived from pre-analytical processes, it is necessary to standardize specimen handling in a broad sense.

A new small-eared shrew of the Cryptotis nigrescens-group from Colombia (Mammalia: Soricomorpha: Soricidae)

USGS Publications Warehouse

Woodman, N.

2003-01-01

Cryptotis colombiana Woodman & Timm, 1993 previously was known from few specimens from two isolated regions in the Cordillera Central and Cordillera Oriental of Colombia. Recent collecting in the northern Cordillera Central and review of older collections from the central Cordillera Oriental in the vicinity of Bogota yielded additional specimens that permit reevaluation of the two geographic populations of these small-eared shrews. Morphological and morphometrical studies indicate that the population inhabiting the Cordillera Oriental represents a distinct, previously unrecognized species that I describe herein as Cryptotis brachyonyx. Study of 54 specimens of shrews from the Cordillera Oriental in systematic collections in North America, South America, and Europe yielded only four specimens of the new species, all collected before 1926. The paucity of modern specimens suggests that C. brachyonyx may be extremely restricted in distribution, or possibly extinct.

iCollections methodology: workflow, results and lessons learned

PubMed Central

Penn, Malcolm; Sadka, Mike; Hine, Adrian; Brooks, Stephen; Siebert, Darrell J.; Sleep, Chris; Cafferty, Steve; Cane, Elisa; Martin, Geoff; Toloni, Flavia; Wing, Peter; Chainey, John; Duffell, Liz; Huxley, Rob; Ledger, Sophie; McLaughlin, Caitlin; Mazzetta, Gerardo; Perera, Jasmin; Crowther, Robyn; Douglas, Lyndsey; Durant, Joanna; Scialabba, Elisabetta; Honey, Martin; Huertas, Blanca; Howard, Theresa; Carter, Victoria; Albuquerque, Sara; Paterson, Gordon; Kitching, Ian J.

2017-01-01

Abstract The Natural History Museum, London (NHMUK) has embarked on an ambitious programme to digitise its collections. The first phase of this programme was to undertake a series of pilot projects to develop the workflows and infrastructure needed to support mass digitisation of very large scientific collections. This paper presents the results of one of the pilot projects – iCollections. This project digitised all the lepidopteran specimens usually considered as butterflies, 181,545 specimens representing 89 species from the British Isles and Ireland. The data digitised includes, species name, georeferenced location, collector and collection date - the what, where, who and when of specimen data. In addition, a digital image of each specimen was taken. A previous paper explained the way the data were obtained and the background to the collections that made up the project. The present paper describes the technical, logistical, and economic aspects of managing the project. PMID:29104442

iCollections methodology: workflow, results and lessons learned

PubMed Central

Penn, Malcolm; Sadka, Mike; Hine, Adrian; Brooks, Stephen; Siebert, Darrell J.; Sleep, Chris; Cafferty, Steve; Cane, Elisa; Martin, Geoff; Toloni, Flavia; Wing, Peter; Chainey, John; Duffell, Liz; Huxley, Rob; Ledger, Sophie; McLaughlin, Caitlin; Mazzetta, Gerardo; Perera, Jasmin; Crowther, Robyn; Douglas, Lyndsey; Durant, Joanna; Honey, Martin; Huertas, Blanca; Howard, Theresa; Carter, Victoria; Albuquerque, Sara; Paterson, Gordon; Kitching, Ian J.

2017-01-01

Abstract The Natural History Museum, London (NHMUK) has embarked on an ambitious programme to digitise its collections. The first phase of this programme was to undertake a series of pilot projects to develop the workflows and infrastructure needed to support mass digitisation of very large scientific collections. This paper presents the results of one of the pilot projects – iCollections. This project digitised all the lepidopteran specimens usually considered as butterflies, 181,545 specimens representing 89 species from the British Isles and Ireland. The data digitised includes, species name, georeferenced location, collector and collection date - the what, where, who and when of specimen data. In addition, a digital image of each specimen was taken. A previous paper explained the way the data were obtained and the background to the collections that made up the project. The present paper describes the technical, logistical, and economic aspects of managing the project. PMID:29104435

iCollections methodology: workflow, results and lessons learned.

PubMed

Blagoderov, Vladimir; Penn, Malcolm; Sadka, Mike; Hine, Adrian; Brooks, Stephen; Siebert, Darrell J; Sleep, Chris; Cafferty, Steve; Cane, Elisa; Martin, Geoff; Toloni, Flavia; Wing, Peter; Chainey, John; Duffell, Liz; Huxley, Rob; Ledger, Sophie; McLaughlin, Caitlin; Mazzetta, Gerardo; Perera, Jasmin; Crowther, Robyn; Douglas, Lyndsey; Durant, Joanna; Honey, Martin; Huertas, Blanca; Howard, Theresa; Carter, Victoria; Albuquerque, Sara; Paterson, Gordon; Kitching, Ian J

2017-01-01

The Natural History Museum, London (NHMUK) has embarked on an ambitious programme to digitise its collections. The first phase of this programme was to undertake a series of pilot projects to develop the workflows and infrastructure needed to support mass digitisation of very large scientific collections. This paper presents the results of one of the pilot projects - iCollections. This project digitised all the lepidopteran specimens usually considered as butterflies, 181,545 specimens representing 89 species from the British Isles and Ireland. The data digitised includes, species name, georeferenced location, collector and collection date - the what, where, who and when of specimen data. In addition, a digital image of each specimen was taken. A previous paper explained the way the data were obtained and the background to the collections that made up the project. The present paper describes the technical, logistical, and economic aspects of managing the project.

Investigation of Fossil Insect Systematics of Specimens Collected at the Clare Quarry Site in the Florissant Fossil Beds, Florissant, Colorado from 1996 to Present

NASA Astrophysics Data System (ADS)

Cancellare, J. A.; Villalobos, J. I.; Lemone, D.

2012-12-01

The Clare Quarry is located in the town of Florissant, Teller County, Colorado, approximately 30 miles west of Colorado Springs on State Highway 27. The elevation at the quarry face is 2500 meters ASL. Ar40/Ar39 dating of the upper beds of the Florissant Formation indicates an age of 34.07 +/- 0.10 Ma.An Oreodont fossil jaw and other mammalian fossils place the formation in the Chadronian Age.The basin in which the formation lies is undergirded by Wall Mountain Tuff dated at 37Ma, which sits on Pike's Peak Granite, which is dated at1080 Ma. In the Late Eocene the Florissant region was lacustrine in nature due to the damning of the river valley which runs north into Florissant. The ash and lahars from volcanic eruptions from the Thirty-nine Mile Volcano Field formed impoundments that produced shallow lakes for what is thought to been a period for 5000 years. Repeated ash falls placed plant matter and insect material in the lakes and streams that were formed intermittently during the period. The ash layers in the Florissant Formation are very fine grained, and contain diatomaceous mats that formed on the lake deposited ash layers aiding in the preservation of plant and insects material. Previous work on Florissant Fossils has been done by Lesquereaux (plants) 1878, Scudder (insects) 1890, and Mc Ginitie (plants) 1953. This project began 17 years ago and has consisted of collection trips ranging from one to eight days in the summers at a proprietary quarry owned land adjacent to The Florissant Fossil Beds National Monument. The collection consists of 2700 catalogued plants, insects, and fish fossils. Of this number, 513 are insect fossils (19% of the total collection). Quality of preservation ranges from very poor to very good with the average qualitative evaluation between poor to fair. The largest series identied to family are Tipulids (Craneflies) with 23 specimens in the series. In this series wing venation is often incomplete and smaller characters including antennae,and leg structures are problematic in most specimens. Other factors affecting specimen quality include specimen orientation, partial specimens due to breaks in the matrix, the degree of preservation and effects of weathering. To date classification is strictly superficial. One of the early objectives of this work was to collect series of the same genera however there is no discernible pattern below the ordinal level. In this phase the primary objective will be to place as many insect specimens into families as possible. Many insect families (but no genera) found in the Florissant persist today. Tools used in the initial sorting and extraction process are pin vices, Exacto Knives, razor blades and a Bausch and Lomb zoom dissecting scope fitted with a circular fluorescent illumination ring with magnification ranging from 7 to 45 diameters. During the summer of 2012, twenty one Tipulid specimens were photographed by the Mid - Atlantic Geo - Image Collection (M.A.G. I. C.), Northern Virginia Community College, in order to test the system's efficacy in specimen comparison within series. Preservation of specimens in the Florissant Fossil Beds occurred during the Eocene - Oligocene Transition. Future use of the results generated in this study may have application in the study of climate change.

Alfredo Dugès' type specimens of amphibians and reptiles revisited.

PubMed

Flores-Villela, Oscar; Ríos-Muñoz, César A; Magaña-Cota, Gloria E; Quezadas-Tapia, Néstor L

2016-03-14

The type specimens of amphibians and reptiles of the Museo de Historia Natural Alfredo Dugès, at the University of Guanajuato (MADUG) were reviewed following Smith & Necker's (1943) summary. Owing to this collection's eventful history and its historical importance as the oldest herpetological collection in Mexico, a review of its conservation status was needed. After many years, the collection has received proper recognition at the University of Guanajuato with a portion of the herpetological types considered "Precious Assets" of the university. We found 34 type specimens pertaining to 18 taxa; six are additional specimens to those previously reported; six herpetological types are missing, including the body of the type of Adelophis copei. All specimens are in good to reasonable condition except for the type of Rhinocheilus antonii, which has dried out completely. All specimens are illustrated to show their condition.

An Evaluation of the Cobas4800 HPV Test on Cervico-Vaginal Specimens in Liquid versus Solid Transport Media.

PubMed

Luo, Hongxue; Du, Hui; Maurer, Kathryn; Belinson, Jerome L; Wang, Guixiang; Liu, Zhihong; Zhang, Lijie; Zhou, Yanqiu; Wang, Chun; Tang, Jinlong; Qu, Xinfeng; Wu, Ruifang

2016-01-01

Determine the ability of the Cobas 4800 assay to detect high-risk human papillomavirus (HrHPV) and high-grade cervical lesions when using cervico-vaginal samples applied to liquid medium and solid media cards compared to a direct cervical sample. Two cervico-vaginal specimens (pseudo self-collected) were obtained from 319 women. One was applied to an iFTA Card (FTA) then the brush placed in liquid-based medium (LSELF); the other was applied to a new solid media: POI card (POI). The clinical performance of Cobas4800 assay using the three aforementioned specimens was compared to direct collected endocervical specimens in liquid media (LDOC). The overall agreements of HrHPV detection were 84.2% (LSELF vs. LDOC), 81.0% (FTA vs. LDOC), and 82.3% (POI vs. LDOC). LSELF, FTA and POI identified 98.0%, 79.6%, and 97.5% positive cases of LDOC. Sensitivity to identify CIN2+ were 98.4% (LSELF), 73.8% (FTA), 95.1% (POI), and 93.4% (LDOC) respectively. FTA had 78.1% and 90.4% agreement with the LSELF samples for all HrHPV and HPV16/18 detection respectively, while POI had 91.6% for both. Cobas4800 HPV test combined with cervico-vaginal specimens applied to both liquid media and POI solid card are accurate to detect HrHPV infection and high-grade cervical lesions as compared with direct endocervical samples in liquid media.

An Evaluation of the Cobas4800 HPV Test on Cervico-Vaginal Specimens in Liquid versus Solid Transport Media

PubMed Central

Luo, Hongxue; Du, Hui; Maurer, Kathryn; Belinson, Jerome L.; Wang, Guixiang; Liu, Zhihong; Zhang, Lijie; Zhou, Yanqiu; Wang, Chun; Tang, Jinlong; Qu, Xinfeng; Wu, Ruifang

2016-01-01

Objectives Determine the ability of the Cobas 4800 assay to detect high-risk human papillomavirus (HrHPV) and high-grade cervical lesions when using cervico-vaginal samples applied to liquid medium and solid media cards compared to a direct cervical sample. Methods Two cervico-vaginal specimens (pseudo self-collected) were obtained from 319 women. One was applied to an iFTA Card (FTA) then the brush placed in liquid-based medium (LSELF); the other was applied to a new solid media: POI card (POI). The clinical performance of Cobas4800 assay using the three aforementioned specimens was compared to direct collected endocervical specimens in liquid media (LDOC). Results The overall agreements of HrHPV detection were 84.2% (LSELF vs. LDOC), 81.0% (FTA vs. LDOC), and 82.3% (POI vs. LDOC). LSELF, FTA and POI identified 98.0%, 79.6%, and 97.5% positive cases of LDOC. Sensitivity to identify CIN2+ were 98.4% (LSELF), 73.8% (FTA), 95.1% (POI), and 93.4% (LDOC) respectively. FTA had 78.1% and 90.4% agreement with the LSELF samples for all HrHPV and HPV16/18 detection respectively, while POI had 91.6% for both. Conclusions Cobas4800 HPV test combined with cervico-vaginal specimens applied to both liquid media and POI solid card are accurate to detect HrHPV infection and high-grade cervical lesions as compared with direct endocervical samples in liquid media. PMID:26828360

37 CFR 2.56 - Specimens.

Code of Federal Regulations, 2010 CFR

2010-07-01

... advertising of the services in commerce. (b)(1) A trademark specimen is a label, tag, or container for the... actually used in the sale or advertising of the services. (3) A collective trademark or collective service mark specimen must show how a member uses the mark on the member's goods or in the sale or advertising...

[The fleas of mammals from the Ucayali River basin (the Peruvian Amazonia)].

PubMed

Darskaia, N F; Malygin, V M

1996-01-01

The material collected from 57 specimens of 9 mammalian species in two localities of the Peruvian Amazonia includes 212 specimens of fleas belonging to four species (Polygenis klagesi, Ropalopsyllus lugubris, Rh. australis and Rothschildopsylla noctilionis). This is the first record of fleas in the Ucayali River basin. The majority of flea specimens were collected form three morphologically similar but karyotypically and electrophoretically distinct species of spiny rats of the genus Proechimys. These fleas belong to the species P. klagesi. The subspecies P. k. samuelis was collected from 32-chromosome spiny rats nearby Pucallpa (8 degrees 22' S, 74 degrees 43' W), whereas in the locality nearby the village Jenaro Errera (4 degrees 52' S, 73 degrees 39' W) only the nominative subspecies P. k. klagesi were collected from all three species of spiny rats. Other species of fleas have relatively less abundance. Six fleas Rh. l. lugubris were found on one specimen of Cuniculus paca; a single Rh. australis--on one specimen of Myoprocta pratti; and a single R. noctilionis--on one specimen of Eptesicus brasiliensis.

Steps for successful implementation of proteomic research in the OR.

PubMed

Martin, Chidima Tsion; Henry, Linda; Martin, Lisa; Ad, Niv

2010-02-01

Proteomic studies (ie, the investigation and identification of proteins found in biological samples such as blood and tissue) are at the forefront of the identification of disease biomarkers and the understanding of proteins. These studies promise to enhance diagnostic and prognostic analysis across all disciplines of clinical practice. As the practice of nursing and medicine becomes more preventative in nature and predictive in terms of patient care, successfully integrating and implementing proteomic research will become increasingly important, especially in the OR. It is imperative that perioperative nurses and researchers establish a collaborative process for specimen collection. Steps in establishing and maintaining a successful specimen collection program include implementing and evaluating a protocol, developing good communication, and keeping all participants up to date on the progress of the study. Copyright 2010 AORN, Inc. Published by Elsevier Inc. All rights reserved.

Ultrasonic Phased Array Evaluation of Control Rod Drive Mechanism (CRDM) Nozzle Interference Fit and Weld Region

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

Cinson, Anthony D.; Crawford, Susan L.; MacFarlan, Paul J.

2011-07-31

Ultrasonic phased array data were collected on a removed-from-service CRDM nozzle specimen to assess a previously reported leak path. First a mock-up CRDM specimen was evaluated that contained two 0.076-mm (3.0-mil) interference fit regions formed from an actual Inconel CRDM tube and two 152.4-mm (6.0-in.) thick carbon steel blocks. One interference fit region has a series of precision crafted electric discharge machining (EDM) notches at various lengths, widths, depths, and spatial separations for establishing probe sensitivity, resolution and calibration. The other interference fit has zones of boric acid (crystal form) spaced periodically between the tube and block to represent anmore » actively leaking CRDM nozzle assembly in the field. Ultrasonic phased-array evaluations were conducted using an immersion 8-element annular 5.0-MHz probe from the tube inner diameter (ID). A variety of focal laws were employed to evaluate the interference fit regions and J grove weld, where applicable. Responses from the mock-up specimen were evaluated to determine detection limits and characterization ability as well as contrast the ultrasonic response differences with the presence of boric acid in the fit region. Nozzle 63, from the North Anna Unit-2 nuclear power plant, was evaluated to assess leakage path(s) and was destructively dismantled to allow a visual verification of the leak path(s).« less

Passive cannabis smoke exposure and oral fluid testing.

PubMed

Niedbala, Sam; Kardos, Keith; Salamone, Sal; Fritch, Dean; Bronsgeest, Matth; Cone, Edward J

2004-10-01

Oral fluid testing for Delta(9)-tetrahydrocannabinol (THC) provides a convenient means of detection of recent cannabis usage. In this study, the risk of positive oral fluid tests from passive cannabis smoke exposure was investigated by housing four cannabis-free volunteers in a small, unventilated, and sealed room with an approximate volume of 36 m(3). Five active cannabis smokers were also present in the room, and each smoked a single cannabis cigarette (1.75% THC). Cannabis smoking occurred over the first 20 min of the study session. All subjects remained in the room for approximately 4 h. Oral fluid specimens were collected with the Intercept DOA Oral Specimen Collection Device. Three urine specimens were collected (0, 20, and 245 min). In addition, three air samples were collected for measurement of THC content. All oral fluid specimens were screened by enzyme immunoassay (EIA) for cannabinoids (cutoff concentration = 3 ng/mL) and tested by gas chromatography-tandem mass spectrometry (GC-MS-MS) for THC (LOQ/LOD = 0.75 ng/mL). All urine specimens were screened by EIA for cannabinoids (cutoff concentration = 50 ng/mL) and tested by GC-MS-MS for THCCOOH (LOQ/LOD = 1 ng/mL). Air samples were measured for THC by GC-MS (LOD = 1 ng/L). A total of eight oral fluid specimens (collected 20 to 50 min following initiation of smoking) from the four passive subjects screened and confirmed positive for THC at concentrations ranging from 3.6 to 26.4 ng/mL. Two additional specimens from one passive subject, collected at 50 and 65 min, screened negative but contained THC in concentrations of 4.2 and 1.1 ng/mL, respectively. All subsequent specimens for passive participants tested negative by EIA and GC-MS-MS for the remainder of the 4-h session. In contrast, oral fluid specimens collected from the five cannabis smokers generally screened and confirmed positive for THC throughout the session at concentrations substantially higher than observed for passive subjects. Urine specimens from active cannabis smokers also screened and confirmed positive at conventional cutoff concentrations. A biphasic pattern of decline for THC was observed in oral fluid specimens collected from cannabis smokers, whereas a linear decline was seen for passive subjects suggesting that initial oral fluid contamination is cleared rapidly and is followed by THC sequestration in the oral mucosa. It is concluded that the risk of positive oral fluid tests from passive cannabis smoke inhalation is limited to a period of approximately 30 min following exposure.

Sequence capture of ultraconserved elements from bird museum specimens.

PubMed

McCormack, John E; Tsai, Whitney L E; Faircloth, Brant C

2016-09-01

New DNA sequencing technologies are allowing researchers to explore the genomes of the millions of natural history specimens collected prior to the molecular era. Yet, we know little about how well specific next-generation sequencing (NGS) techniques work with the degraded DNA typically extracted from museum specimens. Here, we use one type of NGS approach, sequence capture of ultraconserved elements (UCEs), to collect data from bird museum specimens as old as 120 years. We targeted 5060 UCE loci in 27 western scrub-jays (Aphelocoma californica) representing three evolutionary lineages that could be species, and we collected an average of 3749 UCE loci containing 4460 single nucleotide polymorphisms (SNPs). Despite older specimens producing fewer and shorter loci in general, we collected thousands of markers from even the oldest specimens. More sequencing reads per individual helped to boost the number of UCE loci we recovered from older specimens, but more sequencing was not as successful at increasing the length of loci. We detected contamination in some samples and determined that contamination was more prevalent in older samples that were subject to less sequencing. For the phylogeny generated from concatenated UCE loci, contamination led to incorrect placement of some individuals. In contrast, a species tree constructed from SNPs called within UCE loci correctly placed individuals into three monophyletic groups, perhaps because of the stricter analytical procedures used for SNP calling. This study and other recent studies on the genomics of museum specimens have profound implications for natural history collections, where millions of older specimens should now be considered genomic resources. © 2015 The Authors. Molecular Ecology Resources Published by John Wiley & Sons Ltd.

Anti-microbial Activity of Urine after Ingestion of Cranberry: A Pilot Study.

PubMed

Lee, Yee Lean; Najm, Wadie I; Owens, John; Thrupp, Laurie; Baron, Sheryl; Shanbrom, Edward; Cesario, Thomas

2010-06-01

We explore the anti-microbial activity of urine specimens after the ingestion of a commercial cranberry preparation. Twenty subjects without urinary infection, off antibiotics and all supplements or vitamins were recruited. The study was conducted in two phases: in phase 1, subjects collected the first morning urine prior to ingesting 900 mg of cranberry and then at 2, 4 and 6 h. In phase 2, subjects collected urine on 2 consecutive days: on Day 1 no cranberry was ingested (control specimens), on Day 2, cranberry was ingested. The pH of all urine specimens were adjusted to the same pH as that of the first morning urine specimen. Aliquots of each specimen were independently inoculated with Escherichia coli, Klebsiella pneumoniae or Candida albicans. After incubation, colony forming units/ml (CFU ml(-1)) in the control specimen was compared with CFU ml(-1) in specimens collected 2, 4 and 6 h later. Specimens showing ≥50% reduction in CFU ml(-1) were considered as having 'activity' against the strains tested. In phase 1, 7/20 (35%) subjects had anti-microbial activity against E. coli, 13/20 (65%) against K. pneumoniae and 9/20 (45%) against C. albicans in specimens collected 2-6 h after ingestion of cranberry. In phase 2, 6/9 (67%) of the subjects had activity against K. pneumoniae. This pilot study demonstrates weak anti-microbial activity in urine specimens after ingestion of a single dose of commercial cranberry. Anti-microbial activity was noted only against K. pneumoniae 2-6 h after ingestion of the cranberry preparation.

Comparison of Ahlstrom grade 226, Munktell TFN, and Whatman 903 filter papers for dried blood spot specimen collection and subsequent HIV-1 load and drug resistance genotyping analysis.

PubMed

Rottinghaus, Erin; Bile, Ebi; Modukanele, Mosetsanagape; Maruping, Maruping; Mine, Madisa; Nkengasong, John; Yang, Chunfu

2013-01-01

Dried blood spots (DBS) collected onto filter paper have eased the difficulty of blood collection in resource-limited settings. Currently, Whatman 903 (W-903) filter paper is the only filter paper that has been used for HIV load and HIV drug resistance (HIVDR) testing. We therefore evaluated two additional commercially available filter papers, Ahlstrom grade 226 (A-226) and Munktell TFN (M-TFN), for viral load (VL) testing and HIVDR genotyping using W-903 filter paper as a comparison group. DBS specimens were generated from 344 adult patients on antiretroviral therapy (ART) in Botswana. The VL was measured with NucliSENS EasyQ HIV-1 v2.0, and genotyping was performed for those specimens with a detectable VL (≥ 2.90 log(10) copies/ml) using an in-house method. Bland-Altman analysis revealed a strong concordance in quantitative VL analysis between W-903 and A-226 (bias = -0.034 ± 0.246 log(10) copies/ml [mean difference ± standard deviation]) and W-903 and M-TFN (bias = -0.028 ± 0.186 log(10) copies/ml) filter papers, while qualitative VL analysis for virological failure determination, defined as a VL of ≥ 3.00 log(10) copies/ml, showed low sensitivities for A-266 (71.54%) and M-TFN (65.71%) filter papers compared to W-903 filter paper. DBS collected on M-TFN filter paper had the highest genotyping efficiency (100%) compared to W-903 and A-226 filter papers (91.7%) and appeared more sensitive in detecting major HIVDR mutations. DBS collected on A-226 and M-TFN filter papers performed similarly to DBS collected on W-903 filter paper for quantitative VL analysis and HIVDR detection. Together, the encouraging genotyping results and the variability observed in determining virological failure from this small pilot study warrant further investigation of A-226 and M-TFN filter papers as specimen collection devices for HIVDR monitoring surveys.

Comparing Species Composition of Passive Trapping of Adult Flies with Larval Collections from the Body during Scene-Based Medicolegal Death Investigations

PubMed Central

Sanford, Michelle R.

2017-01-01

Collection of insects at the scene is one of the most important aspects of forensic entomology and proper collection is one of the biggest challenges for any investigator. Adult flies are highly mobile and ubiquitous at scenes, yet their link to the body and the time of colonization (TOC) and post-mortem interval (PMI) estimates is not well established. Collection of adults is widely recommended for casework but has yet to be rigorously evaluated during medicolegal death investigations for its value to the investigation. In this study, sticky card traps and immature collections were compared for 22 cases investigated by the Harris County Institute of Forensic Sciences, Houston, TX, USA. Cases included all manner of death classifications and a range of decomposition stages from indoor and outdoor scenes. Overall, the two methods successfully collected at least one species in common only 65% of the time, with at least one species unique to one of the methods 95% of the time. These results suggest that rearing of immature specimens collected from the body should be emphasized during training to ensure specimens directly associated with the colonization of the body can be identified using adult stages if necessary. PMID:28338605

Uranium mineralization in the Wilson Creek and Cranberry Gneisses and the Grandfather Mountain Formation, North Carolina and Tennessee. National Uranium Resource Evaluation

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

Wagener, H.D.; McHone, J.G.

1982-10-01

Detailed petrologic investigations were conducted at 74 anomalies that have surface radioactivities of 5 to 300 times background in the Grandfather Mountain region of North Carolina and Tennessee. One or more specimens of radioactive rock and one specimen of nonanomalous (barren) rock were taken for chemical analysis from each of the 74 sites. The specimens were analyzed fluorometrically for uranium (U/sub 3/O/sub 8/) and for 29 other elements by emission spectroscopy. Of the radioactive specimens, 23 contained less than 100 ppM U/sub 3/O/sub 8/ and were either depleted in uranium because of leaching or were rich in thorium; 25 containedmore » more than 500 ppM U/sub 3/O/sub 8/, with a maximum of 33,000 ppM. Specimens collected as barren contained up to 65 ppM U/sub 3/O/sub 8/. The more uraniferous rocks of the region tend to contain the larger concentrations of trace amounts of base metals.« less

Progressive Consent and Specimen Accrual Models to Address Sustainability: A Decade's Experience at an Oregon Biorepository.

PubMed

Ost, John A; Newton, Paul W; Neilson, Duncan R; Cioffi, Joseph A; Wackym, P Ashley; Perkins, R Serene

2017-02-01

The Legacy Biorepository is a College of American Pathologists-accredited biorepository operating within a seven-hospital healthcare system, with a decade's experience in specimen accrual, storage, and distribution. While standardization of our practices through accreditation remains a priority, we along with others face challenges with regard to sustainability. Purposeful changes in our consent process, which we term "progressive consent," are expected to improve sustainability and operational flexibility while increasing our scientific impact. Until 2015, informed consent was performed primarily by biorepository staff at an estimated time of 1 hour per case. After a process improvement exercise, we successfully changed our informed consent process to a modified front-door model, with use of material and data for research as an opt-in or opt-out selection on the institutional patient informed consent form provided to surgery patients in the healthcare system. Successful implementation of this change required the engagement and participation of multiple stakeholders in healthcare system leadership, hospital administration, research, legal, regulatory, and patient care levels. A modified front-door consent enabled us to collect an additional 38 specimens in the first two quarters of 2016, with a time commitment of 15.75 hours, a time savings per specimen increasing in Q2 over Q1. We estimate a potential savings of 43 hours in 2016. This progressive model allowed us to maintain our frozen sample collection while increasing the availability of paraffin-embedded tissue and bodily fluids. Augmenting our tissue collection added little expense per case (approximately half that of each frozen tissue aliquot) and increased the range of biospecimens collected. Biorepository financial sustainability is a critical issue. Thorough evaluation and modification of existing procedures and collection models, as well as cost recovery initiatives, can translate into savings. Sustainability, process improvement, and scientific impact broadly overlap and continue to require operational critique and implementation of strategic changes.

[Establishment and Management of Multiple Myeloma Specimen Bank Applied for Molecular Biological Researches].

PubMed

Li, Han-Qing; Mei, Jian-Gang; Cao, Hong-Qin; Shao, Liang-Jing; Zhai, Yong-Ping

2017-12-01

To establish a multiple myeloma specimen bank applied for molecular biological researches and to explore the methods of specimen collection, transportation, storage, quality control and the management of specimen bank. Bone marrow and blood samples were collected from multiple myeloma patients, plasma cell sorting were operated after the separation of mononuclear cells from bone marrow specimens. The plasma cells were divided into 2 parts, one was added with proper amount of TRIzol and then kept in -80 °C refrigerator for subsequent RNA extraction, the other was added with proper amount of calf serum cell frozen liquid and then kept in -80 °C refrigerator for subsequent cryopreservation of DNA extraction after numbered respectively. Serum and plasma were separated from peripheral blood, specimens of serum and plasma were then stored at -80 °C refrigerator after registration. Meantime, the myeloma specimen information management system was established, managed and maintained by specially-assigned persons and continuous modification and improvement in the process of use as to facilitate the rapid collection, management, query of the effective samples and clinical data. A total of 244 portions plasma cells, 564 portions of serum, and 1005 portions of plasma were collected, clinical characters were documented. A multiple myeloma specimen bank have been established initially, which can provide quality samples and related clinical information for molecular biological research on multiple myeloma.

A digital reference collection for aquatic macroinvertebrates of North America

USGS Publications Warehouse

Walters, David; Ford, Morgan A; Zuellig, Robert E.

2017-01-01

Aquatic invertebrates are a key component of freshwater ecosystems, and understanding aquatic invertebrate taxonomy is a cornerstone of freshwater science. Physical reference collections of expertly identified voucher specimens are the ‘gold-standard’ used to confirm specimen identifications. However, most biologists lack access to such collections, which themselves tend to be highly regionalized and somewhat limited in terms of taxonomic scope. The North American Aquatic Macroinvertebrate Digital Reference Collection (NAAMDRC; https://sciencebase.usgs.gov/naamdrc) was developed by the US Geological Survey (USGS) to overcome these limitations of physical collections. NAAMDRC provides users with public-domain, high-quality digital photographs to help verify specimen identifications.

DNA barcode assessment of Ceramiales (Rhodophyta) in the intertidal zone of the northwestern Yellow Sea

NASA Astrophysics Data System (ADS)

Du, Guoying; Wu, Feifei; Guo, Hao; Xue, Hongfan; Mao, Yunxiang

2015-05-01

A total of 142 specimens of Ceramiales (Rhodophyta) were collected each month from October 2011 to November 2012 in the intertidal zone of the northwestern Yellow Sea. These specimens covered 21 species, 14 genera, and four families. Cluster analyses show that the specimens had a high diversity for the three DNA markers, namely, partial large subunit rRNA gene (LSU), universal plastid amplicon (UPA), and partial mitochondrial cytochrome c oxidase subunit I gene (COI). No intraspecific divergence was found in our collection for these markers, except for a 1-3 bp divergence in the COI of Ceramium kondoi, Symphyocladia latiuscula, and Neosiphonia japonica. Because short DNA markers were used, the phylogenetic relationships of higher taxonomic levels were hard to evaluate with poor branch support. More than half species of our collection failed to find their matched sequences owing to shortage information of DNA barcodes for macroalgae in GenBank or BOLD (Barcode of Life Data) Systems. Three specimens were presumed as Heterosiphonia crispella by cluster analyses on DNA barcodes assisted by morphological identification, which was the first record in the investigated area, implying that it might be a cryptic or invasive species in the coastal area of northwestern Yellow Sea. In the neighbor-joining trees of all three DNA markers, Heterosiphonia japonica converged with Dasya spp. and was distant from the other Heterosiphonia spp., implying that H. japonica had affinities to the genus Dasya. The LSU and UPA markers amplified and sequenced easier than the COI marker across the Ceramiales species, but the COI had a higher ability to discriminate between species.

Coherent Raman Scattering Microscopy for Evaluation of Head and Neck Carcinoma.

PubMed

Hoesli, Rebecca C; Orringer, Daniel A; McHugh, Jonathan B; Spector, Matthew E

2017-09-01

Objective We aim to describe a novel, label-free, real-time imaging technique, coherent Raman scattering (CRS) microscopy, for histopathological evaluation of head and neck cancer. We evaluated the ability of CRS microscopy to delineate between tumor and nonneoplastic tissue in tissue samples from patients with head and neck cancer. Study Design Prospective case series. Setting Tertiary care medical center. Subjects and Methods Patients eligible were surgical candidates with biopsy-proven, previously untreated head and neck carcinoma and were consented preoperatively for participation in this study. Tissue was collected from 50 patients, and after confirmation of tumor and normal specimens by hematoxylin and eosin (H&E), there were 42 tumor samples and 42 normal adjacent controls. Results There were 42 confirmed carcinoma specimens on H&E, and CRS microscopy identified 37 as carcinoma. Of the 42 normal specimens, CRS microscopy identified 40 as normal. This resulted in a sensitivity of 88.1% and specificity of 95.2% in distinguishing between neoplastic and nonneoplastic images. Conclusion CRS microscopy is a unique label-free imaging technique that can provide rapid, high-resolution images and can accurately determine the presence of head and neck carcinoma. This holds potential for implementation into standard practice, allowing frozen margin evaluation even at institutions without a histopathology laboratory.

49 CFR Appendix D to Part 40 - Report Format: Split Specimen Failure To Reconfirm

Code of Federal Regulations, 2010 CFR

2010-10-01

.... The following items are required on each report: 1. MRO name, address, phone number, and fax number. 2. Collection site name, address, and phone number. 3. Date of collection. 4. Specimen I.D. number. 5. Laboratory accession number. 6. Primary specimen laboratory name, address, and phone number. 7. Date result...

49 CFR Appendix D to Part 40 - Report Format: Split Specimen Failure To Reconfirm

Code of Federal Regulations, 2014 CFR

2014-10-01

.... The following items are required on each report: 1. MRO name, address, phone number, and fax number. 2. Collection site name, address, and phone number. 3. Date of collection. 4. Specimen I.D. number. 5. Laboratory accession number. 6. Primary specimen laboratory name, address, and phone number. 7. Date result...

49 CFR Appendix D to Part 40 - Report Format: Split Specimen Failure To Reconfirm

Code of Federal Regulations, 2013 CFR

2013-10-01

.... The following items are required on each report: 1. MRO name, address, phone number, and fax number. 2. Collection site name, address, and phone number. 3. Date of collection. 4. Specimen I.D. number. 5. Laboratory accession number. 6. Primary specimen laboratory name, address, and phone number. 7. Date result...

49 CFR Appendix D to Part 40 - Report Format: Split Specimen Failure To Reconfirm

Code of Federal Regulations, 2012 CFR

2012-10-01

.... The following items are required on each report: 1. MRO name, address, phone number, and fax number. 2. Collection site name, address, and phone number. 3. Date of collection. 4. Specimen I.D. number. 5. Laboratory accession number. 6. Primary specimen laboratory name, address, and phone number. 7. Date result...

Detection of Plasmodium falciparum Infection in Anopheles squamosus (Diptera: Culicidae) in an Area Targeted for Malaria Elimination, Southern Zambia

PubMed Central

Stevenson, Jennifer C.; Simubali, Limonty; Mbambara, Saidon; Musonda, Michael; Mweetwa, Sydney; Mudenda, Twig; Pringle, Julia C.; Jones, Christine M.; Norris, Douglas E.

2016-01-01

Southern Zambia is the focus of strategies to create malaria-free zones. Interventions being rolled out include test and treat strategies and distribution of insecticide-treated bed nets that target vectors that host-seek indoors and late at night. In Macha, Choma District, collections of mosquitoes were made outdoors using barrier screens within homesteads or UV bulb light traps set next to goats, cattle, or chickens during the rainy season of 2015. Anopheline mosquitoes were identified to species using molecular methods and Plasmodium falciparum infectivity was determined by ELISA and real-time qPCR methods. More than 40% of specimens caught were identified as Anopheles squamosus Theobald, 1901 of which six were found harboring malaria parasites. A single sample, morphologically identified as Anopheles coustani Laveran, 1900, was also found to be infectious. All seven specimens were caught outdoors next to goat pens. Parasite-positive specimens as well as a subset of An. squamosus specimens from either the same study or archive collections from the same area underwent sequencing of the mitochondrial cytochrome oxidase subunit I gene. Maximum parsimony trees constructed from the aligned sequences indicated presence of at least two clades of An. squamosus with infectious specimens falling in each clade. The single infectious specimen identified morphologically as An. coustani could not be matched to reference sequences. This is the first report from Zambia of infections in An. squamosus, a species which is described in literature to display exophagic traits. The bionomic characteristics of this species needs to be studied further to fully evaluate the implications for indoor-targeted vector control. PMID:27297214

Clinical Evaluation of the Cepheid Xpert TV Assay for Detection of Trichomonas vaginalis with Prospectively Collected Specimens from Men and Women.

PubMed

Schwebke, Jane R; Gaydos, C A; Davis, T; Marrazzo, J; Furgerson, D; Taylor, S N; Smith, B; Bachmann, L H; Ackerman, R; Spurrell, T; Ferris, D; Burnham, C A; Reno, H; Lebed, J; Eisenberg, D; Kerndt, P; Philip, S; Jordan, J; Quigley, N

2018-02-01

Trichomoniasis is the most prevalent curable sexually transmitted disease (STD). It has been associated with preterm birth and the acquisition and transmission of HIV. Recently, nucleic acid amplification tests (NAAT) have been FDA cleared in the United States for detection of Trichomonas vaginalis in specimens from both women and men. This study reports the results of a multicenter study recently conducted using the Xpert TV ( T. vaginalis ) assay to test specimens from both men and women. On-demand results were available in as little as 40 min for positive specimens. A total of 1,867 women and 4,791 men were eligible for inclusion in the analysis. In women, the performance of the Xpert TV assay was compared to the patient infected status (PIS) derived from the results of InPouch TV broth culture and Aptima NAAT for T. vaginalis The diagnostic sensitivities and specificities of the Xpert TV assay for the combined female specimens (urine samples, self-collected vaginal swabs, and endocervical swabs) ranged from 99.5 to 100% and 99.4 to 99.9%, respectively. For male urine samples, the diagnostic sensitivity and specificity were 97.2% and 99.9%, respectively, compared to PIS results derived from the results of broth culture for T. vaginalis and bidirectional gene sequencing of amplicons. Excellent performance characteristics were seen using both female and male specimens. The ease of using the Xpert TV assay should result in opportunities for enhanced screening for T. vaginalis in both men and women and, hopefully, improved control of this infection. Copyright © 2018 Schwebke et al.

Performance of the Xpert MTB/RIF assay for the diagnosis of pulmonary tuberculosis and rifampin resistance in a low-incidence, high-resource setting.

PubMed

Rice, Jason P; Seifert, Marva; Moser, Kathleen S; Rodwell, Timothy C

2017-01-01

Performance of the Xpert MTB/RIF assay, designed to simultaneously detect Mycobacterium tuberculosis complex (MTBC) and rifampin (RIF) resistance, has been well documented in low-resource settings with high TB-incidence. However, few studies have assessed its accuracy in low TB incidence settings. We evaluated the performance of Xpert MTB/RIF using clinical sputum specimens routinely collected from suspect pulmonary TB patients over a 4-year time period in San Diego County, California. Xpert MTB/RIF results were compared to acid-fast bacilli (AFB) smear microscopy, mycobacterial culture, and phenotypic drug susceptibility testing (DST). Of 751 sputum specimens, 134 (17.8%) were MTBC culture-positive and 2 (1.5%) were multidrug-resistant (MDR). For the detection of MTBC, Xpert MTB/RIF sensitivity was 89.6% (97.7% and 74.5% in smear-positive and -negative sputa, respectively) and specificity was 97.2%; while AFB smear sensitivity and specificity were 64.9% and 77.8%, respectively. Xpert MTB/RIF detected 35 of 47 smear-negative culture-positive specimens, and excluded 124 of 137 smear-positive culture-negative specimens. Xpert MTB/RIF also correctly excluded 99.2% (121/122) of nontuberculous mycobacteria (NTM) specimens, including all 33 NTM false-positives by smear microscopy. For the detection of RIF resistance, Xpert MTB/RIF sensitivity and specificity were 100% and 98.3%, respectively. Our findings demonstrate that Xpert MTB/RIF is able to accurately detect MTBC and RIF resistance in routinely collected respiratory specimens in a low TB-incidence setting, with comparable performance to that achieved in high-incidence settings; and suggest that under these conditions the assay has particular utility in detecting smear-negative TB cases, excluding smear-positive patients without MTBC disease, and differentiating MTBC from NTM.

Performance of the Xpert MTB/RIF assay for the diagnosis of pulmonary tuberculosis and rifampin resistance in a low-incidence, high-resource setting

PubMed Central

Rice, Jason P.; Moser, Kathleen S.; Rodwell, Timothy C.

2017-01-01

Performance of the Xpert MTB/RIF assay, designed to simultaneously detect Mycobacterium tuberculosis complex (MTBC) and rifampin (RIF) resistance, has been well documented in low-resource settings with high TB-incidence. However, few studies have assessed its accuracy in low TB incidence settings. We evaluated the performance of Xpert MTB/RIF using clinical sputum specimens routinely collected from suspect pulmonary TB patients over a 4-year time period in San Diego County, California. Xpert MTB/RIF results were compared to acid-fast bacilli (AFB) smear microscopy, mycobacterial culture, and phenotypic drug susceptibility testing (DST). Of 751 sputum specimens, 134 (17.8%) were MTBC culture-positive and 2 (1.5%) were multidrug-resistant (MDR). For the detection of MTBC, Xpert MTB/RIF sensitivity was 89.6% (97.7% and 74.5% in smear-positive and -negative sputa, respectively) and specificity was 97.2%; while AFB smear sensitivity and specificity were 64.9% and 77.8%, respectively. Xpert MTB/RIF detected 35 of 47 smear-negative culture-positive specimens, and excluded 124 of 137 smear-positive culture-negative specimens. Xpert MTB/RIF also correctly excluded 99.2% (121/122) of nontuberculous mycobacteria (NTM) specimens, including all 33 NTM false-positives by smear microscopy. For the detection of RIF resistance, Xpert MTB/RIF sensitivity and specificity were 100% and 98.3%, respectively. Our findings demonstrate that Xpert MTB/RIF is able to accurately detect MTBC and RIF resistance in routinely collected respiratory specimens in a low TB-incidence setting, with comparable performance to that achieved in high-incidence settings; and suggest that under these conditions the assay has particular utility in detecting smear-negative TB cases, excluding smear-positive patients without MTBC disease, and differentiating MTBC from NTM. PMID:29016684

Inselect: Automating the Digitization of Natural History Collections

PubMed Central

Hudson, Lawrence N.; Blagoderov, Vladimir; Heaton, Alice; Holtzhausen, Pieter; Livermore, Laurence; Price, Benjamin W.; van der Walt, Stéfan; Smith, Vincent S.

2015-01-01

The world’s natural history collections constitute an enormous evidence base for scientific research on the natural world. To facilitate these studies and improve access to collections, many organisations are embarking on major programmes of digitization. This requires automated approaches to mass-digitization that support rapid imaging of specimens and associated data capture, in order to process the tens of millions of specimens common to most natural history collections. In this paper we present Inselect—a modular, easy-to-use, cross-platform suite of open-source software tools that supports the semi-automated processing of specimen images generated by natural history digitization programmes. The software is made up of a Windows, Mac OS X, and Linux desktop application, together with command-line tools that are designed for unattended operation on batches of images. Blending image visualisation algorithms that automatically recognise specimens together with workflows to support post-processing tasks such as barcode reading, label transcription and metadata capture, Inselect fills a critical gap to increase the rate of specimen digitization. PMID:26599208

Inselect: Automating the Digitization of Natural History Collections.

PubMed

Hudson, Lawrence N; Blagoderov, Vladimir; Heaton, Alice; Holtzhausen, Pieter; Livermore, Laurence; Price, Benjamin W; van der Walt, Stéfan; Smith, Vincent S

2015-01-01

The world's natural history collections constitute an enormous evidence base for scientific research on the natural world. To facilitate these studies and improve access to collections, many organisations are embarking on major programmes of digitization. This requires automated approaches to mass-digitization that support rapid imaging of specimens and associated data capture, in order to process the tens of millions of specimens common to most natural history collections. In this paper we present Inselect-a modular, easy-to-use, cross-platform suite of open-source software tools that supports the semi-automated processing of specimen images generated by natural history digitization programmes. The software is made up of a Windows, Mac OS X, and Linux desktop application, together with command-line tools that are designed for unattended operation on batches of images. Blending image visualisation algorithms that automatically recognise specimens together with workflows to support post-processing tasks such as barcode reading, label transcription and metadata capture, Inselect fills a critical gap to increase the rate of specimen digitization.

Clinical biochemistry laboratory rejection rates due to various types of preanalytical errors.

PubMed

Atay, Aysenur; Demir, Leyla; Cuhadar, Serap; Saglam, Gulcan; Unal, Hulya; Aksun, Saliha; Arslan, Banu; Ozkan, Asuman; Sutcu, Recep

2014-01-01

Preanalytical errors, along the process from the beginning of test requests to the admissions of the specimens to the laboratory, cause the rejection of samples. The aim of this study was to better explain the reasons of rejected samples, regarding to their rates in certain test groups in our laboratory. This preliminary study was designed on the rejected samples in one-year period, based on the rates and types of inappropriateness. Test requests and blood samples of clinical chemistry, immunoassay, hematology, glycated hemoglobin, coagulation and erythrocyte sedimentation rate test units were evaluated. Types of inappropriateness were evaluated as follows: improperly labelled samples, hemolysed, clotted specimen, insufficient volume of specimen and total request errors. A total of 5,183,582 test requests from 1,035,743 blood collection tubes were considered. The total rejection rate was 0.65 %. The rejection rate of coagulation group was significantly higher (2.28%) than the other test groups (P < 0.001) including insufficient volume of specimen error rate as 1.38%. Rejection rates of hemolysis, clotted specimen and insufficient volume of sample error were found to be 8%, 24% and 34%, respectively. Total request errors, particularly, for unintelligible requests were 32% of the total for inpatients. The errors were especially attributable to unintelligible requests of inappropriate test requests, improperly labelled samples for inpatients and blood drawing errors especially due to insufficient volume of specimens in a coagulation test group. Further studies should be performed after corrective and preventive actions to detect a possible decrease in rejecting samples.

Front-Loading Sputum Microscopy Services: An Opportunity to Optimise Smear-Based Case Detection of Tuberculosis in High Prevalence Countries

PubMed Central

Ramsay, Andy; Yassin, Mohammed Ahmed; Cambanis, Alexis; Hirao, Susumu; Almotawa, Ahmad; Gammo, Mohamed; Lawson, Lovett; Arbide, Izabel; Al-Aghbari, Nasher; Al-Sonboli, Najla; Sherchand, Jeevan Bahadur; Gauchan, Punita; Cuevas, Luis Eduardo

2009-01-01

Setting. Ethiopia, Nepal, Nigeria, and Yemen. Objective. To reduce the time to complete sputum microscopy. Design. Cross-sectional surveys enrolling 923 patients with chronic cough in the 4 countries and using similar protocols. Spot-morning-spot sputum specimens were collected. An additional sputum specimen (Xspot) was collected one hour after the first, and the yields of the first two or the three specimens collected as spot-morning-spot or spot-Xspot-morning were compared. Results. 216 patients had ≥ one positive smear. 210 (97%) were identified by the spot-morning-spot, and 210 (97%) were identified by the spot-Xspot-morning specimens, with 203 and 200 identified by the first 2 specimens of each approach, respectively. Neither difference was significant. Conclusions. The time to complete smear microscopy could be reduced. PMID:20309419

Evaluation of Solubility and Microleakage of Glass Carbomer Sealant.

PubMed

Subramaniam, P; Girish Babu, K L; Jayasurya, S

2015-01-01

This study was carried out to evaluate and compare solubility and microleakage of the newly introduced moisture tolerant glass carbomer sealant. For evaluation of solubility, 20 specimens of glass carbomer and conventional glass ionomer were prepared and immersed in artificial saliva of pH 4 and 6 for seven days. The difference between initial and final weight was calculated. For evaluation of microleakage, glass carbomer was compared with a conventional resin sealant. 20 premolar teeth indicated for orthodontic extraction were collected and divided into two groups and the respective sealants were applied. It was subjected to thermocycling and then kept immersed in methylene blue for 24 hours. Dye penetration was scored. The glass carbomer specimens were less soluble than the conventional glass ionomer at both pH values. There was no significant difference in the microleakage. Being moisture resistant, glass carbomer can be used as an alternative fissure sealant material; especially in young children with partially erupted teeth and where obtaining moisture control is difficult.

Rotary powered device for bone marrow aspiration and biopsy yields excellent specimens quickly and efficiently.

PubMed

Swords, Ronan T; Kelly, Kevin R; Cohen, Stephen C; Miller, Larry J; Philbeck, Thomas E; Hacker, Sander O; Spadaccini, Cathy J; Giles, Francis J; Brenner, Andrew J

2010-06-01

Recently, a new FDA-cleared battery powered bone marrow biopsy system was developed to allow operators access to the bone marrow space quickly and efficiently. A pre-clinical evaluation of the device (OnControl, Vidacare Corporation, San Antonio, TX, USA) on anesthetized pigs was conducted, in addition to a clinical evaluation in hematology clinic patients requiring a bone marrow biopsy. Twenty-six samples were collected from the swine model. No cellular artifact or thermal damage was reported in any of the samples obtained. For the clinical evaluation of the device, 16 patients were recruited. Mean time from needle contact with skin to needle removal was 38.5 +/- 13.94 seconds. No complications were reported. In this study, the manual and powered samples were equivalent in specimen quality. In the patients evaluated, the device was safe, easy to use and the mean procedural time was significantly faster than previously reported with a manual technique.

Comparative Field Evaluation of Different Traps for Collecting Adult Phlebotomine Sand Flies (Diptera: Psychodidae) in an Endemic Area of Cutaneous Leishmaniasis in Quintana Roo, Mexico.

PubMed

Rodríguez-Rojas, Jorge J; Arque-Chunga, Wilfredo; Fernández-Salas, Ildefonso; Rebollar-Téllez, Eduardo A

2016-06-01

Phlebotominae are the vectors of Leishmania parasites. It is important to have available surveillance and collection methods for the sand fly vectors. The objectives of the present study were to evaluate and compare traps for the collection of sand fly species and to analyze trap catches along months and transects. Field evaluations over a year were conducted in an endemic area of leishmaniasis in the state of Quintana Roo, Mexico. A randomized-block design was implemented in study area with tropical rainforest vegetation. The study design utilized 4 transects with 11 trap types: 1) Centers for Disease Control and Prevention (CDC) light trap with incandescent bulb (CDC-I), 2) CDC light trap with blue light-emitting diodes (LEDs) (CDC-B), 3) CDC light trap with white LEDs (CDC-W), 4) CDC light trap with red LEDs (CDC-R), 5) CDC light trap with green LEDs (CDC-G), 6) Disney trap, 7) Disney trap with white LEDs, 8) sticky panels, 9) sticky panels with white LEDs, 10) delta-like trap, and 11) delta-like trap with white LEDs. A total of 1,014 specimens of 13 species and 2 genera (Lutzomyia and Brumptomyia) were collected. There were significant differences in the mean number of sand flies caught with the 11 traps; CDC-I was (P  =  0.0000) more effective than the other traps. Other traps exhibited the following results: CDC-W (17.46%), CDC-B (15.68%), CDC-G (14.89%), and CDC-R (14.30%). The relative abundance of different species varied according to trap types used, and the CDC-I trap attracted more specimens of the known vectors of Leishmania spp., such as like Lutzomyia cruciata, Lu. shannoni, and Lu. ovallesi. Disney trap captured more specimens of Lu. olmeca olmeca. Based on abundance and number of species, CDC light traps and Disney traps appeared to be good candidates for use in vector surveillance programs in this endemic area of Mexico.

Interferences from blood collection tube components on clinical chemistry assays

PubMed Central

Bowen, Raffick A.R.; Remaley, Alan T.

2014-01-01

Improper design or use of blood collection devices can adversely affect the accuracy of laboratory test results. Vascular access devices, such as catheters and needles, exert shear forces during blood flow, which creates a predisposition to cell lysis. Components from blood collection tubes, such as stoppers, lubricants, surfactants, and separator gels, can leach into specimens and/or adsorb analytes from a specimen; special tube additives may also alter analyte stability. Because of these interactions with blood specimens, blood collection devices are a potential source of pre-analytical error in laboratory testing. Accurate laboratory testing requires an understanding of the complex interactions between collection devices and blood specimens. Manufacturers, vendors, and clinical laboratorians must consider the pre-analytical challenges in laboratory testing. Although other authors have described the effects of endogenous substances on clinical assay results, the effects/impact of blood collection tube additives and components have not been well systematically described or explained. This review aims to identify and describe blood collection tube additives and their components and the strategies used to minimize their effects on clinical chemistry assays. PMID:24627713

49 CFR 40.65 - What does the collector check for when the employee presents a specimen?

Code of Federal Regulations, 2013 CFR

2013-10-01

... PROCEDURES FOR TRANSPORTATION WORKPLACE DRUG AND ALCOHOL TESTING PROGRAMS Urine Specimen Collections § 40.65.... You must check to ensure that the specimen contains at least 45 mL of urine. (1) If it does not, you... of tampering) also exists. (3) You are never permitted to combine urine collected from separate voids...

49 CFR 40.65 - What does the collector check for when the employee presents a specimen?

Code of Federal Regulations, 2011 CFR

2011-10-01

... PROCEDURES FOR TRANSPORTATION WORKPLACE DRUG AND ALCOHOL TESTING PROGRAMS Urine Specimen Collections § 40.65.... You must check to ensure that the specimen contains at least 45 mL of urine. (1) If it does not, you... of tampering) also exists. (3) You are never permitted to combine urine collected from separate voids...

49 CFR 40.65 - What does the collector check for when the employee presents a specimen?

Code of Federal Regulations, 2010 CFR

2010-10-01

... PROCEDURES FOR TRANSPORTATION WORKPLACE DRUG AND ALCOHOL TESTING PROGRAMS Urine Specimen Collections § 40.65.... You must check to ensure that the specimen contains at least 45 mL of urine. (1) If it does not, you... of tampering) also exists. (3) You are never permitted to combine urine collected from separate voids...

49 CFR 40.65 - What does the collector check for when the employee presents a specimen?

Code of Federal Regulations, 2014 CFR

2014-10-01

... PROCEDURES FOR TRANSPORTATION WORKPLACE DRUG AND ALCOHOL TESTING PROGRAMS Urine Specimen Collections § 40.65.... You must check to ensure that the specimen contains at least 45 mL of urine. (1) If it does not, you... of tampering) also exists. (3) You are never permitted to combine urine collected from separate voids...

49 CFR 40.65 - What does the collector check for when the employee presents a specimen?

Code of Federal Regulations, 2012 CFR

2012-10-01

... PROCEDURES FOR TRANSPORTATION WORKPLACE DRUG AND ALCOHOL TESTING PROGRAMS Urine Specimen Collections § 40.65.... You must check to ensure that the specimen contains at least 45 mL of urine. (1) If it does not, you... of tampering) also exists. (3) You are never permitted to combine urine collected from separate voids...

History and highlights of the teratological collection in the Museum Anatomicum of Leiden University, The Netherlands

PubMed Central

Boek, Peter L. J.; van Dam, Andries J.; Oostra, Roelof‐Jan

2018-01-01

The anatomical collection of the Anatomical Museum of Leiden University Medical Center (historically referred to as Museum Anatomicum Academiae Lugduno‐Batavae) houses and maintains more than 13,000 unique anatomical, pathological and zoological specimens, and include the oldest teratological specimens of The Netherlands. Throughout four centuries hundreds of teratological specimens were acquired by more than a dozen collectors. Due to the rich history of this vast collection, teratological specimens can be investigated in a unique retrospective sight going back almost four centuries. The entire 19th century collection was described in full detail by Eduard Sandifort (1742–1814) and his son Gerard Sandifort (1779–1848). Efforts were made to re‐describe, re‐diagnose and re‐categorize all present human teratological specimens, and to match them with historical descriptions. In the extant collection a total of 642 human teratological specimens were identified, including exceptional conditions such as faciocranioschisis and conjoined twins discordant for cyclopia, and sirenomelia. Both father and son Sandifort differed in their opinion regarding the causative explanation of congenital anomalies. Whereas, their contemporaries Wouter Van Doeveren (1730–1783) and Andreas Bonn (1738–1817) both presented an interesting view on how congenital anomalies were perceived and explained during the 18th and 19th centuries; the golden age of descriptive teratology. Although this enormous collection is almost 400 years old, it still impresses scientists, (bio)medical students, and laymen visiting and exploring the collections of the Museum Anatomicum in Leiden, The Netherlands. PMID:29399953

The NCBI BioCollections Database

PubMed Central

Sharma, Shobha; Ciufo, Stacy; Starchenko, Elena; Darji, Dakshesh; Chlumsky, Larry; Karsch-Mizrachi, Ilene

2018-01-01

Abstract The rapidly growing set of GenBank submissions includes sequences that are derived from vouchered specimens. These are associated with culture collections, museums, herbaria and other natural history collections, both living and preserved. Correct identification of the specimens studied, along with a method to associate the sample with its institution, is critical to the outcome of related studies and analyses. The National Center for Biotechnology Information BioCollections Database was established to allow the association of specimen vouchers and related sequence records to their home institutions. This process also allows cross-linking from the home institution for quick identification of all records originating from each collection. Database URL: https://www.ncbi.nlm.nih.gov/biocollections PMID:29688360

Comparison of FilmArray and Quantitative Real-Time Reverse Transcriptase PCR for Detection of Zaire Ebolavirus from Contrived and Clinical Specimens

PubMed Central

Southern, Timothy R.; Racsa, Lori D.; Albariño, César G.; Fey, Paul D.; Hinrichs, Steven H.; Murphy, Caitlin N.; Herrera, Vicki L.; Sambol, Anthony R.; Hill, Charles E.; Ryan, Emily L.; Kraft, Colleen S.; Campbell, Shelley; Sealy, Tara K.; Schuh, Amy; Ritchie, James C.; Lyon, G. Marshall; Mehta, Aneesh K.; Varkey, Jay B.; Ribner, Bruce S.; Brantly, Kent P.; Ströher, Ute; Iwen, Peter C.

2015-01-01

Rapid, reliable, and easy-to-use diagnostic assays for detection of Zaire ebolavirus (ZEBOV) are urgently needed. The goal of this study was to examine the agreement among emergency use authorization (EUA) tests for the detection of ZEBOV nucleic acids, including the BioFire FilmArray BioThreat (BT) panel, the FilmArray BT-E panel, and the NP2 and VP40 quantitative real-time reverse transcriptase (qRT) PCR assays from the Centers for Disease Control and Prevention (CDC). Specimens used in this study included whole blood spiked with inactivated ZEBOV at known titers and whole-blood, plasma, and urine clinical specimens collected from persons diagnosed with Ebola virus disease (EVD). The agreement for FilmArray and qRT-PCR results using contrived whole-blood specimens was 100% (6/6 specimens) for each ZEBOV dilution from 4 × 107 to 4 × 102 50% tissue culture infective dose (TCID50)/ml, as well as the no-virus negative-control sample. The limit of detection for FilmArray and qRT-PCR assays with inactivated ZEBOV, based on duplicate positive results, was determined to be 4 × 102 TCID50/ml. Rates of agreement between FilmArray and qRT-PCR results for clinical specimens from patients with EVD were 85% (23/27 specimens) for whole-blood specimens, 90% (18/20 specimens) for whole-blood specimens tested by FilmArray testing and matched plasma specimens tested by qRT-PCR testing, and 85% (11/13 specimens) for urine specimens. Among 60 specimens, eight discordant results were noted, with ZEBOV nucleic acids being detected only by FilmArray testing in four specimens and only by qRT-PCR testing in the remaining four specimens. These findings demonstrate that the rapid and easy-to-use FilmArray panels are effective tests for evaluating patients with EVD. PMID:26157148

Karawajew's ant type specimens (Hymenoptera, Formicidae) in the National Museum of Natural History of the National Academy of Sciences of Ukraine.

PubMed

Martynov, Alexander V; Radchenko, Alexander G

2016-03-30

The collection of W.A. Karawajew is one of the richest and most famous ant collections of the World. Much of this collection consists of dry mounted specimens, including types of about 550 taxa, housed in the Shmalhausen Institute of Zoology of the National Academy of Sciences of Ukraine (Kiev). Nevertheless, we located a considerable part of Karawajew's collection, containing about 25,000 specimens in alcohol, that is preserved in the National Museum of Natural History of the National Academy of Sciences of Ukraine (Kiev). The latter material was recently examined and we found types of 24 taxa. This type material was partly mounted, re-ordered and catalogued. In this paper we present a catalogue of these type specimens housed in the National Museum of Natural History.

Identification of type materials of the species of Protypotherium Ameghino, 1885 and Patriarchus Ameghino, 1889 (Notoungulata: Interatheriidae) erected by Florentino Ameghino.

PubMed

FernÁndez, Mercedes; Fernicola, Juan Carlos; CerdeÑo, Esperanza; Reguero, Marcelo A

2018-02-27

The first collections of Interatheriinae (Interatheriidae, Notoungulata) were created by the brothers Florentino and Carlos Ameghino, based on fossil specimens collected from diverse outcrops of Argentina and housed at different national institutions. In order to perform a systematic study of the subfamily, it is essential to revise as much specimens as possible, but first of all those that were used to establish the respective species, that is, the type material. Florentino Ameghino never referred to the collection number of the type specimens of the species he erected in any of his publications; this fact added to the occasional absence of illustrations and adequate descriptions, all of which make their identification a complex task. Thus, when studying the species erected by Florentino Ameghino within Protypotherium and Patriarchus, we recognised a lack of correspondence between some specimens that appeared labelled as types in the collections and the original descriptions of these species. In this contribution, we identify the type specimens of the eleven species of Protypotherium and eight of Patriarchus founded by Florentino Ameghino, housed in the Museo Argentino de Ciencias Naturales "Bernardino Rivadavia" (Buenos Aires, Argentina) and the Zoological Museum of the University of Copenhagen (Denmark). Three case studies are presented: a) specimens correctly identified; b) specimens erroneously catalogued as type material; and c) specimens not established as types in Ameghino's catalogue, but herein recognised as such. Lectotype and paralectotype of P. antiquum are herein designated.

Performance of ARCHITECT HCV core antigen test with specimens from US plasma donors and injecting drug users.

PubMed

Mixson-Hayden, Tonya; Dawson, George J; Teshale, Eyasu; Le, Thao; Cheng, Kevin; Drobeniuc, Jan; Ward, John; Kamili, Saleem

2015-05-01

Hepatitis C virus (HCV) core antigen is a serological marker of current HCV infection. The aim of this study was mainly to evaluate the performance characteristics of the ARCHITECT HCV core antigen assay with specimens from US plasma donors and injecting drug users. A total of 551 serum and plasma samples with known anti-HCV and HCV RNA status were tested for HCV core antigen using the Abbott ARCHITECT HCV core antigen test. HCV core antigen was detectable in 100% of US plasma donor samples collected during the pre-seroconversion phase of infection (anti-HCV negative/HCV RNA positive). Overall sensitivity of the HCV core antigen assay was 88.9-94.3% in samples collected after seroconversion. The correlation between HCV core antigen and HCV RNA titers was 0.959. HCV core antigen testing may be reliably used to identify current HCV infection. Published by Elsevier B.V.

Optimal design of studies of influenza transmission in households. I: case-ascertained studies.

PubMed

Klick, B; Leung, G M; Cowling, B J

2012-01-01

Case-ascertained household transmission studies, in which households including an 'index case' are recruited and followed up, are invaluable to understanding the epidemiology of influenza. We used a simulation approach parameterized with data from household transmission studies to evaluate alternative study designs. We compared studies that relied on self-reported illness in household contacts vs. studies that used home visits to collect swab specimens for virological confirmation of secondary infections, allowing for the trade-off between sample size vs. intensity of follow-up given a fixed budget. For studies estimating the secondary attack proportion, 2-3 follow-up visits with specimens collected from all members regardless of illness were optimal. However, for studies comparing secondary attack proportions between two or more groups, such as controlled intervention studies, designs with reactive home visits following illness reports in contacts were most powerful, while a design with one home visit optimally timed also performed well.

Comparison of two culture approaches, blind passage and dual observation, for detecting Chlamydia trachomatis in various prevalence populations.

PubMed Central

Zimmerman, S J; Moses, E; Sofat, N; Bartholomew, W R; Amsterdam, D

1992-01-01

Chlamydia trachomatis diagnosis in our laboratory consisted of dual inoculation of shell vials and detection of inclusions by using fluorescein-conjugated monoclonal antiserum; the second culture vial was conventionally used for blind passage when the first vial was negative. We compared the increase in positivity using blind passage with that of a strategy utilizing observation of two stained monolayers (dual observation) without blind passage, in an effort to reduce the reporting time and labor associated with the conventional approach. A total of 4,329 specimens were obtained from an obstetrics and gynecology (OB-GYN) clinic (2,563 specimens) and the sexually transmitted disease clinic (1,766 specimens). These specimens were used to compare the two strategies. Blind passage of 1,269 initially culture-negative specimens from the OB-GYN clinic resulted in an additional 6 positive chlamydial diagnoses. In comparison, a similar number of specimens (1,294) from the OB-GYN clinic collected subsequently to the first group were tested by dual observation. There were five additional positive findings. A similar evaluation of specimens from the sexually transmitted disease clinic was performed. Blind passage of 313 initially culture-negative specimens yielded 3 additional positive diagnoses, whereas dual observation of 1,435 similar specimens resulted in 9 positive diagnoses. On the basis of analysis of 4,332 specimens, sensitivity of dual observation is comparable to that of blind passage; labor, cost, and reporting time of dual observation are reduced in comparison to those of blind passage. PMID:1452664

49 CFR 40.33 - What training requirements must a collector meet?

Code of Federal Regulations, 2012 CFR

2012-10-01

... TRANSPORTATION WORKPLACE DRUG AND ALCOHOL TESTING PROGRAMS Urine Collection Personnel § 40.33 What training... about this part, the current “DOT Urine Specimen Collection Procedures Guidelines,” and DOT agency... changes to these materials. The DOT Urine Specimen Collection Procedures Guidelines document is available...

49 CFR 40.33 - What training requirements must a collector meet?

Code of Federal Regulations, 2013 CFR

2013-10-01

... TRANSPORTATION WORKPLACE DRUG AND ALCOHOL TESTING PROGRAMS Urine Collection Personnel § 40.33 What training... about this part, the current “DOT Urine Specimen Collection Procedures Guidelines,” and DOT agency... changes to these materials. The DOT Urine Specimen Collection Procedures Guidelines document is available...

49 CFR 40.33 - What training requirements must a collector meet?

Code of Federal Regulations, 2011 CFR

2011-10-01

... TRANSPORTATION WORKPLACE DRUG AND ALCOHOL TESTING PROGRAMS Urine Collection Personnel § 40.33 What training... about this part, the current “DOT Urine Specimen Collection Procedures Guidelines,” and DOT agency... changes to these materials. The DOT Urine Specimen Collection Procedures Guidelines document is available...

49 CFR 40.33 - What training requirements must a collector meet?

Code of Federal Regulations, 2010 CFR

2010-10-01

... TRANSPORTATION WORKPLACE DRUG AND ALCOHOL TESTING PROGRAMS Urine Collection Personnel § 40.33 What training... about this part, the current “DOT Urine Specimen Collection Procedures Guidelines,” and DOT agency... changes to these materials. The DOT Urine Specimen Collection Procedures Guidelines document is available...

49 CFR 40.33 - What training requirements must a collector meet?

Code of Federal Regulations, 2014 CFR

2014-10-01

... TRANSPORTATION WORKPLACE DRUG AND ALCOHOL TESTING PROGRAMS Urine Collection Personnel § 40.33 What training... about this part, the current “DOT Urine Specimen Collection Procedures Guidelines,” and DOT agency... changes to these materials. The DOT Urine Specimen Collection Procedures Guidelines document is available...

Revolutionizing the Use of Natural History Collections in Education

ERIC Educational Resources Information Center

Powers, Karen E.; Prather, L. Alan; Cook, Joseph A.; Woolley, James; Bart, Henry L., Jr.; Monfils, Anna K.; Sierwald, Petra

2014-01-01

Natural history collections are an irreplaceable and extensive record of life, and form the basis of our understanding of biodiversity on our planet. Broad-scale educational accessibility to these vast specimen collections, specimen images, and their associated data is currently severely hampered. With emerging technologies and massive efforts…

Harvestmen of the BOS Arthropod Collection of the University of Oviedo (Spain) (Arachnida, Opiliones).

PubMed

Merino-Sáinz, Izaskun; Anadón, Araceli; Torralba-Burrial, Antonio

2013-01-01

There are significant gaps in accessible knowledge about the distribution and phenology of Iberian harvestmen (Arachnida: Opiliones). Harvestmen accessible datasets in Iberian Peninsula are unknown, an only two other datasets available in GBIF are composed exclusively of harvestmen records. Moreover, only a few harvestmen data from Iberian Peninsula are available in GBIF network (or in any network that allows public retrieval or use these data). This paper describes the data associated with the Opiliones kept in the BOS Arthropod Collection of the University of Oviedo, Spain (hosted in the Department of Biología de Organismos y Sistemas), filling some of those gaps. The specimens were mainly collected from the northern third of the Iberian Peninsula. The earliest specimen deposited in the collection, dating back to the early 20(th) century, belongs to the P. Franganillo Collection. The dataset documents the collection of 16,455 specimens, preserved in 3,772 vials. Approximately 38% of the specimens belong to the family Sclerosomatidae, and 26% to Phalangidae; six other families with fewer specimens are also included. Data quality control was incorporated at several steps of digitisation process to facilitate reuse and improve accuracy. The complete dataset is also provided in Darwin Core Archive format, allowing public retrieval, use and combination with other biological, biodiversity of geographical variables datasets.

A Diversified Approach to Funding a Paleontology Program

NASA Astrophysics Data System (ADS)

Dooley, A., Jr.

2014-12-01

Routine field collection of fossils and other geologic specimens and maintenance of the resulting collections do not typically receive frequent infusions of large amounts of grant money, in spite of the relatively low costs of these activities and the baseline of data they provide. This type of work is often carried out by chronically-underfunded museums that that must use innovative methods of fundraising to carry out their missions. The Virginia Museum of Natural History (VMNH) is an independent state agency that is not affiliated with a university or any other institution. The VMNH paleontology department carries out frequent excavations of vertebrate fossils at three different localities in Virginia and Wyoming, maintains a collection of several hundred thousand specimens, and conducts original research and participates in professional meetings. Yet the annual operations (non-salary) appropriation for the paleontology department is only $500/year. Since 2007, state appropriations have accounted for only 3% of the department's non-salary funding, while grants (excluding salary-specific funding) have accounted for 27% and cash donations provided 1%. The remaining 69% has come from a diverse suite of alternate fundraising methods. Ecotourism and educational programming fees (37%) include fees paid by students and members of the public to participate in VMNH excavations, as well as fee-based field trips and programs involving fossils or casts. Merchandise sales (15%) are based on casts of specimens held in either the VMNH collections or at smaller museums that have contracted with VMNH to provide paleontology services. Contract work (13%) has included paleo-themed exhibit design, specimen evaluation, and repair of fossil specimens for smaller museums and visitor centers that lack a paleontology staff. A crowdfunding campaign designed to support a specific fossil excavation was responsible for 4% of the department's funds. This diverse range of funding sources has both provided the department with sufficient funds to carry out its operations and insulated it from the effects of reduction of any one funding source. Moreover, as most of these methods involve considerable interaction with the public they serve as additional means of outreach.

Self-collected versus clinician-collected sampling for sexually transmitted infections: a systematic review and meta-analysis protocol.

PubMed

Taylor, Darlene; Lunny, Carole; Wong, Tom; Gilbert, Mark; Li, Neville; Lester, Richard; Krajden, Mel; Hoang, Linda; Ogilvie, Gina

2013-10-10

Three meta-analyses and one systematic review have been conducted on the question of whether self-collected specimens are as accurate as clinician-collected specimens for STI screening. However, these reviews predate 2007 and did not analyze rectal or pharyngeal collection sites. Currently, there is no consensus on which sampling method is the most effective for the diagnosis of genital chlamydia (CT), gonorrhea (GC) or human papillomavirus (HPV) infection. Our meta-analysis aims to be comprehensive in that it will examine the evidence of whether self-collected vaginal, urine, pharyngeal and rectal specimens provide as accurate a clinical diagnosis as clinician-collected samples (reference standard). Eligible studies include both randomized and non-randomized controlled trials, pre- and post-test designs, and controlled observational studies. The databases that will be searched include the Cochrane Database of Systematic Reviews, Web of Science, Database of Abstracts of Reviews of Effects (DARE), EMBASE and PubMed/Medline. Data will be abstracted independently by two reviewers using a standardized pre-tested data abstraction form. Heterogeneity will be assessed using the Q2 test. Sensitivity and specificity estimates with 95% confidence intervals as well as negative and positive likelihood ratios will be pooled and weighted using random effects meta-analysis, if appropriate. A hierarchical summary receiver operating characteristics curve for self-collected specimens will be generated. This synthesis involves a meta-analysis of self-collected samples (urine, vaginal, pharyngeal and rectal swabs) versus clinician-collected samples for the diagnosis of CT, GC and HPV, the most prevalent STIs. Our systematic review will allow patients, clinicians and researchers to determine the diagnostic accuracy of specimens collected by patients compared to those collected by clinicians in the detection of chlamydia, gonorrhea and HPV.

Microscopic and ultrastructural changes of Müller's muscle in patients with simple congenital ptosis.

PubMed

Alshehri, Mohammed D; Al-Fakey, Yasser H; Alkhalidi, Hisham M; Mubark, Mohamed A; Alsuhaibani, Adel H

2014-01-01

To study microscopic and ultrastructural changes of Müller's muscle in patients with isolated congenital ptosis. In this prospective, observational case-control study, Müller's muscle specimens were collected during ptosis surgical correction for 18 consecutive patients. Each specimen was divided into 2 parts. One part was embedded in formalin for light microscopy, and the other one was fixed in 3% glutaraldehyde for electron microscopy. A neuropathologist, serving as a masked evaluator, blindly reviewed all the different features for every case and counted the number of myocytes showing distinct myofilaments in the whole grid for every case. Statistical analysis using compare means and correlation tests was conducted to investigate potential associations and/or differences within and across groups. Twelve Müller's muscle specimens from patients with simple congenital ptosis of various severities and 6 specimens from patients with aponeurotic ptosis (controls) were collected and studied. Under light microscopy, congenital ptosis slides showed a small number of dispersed myocytes in a fibrotic background, whereas acquired ptosis slides showed a greater number of well-defined myocytes. Under electron microscopy, all congenital ptosis specimens had only a very small number of myocytes with clear, distinct myofilaments. Most myocytes in the aponeurotic ptosis group showed clear, distinct myofilaments, indicating a well-preserved muscle. No relationship existed between the number of clear, distinct myofilaments observed in the congenital ptosis group by transmission electron microscopy and patient age or ptosis severity. Substantial Müller's muscle atrophy was observed in patients with different severities of isolated congenital ptosis.

Standard operating procedures for serum and plasma collection: early detection research network consensus statement standard operating procedure integration working group.

PubMed

Tuck, Melissa K; Chan, Daniel W; Chia, David; Godwin, Andrew K; Grizzle, William E; Krueger, Karl E; Rom, William; Sanda, Martin; Sorbara, Lynn; Stass, Sanford; Wang, Wendy; Brenner, Dean E

2009-01-01

Specimen collection is an integral component of clinical research. Specimens from subjects with various stages of cancers or other conditions, as well as those without disease, are critical tools in the hunt for biomarkers, predictors, or tests that will detect serious diseases earlier or more readily than currently possible. Analytic methodologies evolve quickly. Access to high-quality specimens, collected and handled in standardized ways that minimize potential bias or confounding factors, is key to the "bench to bedside" aim of translational research. It is essential that standard operating procedures, "the how" of creating the repositories, be defined prospectively when designing clinical trials. Small differences in the processing or handling of a specimen can have dramatic effects in analytical reliability and reproducibility, especially when multiplex methods are used. A representative working group, Standard Operating Procedures Internal Working Group (SOPIWG), comprised of members from across Early Detection Research Network (EDRN) was formed to develop standard operating procedures (SOPs) for various types of specimens collected and managed for our biomarker discovery and validation work. This report presents our consensus on SOPs for the collection, processing, handling, and storage of serum and plasma for biomarker discovery and validation.

Hyperspectral imaging fluorescence excitation scanning for detecting colorectal cancer: pilot study

NASA Astrophysics Data System (ADS)

Leavesley, Silas J.; Wheeler, Mikayla; Lopez, Carmen; Baker, Thomas; Favreau, Peter F.; Rich, Thomas C.; Rider, Paul F.; Boudreaux, Carole W.

2016-03-01

Optical spectroscopy and hyperspectral imaging have shown the theoretical potential to discriminate between cancerous and non-cancerous tissue with high sensitivity and specificity. To date, these techniques have not been able to be effectively translated to endoscope platforms. Hyperspectral imaging of the fluorescence excitation spectrum represents a new technology that may be well-suited for endoscopic implementation. However, the feasibility of detecting differences between normal and cancerous mucosa using fluorescence excitation-scanning hyperspectral imaging has not been evaluated. The objective of this pilot study was to evaluate the changes in the fluorescence excitation spectrum of resected specimen pairs of colorectal adenocarcinoma and normal colorectal mucosa. Patients being treated for colorectal adenocarcinoma were enrolled. Representative adenocarcinoma and normal colonic mucosa specimens were collected from each case. Specimens were flash frozen in liquid nitrogen. Adenocarcinoma was confirmed by histologic evaluation of H&E permanent sections. Hyperspectral image data of the fluorescence excitation of adenocarcinoma and surrounding normal tissue were acquired using a custom microscope configuration previously developed in our lab. Results demonstrated consistent spectral differences between normal and cancerous tissues over the fluorescence excitation spectral range of 390-450 nm. We conclude that fluorescence excitation-scanning hyperspectral imaging may offer an alternative approach for differentiating adenocarcinoma and surrounding normal mucosa of the colon. Future work will focus on expanding the number of specimen pairs analyzed and will utilize fresh tissues where possible, as flash freezing and reconstituting tissues may have altered the autofluorescence properties.

Cicadidae types (Hemiptera-Cicadomorpha) housed at the Museo de La Plata entomological collection (Argentina).

PubMed

De Remes Lenicov, Ana M Marino; Maciá, Arnaldo; Pianzola, Bruno

2015-06-23

A catalog of the 161 type specimens of species of Hemiptera Cicadidae housed in the collection of the Entomology Division of the Museo de La Plata is presented. This collection represents 52 species grouped in 19 genera. For each species the original and current names, bibliographic references, type category, number of specimens, gender, Museo de La Plata code numbers, and transcription of data from labels (country, province, locality, date of collection, collector's name, and hosts) are given. Information about the state of preservation of the specimens in each series and photographs of each type species are also provided.

Development and Evaluation of Problem-Solving Skills in Microbiology.

ERIC Educational Resources Information Center

Schuytema, Eunice C.; And Others

A problem solving, laboratory experience was devised in which first-year medical students were given a case description and then required to make judgments about what microbiology specimens should be collected and to analyze the results of laboratory tests in terms of implications for patient care. Over a four-year period revisions were made in…

Clinical and Analytical Evaluation of a Single-Vial Stool Collection Device with Formalin-Free Fixative for Improved Processing and Comprehensive Detection of Gastrointestinal Parasites

PubMed Central

Couturier, Brianne A.; Jensen, Ryan; Arias, Nora; Heffron, Michael; Gubler, Elyse; Case, Kristin; Gowans, Jason

2015-01-01

Microscopic examination of feces is a standard laboratory method for diagnosing gastrointestinal parasite infections. In North America, the ovum and parasite (O&P) examination is typically performed using stool that is chemically fixed in polyvinyl alcohol (PVA) and formalin, after which the stool is concentrated by filtration to enhance sensitivity. Mini Parasep solvent-free (SF) tubes allow collection and concentration within a single collection vial. The goal of the study was to determine whether consolidated processing and concentration with the Parasep tubes using an alcohol-based fixative (Alcorfix) provide O&P examinations equivalent to or better than those done by processing of PVA-formalin-fixed stool using a SpinCon concentration device. Parasep tubes revealed filtration performance equivalent to that of the SpinCon concentration device using PVA-formalin-fixed stool containing protozoa. Specimens cocollected in Parasep tubes containing PVA-formalin and Alcorfix revealed comparable morphology and staining for various protozoa. Alcorfix effectively fixed live Cryptosporidium and microsporidia such that morphology and staining were conserved for modified acid-fast and modified trichrome stains. A work flow analysis revealed significant time savings for batches of 10 or 30 O&P specimens in tubes with Alcorfix compared to the amount of time that it took to analyze the same number of specimens in tubes with PVA-formalin. The direct hands-on time savings with Mini Parasep tubes were 17 min and 41 s and 32 min and 1 s for batches of 10 and 30 specimens, respectively. Parasep tubes containing Alcorfix provide significant work flow advantages to laboratories that process medium to high volumes of O&P specimens by streamlining processing and converting to a single tube. These improvements in work flow, reduction of the amount of formalin used in the laboratory, and equivalent microscopy results are attractive advancements in O&P testing for North American diagnostic parasitology laboratories. PMID:26019199

Clinical and Analytical Evaluation of a Single-Vial Stool Collection Device with Formalin-Free Fixative for Improved Processing and Comprehensive Detection of Gastrointestinal Parasites.

PubMed

Couturier, Brianne A; Jensen, Ryan; Arias, Nora; Heffron, Michael; Gubler, Elyse; Case, Kristin; Gowans, Jason; Couturier, Marc Roger

2015-08-01

Microscopic examination of feces is a standard laboratory method for diagnosing gastrointestinal parasite infections. In North America, the ovum and parasite (O&P) examination is typically performed using stool that is chemically fixed in polyvinyl alcohol (PVA) and formalin, after which the stool is concentrated by filtration to enhance sensitivity. Mini Parasep solvent-free (SF) tubes allow collection and concentration within a single collection vial. The goal of the study was to determine whether consolidated processing and concentration with the Parasep tubes using an alcohol-based fixative (Alcorfix) provide O&P examinations equivalent to or better than those done by processing of PVA-formalin-fixed stool using a SpinCon concentration device. Parasep tubes revealed filtration performance equivalent to that of the SpinCon concentration device using PVA-formalin-fixed stool containing protozoa. Specimens cocollected in Parasep tubes containing PVA-formalin and Alcorfix revealed comparable morphology and staining for various protozoa. Alcorfix effectively fixed live Cryptosporidium and microsporidia such that morphology and staining were conserved for modified acid-fast and modified trichrome stains. A work flow analysis revealed significant time savings for batches of 10 or 30 O&P specimens in tubes with Alcorfix compared to the amount of time that it took to analyze the same number of specimens in tubes with PVA-formalin. The direct hands-on time savings with Mini Parasep tubes were 17 min and 41 s and 32 min and 1 s for batches of 10 and 30 specimens, respectively. Parasep tubes containing Alcorfix provide significant work flow advantages to laboratories that process medium to high volumes of O&P specimens by streamlining processing and converting to a single tube. These improvements in work flow, reduction of the amount of formalin used in the laboratory, and equivalent microscopy results are attractive advancements in O&P testing for North American diagnostic parasitology laboratories. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

A new species of Cryptotis (Mammalia, Eulipotyphla, Soricidae) from the Sierra de Perijá, Venezuelan-Colombian Andes

USGS Publications Warehouse

Quiroga-Carmona, Marcial; Woodman, Neal

2015-01-01

The Sierra de Perijá is the northern extension of the Cordillera Oriental of the Andes and includes part of the border between Colombia and Venezuela. The population of small-eared shrews (Mammalia, Eulipotyphla, Soricidae, Cryptotis) inhabiting the Sierra de Perijá previously was known from only a single skull from an individual collected in Colombia in 1989. This specimen had been referred to alternatively as C. thomasi and C. meridensis, but more precise definition of the known Colombian and Venezuelan species of Cryptotis has since excluded the Sierra de Perijá population from any named species. The recent collection of a specimen from the Venezuelan slope of Sierra de Perijá, prompted us to re-evaluate the taxonomic status of this population and determine its relationship with other Andean shrews. Our examination of the available specimens revealed that they possess a unique suite of morphological and morphometrical characters, and we describe the Sierra de Perijá population as a new species in the South American C. thomasi species group. Recognition of this new species adds to our knowledge of this genus in South America and to the biodiversity of the Sierra de Perijá.

Symptomatic Zika Virus Infection in Infants, Children, and Adolescents Living in Puerto Rico.

PubMed

Read, Jennifer S; Torres-Velasquez, Brenda; Lorenzi, Olga; Rivera Sanchez, Aidsa; Torres-Torres, Sanet; Rivera, Lillian V; Capre-Franceschi, Sheila M; Garcia-Gubern, Carlos; Munoz-Jordan, Jorge; Santiago, Gilberto A; Alvarado, Luisa I

2018-05-29

Little information is available regarding Zika virus (ZIKV) infection in children. To describe patients younger than 18 years who were infected with ZIKV and were enrolled in the Sentinel Enhanced Dengue and Acute Febrile Illness Surveillance System (SEDSS). Children infected with ZIKV with 7 or fewer days of fever or emancipated minors aged 14 to 17 years with a generalized maculopapular rash, arthritis or arthralgia, or nonpurulent conjunctivitis were eligible for enrollment on or before December 31, 2016, in Puerto Rico. Patients were evaluated using ZIKV polymerase chain reaction testing at 7 or fewer days after the onset of symptoms. Available ZIKV polymerase chain reaction-positive specimens were evaluated to determine viral loads. Confirmed polymerase chain reaction-positive ZIKV infection. Clinical characteristics and viral loads of symptomatic children with confirmed ZIKV infection. Of 7191 children enrolled in SEDSS on or before December 31, 2016, only those with confirmed ZIKV infection (351 participants) were included in this study. Participants who had confirmed ZIKV infection included 25 infants (7.1%), 69 children (19.7%) aged 1 to 4 years, 95 (27.1%) aged 5 to 9 years, and 162 (46.1%) aged 10 to 17 years. Among these, 260 patients (74.1%) presented for evaluation of ZIKV infection at fewer than 3 days after the onset of symptoms, 340 (96.9%) were discharged to home after evaluation, and 349 (99.4%) had fever, 280 (79.8%) had a rash, 243 (69.2%) had facial or neck erythema, 234 (66.7%) had fatigue, 223 (63.5%) had headache, 212 (60.4%) had chills, 206 (58.7%) had pruritus, and 204 (58.1%) had conjunctival hyperemia. Of 480 specimens collected (317 serum and 163 urine specimens) from 349 children, the median number of days after the onset of symptoms was lower for children who had serum specimens (1 day [interquartile range (IQR), 1-2 days]) than for children who had urine specimens (2 [1-3] days) (P < .001). Of 131 children who had both serum and urine specimens collected on the same day, the median viral load was higher in serum than in urine (median [IQR], 23 098 [8784-88 242] copies/mL for serum vs 9966 [2815-52 774] copies/mL for urine; P = .02). When a single serum sample from each of 317 patients was analyzed, there were no statistically significant differences in median viral loads according to age, sex, or disposition. However, the median serum viral load varied significantly according to the number of days after the onset of symptoms (0 days, 106 778 [IQR, 9772-1 571 718] copies/mL; 1 day, 46 299 [10 663-255 030] copies/mL; 2 days, 20 678 [8763-42 458] copies/mL; and ≥3 days, 15 901 [5135-49 248] copies/mL; P = .001). This study represents the largest study to date of ZIKV infection in the pediatric population. Most children infected with ZIKV had fever, rash, and conjunctival hyperemia. The children usually presented for evaluation at fewer than 3 days after the onset of symptoms. Viral loads for ZIKV were higher in serum vs urine specimens. Median viral loads in serum specimens differed significantly according to the number of days after the onset of symptoms.

Urine culture contamination: a College of American Pathologists Q-Probes study of 127 laboratories.

PubMed

Bekeris, Leonas G; Jones, Bruce Allen; Walsh, Molly K; Wagar, Elizabeth A

2008-06-01

While urine culture contamination may not be completely avoidable, some laboratories have lower contamination rates than others. A College of American Pathologists (CAP) 1998 Q-Probes study showed that many interventions commonly assumed to reduce contamination were not demonstrably effective. This article revisits the issue. To examine the frequency of urine culture contamination, review current laboratory practices in the collection of urine culture specimens, and determine practice characteristics that may be associated with the contamination rate. Laboratories participating in a CAP Q-Probes study were required to prospectively collect data on 120 consecutive urine culture specimens and provide information on the patient's demographics (age and sex), the location where the specimen was collected, how the specimen was handled, the number of isolates in quantities greater than or equal to 10,000 colony-forming units (CFU)/mL, and whether the laboratory considered the specimen to be contaminated. Specific inclusion and exclusion criteria were provided to the participants. Each laboratory completed a supplemental questionnaire that probed for specific laboratory urine culture collection practices. One hundred twenty-seven laboratories participated in the study. Results from a total of 14,739 urine specimens were received. For the purpose of this study, a urine specimen was determined to be contaminated if the culture yielded more than 2 isolates in quantities greater than or equal to 10,000 CFU/mL. Using these criteria the median institution had a contamination rate of 15.0%. Laboratories in the 10th percentile (low performance) had an average contamination rate of 41.7%, while laboratories in the 90th percentile had an average rate of 0.8%. The collection site had no influence on the contamination rate, but postcollection processing, especially refrigeration of the specimen, had a substantial effect. Providing instruction to patients produced a statistically significant lowering of contamination rates for specimens from male patients (P = .006) but not for female patients, except when written instructions were provided in the emergency room, in which case specimen contamination rates for both male and female patients dropped (P = .01). The median contamination rates remain at a level comparable to the results seen in a previous Q-Probes study, and some laboratories have very high contamination rates. Specimen refrigeration is associated with lower overall urine culture specimen contamination rate. Providing patient instruction is also associated with lower contamination rates under specific circumstances.

Catalog of type specimens of recent mammals: Rodentia (Myomorpha, Anomaluromorpha, and Hystricomorpha) in the National Museum of Natural History, Smithsonian Institution

USGS Publications Warehouse

Fisher, Robert D.; Ludwig, Craig A.

2014-01-01

The type collection of Recent mammals in the Division of Mammals, National Museum of Natural History, Smithsonian Institution, contains 945 specimens bearing names of 931 species-group taxa of Rodentia (Myomorpha, Anomaluromorpha, and Hystricomorpha) as of August 2013. This catalog presents an annotated list of these holdings comprised of 905 holotypes, 16 lectotypes, 8 syntypes (48 specimens), and 2 neotypes. In addition, we include 44 specimens that are part of syntype series that should be in the collection but cannot be found or are now known to be in other collections. One hundred and ten of the names are new since the last type catalog covering these suborders A lectotype for Mus peruvianus Peale, 1848, is newly designated herein. Nine specimens previously reported were subsequently sent to the vertebrate paleontology collection and are not included here. Suborders and families are ordered as in Carleton and Musser; within families, currently recognized genera are arranged alphabetically; within each currently recognized genus, accounts are arranged alphabetically by original published name. Information in each account includes original name and abbreviated citation thereto, current name if other than original, citation for first use of current name combination for the taxon (or new name combination if used herein for the first time), type designation, U.S. National Museum catalog number(s), preparation, age and sex, date of collection and collector, original collector number, type locality, and remarks as appropriate. Digital photographs of each specimen will serve as a condition report and will be attached to each electronic specimen record.

Catalog of type specimens of recent mammals: Rodentia (Sciuromorpha and Castorimorpha) in the National Museum of Natural History, Smithsonian Institution

USGS Publications Warehouse

Fisher, Robert D.; Ludwig, Craig A.

2012-01-01

The type collection of Recent mammals in the Division of Mammals, National Museum of Natural History, Smithsonian Institution, contains 843 specimens bearing names of 820 species group taxa of Rodentia (Sciuromorpha and Castorimorpha) as of July 2011. This catalog presents a list of these holdings, which comprise 798 holotypes, 14 lectotypes, seven syntypes (30 specimens), and one neotype. In addition, we include three holotypes and 10 specimens that are part of syntype series that should be in the collection but cannot be found and three syntypes that were originally in this collection but are now known to be in other collections. One specimen that no longer has name-bearing status is included for the record. Forty-one of the names are new since the last type catalog. One new lectotype is designated. Suborders and families are listed as in Wilson and Reeder. Within families, currently recognized genera are arranged alphabetically. Within each currently recognized genus, accounts are arranged alphabetically by original published name. Information in each account includes original name and abbreviated citation thereto, current name if other than original, citation for first use of current name combination for the taxon (or new name combination if used herein for the first time), type designation, U.S. National Museum catalog number(s), preparation, age and sex, type locality, date of collection and name of collector, collector’s original number, and comments or additional information as appropriate. Digital photographs of each specimen serve as a condition report and will be linked to each electronic specimen record.

Catalog of type specimens of recent mammals: orders Didelphimorpha through Chiroptera (Excluding Rodentia) in the National Museum of Natural History, Smithsonian Institution

USGS Publications Warehouse

Fisher, Robert D.; Ludwig, Craig A.

2015-01-01

The type collection of Recent Mammals in the Division of Mammals, National Museum of Natural History, Smithsonian Institution, contains 820 specimens bearing names of 809 species-group taxa of Didelphimorphia through Chiroptera, excluding Rodentia, as of June 2014. This catalog presents an annotated list of these holdings comprised of 788 holotypes, 26 lectotypes, 11 syntypes (22 specimens), and 4 neotypes. Included are several specimens that should be in the collection but cannot be found or are now known to be in other collections. One hundred and twenty-seven of the names are new since the last type catalog covering these orders, Poole and Schantz (1942). Five specimens reported in Poole and Schantz (1942) were subsequently sent to the Vertebrate Paleontology collection and are not included here. Orders and families are ordered as in Wilson and Reeder (2005); within families, currently recognized genera are arranged alphabetically; within each currently recognized genus, accounts are arranged alphabetically by original published name. Information in each account includes original name and abbreviated citation thereto, current name if other than original, citation for first use of current name combination for the taxon (or new name combination if used herein for the first time), type designation, U.S. National Museum catalog number(s), preparation, age and sex, date of collection and collector, original collector number, type locality, and remarks as appropriate. Digital photographs of each specimen will serve as a condition report and will be attached to each electronic specimen record.

Gut Microbiota Dysbiosis and Diarrhea in Kidney Transplant Recipients.

PubMed

Lee, John Richard; Magruder, Matthew; Zhang, Lisa; Westblade, Lars F; Satlin, Michael J; Robertson, Amy; Edusei, Emmanuel; Crawford, Carl; Ling, Lilan; Taur, Ying; Schlueter, Jonas; Lubetzky, Michelle; Dadhania, Darshana; Pamer, Eric; Suthanthiran, Manikkam

2018-06-19

Post-transplant diarrhea is associated with kidney allograft failure and death but its etiology remains unknown in the majority of cases. Because altered gut microbial ecology is a potential basis for diarrhea, we investigated whether post-transplant diarrhea is associated with gut dysbiosis. We enrolled 71 kidney allograft recipients for serial fecal specimen collections in the first 3 months of transplantation and profiled the gut microbiota using 16S rRNA gene V4-V5 deep sequencing. The Shannon diversity index was significantly lower in 28 diarrheal fecal specimens from 25 recipients with post-transplant diarrhea than in 112 fecal specimens from 46 recipients without post-transplant diarrhea. We found lower relative abundance of 13 commensal genera (Benjamini-Hochberg adjusted p value ≤ 0.15) in the diarrheal fecal specimens including the same 4 genera identified in our prior study. The 28 diarrheal fecal specimens were also evaluated by a multiplexed PCR assay for 22 bacterial, viral, and protozoan gastrointestinal pathogens, and 26 specimens were negative for infectious etiologies. Using PICRUSt to predict metagenomic functions, we found diarrheal fecal specimens had a lower abundance of metabolic genes. Our findings suggest that post-transplant diarrhea is not associated with common infectious diarrheal pathogens but with a gut dysbiosis. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

The genus Milnesium (Tardigrada: Eutardigrada: Milnesiidae) in the Great Smoky Mountains National Park (North Carolina and Tennessee, USA), with the description of Milnesium bohleberi sp. nov.

PubMed

Bartels, Paul J; Nelson, Diane R; Kaczmarek, Lukasz; Michalczyk, Lukasz

2014-06-30

For many decades the genus Milnesium was thought to consist of a single, cosmopolitan species: Milnesium tardigradum Doyère, 1840. However, recently the genus has been re-evaluated, and numerous new species have been described. Currently, over twenty extant species and one fossil are recognised, and most appear to have very narrow geographic ranges. It is doubtful that M. tardigradum sensu stricto is truly cosmopolitan, but to evaluate this hypothesis, specimens previously identified as M. tardigradum must be re-examined using newly proposed taxonomic characters. As part of the All Taxa Biodiversity Inventory (ATBI) we collected Milnesium specimens from various locations in the Great Smoky Mountains National Park (GSMNP). Two Milnesium species have been evaluated, and one of them, Milnesium bohleberi sp. nov., is new to science. The new species is most similar to M. eurystomum but differs by shorter claws and a shorter, narrower, and more cylindrical buccal tube. The other Milnesium species, very rare in our collection, is morphologically indistinguishable from Milnesium granulatum Ramazzotti 1962, which was previously known only from Chile, Italy and Romania. Based on the recently revised description of M. tardigradum sensu stricto, this nominal species for the genus has not been found in the GSMNP samples. 

Neoplastic lesions in the nasal cavities of dogs.

PubMed

Spuzak, J; Jankowski, M; Kubiak, K; Glińska-Suchocka, K; Grzegory, M; Hałoń, A

2014-01-01

This paper aims at evaluating the frequency of nasal cavity tumors in dogs as well as comparing an endoscopic examination with a histopathological evaluation of the collected biopsy specimens. The study was conducted on 68 dogs. During the endoscopic examination, proliferative lesions were recognized in 20 dogs. During the histopathological examination, neoplastic lesions were confirmed in 95% of the dogs in which proliferative lesions were identified in the endoscopic examination. Adenocarcinoma occurred most frequently in the population under study.

Redescription and sexual dimorphism of Andaman leg-skate Cruriraja andamanica (Chondrichthyes: Rajiformes) with comments on the zoogeography of the genus Cruriraja.

PubMed

Vinu, J; Rajeeshkumar, M P; Parmeswaran, U V; Sumod, K S; Akhilesh, K V; Manjebrayakath, H; Sanjeevan, V N

2017-08-01

This paper redescribes sexually dimorphic Cruriraja andamanica based on five juvenile (four males, one female) and four adult specimens (three males, one female) collected from Andaman waters. Morphometric comparison of the present specimens with a female specimen collected off the coast of Tanzania reveals considerable dissimilarities between them. These findings, along with the wide geographical distance between collection locations, support a need for revision of the Tanzanian specimen, which, in all probability, represents a new species in the genus. The paper also addresses zoogeography of genus Cruriraja across the world's oceans and provides a revised key to the species. © 2017 The Fisheries Society of the British Isles.

Diversity of sandflies (Psychodidae: Phlebotominae) captured in sandstone caves from Central Amazonia, Brazil.

PubMed

Alves, Veracilda Ribeiro; Freitas, Rui Alves de; Santos, Francisco Lima; Barrett, Toby Vincent

2011-05-01

In the present paper we describe the diversity of phlebotomine sandflies collected in three sandstone caves in the municipality of Presidente Figueiredo, state of Amazonas, Brazil. The phlebotomines were captured during 2006 with CDC light traps. Guano samples from inside the Gruta Refúgio do Maruaga were collected to investigate the presence of immature specimens. A total of 2,160 adult phlebotomines representing 15 species were captured. Pintomyia pacae was the dominant species in Gruta dos Animais (1,723 specimens) and Gruta dos Lages (50 specimens) and Deanemyia maruaga new comb (280 specimens) was the dominant species in Gruta Refúgio do Maruaga. A total of 18 guano samples were collected and seven of these samples included immature specimens. A total of 507 immature specimens were captured; 495 of these specimens were larvae and 12 were pupae. The presence of paca (Agouti paca) footprints near Gruta dos Animais and Gruta dos Lages suggests the association of Pi. pacae with this rodent. This finding may explain the abundance of Pi. pacae in these locations, while the species is relatively rare in the forest. Deanemyia maruaga is a cave species that uses guano to breed during its immature stages. Adult specimens of this species are apparently parthenogenetic and autogenous and represent the second record of parthenogenesis for the subfamily Phlebotominae.

National environmental specimen bank survey. [Location of 657 collections of environmental specimens

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

Van Hook, R.I.; Huber, E.E.

1976-01-01

This report presents the data base developed in the National Environmental Specimen Bank (NESB) Survey. The methodology utilized in developing the mailing lists and in developing and maintaining the data base records also is included. The NESB Survey Data Base is computerized in the Oak Ridge Computerized Hierarchical Information System, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37830. The NESB Survey mailing list consisted of 4500 names and addresses. The 657 environmental specimen collections that were located and documented in the NESB Survey Data Base include the following categories: animal, atmospheric, geological, microbiological, plant, and water. However, the majority ofmore » the collections identified are biological in nature. Three indices of the NESB Survey Data Base are included in this report: respondents names and addresses categorized by organizational affiliation; (2) alphabetical listing of respondents; and geographical sampling location for materials in collections.« less

The reptile type specimens preserved in the Museo Nacional de Ciencias Naturales (CSIC) of Madrid, Spain.

PubMed

García-Díez, Teresa; González-Fernández, José E

2013-01-01

A first complete list of the reptile type specimens preserved in the Museo Nacional de Ciencias Naturales (CSIC) of Madrid (updated until 15 July 2012) is provided. The collection houses a total of 319 type specimens representing 24 taxa belonging to 6 families and 12 genera. There are 22 taxa represented by primary types (19 holotypes, 2 neotypes and 1lectotype) and at least one paratype, and only two taxa are exclusively represented by one secondary type (paratype). The collection is specially rich in Spanish endemisms. Special attention is deserved by the type series of many subspecies of Podarcis lilfordi described by A. Salvador and V. Pdéez-Mellado. All type specimens are housed in the Herpetological collection except Blanus mariae and Psaimodroims occidentalis type series and Psammodroims hispanicus (neotype) which are preserved in the DNA/Tissues Collection.

Morphometric and molecular analyses of the sand fly species Lutzomyia shannoni (Diptera: Psychodidae: Phlebotominae) collected from seven different geographical areas in the southeastern United States.

PubMed

Florin, David A; Davies, Stephen J; Olsen, Cara; Lawyer, Phillip; Lipnick, Robert; Schultz, George; Rowton, Edgar; Wilkerson, Richard; Keep, Lisa

2011-03-01

A morphometric and molecular study of adult male and female Lutzomyia shannoni (Dyar 1929) collected at seven different locations within the southeastern United States was conducted to assess the degree of divergence between the grouped specimens from each location. The collection locations were as follows: Fort Bragg, NC; Fort Campbell, KY; Fort Rucker, AL; Ossabaw Island, GA; Patuxent National Wildlife Research Refuge, MD; Suwannee National Wildlife Refuge, FL; and Baton Rouge, LA. Forty males and forty females from each location were analyzed morphometrically from 54 and 49 character measurements, respectively. In addition, the molecular markers consisting of the partial cytochrome c oxidase subunit I (from 105 sand flies: 15 specimens/collection site) and the partial internal transcribed spacer 2 (from 42 sand flies: six specimens/collection site) were compared. Multivariate analyses indicate that the low degree of variation between the grouped specimens from each collection site prevents the separation of any collection site into an entity that could be interpreted as a distinct population. The molecular analyses were in concordance with the morphometric study as no collection location grouped into a separate population based on the two partial markers. The grouped specimens from each collection site appear to be within the normal variance of the species, indicating a single population in the southeast United States. It is recommended that additional character analyses of L. shannoni based on more molecular markers, behavioral, ecological, and physiological characteristics, be conducted before ruling out the possibility of populations or a cryptic species complex within the southeastern United States.

Monitoring cocaine use in substance-abuse-treatment patients by sweat and urine testing.

PubMed

Preston, K L; Huestis, M A; Wong, C J; Umbricht, A; Goldberger, B A; Cone, E J

1999-09-01

Sweat and urine specimens were collected from 44 methadone-maintenance patients to evaluate the use of sweat testing to monitor cocaine use. Paired sweat patches that were applied and removed weekly (on Tuesdays) were compared with 3-5 consecutive urine specimens collected Mondays, Wednesdays, and Fridays. All patches (N = 930) were extracted in 2.5 mL of solvent and analyzed by ELISA immunoassay (cutoff concentration 10 ng/mL); a subset of patches (N = 591) was also analyzed by gas chromatography-mass spectrometry (GC-MS) for cocaine, benzoylecgonine (BZE), and ecgonine methyl ester (EME) (cutoff concentration 5 ng/mL). Urine specimens were subjected to qualitative analysis by EMIT (cutoff 300 ng/mL) and subsets were analyzed by TDx (semiquantitative, LOD 30 ng/mL) and by GC-MS for cocaine (LOD 5 ng/mL). Results were evaluated to (1) determine the relative amounts of cocaine and its metabolites in sweat; (2) assess replicability in duplicate patches; (3) compare ELISA and GC-MS results for cocaine in sweat; and (4) compare the detection of cocaine use by sweat and urine testing. Cocaine was detected by GC-MS in 99% of ELISA-positive sweat patches; median concentrations of cocaine, BZE, and EME were 378, 78.7, and 74 ng/mL, respectively. Agreement in duplicate patches was approximately 90% by ELISA analysis. The sensitivity, specificity, and efficiency of sweat ELISA cocaine results as compared with sweat GC-MS results were 93.6%, 91.3%, and 93.2%, respectively. The sensitivity, specificity, and efficiency between ELISA sweat patch and EMIT urine results were 97.6%, 60.5%, and 77.7%, respectively. These results support the use of sweat patches for monitoring cocaine use, though further evaluation is needed.

HIV-1 infection using dried blood spots can be confirmed by Bio-Rad Geenius™ HIV 1/2 confirmatory assay.

PubMed

Fernández McPhee, Carolina; Álvarez, Patricia; Prieto, Luis; Obiang, Jacinta; Avedillo, Pedro; Vargas, Antonio; Rojo, Pablo; Abad, Carlota; Ramos, José Tomás; Holguín, Africa

2015-02-01

Confirmatory assays for HIV diagnosis are not well implemented in low-income countries with limited infrastructures. Geenius™ HIV 1/2 Confirmatory Assay is a single-use immunochromatographic test for the confirmation and differentiation of individual HIV-1/2 antibodies validated in venous whole blood, serum and plasma. However, dried blood specimens (DBS) are easier to collect, store and transport than plasma/serum in remote settings from limited resource countries and mobile populations. To evaluate the confirmatory assay Geenius™ HIV 1/2 for HIV diagnosis using DBS specimens. We collected DBS from 70 Guinean women previously diagnosed as HIV-1 infected by rapid tests using whole blood samples in Equatorial Guinea and from 25 HIV-negative Guinean women and HIV-exposed infants diagnosed by molecular testing in Madrid. Geenius HIV 1/2 was performed by eluting two drops of dried blood from each patient and following the manufacturer instructions for the assay but using 40μl of the eluted blood as specimen. The results obtained were confirmed by western blot. Geenius™ HIV 1/2 successfully confirmed the HIV-1 positive and negative infection in all tested DBS specimens, providing 100% specificity [95% Confidence Interval (CI): 86.2%-100%]. No HIV 1/2 coinfections were found in the study cohort. This is the first report that proves a good performance of Geenius™ HIV 1/2 for the HIV-1 infection confirmation using only two drops of dried blood. Our results approve the utility of this confirmatory assay using DBS when a lack of adequate infrastructure to collect, store or transport plasma/serum is found. DBS are a practical alternative to plasma/serum for HIV serological diagnosis. Copyright © 2015 Elsevier B.V. All rights reserved.

NASA Biological Specimen Repository

NASA Technical Reports Server (NTRS)

McMonigal, K. A.; Pietrzyk, R. A.; Sams, C. F.; Johnson, M. A.

2010-01-01

The NASA Biological Specimen Repository (NBSR) was established in 2006 to collect, process, preserve and distribute spaceflight-related biological specimens from long duration ISS astronauts. This repository provides unique opportunities to study longitudinal changes in human physiology spanning may missions. The NBSR collects blood and urine samples from all participating ISS crewmembers who have provided informed consent. These biological samples are collected once before flight, during flight scheduled on flight days 15, 30, 60, 120 and within 2 weeks of landing. Postflight sessions are conducted 3 and 30 days after landing. The number of in-flight sessions is dependent on the duration of the mission. Specimens are maintained under optimal storage conditions in a manner that will maximize their integrity and viability for future research The repository operates under the authority of the NASA/JSC Committee for the Protection of Human Subjects to support scientific discovery that contributes to our fundamental knowledge in the area of human physiological changes and adaptation to a microgravity environment. The NBSR will institute guidelines for the solicitation, review and sample distribution process through establishment of the NBSR Advisory Board. The Advisory Board will be composed of representatives of all participating space agencies to evaluate each request from investigators for use of the samples. This process will be consistent with ethical principles, protection of crewmember confidentiality, prevailing laws and regulations, intellectual property policies, and consent form language. Operations supporting the NBSR are scheduled to continue until the end of U.S. presence on the ISS. Sample distribution is proposed to begin with selections on investigations beginning in 2017. The availability of the NBSR will contribute to the body of knowledge about the diverse factors of spaceflight on human physiology.

Discrimination of Venezuelan spirituous beverages by a trace element-radial basis neural network approach.

PubMed

Hernández-Caraballo, Edwin A; Avila de Hernández, Rita M; Rivas-Echeverría, Francklin; Capote-Luna, Tarcisio

2008-01-15

Radial basis neural networks (RBNNs) were developed and evaluated for discrimination of specimens of 'aguardiente de Cocuy', a spirituous beverage produced in the northwestern region of Venezuela. The beverage is distilled from the must of Agave cocui Trelease in an artisanship fashion with little quality control. Forty specimens, with known concentrations of copper, iron, and zinc, were used in this study. The specimens were previously collected in various locations around Sucre Municipality (Falcón State) and Urdaneta Municipality (Lara State). The normalized concentrations of these elements served as indirect descriptors of origin (input data). They were presented to the neural networks through 1-3 input nodes in seven different combinations. In addition, two categories (two collection sites) and four categories (two collection sites+two manufacturing conditions) were designated as output data, in order to assess the impact of such selection on the discrimination performance. The overall performance of the four-category RBNNs was as follows (the input data is indicated in parentheses): (Cu-Fe)>(Cu-Zn)>(Cu)>(Zn)>(Fe-Zn)>(Cu-Fe-Zn)>(Fe). In this case, the highest percentage of correct hits was 82.5%. For the two-category RBNNs, the performance decreased as indicated below: (Cu)>(Cu-Fe)>(Cu-Zn)>(Fe-Zn)>(Zn) approximately (Cu-Fe-Zn)>(Fe). The reduction in the number of categories led to an increase in the discrimination performance of all the RBNNs, the best of which was 90.0%. The possibility of discriminating specimens of 'aguardiente de Cocuy' with such an accuracy, based on a single-element determination, is particularly attractive as it would result in a reduction of analysis' costs and laboratory's response time.

Usefulness of lavage cytology during endoscopic transpapillary catheterization into the gallbladder in the cytological diagnosis of gallbladder disease.

PubMed

Naito, Yoshiki; Okabe, Yoshinobu; Kawahara, Akihiko; Taira, Tomoki; Isida, Yusuke; Kaji, Ryouhei; Sata, Michio; Ureshino, Hiroki; Mikagi, Kazuhiro; Kinoshita, Hisafumi; Yasumoto, Makiko; Kusano, Hironori; Kage, Masayoshi; Yano, Hirohisa

2009-06-01

Many studies have reported methods of cell collection involving percutaneous transhepatic cholangiodrainage (PTCD) and fine-needle aspiration cytology for the diagnosis of gallbladder disease. However, few studies have described the use of a transpapillary approach, i.e., endoscopic transpapillary catheterization into the gallbladder (ETCG). In this study, we analyzed cells collected by ETCG to evaluate its usefulness in the cytological diagnosis of gallbladder disease. The subjects were 19 patients who had undergone ETCG for the diagnosis of gallbladder disease. Of these patients, 11 and 8 had gallbladder cancer and benign gallbladder disease, respectively. We also evaluated the diagnostic accuracy of PTCD cytology performed in 15 patients with gallbladder cancer.Specimens were cytologically diagnosed as normal or benign, indeterminate, suspected malignancy, malignant, and inadequate in 47% (9/19), 11% (2/19), 0% (0/19), 37% (7/19), and 5% (1/19) of patients, respectively. Specimens were diagnosed as malignant, indeterminate, normal or benign, and inadequate in 7, 2, 1, and 1, respectively, of the 11 patients diagnosed with gallbladder cancer. The sensitivity and specificity of ETCG cytology were 78 and 100%, respectively, whereas the diagnostic accuracy of PTCD cytology was 20% (3/15). None of the patients developed complications of ETCG. Despite its technical difficulty, ETCG for bile cytology allows the collection of adequate cell numbers from patients with benign disease or gallbladder cancer and facilitates a cytological diagnosis, making it a useful method for collecting cells. (c) 2009 Wiley-Liss, Inc.

49 CFR 40.193 - What happens when an employee does not provide a sufficient amount of urine for a drug test?

Code of Federal Regulations, 2010 CFR

2010-10-01

...) If the employee refuses to make the attempt to provide a new urine specimen or leaves the collection site before the collection process is complete, you must discontinue the collection, note the fact on... attempt to provide the specimen, you must discontinue the collection, note the fact on the “Remarks” line...

Improving the pathologic evaluation of lung cancer resection specimens.

PubMed

Osarogiagbon, Raymond U; Hilsenbeck, Holly L; Sales, Elizabeth W; Berry, Allen; Jarrett, Robert W; Giampapa, Christopher S; Finch-Cruz, Clara N; Spencer, David

2015-08-01

Accurate post-operative prognostication and management heavily depend on pathologic nodal stage. Patients with nodal metastasis benefit from post-operative adjuvant chemotherapy, those with mediastinal nodal involvement may also benefit from adjuvant radiation therapy. However, the quality of pathologic nodal staging varies significantly, with major survival implications in large populations of patients. We describe the quality gap in pathologic nodal staging, and provide evidence of its potential reversibility by targeted corrective interventions. One intervention, designed to improve the surgical lymphadenectomy, specimen labeling, and secure transfer between the operating theatre and the pathology laboratory, involves use of pre-labeled specimen collection kits. Another intervention involves application of an improved method of gross dissection of lung resection specimens, to reduce the inadvertent loss of intrapulmonary lymph nodes to histologic examination for metastasis. These corrective interventions are the subject of a regional dissemination and implementation project in diverse healthcare systems in a tri-state region of the United States with some of the highest lung cancer incidence and mortality rates. We discuss the potential of these interventions to significantly improve the accuracy of pathologic nodal staging, risk stratification, and the quality of specimens available for development of stage-independent prognostic markers in lung cancer.

Reliability of the Xpert HPV assay to detect high-risk human papillomavirus DNA in a colposcopy referral population.

PubMed

Castle, Philip E; Smith, Katherine M; Davis, Thomas E; Schmeler, Kathleen M; Ferris, Daron G; Savage, Ashlyn H; Gray, Jermaine E; Stoler, Mark H; Wright, Thomas C; Ferenczy, Alex; Einstein, Mark H

2015-01-01

The Xpert HPV Assay (Xpert; Cepheid, Sunnyvale, CA) was developed for the multianalytic GeneXpert platform. In a colposcopy referral population of 708 women living in the United States, two cervical specimens, A and B, were collected, and both were tested by the Xpert assay for high-risk human papillomavirus (hrHPV) DNA, permitting an evaluation of its test reliability. Specimen B was also tested by Hybrid Capture 2 (hc2; Qiagen, Germantown, MD) and the cobas HPV Test (cobas; Roche Molecular Systems, Pleasanton, CA). The κ and percent agreement for any hrHPV for the two Xpert results were 0.88 and 94.5%, respectively. There was no statistical difference in testing positive on both specimens by Xpert (P = .62). The sensitivity for detection of cervical intraepithelial neoplasia grade 2 or more severe (CIN2+) was 89.0% using specimen A and 90.4% using specimen B for Xpert, 90.4% for cobas, and 81.6% for hc2. The Xpert assay was sensitive and reliable for the detection of hrHPV and the identification of women with CIN2+. Copyright© by the American Society for Clinical Pathology.

High degree of mitochondrial gene heterogeneity in the bat tick species Ixodes vespertilionis, I. ariadnae and I. simplex from Eurasia.

PubMed

Hornok, Sándor; Estrada-Peña, Agustín; Kontschán, Jenő; Plantard, Olivier; Kunz, Bernd; Mihalca, Andrei D; Thabah, Adora; Tomanović, Snežana; Burazerović, Jelena; Takács, Nóra; Görföl, Tamás; Estók, Péter; Tu, Vuong Tan; Szőke, Krisztina; Fernández de Mera, Isabel G; de la Fuente, José; Takahashi, Mamoru; Yamauchi, Takeo; Takano, Ai

2015-09-17

Phylogeographical studies allow precise genetic comparison of specimens, which were collected over large geographical ranges and belong to the same or closely related animal species. These methods have also been used to compare ticks of veterinary-medical importance. However, relevant data are missing in the case of ixodid ticks of bats, despite (1) the vast geographical range of both Ixodes vespertilionis and Ixodes simplex, and (2) the considerable uncertainty in their taxonomy, which is currently unresolvable by morphological clues. In the present study 21 ticks were selected from collections or were freshly removed from bats or cave walls in six European and four Asian countries. The DNA was extracted and PCRs were performed to amplify part of the cytochrome oxidase I (COI), 16S and 12S rDNA genes, followed by sequencing for identification and molecular-phylogenetic comparison. No morphological differences were observed between Ixodes vespertilionis specimens from Spain and from other parts of Europe, but corresponding genotypes had only 94.6 % COI sequence identity. An I. vespertilionis specimen collected in Vietnam was different both morphologically and genetically (i.e. with only 84.1 % COI sequence identity in comparison with I. vespertilionis from Europe). Two ticks (collected in Vietnam and in Japan) formed a monophyletic clade and shared morphological features with I. ariadnae, recently described and hitherto only reported in Europe. In addition, two Asiatic specimens of I. simplex were shown to differ markedly from European genotypes of the same species. Phylogenetic relationships of ticks showed similar clustering patterns with those of their associated bat host species. Although all three ixodid bat tick species evaluated in the present study appear to be widespread in Eurasia, they exhibit pronounced genetic differences. Data of this study also reflect that I. vespertilionis may represent a species complex.

An Analysis of Factors Affecting Genotyping Success from Museum Specimens Reveals an Increase of Genetic and Morphological Variation during a Historical Range Expansion of a European Spider.

PubMed

Krehenwinkel, Henrik; Pekar, Stano

2015-01-01

Natural history collections house an enormous amount of plant and animal specimens, which constitute a promising source for molecular analyses. Storage conditions differ among taxa and can have a dramatic effect on the success of DNA work. Here, we analyze the feasibility of DNA extraction from ethanol preserved spiders (Araneae). We tested genotyping success using several hundred specimens of the wasp spider, Argiope bruennichi, deposited in two large German natural history collections. We tested the influence of different factors on the utility of specimens for genotyping. Our results show that not the specimen's age, but the museum collection is a major predictor of genotyping success. These results indicate that long term storage conditions should be optimized in natural history museums to assure the utility of collections for DNA work. Using historical material, we also traced historical genetic and morphological variation in the course of a poleward range expansion of A. bruennichi by comparing contemporary and historical specimens from a native and an invasive population in Germany. We show that the invasion of A. bruennichi is tightly correlated with an historical increase of genetic and phenotypic variation in the invasive population.

Digital Management and Curation of the National Rock and Ore Collections at NMNH, Smithsonian

NASA Astrophysics Data System (ADS)

Cottrell, E.; Andrews, B.; Sorensen, S. S.; Hale, L. J.

2011-12-01

The National Museum of Natural History, Smithsonian Institution, is home to the world's largest curated rock collection. The collection houses 160,680 physical rock and ore specimen lots ("samples"), all of which already have a digital record that can be accessed by the public through a searchable web interface (http://collections.mnh.si.edu/search/ms/). In addition, there are 66 accessions pending that when catalogued will add approximately 60,000 specimen lots. NMNH's collections are digitally managed on the KE EMu° platform which has emerged as the premier system for managing collections in natural history museums worldwide. In 2010 the Smithsonian released an ambitious 5 year Digitization Strategic Plan. In Mineral Sciences, new digitization efforts in the next five years will focus on integrating various digital resources for volcanic specimens. EMu sample records will link to the corresponding records for physical eruption information housed within the database of Smithsonian's Global Volcanism Program (GVP). Linkages are also planned between our digital records and geochemical databases (like EarthChem or PetDB) maintained by third parties. We anticipate that these linkages will increase the use of NMNH collections as well as engender new scholarly directions for research. Another large project the museum is currently undertaking involves the integration of the functionality of in-house designed Transaction Management software with the EMu database. This will allow access to the details (borrower, quantity, date, and purpose) of all loans of a given specimen through its catalogue record. We hope this will enable cross-referencing and fertilization of research ideas while avoiding duplicate efforts. While these digitization efforts are critical, we propose that the greatest challenge to sample curation is not posed by digitization and that a global sample registry alone will not ensure that samples are available for reuse. We suggest instead that the ability of the Earth science community to identify and preserve important collections and make them available for future study is limited by personnel and space resources from the level of the individual PI to the level of national facilities. Moreover, when it comes to specimen "estate planning," the cultural attitudes of scientists, institutions, and funding agencies are often inadequate to provide for long-term specimen curation - even if specimen discovery is enabled by digital registry. Timely access to curated samples requires that adequate resources be devoted to the physical care of specimens (facilities) and to the personnel costs associated with curation - from the conservation, storage, and inventory management of specimens, to the dispersal of samples for research, education, and exhibition.

Catalog of type specimens of recent mammals: Orders Carnivora, Perissodactyla, Artiodactyla, and Cetacea in the National Museum of Natural History, Smithsonian Institution

USGS Publications Warehouse

Fisher, Robert D.; Ludwig, Craig A.

2016-01-01

The type collection of Recent mammals in the Division of Mammals, National Museum of Natural History, Smithsonian Institution, contains 612 specimens bearing names of 604 species-group taxa of Carnivora, Perissodactyla, Artiodactyla, and Cetacea as of May 2016. This catalog presents an annotated list of these holdings comprising 582 holotypes; 16 lectotypes, two of which are newly designated herein; 7 syntypes (15 specimens); and 1 neotype. Included are several specimens that should be in the collection but cannot be found or are now known to be in other collections and therefore are not in the database. Thirty-seven of the names are new since the last type catalog covering these orders, Arthur J. Poole and Viola S. Schantz’s 1942 “Catalog of the Type Specimens of Mammals in the United States National Museum, Including the Biological Surveys Collection” (Bulletin of the United States National Museum, 178). One of these, Lutra iowa Goldman, 1941, was transferred to the National Museum’s Paleobiology Department collection and is mentioned only briefly in this work. Orders and families are arranged systematically following D. E. Wilson and D. M. Reeder’s 2005 Mammal Species of the World: A Taxonomic and Geographic Reference, third edition, volume 1; within families, currently recognized genera are arranged alphabetically, and within each currently recognized genus, species and subspecies accounts are arranged alphabetically by original published name. Information in each account includes original name and abbreviated citation thereto, current name if other than original, citation for first use of current name combination for the taxon, type designation, U.S. National Museum catalog number(s), preparation, age and sex, date of collection and collector, original collector number, type locality, and remarks as appropriate. Digital photographs of each specimen will serve as a condition report and will be attached to each electronic specimen record. An addendum contains two accounts for holotypes added to the collection subsequent to the publication of the catalog for their taxa. Appendices tabulate summary data for all four of our recent type catalogs (Fisher and Ludwig, 2012, 2014, 2015, and this volume) and include authors of names, collectors of type specimens, countries, islands, and provinces or states in which type specimens were collected, numbers of new names per decade, and summary numbers for holotypes, lectotypes, syntypes, neotypes, and new taxa since the last type catalog (Poole and Schantz, 1942) covering the entire type collection.

Structured pathology reporting improves the macroscopic assessment of rectal tumour resection specimens.

PubMed

King, Simon; Dimech, Margaret; Johnstone, Susan

2016-06-01

We examined whether introduction of a structured macroscopic reporting template for rectal tumour resection specimens improved the completeness and efficiency in collecting key macroscopic data elements. Fifty free text (narrative) macroscopic reports retrieved from 2012 to 2014 were compared with 50 structured macroscopic reports from 2013 to 2015, all of which were generated at John Hunter Hospital, Newcastle, NSW. The six standard macroscopic data elements examined in this study were reported in all 50 anatomical pathology reports using a structured macroscopic reporting dictation template. Free text reports demonstrated significantly impaired data collection when recording intactness of mesorectum (p<0.001), relationship to anterior peritoneal reflection (p=0.028) and distance of tumour to the non-peritonealised circumferential margin (p<0.001). The number of words used was also significantly (p<0.001) reduced using pre-formatted structured reports compared to free text reports. The introduction of a structured reporting dictation template improves data collection and may reduce the subsequent administrative burden when macroscopically evaluating rectal resections. Copyright © 2016 Royal College of Pathologists of Australasia. Published by Elsevier B.V. All rights reserved.

Development and Clinical Evaluation of a Recombinant-Antigen-Based Cytomegalovirus Immunoglobulin M Automated Immunoassay Using the Abbott AxSYM Analyzer

PubMed Central

Maine, G. T.; Stricker, R.; Schuler, M.; Spesard, J.; Brojanac, S.; Iriarte, B.; Herwig, K.; Gramins, T.; Combs, B.; Wise, J.; Simmons, H.; Gram, T.; Lonze, J.; Ruzicki, D.; Byrne, B.; Clifton, J. D.; Chovan, L. E.; Wachta, D.; Holas, C.; Wang, D.; Wilson, T.; Tomazic-Allen, S.; Clements, M. A.; Wright, G. L.; Lazzarotto, T.; Ripalti, A.; Landini, M. P.

2000-01-01

A new microparticle enzyme immunoassay (MEIA), the Cytomegalovirus (CMV) Immunoglobulin M (IgM) test, was developed on the Abbott AxSYM analyzer. This test uses recombinant CMV antigens derived from portions of four structural and nonstructural proteins of CMV: pUL32 (pp150), pUL44 (pp52), pUL83 (pp65), and pUL80a (pp38). A total of 1,608 specimens from random volunteer blood donors (n = 300), pregnant women (n = 1,118), transplant recipients (n = 6), and patients with various clinical conditions and disease states (n = 184) were tested during development and evaluation of this new assay. In a preliminary clinical evaluation we tested specimens collected prospectively from pregnant women (n = 799) and selected CMV IgM-positive archived specimens from pregnant women (n = 39). The results from the new CMV IgM immunoassay were compared to the results of a consensus interpretation of the results obtained with three commercial CMV IgM immunoassays. The results for specimens with discordant results were resolved by a CMV IgM immunoblot assay. The relative sensitivity, specificity, and agreement for the AxSYM CMV IgM assay were 94.29, 96.28, and 96.19%, respectively, and the resolved sensitivity, specificity, and agreement were 95.83, 97.47, and 97.37%, respectively. We also tested serial specimens from women who experienced seroconversion or a recent CMV infection during gestation (n = 17) and potentially cross-reactive specimens negative for CMV IgM antibody by the consensus tests (n = 184). The AxSYM CMV IgM assay was very sensitive for the detection of CMV IgM during primary CMV infection, as shown by the detection of CMV IgM at the same time as or just prior to the detection of CMV IgG. Specimens from individuals with lupus (n = 16) or parvovirus B19 infection (n = 6) or specimens containing hyper IgM (n = 9), hyper IgG (n = 8), or rheumatoid factor (n = 55) did not cross-react with the AxSYM assay. One specimen each from individuals infected with Epstein-Barr virus (n = 26), measles virus (n = 10), herpes simplex virus (n = 12), or varicella-zoster virus (n = 13) infection, one specimen from an influenza vaccinee (n = 14), and one specimen containing antinuclear antibody cross-reacted with the assay. The overall rate of cross-reactivity of the specimens with the assay was 3.3% (6 of 184). The AxSYM CMV IgM assay is a sensitive and specific assay for the detection of CMV-specific IgM. PMID:10747129

Wildlife species, Ixodid fauna and new host records for ticks in an Amazon forest area, Rondônia, Brazil.

PubMed

Zimmermann, Namor Pinheiro; Aguirre, André de Abreu Rangel; Rodrigues, Vinicius da Silva; Garcia, Marcos Valério; Medeiros, Jansen Fernandes; Blecha, Isabella Maiumi Zaidan; Duarte, Pamella Oliveira; Cruz, Breno Cayeiro; Cunha, Rodrigo Casquero; Martins, Thiago Fernandes; Andreotti, Renato

2018-01-01

The objective of this work was to evaluate the diversity of ticks associated with free-living animals and to investigate new host records for ticks. Ticks were collected from animals rescued during the flood of the Jamari River in the municipality of Ariquemes, state of Rondônia, North Region of Brazil. A total of 39 animals were captured, out of which 10 were amphibians, 19 were reptiles and 10 were mammals. A total of 127 ticks of the Amblyomma genus were collected from these animals, distributed among seven species: Amblyomma dissimile, Amblyomma geayi, Amblyomma humerale , Amblyomma longirostre, Amblyomma nodosum , Amblyomma rotundatum and Amblyomma varium. In addition, one specimen of Rhipicephalus (Boophilus) microplus was collected. Among these specimens, 85 were adults and 42 were nymphs, with A. rotundatum being the most prevalent species. An Amblyomma spp. larvae was also collected from a lizard (Uranoscodon superciliosus), and one Amblyomma calcaratum and one Amblyomma dubitatum were recovered from the environment, thus totaling 130 ticks. Among the Ixodidae collected from different hosts, we provide the first report for the species A. rotundatum parasitizing Rhinella major, U. superciliosus, Leptophis ahaetulla, Chironius multiventris, and Mastigodryas boddaerti, as well as of A. humerale parasitizing U. superciliosus, A. geayi parasitizing Choloepus didactylus, and Rhipicephalus (B.) microplus parasitizing Alouatta puruensis.

Evaluation of five enzyme immunoassays compared with the cytotoxicity assay for diagnosis of Clostridium difficile-associated diarrhea in dogs.

PubMed

Chouicha, Nadira; Marks, Stanley L

2006-03-01

Clostridium difficile-associated-diarrhea (CDAD) is a nosocomial infection in dogs. Diagnosis of this infection is dependent on clinical signs of disease supported by laboratory detection of C. difficile toxins A or B, or both, in fecal specimens via enzyme-linked immunosorbent assay (ELISA). Unfortunately, to the authors' knowledge, commercially available ELISAs have not been validated in dogs to date. We evaluated 5 ELISAs done on 143 canine fecal specimens (100 diarrheic and 43 nondiarrheic dogs) and on 29 C. difficile isolates. The results of each ELISA were compared with the cytotoxin B tissue culture assay (CTA). Clostridium difficile was isolated from 23% of the fecal specimens. Eighteen of the 143 fecal specimens were toxin positive (15 diarrheic and 3 nondiarrheic dogs). On the basis of multiplex polymerase chain reaction (PCR) analysis for toxin-A and -B genes, 72% of the isolates were toxigenic. The carriage rate of toxigenic isolates in diarrheic dogs was higher than that in the nondiarrheic dogs; however, these differences were not statistically significant. A good correlation was found between CTA, PCR, and culture results. The ELISAs done on fecal specimens collected from diarrheic dogs had low sensitivity (7-33%). In contrast, ELISA for toxin A or B, or both, performed on toxigenic isolates had high sensitivity (93%). These results suggest that commercially available human ELISAs are inadequate for the diagnosis of canine C. difficile-associated diarrhea when tested on fecal specimens. In contrast, the Premier ToxinA/B and Techlab ToxinA/B ELISAs may be useful for the diagnosis of canine CDAD when used on toxigenic isolates.

Standard Operating Procedures, ethical and legal regulations in BTB (Brain/Tissue/Bio) banking: what is still missing?

PubMed

Ravid, Rivka

2008-09-01

The use of human biological specimens in scientific research is the focus of current international public and professional concern and a major issue in bioethics in general. Brain/Tissue/Bio banks (BTB-banks) are a rapid developing sector; each of these banks acts locally as a steering unit for the establishment of the local Standard Operating Procedures (SOPs) and the legal regulations and ethical guidelines to be followed in the procurement and dissemination of research specimens. An appropriat Code of Conduct is crucial to a successful operation of the banks and the research application they handle. What are we still missing ? (1) Adequate funding for research BTB-banks. (2) Standard evaluation protocls for audit of BTB-bank performance. (3) Internationally accepted SOP's which will facilitate exchange and sharing of specimens and data with the scientific community. (4) Internationally accepted Code of Conduct. In the present paper we review the most pressing organizational, methodological, medico-legal and ethical issues involved in BTB-banking; funding, auditing, procurement, management/handling, dissemination and sharing of specimens, confidentiality and data protection, genetic testing, "financial gain" and safety measures. Taking into consideration the huge variety of the specimens stored in different repositories and the enormous differences in medico-legal systems and ethics regulations in different countries it is strongly recommend that the health-care systems and institutions who host BTB-Banks will put more efforts in getting adequate funding for the infrastructure and daily activities. The BTB-banks should define evaluation protocols, SOPs and their Code of Conduct. This in turn will enable the banks to share the collected specimens and data with the largest possible number of researchers and aim at a maximal scientific spin-off and advance in public health research.

Evaluation of RIDA®GENE norovirus GI/GII real time RT-PCR using stool specimens collected from children and adults with acute gastroenteritis.

PubMed

Kanwar, N; Hassan, F; Barclay, L; Langley, C; Vinjé, J; Bryant, P W; George, K St; Mosher, L; Matthews-Greer, J M; Rocha, M A; Beenhouwer, D O; Harrison, C J; Moffatt, M; Shastri, N; Selvarangan, R

2018-04-10

Norovirus is the leading cause of epidemic and sporadic acute gastroenteritis (AGE) in the United States. Widespread prevalence necessitates implementation of accurate norovirus detection assays in clinical diagnostic laboratories. To evaluate RIDA ® GENE norovirus GI/GII real-time RT-PCR assay (RGN RT-PCR) using stool samples from patients with sporadic AGE. Patients between 14 days to 101 years of age with symptoms of AGE were enrolled prospectively at four sites across the United States during 2014-2015. Stool specimens were screened for the presence of norovirus RNA by the RGN RT-PCR assay. Results were compared with a reference method that included conventional RT-PCR and sequencing of a partial region of the 5'end of the norovirus ORF2 gene. A total of 259 (36.0%) of 719 specimens tested positive for norovirus by the reference method. The RGN RT-PCR assay detected norovirus in 244 (94%) of these 259 norovirus positive specimens. The sensitivity and specificity (95% confidence interval) of the RGN RT-PCR assay for detecting norovirus genogroup (G) I was 82.8% (63.5-93.5) and 99.1% (98.0-99.6) and for GII was 94.8% (90.8-97.2) and 98.6% (96.9-99.4), respectively. Seven specimens tested positive by the RGN-RT PCR that were negative by the reference method. The fifteen false negative samples were typed as GII.4 Sydney, GII.13, GI.3, GI.5, GI.2, GII.1, and GII.3 in the reference method. The RGN RT-PCR assay had a high sensitivity and specificity for the detection of norovirus in stool specimens from patients with sporadic AGE. Copyright © 2018. Published by Elsevier B.V.

High-Performance X-ray Detection in a New Analytical Electron Microscope

NASA Technical Reports Server (NTRS)

Lyman, C. E.; Goldstein, J. I.; Williams, D. B.; Ackland, D. W.; vonHarrach, S.; Nicholls, A. W.; Statham, P. J.

1994-01-01

X-ray detection by energy-dispersive spectrometry in the analytical electron microscope (AEM) is often limited by low collected X-ray intensity (P), modest peak-to-background (P/B) ratios, and limitations on total counting time (tau) due to specimen drift and contamination. A new AFM has been designed with maximization of P. P/B, and tau as the primary considerations. Maximization of P has been accomplished by employing a field-emission electron gun, X-ray detectors with high collection angles, high-speed beam blanking to allow only one photon into the detector at a time, and simultaneous collection from two detectors. P/B has been maximized by reducing extraneous background signals generated at the specimen holder, the polepieces and the detector collimator. The maximum practical tau has been increased by reducing specimen contamination and employing electronic drift correction. Performance improvments have been measured using the NIST standard Cr thin film. The 0-3 steradian solid angle of X-ray collection is the highest value available. The beam blanking scheme for X-ray detection provides 3-4 times greater throughput of X-rays at high count rates into a recorded spectrum than normal systems employing pulse-pileup rejection circuits. Simultaneous X-ray collection from two detectors allows the highest X-ray intensity yet recorded to be collected from the NIST Cr thin film. The measured P/B of 6300 is the highest level recorded for an AEM. In addition to collected X-ray intensity (cps/nA) and P/B measured on the standard Cr film, the product of these can be used as a figure-of-merit to evaluate instruments. Estimated minimum mass fraction (MMF) for Cr measured on the standard NIST Cr thin film is also proposed as a figure-of-merit for comparing X-ray detection in AEMs. Determinations here of the MMF of Cr detectable show at least a threefold improvement over previous instruments.

Harvestmen of the BOS Arthropod Collection of the University of Oviedo (Spain) (Arachnida, Opiliones)

PubMed Central

Merino-Sáinz, Izaskun; Anadón, Araceli; Torralba-Burrial, Antonio

2013-01-01

Abstract There are significant gaps in accessible knowledge about the distribution and phenology of Iberian harvestmen (Arachnida: Opiliones). Harvestmen accessible datasets in Iberian Peninsula are unknown, an only two other datasets available in GBIF are composed exclusively of harvestmen records. Moreover, only a few harvestmen data from Iberian Peninsula are available in GBIF network (or in any network that allows public retrieval or use these data). This paper describes the data associated with the Opiliones kept in the BOS Arthropod Collection of the University of Oviedo, Spain (hosted in the Department of Biología de Organismos y Sistemas), filling some of those gaps. The specimens were mainly collected from the northern third of the Iberian Peninsula. The earliest specimen deposited in the collection, dating back to the early 20th century, belongs to the P. Franganillo Collection. The dataset documents the collection of 16,455 specimens, preserved in 3,772 vials. Approximately 38% of the specimens belong to the family Sclerosomatidae, and 26% to Phalangidae; six other families with fewer specimens are also included. Data quality control was incorporated at several steps of digitisation process to facilitate reuse and improve accuracy. The complete dataset is also provided in Darwin Core Archive format, allowing public retrieval, use and combination with other biological, biodiversity of geographical variables datasets. PMID:24146596

Building a Zoological Teaching Collection of Invertebrates Using Alcoholic Gel

ERIC Educational Resources Information Center

Mugnai, Riccardo; Barbosa, Julio Vianna; Baptista, Darcilio Fernandes

2012-01-01

Teaching collections are of great importance for science instruction at any level. There are several problems linked to the handling and curatorial management of this kind of collection. Among these is the relatively short life-span of specimens, due to the damage from continuous handling by students. Often the specimens used to replenish the…

Self-Collected Nasal Swabs for Respiratory Virus Surveillance

PubMed Central

Jackson, Michael L.; Nguyen, Matthew; Kirlin, Beth; Madziwa, Lawrence

2015-01-01

We tested whether 135 patients reporting acute respiratory illness (ARI) could self-collect nasal swab specimens and ship them for laboratory testing. Most subjects (78.2%) collected and shipped their specimens without errors; 10.5% excluded ≥1 packing components; 12.9% made ≥1 packing errors. Self-swabbing at home is feasible for confirming ARI etiology. PMID:26613095

Search for biological specimens from midwestern parks: pitfalls and solutions

USGS Publications Warehouse

Bennett, J.P.

2001-01-01

This paper describes the results of searches of herbarium and museum collections and databases for records of vertebrate and vascular plant specimens that had been collected in 15 midwestern National Park System units. The records of these specimens were previously unknown to the National Park Service (NPS). In the course of our searches, numerous obstacles were encountered that prevented us from fully completing our task. These ranged from difficulties with the way databases are structured, to poor record-keeping, to incomplete or incorrect information on the actual location of specimens within collections. Despite these problems, we are convinced that the information to be gained from such searches in invaluable, and we believe that our experience, and the recommendations we offer, may well prove instructive to others undertaking this kind of work.

A snail in the long tail: a new Plekocheilus species collected by the ‘Comisión Científica del Pacífico’ (Mollusca, Gastropoda, Amphibulimidae)

PubMed Central

Breure, Abraham S. H.; Araujo, Rafael

2015-01-01

Abstract Among the historical collection gathered by the ‘Comisión Científica del Pacífico’ during 1862–1865, type material was found of one of the species described on the basis of the material collected shortly afterwards. Inspection of the types revealed that only one specimen may be considered as type material of Bulimus aristaceus Crosse, 1869; this specimen is now designated as the lectotype. The other specimens are described as a new species, Plekocheilus (Plekocheilus) cecepeus. PMID:26312021

Drug Resistance and R Factors in the Bowel Bacteria of London Patients before and after Admission to Hospital

PubMed Central

Datta, Naomi

1969-01-01

The content of drug-resistant coliform bacteria in faecal specimens collected before admission from patients awaiting non-urgent surgery were compared with specimens collected in hospital. Resistant strains of Escherichia coli were isolated from 52% of preadmission specimens and were present in large numbers in 28%. Tetracycline, sulphonamide, and streptomycin resistance were commonest: 60% of resistant strains carried transmissible R factors and multiple resistance was commoner than single. No characteristically resistant intestinal bacteria of any genera were found in hospital specimens as compared with those from outside. PMID:4976456

Public biobanks: calculation and recovery of costs.

PubMed

Clément, Bruno; Yuille, Martin; Zaltoukal, Kurt; Wichmann, Heinz-Erich; Anton, Gabriele; Parodi, Barbara; Kozera, Lukasz; Bréchot, Christian; Hofman, Paul; Dagher, Georges

2014-11-05

A calculation grid developed by an international expert group was tested across biobanks in six countries to evaluate costs for collections of various types of biospecimens. The assessment yielded a tool for setting specimen-access prices that were transparently related to biobank costs, and the tool was applied across three models of collaborative partnership. Copyright © 2014, American Association for the Advancement of Science.

The Yale Peabody Museum Mineral Collection: Past, Present, and Future

NASA Astrophysics Data System (ADS)

Nicolescu, S.; Ague, J.

2012-12-01

The beginnings of what became the Yale Peabody Museum (YPM) mineral collection are intimately associated with the emergence of science teaching and scientific research in the US. In 1802 Yale College graduate Benjamin Silliman was offered the first Yale "Chymistry" and Natural History professorship. In order to fulfill his academic duties he needed a mineral collection, but in 1802 only a few specimens were available to him. Through his determined efforts and with the critical support of two Yale College presidents, by 1825 Yale was in possession of what was arguably the best mineral collection in the US. The quality of the scientific education pioneered by Silliman attracted many bright students, including future pillars of 19th century science J. D. Dana, O. C. Marsh and G. J. Brush. Silliman was also the founder of an illustrious mineralogical "dynasty", members of which, starting with his son-in-law J. D. Dana and continuing with son, B. Silliman, Jr. and grandson E. S. Dana, contributed in seminal ways to the development of mineralogy. Having access to specimens collected by the Sillimans, or the many ones described in successive editions of Dana's System of Mineralogy, is a rare privilege. The YPM was founded in 1866 and the mineral collection started by Silliman became part of it. The collection has now grown to some 40,000 specimens, at least 38 of which are type minerals (roughly one percent of all presently known mineral species). Any collection is a valuable asset only if it is "alive" through use and development; hence, further enhancing the holdings of the YPM mineral collection is a continuing effort. Preservation of historic and scientifically relevant specimens is only one of many purposes served by the collection. An important intellectual value resides in the fact that many specimens are from localities lost to anthropogenic activities. The REE and U-Th bearing pegmatites at Barringer Hill, TX are such an example. Barringer Hill has been under the waters of Lake Buchanan since 1938. However, a significant mineral suite collected in the late 1800s/early 1900s is preserved in the YPM. The same holds true for mineral specimens from localities on Manhattan Island, NY, lost to urban development over the last 100 plus years, and many other US and world localities. Following the tradition instilled by Silliman, the specimens of the YPM mineral collection are actively used for undergraduate and graduate teaching in a large spectrum of Yale classes in several disciplines, ranging from Geology to Art and Architecture. Yale graduate and post-graduate students, as well as faculty and research personnel, are actively using collection material for research. Moreover, ongoing US and international projects are making use of YPM mineral specimens either for refining or redefining mineral chemical and structural data. In line with this last line of research, one of our future projects is the in-depth investigation of the type mineral specimens in the collection using state-of-the-art analytical techniques. The Petrology Collection, which also dates back to the 19th century, was recently acquired from the Yale Department of Geology and Geophysics and will be the focus of future research projects as well.

Investigation of solidification in zero-gravity environment; M553 sphere forming experiment. Phase C: Evaluation of Skylab specimens. [physical and mechanical properties of metal spheres formed under weightless conditions

NASA Technical Reports Server (NTRS)

Kattamis, T. Z.

1973-01-01

Results on specimen evaluation and discussion of solidification behavior in each case are reported in the following order: (1) specimen SL-1.6, (2) specimen SL-2.8, (3) specimen SL-2.4, (4) specimen SL-1.10 and (5) specimen SL-1.11. Comparison is made with ground-processed specimens of similar composition, whenever pertinent and meaningful. Among the nondestructive evaluation methods the measurement of sphericity was conducted by micrometric and shadowgraphic techniques. The intricate shape of specimens in some cases appeared difficult to define. In measuring the density, liquid penetration inside cavities that outcrop on the surface was avoided by sealing off these cavities. Among the destructive evaluation methods the use of the Quantimet 720 required particular attention, because of the small difference in contrast between second phases and micropores. With regard to microporosity microvoids in the core of some specimens were so fine that X-ray microradiography had to be used.

Performance of self-collected cervical samples in screening for future precancer using human papillomavirus DNA testing.

PubMed

Porras, Carolina; Hildesheim, Allan; González, Paula; Schiffman, Mark; Rodríguez, Ana Cecilia; Wacholder, Sholom; Jiménez, Silvia; Quint, Wim; Guillen, Diego; Kreimer, Aimée R; Herrero, Rolando

2015-01-01

Self-collected human papillomavirus (HPV) testing could reduce barriers to cervical cancer screening, with performance comparable to clinician-collected specimens. The ability of self-collected specimens to cross-sectionally and prospectively detect precursor lesions was investigated in an HPV vaccine randomized trial in Costa Rica. In the trial, 7466 women age 18 to 25 years received an HPV16/18 or control vaccine and were followed at least annually for four years. In this secondary analysis, we included all women who provided a self-collected cervicovaginal specimen six months after enrollment (5109 women = full analytical cohort). A subset (615 women = restricted cohort) also had clinician-collected specimens at the six-month postenrollment visit. High-grade squamous intraepithelial lesion or repeat low-grade squamous intraepithelial lesion prompted colposcopic referral throughout the study. HPV testing was performed with SPF10PCR/DEIA/LiPA25. Cross-sectional and prospective sensitivity, specificity, and predictive values were estimated. In the full cohort, one-time HPV testing on self-collected samples detected prevalent CIN2+ with a sensitivity of 88.7% (95% confidence interval [CI] =77.0% to 95.7%) and a specificity of 68.9% (95% CI = 67.6% to 70.1%). For predicting incident CIN2+ in the subsequent four years, sensitivity was 73.9% (95% CI = 65.8% to 81.0%) and specificity 69.4% (95% CI = 68.1% to 70.7%). In the restricted cohort, for incident CIN2+, self-collected HPV was much more sensitive than cytology (80.0% vs 10.0%); relative sensitivity was 0.1 (95% CI = 0.03% to 0.5%). Furthermore, three times more women with normal baseline cytology developed incident CIN2+ than those with negative self-collected HPV. Self-collected and clinician-collected HPV testing had comparable performance. Agreement between self- and clinician-collected samples was 89.7% (kappa = 0.78, McNemar χ2 = 0.62) for carcinogenic HPV types. Self-collected specimens can be used for HPV-based screening, providing sensitivity and specificity comparable with clinician-collected specimens and detecting disease earlier than cytology. © The Author 2014. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

Collection of biological samples in forensic toxicology.

PubMed

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

2010-09-01

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

NASA Biological Specimen Repository

NASA Technical Reports Server (NTRS)

Pietrzyk, Robert; McMonigal, K. A.; Sams, C. F.; Johnson, M. A.

2009-01-01

The NASA Biological Specimen Repository (NBSR) has been established to collect, process, annotate, store, and distribute specimens under the authority of the NASA/JSC Committee for the Protection of Human Subjects. The International Space Station (ISS) provides a platform to investigate the effects of microgravity on human physiology prior to lunar and exploration class missions. The NBSR is a secure controlled storage facility that is used to maintain biological specimens over extended periods of time, under well-controlled conditions, for future use in approved human spaceflight-related research protocols. The repository supports the Human Research Program, which is charged with identifying and investigating physiological changes that occur during human spaceflight, and developing and implementing effective countermeasures when necessary. The storage of crewmember samples from many different ISS flights in a single repository will be a valuable resource with which researchers can validate clinical hypotheses, study space-flight related changes, and investigate physiological markers All samples collected require written informed consent from each long duration crewmember. The NBSR collects blood and urine samples from all participating long duration ISS crewmembers. These biological samples are collected pre-flight at approximately 45 days prior to launch, during flight on flight days 15, 30, 60 120 and within 2 weeks of landing. Postflight sessions are conducted 3 and 30 days following landing. The number of inflight sessions is dependent on the duration of the mission. Operations began in 2007 and as of October 2009, 23 USOS crewmembers have completed or agreed to participate in this project. As currently planned, these human biological samples will be collected from crewmembers covering multiple ISS missions until the end of U.S. presence on the ISS or 2017. The NBSR will establish guidelines for sample distribution that are consistent with ethical principles, protection of crewmember confidentiality, prevailing laws and regulations, intellectual property policies, and consent form language. A NBSR Advisory Board composed of representatives of all participating agencies will be established to evaluate each request by an investigator for use of the samples to ensure the request reflects the mission of the NBSR.

SPORE/EDRN/PRE-PLCO Ovarian Phase II Validation Study — EDRN Public Portal

Cancer.gov

Create a new set of phase II specimens (160 cases with pre-operative bloods representing major histologic types and including 80 early-staged and 80 late-staged cases, 160 controls with benign disease, 480 general population controls, and a small set of serial Samples collected either at least 3 months apart, but not more than 6 months apart OR between 10 months apart and no more than 14 months apart in 40 healthy controls) will be used to evaluate markers identified in preliminary work. The top 5-10 markers, plus an expanded panel of Luminex markers, will comprise a “working consensus panel” for subsequent analysis in PLCO specimens.

Creating & using specimen images for collection documentation, research, teaching and outreach

NASA Astrophysics Data System (ADS)

Demouthe, J. F.

2012-12-01

In this age of digital media, there are many opportunities for use of good images of specimens. On-line resources such as institutional web sites and global sites such as PaleoNet and the Paleobiology Database provide venues for collection information and images. Pictures can also be made available to the general public through popular media sites such as Flickr and Facebook, where they can be retrieved and used by teachers, students, and the general public. The number of requests for specimen loans can be drastically reduced by offering the scientific community access to data and specimen images using the internet. This is an important consideration in these days of limited support budgets, since it reduces the amount of staff time necessary for giving researchers and educators access to collections. It also saves wear and tear on the specimens themselves. Many institutions now limit or refuse to send specimens out of their own countries because of the risks involved in going through security and customs. The internet can bridge political boundaries, allowing everyone equal access to collections. In order to develop photographic documentation of a collection, thoughtful preparation will make the process easier and more efficient. Acquire the necessary equipment, establish standards for images, and develop a simple workflow design. Manage images in the camera, and produce the best possible results, rather than relying on time-consuming editing after the fact. It is extremely important that the images of each specimen be of the highest quality and resolution. Poor quality, low resolution photos are not good for anything, and will often have to be retaken when another need arises. Repeating the photography process involves more handling of specimens and more staff time. Once good photos exist, smaller versions can be created for use on the web. The originals can be archived and used for publication and other purposes.

Matthew baillie's specimens and engravings.

PubMed

Spear, Caitlin; Reilly, Maggie; McDonald, Stuart W

2017-08-17

In 1799, Matthew Baillie, William Hunter's nephew, published his famous atlas of pathology. It was entitled A Series of Engravings Accompanied with Explanations which are Intended to Illustrate the Morbid Anatomy of Some of the Most Important Parts of the Human Body. The present study aims to match the illustrations to extant specimens in the collections of William and John Hunter, preserved at the University of Glasgow and at the Royal College of Surgeons of England respectively. Baillie's book contains 10 fasciculi, consisting of 73 plates and 206 figures. The specimens Baillie illustrated came from his own collection and those of ten others, including his uncles, William and John Hunter. The book was illustrated by William Clift and engraved by James Basire, William Skelton and James Heath. Excluding eight illustrations of intestinal worms where the provenance of the specimens is uncertain, a total of 98 specimens from William Hunter's collection were illustrated in 104 figures. Eight of the specimens were calculi impossible to identify specifically. Excluding worms and calculi, 72 of William Hunter's specimens illustrated by Baillie are extant in the Hunterian Collection at the University of Glasgow. All but one of the 20 specimens illustrated that had belonged to John Hunter were identified in the on-line catalog of the Royal College of Surgeons of England. Baillie's own collection was destroyed when the Royal College of Surgeons of England was bombed in 1941. Baillie is credited with being the first to produce an illustrated systematic textbook of morbid anatomy and probably the first to illustrate emphysema and transposition of the great vessels. His book, however, was not comprehensive. It did not cover a number of topics such as muscles and bones and there is little coverage of the nervous system. Baillie's book, however, was an original concept as an atlas of morbid anatomy and showed his deep insight into pathology. Clin. Anat., 2017. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Comparison of quantitative cytomegalovirus (CMV) PCR in plasma and CMV antigenemia assay: clinical utility of the prototype AMPLICOR CMV MONITOR test in transplant recipients.

PubMed

Caliendo, A M; St George, K; Kao, S Y; Allega, J; Tan, B H; LaFontaine, R; Bui, L; Rinaldo, C R

2000-06-01

The correlation between the prototype AMPLICOR CMV MONITOR test (Roche Molecular Systems), a quantitative PCR assay, and the cytomegalovirus (CMV) pp65 antigenemia assay was evaluated in transplant recipients. Sequential blood specimens were collected on 29 patients (491 specimens), the leukocyte fraction was tested by CMV antigenemia, and quantitative PCR was performed on plasma specimens. None of the 15 patients (242 specimens) who were antigenemia negative were positive for CMV DNA by PCR, and none of these patients developed active CMV disease. There were 14 antigenemia-positive patients, 8 of whom developed active CMV disease. In all patients, there was a good association between the antigenemia and PCR assays. Ganciclovir-resistant virus was isolated from three patients with active CMV disease. These three patients had persistently elevated levels of antigenemia and CMV DNA by PCR when resistance to ganciclovir developed. This standardized, quantitative CMV PCR assay on plasma has clinical utility for the diagnosis of active disease and in monitoring the response to antiviral therapy in transplant recipients.

Comparison of Quantitative Cytomegalovirus (CMV) PCR in Plasma and CMV Antigenemia Assay: Clinical Utility of the Prototype AMPLICOR CMV MONITOR Test in Transplant Recipients

PubMed Central

Caliendo, Angela M.; St. George, Kirsten; Kao, Shaw-Yi; Allega, Jessica; Tan, Ban-Hock; LaFontaine, Robert; Bui, Larry; Rinaldo, Charles R.

2000-01-01

The correlation between the prototype AMPLICOR CMV MONITOR test (Roche Molecular Systems), a quantitative PCR assay, and the cytomegalovirus (CMV) pp65 antigenemia assay was evaluated in transplant recipients. Sequential blood specimens were collected on 29 patients (491 specimens), the leukocyte fraction was tested by CMV antigenemia, and quantitative PCR was performed on plasma specimens. None of the 15 patients (242 specimens) who were antigenemia negative were positive for CMV DNA by PCR, and none of these patients developed active CMV disease. There were 14 antigenemia-positive patients, 8 of whom developed active CMV disease. In all patients, there was a good association between the antigenemia and PCR assays. Ganciclovir-resistant virus was isolated from three patients with active CMV disease. These three patients had persistently elevated levels of antigenemia and CMV DNA by PCR when resistance to ganciclovir developed. This standardized, quantitative CMV PCR assay on plasma has clinical utility for the diagnosis of active disease and in monitoring the response to antiviral therapy in transplant recipients. PMID:10834964

10 CFR 26.111 - Checking the acceptability of the urine specimen.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 1 2013-01-01 2013-01-01 false Checking the acceptability of the urine specimen. 26.111 Section 26.111 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for..., the collector shall measure the temperature of the specimen. The temperature-measuring device used...

10 CFR 26.111 - Checking the acceptability of the urine specimen.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 1 2012-01-01 2012-01-01 false Checking the acceptability of the urine specimen. 26.111 Section 26.111 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for..., the collector shall measure the temperature of the specimen. The temperature-measuring device used...

10 CFR 26.111 - Checking the acceptability of the urine specimen.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 1 2014-01-01 2014-01-01 false Checking the acceptability of the urine specimen. 26.111 Section 26.111 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for..., the collector shall measure the temperature of the specimen. The temperature-measuring device used...

10 CFR 26.113 - Splitting the urine specimen.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 1 2013-01-01 2013-01-01 false Splitting the urine specimen. 26.113 Section 26.113 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.113 Splitting the urine specimen. (a) Licensees and other entities may, but are not required to, use split...

10 CFR 26.113 - Splitting the urine specimen.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 1 2012-01-01 2012-01-01 false Splitting the urine specimen. 26.113 Section 26.113 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.113 Splitting the urine specimen. (a) Licensees and other entities may, but are not required to, use split...

10 CFR 26.113 - Splitting the urine specimen.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 1 2014-01-01 2014-01-01 false Splitting the urine specimen. 26.113 Section 26.113 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.113 Splitting the urine specimen. (a) Licensees and other entities may, but are not required to, use split...

10 CFR 26.109 - Urine specimen quantity.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Urine specimen quantity. 26.109 Section 26.109 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.109 Urine specimen quantity. (a) Licensees and other entities who are subject to this subpart shall establish a...

10 CFR 26.113 - Splitting the urine specimen.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false Splitting the urine specimen. 26.113 Section 26.113 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.113 Splitting the urine specimen. (a) Licensees and other entities may, but are not required to, use split...

10 CFR 26.109 - Urine specimen quantity.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false Urine specimen quantity. 26.109 Section 26.109 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.109 Urine specimen quantity. (a) Licensees and other entities who are subject to this subpart shall establish a...

10 CFR 26.113 - Splitting the urine specimen.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Splitting the urine specimen. 26.113 Section 26.113 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.113 Splitting the urine specimen. (a) Licensees and other entities may, but are not required to, use split...

[Evaluation of Consistency in detection of epidermal growth factor receptor gene T790M mutation in plasma and tumor specimens of patients with lung adenocarcinoma].

PubMed

Du, J; Wang, Z; Yang, L; Di, J; Zhang, J G; Wang, T Y; Liu, D G

2018-01-23

Objective: To evaluate the consistency in detection of T790M mutation of epidermal growth factor receptor gene (EGFR) in plasma and tumor samples of patients with lung adenocarcinoma. Methods: The tumor tissues or cytological specimens of 12 patients with operable lung adenocarcinoma(stage Ⅰ-ⅢA) and 100 patients with advanced stage ⅢB-Ⅳ lung adenocarcinoma were collected, among which 11 patients showed acquired resistance for gefitinib (11/100). In the same period, peripheral blood samples were collected from all patients and 50 healthy volunteers. Amplification refractory mutation system (ARMS) was used to detect EGFR mutations in tumor specimens. Next Generation Sequencing(NGS) based circulating single-molecule amplification and resequencing technology (cSMART)was performed to quantitatively detect the EGFR mutations in circulating tumor DNA (ctDNA) from plasma specimens. Results: The sensitivity, specificity and concordance rate of EGFR T790M mutation between plasma and tissue specimens from 100 advanced stage patients were 50.0%, 72.9% and 72.0%, respectively. For L858R mutation and exon 19 deletion mutations, the above mentioned sensitivity, specificity and concordance rate were 91.7%, 100.0%, and 98.0%, as well as 79.2%, 100.0% and 95.0%, respectively. The L858R mutation and exon 19 deletion mutations were not detected in plasma of 50 healthy volunteers, whereasT790M mutation(1.0±0.0 copies) was found in 7 individuals(7/50, 14.0%). Similarly, in 12 resectable patients, 4 (4/12, 33.3%) T790M mutations were found in plasma (1.2±0.2 copies), but no L858R mutation and 19 exon deletion mutations. In comparison, 28.0% of patients with advanced lung adenocarcinoma (28/100)had detectable T790M mutation in plasma with copy numbers (34.0±22.7 copies). Furthermore, the copy numbers of T790M were 268.2±119.9 in plasma of 5 cases with acquired gefitinib-resistance. Conclusions: In patients with advanced stages of lung adenocarcinoma, the detection of T790M mutation in plasma and tumor specimens is low. The T790M mutation also exists in the plasma of some healthy controls, suggesting that T790M mutation participates in EGFR signaling pathway and it might function in healthy population.

Molecular markers: Implications for cytopathology and specimen collection.

PubMed

VanderLaan, Paul A

2015-08-01

Cytologic specimens obtained through minimally invasive biopsy techniques are increasingly being used as principle diagnostic specimens for tumors arising in multiple sites. The number and scope of ancillary tests performed on these specimens have grown substantially over the past decade, including many molecular markers that not only can aid in formulating accurate and specific diagnoses but also can provide prognostic or therapeutic information to help direct clinical decisions. Thus, the cytopathologist needs to ensure that adequate material is collected and appropriately processed for the study of relevant molecular markers, many of which are specific to tumor site. This brief review covers considerations for effective cytologic specimen collection and processing to ensure diagnostic and testing success. In addition, a general overview is provided of molecular markers pertinent to tumors from a variety of sites. The recognition of these established and emerging molecular markers by cytopathologists is an important step toward realizing the promise of personalized medicine. © 2015 American Cancer Society.

Macrophage activation by heparanase is mediated by TLR-2 and TLR-4 and associates with plaque progression.

PubMed

Blich, Miry; Golan, Amnon; Arvatz, Gil; Sebbag, Anat; Shafat, Itay; Sabo, Edmond; Cohen-Kaplan, Victoria; Petcherski, Sirouch; Avniel-Polak, Shani; Eitan, Amnon; Hammerman, Haim; Aronson, Doron; Axelman, Elena; Ilan, Neta; Nussbaum, Gabriel; Vlodavsky, Israel

2013-02-01

Factors and mechanisms that activate macrophages in atherosclerotic plaques are incompletely understood. We examined the capacity of heparanase to activate macrophages. Highly purified heparanase was added to mouse peritoneal macrophages and macrophage-like J774 cells, and the levels of tumor necrosis factor-α, matrix metalloproteinase-9, interlukin-1, and monocyte chemotactic protein-1 were evaluated by ELISA. Gene expression was determined by RT-PCR. Cells collected from Toll-like receptor-2 and Toll-like receptor-4 knockout mice were evaluated similarly. Heparanase levels in the plasma of patients with acute myocardial infarction, stable angina, and healthy subjects were determined by ELISA. Immunohistochemistry was applied to detect the expression of heparanase in control specimens and specimens of patients with stable angina or acute myocardial infarction. Addition or overexpression of heparanase variants resulted in marked increase in tumor necrosis factor-α, matrix metalloproteinase-9, interlukin-1, and monocyte chemotactic protein-1 levels. Mouse peritoneal macrophages harvested from Toll-like receptor-2 or Toll-like receptor-4 knockout mice were not activated by heparanase. Plasma heparanase level was higher in patients with acute myocardial infarction, compared with patients with stable angina and healthy subjects. Pathologic coronary specimens obtained from vulnerable plaques showed increased heparanase staining compared with specimens of stable plaque and controls. Heparanase activates macrophages, resulting in marked induction of cytokine expression associated with plaque progression toward vulnerability.

Decline of measles-specific immunoglobulin M antibodies after primary measles, mumps, and rubella vaccination.

PubMed

Helfand, R F; Gary, H E; Atkinson, W L; Nordin, J D; Keyserling, H L; Bellini, W J

1998-03-01

Detection of measles-specific immunoglobulin M (IgM) has become the standard diagnostic method for laboratory confirmation of measles. In outbreaks, the interpretation of an IgM-positive result can be complicated when persons with suspected measles receive a dose of measles vaccine as part of outbreak control measures. This investigation evaluated the decay of measles-specific IgM antibodies 1 to 4 months after primary vaccination with measles, mumps, and rubella vaccine (MMRII). Serum samples were obtained from 536 infants vaccinated when they were 15 months old as part of a study to assess primary and secondary measles vaccine failure. Sixty serum specimens per week were selected from specimens collected between 4 and 9 weeks after MMRII vaccination; all 176 available serum specimens collected between 10 and > or = 16 weeks were included. Specimens were tested for the presence of measles-specific IgM by an antibody-capture enzyme immunoassay. The proportion of IgM-positive specimens dropped from 73% at 4 weeks after vaccination to 52% at 5 weeks after vaccination and then declined to 7% by 8 weeks after vaccination. Less than 10% of children remained IgM positive between 9 and 11 weeks. An IgM-negative result helps rule out the diagnosis of measles in a person with suspected infection and a history of recent vaccination. The interpretation of a positive IgM result from a person with a clinically suspected case of measles and a recent history of measles vaccination (especially within 8 weeks) is problematic, and the diagnosis of measles should be based on epidemiologic linkage to a confirmed case or on detection of wild-type measles virus.

Evaluation of lateral flow devices for identification of infected poultry by testing swab and feather specimens during H5N1 highly pathogenic avian influenza outbreaks in Vietnam

PubMed Central

Slomka, Marek J.; To, Thanh L.; Tong, Hien H.; Coward, Vivien J.; Mawhinney, Ian C.; Banks, Jill; Brown, Ian H.

2011-01-01

Please cite this paper as: Slomka et al. (2012) Evaluation of lateral flow devices for identification of infected poultry by testing swab and feather specimens during H5N1 highly pathogenic avian influenza outbreaks in Vietnam. Influenza and Other Respiratory Viruses 6(5), 318–327. Background  Evaluation of two commercial lateral flow devices (LFDs) for avian influenza (AI) detection in H5N1 highly pathogenic AI infected poultry in Vietnam. Objectives  Determine sensitivity and specificity of the LFDs relative to a validated highly sensitive H5 RRT PCR. Methods  Swabs (cloacal and tracheal) and feathers were collected from 46 chickens and 48 ducks (282 clinical specimens) and tested by both LFDs and H5 RRT PCR. A subset of 59 chicken and 34 duck specimens was also tested by virus isolation (VI), the ‘gold standard’. Results  Twenty‐six chickens and 15 ducks were shown to be infected by at least one RRT PCR positive clinical specimen per bird. Bird‐level sensitivity for the Anigen LFD was 84·6% for chickens and 53·3% for ducks, and for the Quickvue LFD 65·4% for chickens and 33·3% for ducks. Comparison of the three clinical specimens revealed that chicken feathers were the most sensitive with 84% and 56% sensitivities for Anigen and Quickvue respectively. All 21 RRT PCR positive swabs from ducks were negative by both LFDs. However, duck feather testing gave sensitivities of 53·3% and 33·3% for Anigen and Quickvue respectively. Specificity was 100% for both LFDs in all investigations. Conclusions  Although LFDs were less sensitive than AI RRT PCR and VI, high titre viral shedding in H5N1 highly pathogenic avian influenza (HPAI) infected and diseased chickens is sufficient for a proportion of birds to be identified as AI infected by LFDs. Feathers were the optimal specimen for LFD testing in such diseased HPAI scenarios, particularly for ducks where swab testing by LFDs failed to identify any infected birds. However, specimens should be forwarded to the laboratory for confirmation by more sensitive diagnostic techniques. PMID:22151025

Rescue karyotyping: a case series of array-based comparative genomic hybridization evaluation of archival conceptual tissue

PubMed Central

2014-01-01

Background Determination of fetal aneuploidy is central to evaluation of recurrent pregnancy loss (RPL). However, obtaining this information at the time of a miscarriage is not always possible or may not have been ordered. Here we report on “rescue karyotyping”, wherein DNA extracted from archived paraffin-embedded pregnancy loss tissue from a prior dilation and curettage (D&C) is evaluated by array-based comparative genomic hybridization (aCGH). Methods A retrospective case series was conducted at an academic medical center. Patients included had unexplained RPL and a prior pregnancy loss for which karyotype information would be clinically informative but was unavailable. After extracting DNA from slides of archived tissue, aCGH with a reduced stringency approach was performed, allowing for analysis of partially degraded DNA. Statistics were computed using STATA v12.1 (College Station, TX). Results Rescue karyotyping was attempted on 20 specimens from 17 women. DNA was successfully extracted in 16 samples (80.0%), enabling analysis at either high or low resolution. The longest interval from tissue collection to DNA extraction was 4.2 years. There was no significant difference in specimen sufficiency for analysis in the collection-to-extraction interval (p = 0.14) or gestational age at pregnancy loss (p = 0.32). Eight specimens showed copy number variants: 3 trisomies, 2 partial chromosomal deletions, 1 mosaic abnormality and 2 unclassified variants. Conclusions Rescue karyotyping using aCGH on DNA extracted from paraffin-embedded tissue provides the opportunity to obtain critical fetal cytogenetic information from a prior loss, even if it occurred years earlier. Given the ubiquitous archiving of paraffin embedded tissue obtained during a D&C and the ease of obtaining results despite long loss-to-testing intervals or early gestational age at time of fetal demise, this may provide a useful technique in the evaluation of couples with recurrent pregnancy loss. PMID:24589081

Specimen banking of marine organisms in the United States: Current status and long-term prospective

USGS Publications Warehouse

Becker, P.R.; Wise, S.A.; Thorsteinson, L.; Koster, B.J.; Rowles, T.

1997-01-01

A major part of the activities conducted over the last decade by the National Biomonitoring Specimen Bank (NBSB) has involved the archival of marine specimens collected by ongoing environmental monitoring programs. These archived specimens include bivalves, marine sediments, and fish tissues collected by the National Status and Trends and the Exxon Valdez Oil Spill Damage Assessment programs, and marine mammal tissues collected by the Marine Mammal Health and Stranding Response Program and the Alaska Marine Mammal Tissue Archival Project. In addition to supporting these programs, the specimens have been used to investigate circumpolar patterns of chlorinated hydrocarbon concentrations, genetic separation of marine animal stocks, baseline levels of essential and nonessential elements in marine mammals, and the potential risk to human consumers in the Arctic from anthropogenic contaminants found in local subsistence foods. The NBSB specimens represent a resource that has the potential for addressing future issues of marine environmental quality and ecosystem changes through retrospective analysis; however, an ecosystem-based food web approach would maximize this potential. The current status of the NBSB activities related to the banking of marine organisms is presented and discussed, the long-term prospective of these activities is presented, and the importance of an ecosystem-based food web monitoring approach to the value of specimen banking is discussed.

Increasing the efficiency of digitization workflows for herbarium specimens.

PubMed

Tulig, Melissa; Tarnowsky, Nicole; Bevans, Michael; Anthony Kirchgessner; Thiers, Barbara M

2012-01-01

The New York Botanical Garden Herbarium has been databasing and imaging its estimated 7.3 million plant specimens for the past 17 years. Due to the size of the collection, we have been selectively digitizing fundable subsets of specimens, making successive passes through the herbarium with each new grant. With this strategy, the average rate for databasing complete records has been 10 specimens per hour. With 1.3 million specimens databased, this effort has taken about 130,000 hours of staff time. At this rate, to complete the herbarium and digitize the remaining 6 million specimens, another 600,000 hours would be needed. Given the current biodiversity and economic crises, there is neither the time nor money to complete the collection at this rate.Through a combination of grants over the last few years, The New York Botanical Garden has been testing new protocols and tactics for increasing the rate of digitization through combinations of data collaboration, field book digitization, partial data entry and imaging, and optical character recognition (OCR) of specimen images. With the launch of the National Science Foundation's new Advancing Digitization of Biological Collections program, we hope to move forward with larger, more efficient digitization projects, capturing data from larger portions of the herbarium at a fraction of the cost and time.

Increasing the efficiency of digitization workflows for herbarium specimens

PubMed Central

Tulig, Melissa; Tarnowsky, Nicole; Bevans, Michael; Anthony Kirchgessner; Thiers,  Barbara M.

2012-01-01

Abstract The New York Botanical Garden Herbarium has been databasing and imaging its estimated 7.3 million plant specimens for the past 17 years. Due to the size of the collection, we have been selectively digitizing fundable subsets of specimens, making successive passes through the herbarium with each new grant. With this strategy, the average rate for databasing complete records has been 10 specimens per hour. With 1.3 million specimens databased, this effort has taken about 130,000 hours of staff time. At this rate, to complete the herbarium and digitize the remaining 6 million specimens, another 600,000 hours would be needed. Given the current biodiversity and economic crises, there is neither the time nor money to complete the collection at this rate. Through a combination of grants over the last few years, The New York Botanical Garden has been testing new protocols and tactics for increasing the rate of digitization through combinations of data collaboration, field book digitization, partial data entry and imaging, and optical character recognition (OCR) of specimen images. With the launch of the National Science Foundation’s new Advancing Digitization of Biological Collections program, we hope to move forward with larger, more efficient digitization projects, capturing data from larger portions of the herbarium at a fraction of the cost and time. PMID:22859882

Evaluation of lateral flow devices for identification of infected poultry by testing swab and feather specimens during H5N1 highly pathogenic avian influenza outbreaks in Vietnam.

PubMed

Slomka, Marek J; To, Thanh L; Tong, Hien H; Coward, Vivien J; Mawhinney, Ian C; Banks, Jill; Brown, Ian H

2012-09-01

Evaluation of two commercial lateral flow devices (LFDs) for avian influenza (AI) detection in H5N1 highly pathogenic AI infected poultry in Vietnam. Determine sensitivity and specificity of the LFDs relative to a validated highly sensitive H5 RRT PCR. Swabs (cloacal and tracheal) and feathers were collected from 46 chickens and 48 ducks (282 clinical specimens) and tested by both LFDs and H5 RRT PCR. A subset of 59 chicken and 34 duck specimens was also tested by virus isolation (VI), the 'gold standard'. Twenty-six chickens and 15 ducks were shown to be infected by at least one RRT PCR positive clinical specimen per bird. Bird-level sensitivity for the Anigen LFD was 84·6% for chickens and 53·3% for ducks, and for the Quickvue LFD 65·4% for chickens and 33·3% for ducks. Comparison of the three clinical specimens revealed that chicken feathers were the most sensitive with 84% and 56% sensitivities for Anigen and Quickvue respectively. All 21 RRT PCR positive swabs from ducks were negative by both LFDs. However, duck feather testing gave sensitivities of 53·3% and 33·3% for Anigen and Quickvue respectively. Specificity was 100% for both LFDs in all investigations. Although LFDs were less sensitive than AI RRT PCR and VI, high titre viral shedding in H5N1 highly pathogenic avian influenza (HPAI) infected and diseased chickens is sufficient for a proportion of birds to be identified as AI infected by LFDs. Feathers were the optimal specimen for LFD testing in such diseased HPAI scenarios, particularly for ducks where swab testing by LFDs failed to identify any infected birds. However, specimens should be forwarded to the laboratory for confirmation by more sensitive diagnostic techniques. © 2011 Blackwell Publishing Ltd.

Utility of pooled urine specimens for detection of Chlamydia trachomatis and Neisseria gonorrhoeae in men attending public sexually transmitted infection clinics in Mumbai, India, by PCR.

PubMed

Lindan, Christina; Mathur, Meenakshi; Kumta, Sameer; Jerajani, Hermangi; Gogate, Alka; Schachter, Julius; Moncada, Jeanne

2005-04-01

Pooling urogenital specimens for the detection of Chlamydia trachomatis and Neisseria gonorrhoeae by nucleic acid amplification tests is an attractive alternative to individual testing. As pooling can reduce the costs of testing as well as labor, it has been advocated for use in resource-poor settings. However, it has neither been widely adopted nor evaluated for use in developing countries. We evaluated the practical use of pooling first-catch urine (FCU) specimens for the detection of C. trachomatis and N. gonorrhoeae from 690 men in Mumbai, India, by PCR. FCU, urethral smears, and swabs were collected from men seen at two sexually transmitted infection (STI) clinics. All laboratory testing was done at the Lokmanya Tilak General Hospital. Gram stain smears and culture isolation for N. gonorrhoeae were performed. Each FCU was tested individually and in pools using the Roche Amplicor PCR for C. trachomatis and N. gonorrhoeae with an internal control for inhibition. Specimen pools consisted of aliquots from five consecutively processed FCUs combined into an amplification tube. An optical density reading of > or =0.20 indicated a pool for which subsequent testing of individual samples was required. Prevalence by PCR on single specimens was 2.2% (15/690) for C. trachomatis and 5.4% (37/690) for N. gonorrhoeae. Compared to individual FCU results, pooling for C. trachomatis and N. gonorrhoeae had an overall sensitivity of 96.1% (50/52). Specificity was 96.5% (83/86) in that three pools required single testing that failed to identify a positive specimen. Pooling missed two positive specimens, decreased the inhibition rate, and saved 50.3% of reagent costs. In this resource-limited setting, the use of pooling to detect C. trachomatis and N. gonorrhoeae by PCR proved to be a simple, accurate, and cost-effective procedure compared to individual testing.

Evaluation of the CDC proposed laboratory HIV testing algorithm among men who have sex with men (MSM) from five US metropolitan statistical areas using specimens collected in 2011.

PubMed

Masciotra, Silvina; Smith, Amanda J; Youngpairoj, Ae S; Sprinkle, Patrick; Miles, Isa; Sionean, Catlainn; Paz-Bailey, Gabriela; Johnson, Jeffrey A; Owen, S Michele

2013-12-01

Until recently most testing algorithms in the United States (US) utilized Western blot (WB) as the supplemental test. CDC has proposed an algorithm for HIV diagnosis which includes an initial screen with a Combo Antigen/Antibody 4th generation-immunoassay (IA), followed by an HIV-1/2 discriminatory IA of initially reactive-IA specimens. Discordant results in the proposed algorithm are resolved by nucleic acid-amplification testing (NAAT). Evaluate the results obtained with the CDC proposed laboratory-based algorithm using specimens from men who have sex with men (MSM) obtained in five metropolitan statistical areas (MSAs). Specimens from 992 MSM from five MSAs participating in the CDC's National HIV Behavioral Surveillance System in 2011 were tested at local facilities and CDC. The five MSAs utilized algorithms of various screening assays and specimen types, and WB as the supplemental test. At the CDC, serum/plasma specimens were screened with 4th generation-IA and the Multispot HIV-1/HIV-2 discriminatory assay was used as the supplemental test. NAAT was used to resolve discordant results and to further identify acute HIV infections from all screened-non-reactive missed by the proposed algorithm. Performance of the proposed algorithm was compared to site-specific WB-based algorithms. The proposed algorithm detected 254 infections. The WB-based algorithms detected 19 fewer infections; 4 by oral fluid (OF) rapid testing and 15 by WB supplemental testing (12 OF and 3 blood). One acute infection was identified by NAAT from all screened-non-reactive specimens. The proposed algorithm identified more infections than the WB-based algorithms in a high-risk MSM population. OF testing was associated with most of the discordant results between algorithms. HIV testing with the proposed algorithm can increase diagnosis of infected individuals, including early infections. Published by Elsevier B.V.

Expression of p53, p21 and cyclin D1 in penile cancer: p53 predicts poor prognosis.

PubMed

Gunia, Sven; Kakies, Christoph; Erbersdobler, Andreas; Hakenberg, Oliver W; Koch, Stefan; May, Matthias

2012-03-01

To evaluate the role of p53, p21 and cyclin D1 expression in patients with penile cancer (PC). Paraffin-embedded tissues from PC specimens from six pathology departments were subjected to a central histopathological review performed by one pathologist. The tissue microarray technique was used for immunostaining which was evaluated by two independent pathologists and correlated with cancer-specific survival (CSS). κ-statistics were used to assess interobserver variability. Uni- and multivariable Cox proportional hazards analysis was applied to assess the independent effects of several prognostic factors on CSS over a median of 32 months (IQR 6-66 months). Specimens and clinical data from 110 men treated surgically for primary PC were collected. p53 staining was positive in 30 and negative in 62 specimens. κ-statistics showed substantial interobserver reproducibility of p53 staining evaluation (κ=0.73; p<0.001). The 5-year CSS rate for the entire study cohort was 74%. Five-year CSS was 84% in p53-negative and 51% in p53-positive PC patients (p=0.003). Multivariable analysis showed p53 (HR=3.20; p=0.041) and pT-stage (HR=4.29; p<0.001) as independent significant prognostic factors for CSS. Cyclin D1 and p21 expression were not correlated with survival. However, incorporating p21 into a multivariable Cox model did contribute to improved model quality for predicting CSS. In patients with PC, the expression of p53 in the primary tumour specimen can be reproducibly assessed and is negatively associated with cancer specific survival.

Effect of diet on results obtained by use of two commercial test kits for detection of occult blood in feces of dogs.

PubMed

Cook, A K; Gilson, S D; Fischer, W D; Kass, P H

1992-10-01

To evaluate the effect of diet on results obtained by use of 2 commercial test kits for detection of occult blood in feces, 5 dogs were fed 7 diets in randomized sequence. Dry and canned diets with various principal ingredients were evaluated. Each diet was offered twice over a 24-hour period, followed by a 36-hour nonfeeding period. Fecal specimens were collected twice daily, and tests for occult blood were performed within 12 hours. The dietary origin of fecal specimens was confirmed by use of colored markers fed with each diet, and was correlated with estimates of gastrointestinal tract transit time. A modified guaiac paper test and an o-tolidine tablet test were performed on each specimen. Of 59 specimens, 4 were positive for occult blood, using the o-tolidine tablet test. Three positive results were associated with a mutton-based canned diet, and 1 positive result was associated with a canned beef-based diet. Of 59 specimens, 11 were positive for occult blood, using the modified guaiac paper test. Four positive results were associated with the mutton diet, and 3 positive results were associated with the beef diet. Of the remaining 5 diets, 4 caused 1 positive reaction. Results were inconsistent with the null hypothesis that the distribution of positive occult blood test results is not affected by diet (P < 0.025), and indicate that diet can affect the specificity of peroxidase-based tests for detection of occult blood in canine feces. Diet modification prior to testing is recommended.

Herpetofauna of the Oak Ridge area

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

Johnson, R.M.

1964-12-01

The herpetofauna of the Oak Ridge area was investigated to ascertain th kinds of amphibians and reptiles (herptiles) occurring in th area, to evaluate habitat preferences of the herptiles, to evaluate the suitability of the various species populations for ecological investigations, and to prepare a reference collection of herptiles of the area. The numbers of monotypic species of herptiles collected are as follows: salamanders, 3; anurans, 2; turtles, 2; lizards, 4; and snakes, 2. The numbers of polytypic species collected are as follows (numbers in parentheses are subspecies represented): salamanders, 4 (4); anurans, 10 (12); turtles, 8(1); lizards, 1 (1);more » and snakes, 15 (18). The largest numbers of species and specimens were collected in flood-plain and pond habitats; the least numbers were collected in pine plantations. Herptiles judged as occurring in populations of sufficient size, seasonal availability, and ease of sampling for extensive field and laboratory investigations are as follows: Desmognathus fuscus; Hyla versicolor; Acris crepitans; Rana clamitans; R. palustris; Chrysemys picta; Pseudemys scripta; Natrix septemvittata; and N. sipedon.« less

Applications of deep convolutional neural networks to digitized natural history collections.

PubMed

Schuettpelz, Eric; Frandsen, Paul B; Dikow, Rebecca B; Brown, Abel; Orli, Sylvia; Peters, Melinda; Metallo, Adam; Funk, Vicki A; Dorr, Laurence J

2017-01-01

Natural history collections contain data that are critical for many scientific endeavors. Recent efforts in mass digitization are generating large datasets from these collections that can provide unprecedented insight. Here, we present examples of how deep convolutional neural networks can be applied in analyses of imaged herbarium specimens. We first demonstrate that a convolutional neural network can detect mercury-stained specimens across a collection with 90% accuracy. We then show that such a network can correctly distinguish two morphologically similar plant families 96% of the time. Discarding the most challenging specimen images increases accuracy to 94% and 99%, respectively. These results highlight the importance of mass digitization and deep learning approaches and reveal how they can together deliver powerful new investigative tools.

New records for millipedes from southern Chile (Polydesmida: Dalodesmidae; Polyzoniida: Siphonotidae).

PubMed

Mesibov, Robert Evan

2017-01-01

Millipedes from 1983 collections by the author in southern Chile have been identified and registered as specimen lots at the Queen Victoria Museum and Art Gallery (QVMAG) in Launceston, Tasmania. Collection and specimen data from the new QVMAG specimen lots have been archived in Darwin Core format together with a KML file of occurrences. The 31 occurrence records in the Darwin Core Archive list 13 millipede taxa from 16 sites in Llanquihue and Osorno provinces, Chile.

Evaluation of gastroscopy and biopsy of the proventriculus and ventriculus in pigeons (Columba livia).

PubMed

Sladakovic, Izidora; Ellis, Angela E; Divers, Stephen J

2017-01-01

OBJECTIVE To evaluate the efficacy and safety of gastroscopy and biopsy of the proventriculus and ventriculus in pigeons (Columba livia). ANIMALS 15 adult pigeons. PROCEDURES Each pigeon was anesthetized, and the upper gastrointestinal tract (from the cervical portion of the esophagus to the ventriculus) was endoscopically evaluated by use of a rigid endoscope inserted orally. Saline (0.9% NaCl) solution was orally infused to achieve lumen dilation and visibility. Two mucosal biopsy specimens were collected from each of the proventriculus and ventriculus, histologically evaluated, and graded for crush artifacts and depth. Pigeons were monitored for adverse effects for 3 to 6 days after the procedure, after which they were euthanized for necropsy. RESULTS Gastroscopy via the oral approach provided excellent visibility of the lumen and mucosal surfaces of the proventriculus and cranial portion of the ventriculus and was safe provided that appropriate precautions were taken. Two intraoperative deaths occurred at the beginning of the study; following procedure refinement, no additional deaths occurred. No major adverse effects of the procedure were detected in the remaining 13 pigeons during the postoperative monitoring period or at necropsy. Diagnostic quality of proventriculus specimens was adequate for 10 of 13 pigeons. Eight of 13 ventriculus specimens were of inadequate quality, and only 3 were of adequate quality. CONCLUSIONS AND CLINICAL RELEVANCE Gastroscopy was useful for evaluating the lumen and mucosal surface of the proventriculus and ventriculus in pigeons, and biopsy of those organs was safely performed with the appropriate technique. Further evaluation of these techniques is needed in birds with clinical disease and birds of other species.

A framework for assessing supply-side wildlife conservation.

PubMed

Phelps, J; Carrasco, L R; Webb, E L

2014-02-01

Market-based, supply-side interventions such as domestication, cultivation, and wildlife farming have been proposed as legal substitutes for wild-collected plants and animals in the marketplace. Based on the literature, we devised a list of the conditions under which supply-side interventions may yield positive conservation outcomes. We applied it to the trade of the orchid Rhynchostylis gigantea, a protected ornamental plant. We conducted a survey of R. gigantea at Jatujak Market in Bangkok, Thailand. Farmed (legal) and wild (illegal, protected) specimens of R. gigantea were sold side-by-side at market. These results suggest farmed specimens are not being substituted for wild plants in the marketplace. For any given set of physical plant characteristics (size, condition, flowers), the origin of the plants (wild vs. farmed) did not affect price. For all price classes, farmed plants were of superior quality to wild-collected plants on the basis of most physical variables. These results suggest wild and farmed specimens represent parallel markets and may not be substitutable goods. Our results with R. gigantea highlight a range of explanations for why supply-side interventions may lack effectiveness, for example, consumer preferences for wild-collected products and low financial incentives for farming. Our results suggest that market-based conservation strategies may not be effective by themselves and may be best utilized as supplements to regulation and education. This approach represents a broad, multidisciplinary evaluation of supply-side interventions that can be applied to other plant and animal species. © 2013 Society for Conservation Biology.

Field evaluation of a new light trap for phlebotomine sand flies.

PubMed

Gaglio, Gabriella; Napoli, Ettore; Falsone, Luigi; Giannetto, Salvatore; Brianti, Emanuele

2017-10-01

Light traps are one of the most common attractive method for the collection of nocturnal insects. Although light traps are generally referred to as "CDC light traps", different models, equipped with incandescent or UV lamps, have been developed. A new light trap, named Laika trap 3.0, equipped with LED lamps and featured with a light and handy design, has been recently proposed into the market. In this study we tested and compared the capture performances of this new trap with those of a classical light trap model under field conditions. From May to November 2013, a Laika trap and a classical light trap were placed biweekly in an area endemic for sand flies. A total of 256 sand fly specimens, belonging to 3 species (Sergentomyia minuta, Phlebotomus perniciosus, Phlebotomus neglectus) were collected during the study period. The Laika trap captured 126 phlebotomine sand flies: P. perniciosus (n=38); S. minuta (n=88), a similar number of specimens (130) and the same species were captured by classical light trap which collected also 3 specimens of P. neglectus. No significant differences in the capture efficiency at each day of trapping, neither in the number of species or in the sex of sand flies were observed. According to results of this study, the Laika trap may be a valid alternative to classical light trap models especially when handy design and low power consumption are key factors in field studies. Copyright © 2017 Elsevier B.V. All rights reserved.

Digitization workflows for flat sheets and packets of plants, algae, and fungi1

PubMed Central

Nelson, Gil; Sweeney, Patrick; Wallace, Lisa E.; Rabeler, Richard K.; Allard, Dorothy; Brown, Herrick; Carter, J. Richard; Denslow, Michael W.; Ellwood, Elizabeth R.; Germain-Aubrey, Charlotte C.; Gilbert, Ed; Gillespie, Emily; Goertzen, Leslie R.; Legler, Ben; Marchant, D. Blaine; Marsico, Travis D.; Morris, Ashley B.; Murrell, Zack; Nazaire, Mare; Neefus, Chris; Oberreiter, Shanna; Paul, Deborah; Ruhfel, Brad R.; Sasek, Thomas; Shaw, Joey; Soltis, Pamela S.; Watson, Kimberly; Weeks, Andrea; Mast, Austin R.

2015-01-01

Effective workflows are essential components in the digitization of biodiversity specimen collections. To date, no comprehensive, community-vetted workflows have been published for digitizing flat sheets and packets of plants, algae, and fungi, even though latest estimates suggest that only 33% of herbarium specimens have been digitally transcribed, 54% of herbaria use a specimen database, and 24% are imaging specimens. In 2012, iDigBio, the U.S. National Science Foundation’s (NSF) coordinating center and national resource for the digitization of public, nonfederal U.S. collections, launched several working groups to address this deficiency. Here, we report the development of 14 workflow modules with 7–36 tasks each. These workflows represent the combined work of approximately 35 curators, directors, and collections managers representing more than 30 herbaria, including 15 NSF-supported plant-related Thematic Collections Networks and collaboratives. The workflows are provided for download as Portable Document Format (PDF) and Microsoft Word files. Customization of these workflows for specific institutional implementation is encouraged. PMID:26421256

Comparison of the gas-liquid dual support fixation and Heitzman fixation techniques for preparing lung specimens

PubMed Central

Yu, Dongsheng; Qu, Weili; Xia, Haipeng; Li, Xiaofeng; Luan, Zhenfeng; Yan, Renjie; Lu, Xiaodong; Zhao, Peng

2017-01-01

The aim of the present study was to compare the gas-liquid dual support fixation and Heitzman fixation techniques for the preparation of lung specimens. A total of 40 fresh lung samples were surgically collected from 40 male patients with lung cancer by biopsy. Patients were recruited from the Affiliated Hospital of Qingdao University Medical College (Qingdao, China) between July 2007 and June 2014. Samples were prepared using either the gas-liquid dual support fixation method (group A; n=26) or the Heitzman fixation method (group B; n=14). High-resolution computed tomography (HRCT) scanning was performed prior to surgery and corresponding postoperative HRCT scanning was conducted for the lung specimens; the gross transverse specimen section, cord photography images and histological sections were evaluated. Morphological observations of lung specimens indicated that there were 22 cases in group A with grade I (84.6%) and 4 cases with grade II (15.4%), whereas, in group B, there were 5 cases with grade II (35.7%) and 9 cases with grade III (64.3%). Statistical analysis demonstrated that the grades of specimens between the two groups were significantly different (P<0.01). Results from imaging and histological studies found that the quality of lung specimens was superior in group A, compared with group B. In conclusion, the present study demonstrated that, compared with the Heitzman fixation method, gas-liquid dual support fixation may be a superior technique for the preparation of lung specimens. This finding may facilitate the improvement of lung HRCT and pathological studies. PMID:28673006

Comparison of the gas-liquid dual support fixation and Heitzman fixation techniques for preparing lung specimens.

PubMed

Yu, Dongsheng; Qu, Weili; Xia, Haipeng; Li, Xiaofeng; Luan, Zhenfeng; Yan, Renjie; Lu, Xiaodong; Zhao, Peng

2017-07-01

The aim of the present study was to compare the gas-liquid dual support fixation and Heitzman fixation techniques for the preparation of lung specimens. A total of 40 fresh lung samples were surgically collected from 40 male patients with lung cancer by biopsy. Patients were recruited from the Affiliated Hospital of Qingdao University Medical College (Qingdao, China) between July 2007 and June 2014. Samples were prepared using either the gas-liquid dual support fixation method (group A; n=26) or the Heitzman fixation method (group B; n=14). High-resolution computed tomography (HRCT) scanning was performed prior to surgery and corresponding postoperative HRCT scanning was conducted for the lung specimens; the gross transverse specimen section, cord photography images and histological sections were evaluated. Morphological observations of lung specimens indicated that there were 22 cases in group A with grade I (84.6%) and 4 cases with grade II (15.4%), whereas, in group B, there were 5 cases with grade II (35.7%) and 9 cases with grade III (64.3%). Statistical analysis demonstrated that the grades of specimens between the two groups were significantly different (P<0.01). Results from imaging and histological studies found that the quality of lung specimens was superior in group A, compared with group B. In conclusion, the present study demonstrated that, compared with the Heitzman fixation method, gas-liquid dual support fixation may be a superior technique for the preparation of lung specimens. This finding may facilitate the improvement of lung HRCT and pathological studies.

Evaluation of the Hologic gen-probe PANTHER, APTIMA Combo 2 assay in a tertiary care teaching hospital.

PubMed

Cheng, Annie; Kirby, James E

2014-03-01

To evaluate the performance of the Hologic Gen-Probe (San Diego, CA) PANTHER system. The performance of PANTHER was compared with the Hologic Gen-Probe TIGRIS and/or Roche (Indianapolis, IN) COBAS AMPLICOR systems through testing of patient specimens and the spiked-urine matrix. After discrepant resolution, PANTHER demonstrated a 99.3% (95% confidence interval [CI], 96.0%-99.9%) positive and 100% (98.5%-100.0%) negative agreement for Chlamydia trachomatis (CT) and 100% (96.6%-100.0%) positive and 100% (98.6%-100.0%) negative agreement for Neisseria gonorrhoeae (NG) for all male, female, unsexed, and NG-spiked female urine specimens combined. For other specimen types collectively, the PANTHER demonstrated 100% (95% CI, 90.6%-100.0%) positive and 100% (88.3%-100.0%) negative agreement for CT and 90.9% (62.8%-98.4%) positive and 100% (93.5%-100.0%) negative agreement for NG. Analytical sensitivity of the PANTHER in urine matrix was similar to the TIGRIS system. The PANTHER system provides an excellent new addition to options for detecting CT and NG, is appropriate for testing urine samples, and will facilitate high-throughput testing in the clinical laboratory.

The Alaska Area Specimen Bank: a tribal-federal partnership to maintain and manage a resource for health research.

PubMed

Parkinson, Alan J; Hennessy, Thomas; Bulkow, Lisa; Smith, H Sally

2013-01-01

Banked biospecimens from a defined population are a valuable resource that can be used to assess early markers for illness or to determine the prevalence of a disease to aid the development of intervention strategies to reduce morbidity and mortality. The Alaska Area Specimen Bank (AASB) currently contains 266,353 residual biologic specimens (serum, plasma, whole blood, tissue, bacterial cultures) from 83,841 persons who participated in research studies, public health investigations and clinical testing conducted by the U.S. Public Health Service and Alaska Native tribal health organisations dating back to 1961. The majority (95.7%) are serum specimens, 77% were collected between 1981 and 1994 and 85% were collected from Alaska Native people. Oversight of the specimen bank is provided by a working group with representation from tribal, state and federal health organisations, the Alaska Area IRB and a specimen bank committee which ensures the specimens are used in accordance with policies and procedures developed by the working group.

DNA Barcode Authentication and Library Development for the Wood of Six Commercial Pterocarpus Species: the Critical Role of Xylarium Specimens.

PubMed

Jiao, Lichao; Yu, Min; Wiedenhoeft, Alex C; He, Tuo; Li, Jianing; Liu, Bo; Jiang, Xiaomei; Yin, Yafang

2018-01-31

DNA barcoding has been proposed as a useful tool for forensic wood identification and development of a reliable DNA reference library is an essential first step. Xylaria (wood collections) are potentially enormous data repositories if DNA information could be extracted from wood specimens. In this study, 31 xylarium wood specimens and 8 leaf specimens of six important commercial species of Pterocarpus were selected to investigate the reliability of DNA barcodes for authentication at the species level and to determine the feasibility of building wood DNA barcode reference libraries from xylarium specimens. Four DNA barcodes (ITS2, matK, ndhF-rpl32 and rbcL) and their combination were tested to evaluate their discrimination ability for Pterocarpus species with both TaxonDNA and tree-based analytical methods. The results indicated that the combination barcode of matK + ndhF-rpl32 + ITS2 yielded the best discrimination for the Pterocarpus species studied. The mini-barcode ndhF-rpl32 (167-173 bps) performed well distinguishing P. santalinus from its wood anatomically inseparable species P. tinctorius. Results from this study verified not only the feasibility of building DNA barcode libraries using xylarium wood specimens, but the importance of using wood rather than leaves as the source tissue, when wood is the botanical material to be identified.

Comparison between Saliva and Nasopharyngeal Swab Specimens for Detection of Respiratory Viruses by Multiplex Reverse Transcription-PCR

PubMed Central

Kim, Young-gon; Kim, Min Young; Park, Kwisung; Cho, Chi Hyun; Yoon, Soo Young; Nam, Myung Hyun; Lee, Chang Kyu; Cho, Yun-Jung; Lim, Chae Seung

2016-01-01

ABSTRACT Nasopharyngeal swabs (NPSs) are being widely used as specimens for multiplex real-time reverse transcription (RT)-PCR for respiratory virus detection. However, it remains unclear whether NPS specimens are optimal for all viruses targeted by multiplex RT-PCR. In addition, the procedure to obtain NPS specimens causes coughing in most patients, which possibly increases the risk of nosocomial spread of viruses. In this study, paired NPS and saliva specimens were collected from 236 adult male patients with suspected acute respiratory illnesses. Specimens were tested for 16 respiratory viruses by multiplex real-time RT-PCR. Among the specimens collected from the 236 patients, at least 1 respiratory virus was detected in 183 NPS specimens (77.5%) and 180 saliva specimens (76.3%). The rates of detection of respiratory viruses were comparable for NPS and saliva specimens (P = 0.766). Nine virus species and 349 viruses were isolated, 256 from NPS specimens and 273 from saliva specimens (P = 0.1574). Adenovirus was detected more frequently in saliva samples (P < 0.0001), whereas influenza virus type A and human rhinovirus were detected more frequently in NPS specimens (P = 0.0001 and P = 0.0289, respectively). The possibility of false-positive adenovirus detection from saliva samples was excluded by direct sequencing. In conclusion, neither of the sampling methods was consistently more sensitive than the other. We suggest that these cost-effective methods for detecting respiratory viruses in mixed NPS-saliva specimens might be valuable for future studies. PMID:27807150

10 CFR 26.117 - Preparing urine specimens for storage and shipping.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 1 2013-01-01 2013-01-01 false Preparing urine specimens for storage and shipping. 26.117 Section 26.117 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.117 Preparing urine specimens for storage and shipping. (a) Both the donor and the collector...

10 CFR 26.117 - Preparing urine specimens for storage and shipping.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 1 2014-01-01 2014-01-01 false Preparing urine specimens for storage and shipping. 26.117 Section 26.117 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.117 Preparing urine specimens for storage and shipping. (a) Both the donor and the collector...

10 CFR 26.117 - Preparing urine specimens for storage and shipping.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 1 2012-01-01 2012-01-01 false Preparing urine specimens for storage and shipping. 26.117 Section 26.117 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.117 Preparing urine specimens for storage and shipping. (a) Both the donor and the collector...

10 CFR 26.117 - Preparing urine specimens for storage and shipping.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Preparing urine specimens for storage and shipping. 26.117 Section 26.117 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.117 Preparing urine specimens for storage and shipping. (a) Both the donor and the collector...

10 CFR 26.117 - Preparing urine specimens for storage and shipping.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false Preparing urine specimens for storage and shipping. 26.117 Section 26.117 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.117 Preparing urine specimens for storage and shipping. (a) Both the donor and the collector...

10 CFR 26.111 - Checking the acceptability of the urine specimen.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Checking the acceptability of the urine specimen. 26.111 Section 26.111 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.111 Checking the acceptability of the urine specimen. (a) Immediately after the donor...

10 CFR 26.111 - Checking the acceptability of the urine specimen.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false Checking the acceptability of the urine specimen. 26.111 Section 26.111 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.111 Checking the acceptability of the urine specimen. (a) Immediately after the donor...

Anthrax: Diagnosis

MedlinePlus

... Laboratory Testing Confirming Anthrax Through the Laboratory Response Network FAQs Information for Specific Groups Laboratory Professionals Collecting Specimens Recommended Specimens Worker Safety ...

KOTOBUKI-1 apparatus for cryogenic coherent X-ray diffraction imaging.

PubMed

Nakasako, Masayoshi; Takayama, Yuki; Oroguchi, Tomotaka; Sekiguchi, Yuki; Kobayashi, Amane; Shirahama, Keiya; Yamamoto, Masaki; Hikima, Takaaki; Yonekura, Koji; Maki-Yonekura, Saori; Kohmura, Yoshiki; Inubushi, Yuichi; Takahashi, Yukio; Suzuki, Akihiro; Matsunaga, Sachihiro; Inui, Yayoi; Tono, Kensuke; Kameshima, Takashi; Joti, Yasumasa; Hoshi, Takahiko

2013-09-01

We have developed an experimental apparatus named KOTOBUKI-1 for use in coherent X-ray diffraction imaging experiments of frozen-hydrated non-crystalline particles at cryogenic temperature. For cryogenic specimen stage with small positional fluctuation for a long exposure time of more than several minutes, we here use a cryogenic pot cooled by the evaporation cooling effect for liquid nitrogen. In addition, a loading device is developed to bring specimens stored in liquid nitrogen to the specimen stage in vacuum. The apparatus allows diffraction data collection for frozen-hydrated specimens at 66 K with a positional fluctuation of less than 0.4 μm and provides an experimental environment to easily exchange specimens from liquid nitrogen storage to the specimen stage. The apparatus was developed and utilized in diffraction data collection of non-crystalline particles with dimensions of μm from material and biological sciences, such as metal colloid particles and chloroplast, at BL29XU of SPring-8. Recently, it has been applied for single-shot diffraction data collection of non-crystalline particles with dimensions of sub-μm using X-ray free electron laser at BL3 of SACLA.

DNA Quantity and Quality in Remnants of Traffic-Killed Specimens of an Endangered Longhorn Beetle: A Comparison of Different Methods.

PubMed

Rusterholz, Hans-Peter; Ursenbacher, Sylvain; Coray, Armin; Weibel, Urs; Baur, Bruno

2015-01-01

The sampling of living insects should be avoided in highly endangered species when the sampling would further increase the risk of population extinction. Nonlethal sampling (wing clips or leg removals) can be an alternative to obtain DNA of individuals for population genetic studies. However, nonlethal sampling may not be possible for all insect species. We examined whether remnants of traffic-killed specimens of the endangered and protected flightless longhorn beetle Iberodorcadion fuliginator (L., 1758) can be used as a resource for population genetic analyses. Using insect fragments of traffic-killed specimens collected over 15 yr, we determined the most efficient DNA extraction method in relation to the state of the specimens (crushed, fragment, or intact), preservation (dried, airtight, or in ethanol), storage duration, and weight of the sample by assessing the quantity and quality of genomic DNA. A modified cetyltrimethyl ammonium bromide method provided the highest recovery rate of genomic DNA and the largest yield and highest quality of DNA. We further used traffic-killed specimens to evaluate two DNA amplification techniques (quantitative polymerase chain reaction [qPCR] and microsatellites). Both qPCR and microsatellites revealed successful DNA amplification in all degraded specimens or beetle fragments examined. However, relative qPCR concentration and peak height of microsatellites were affected by the state of specimen and storage duration but not by specimen weight. Our investigation demonstrates that degraded remnants of traffic-killed beetle specimens can serve as a source of high-quality genomic DNA, which allows to address conservation genetic issues. © The Author 2015. Published by Oxford University Press on behalf of the Entomological Society of America.

Leveraging biospecimen resources for discovery or validation of markers for early cancer detection.

PubMed

Schully, Sheri D; Carrick, Danielle M; Mechanic, Leah E; Srivastava, Sudhir; Anderson, Garnet L; Baron, John A; Berg, Christine D; Cullen, Jennifer; Diamandis, Eleftherios P; Doria-Rose, V Paul; Goddard, Katrina A B; Hankinson, Susan E; Kushi, Lawrence H; Larson, Eric B; McShane, Lisa M; Schilsky, Richard L; Shak, Steven; Skates, Steven J; Urban, Nicole; Kramer, Barnett S; Khoury, Muin J; Ransohoff, David F

2015-04-01

Validation of early detection cancer biomarkers has proven to be disappointing when initial promising claims have often not been reproducible in diagnostic samples or did not extend to prediagnostic samples. The previously reported lack of rigorous internal validity (systematic differences between compared groups) and external validity (lack of generalizability beyond compared groups) may be effectively addressed by utilizing blood specimens and data collected within well-conducted cohort studies. Cohort studies with prediagnostic specimens (eg, blood specimens collected prior to development of clinical symptoms) and clinical data have recently been used to assess the validity of some early detection biomarkers. With this background, the Division of Cancer Control and Population Sciences (DCCPS) and the Division of Cancer Prevention (DCP) of the National Cancer Institute (NCI) held a joint workshop in August 2013. The goal was to advance early detection cancer research by considering how the infrastructure of cohort studies that already exist or are being developed might be leveraged to include appropriate blood specimens, including prediagnostic specimens, ideally collected at periodic intervals, along with clinical data about symptom status and cancer diagnosis. Three overarching recommendations emerged from the discussions: 1) facilitate sharing of existing specimens and data, 2) encourage collaboration among scientists developing biomarkers and those conducting observational cohort studies or managing healthcare systems with cohorts followed over time, and 3) conduct pilot projects that identify and address key logistic and feasibility issues regarding how appropriate specimens and clinical data might be collected at reasonable effort and cost within existing or future cohorts. © Published by Oxford University Press 2015.

Leveraging Biospecimen Resources for Discovery or Validation of Markers for Early Cancer Detection

PubMed Central

Carrick, Danielle M.; Mechanic, Leah E.; Srivastava, Sudhir; Anderson, Garnet L.; Baron, John A.; Berg, Christine D.; Cullen, Jennifer; Diamandis, Eleftherios P.; Doria-Rose, V. Paul; Goddard, Katrina A. B.; Hankinson, Susan E.; Kushi, Lawrence H.; Larson, Eric B.; McShane, Lisa M.; Schilsky, Richard L.; Shak, Steven; Skates, Steven J.; Urban, Nicole; Kramer, Barnett S.; Khoury, Muin J.; Ransohoff, David F.

2015-01-01

Validation of early detection cancer biomarkers has proven to be disappointing when initial promising claims have often not been reproducible in diagnostic samples or did not extend to prediagnostic samples. The previously reported lack of rigorous internal validity (systematic differences between compared groups) and external validity (lack of generalizability beyond compared groups) may be effectively addressed by utilizing blood specimens and data collected within well-conducted cohort studies. Cohort studies with prediagnostic specimens (eg, blood specimens collected prior to development of clinical symptoms) and clinical data have recently been used to assess the validity of some early detection biomarkers. With this background, the Division of Cancer Control and Population Sciences (DCCPS) and the Division of Cancer Prevention (DCP) of the National Cancer Institute (NCI) held a joint workshop in August 2013. The goal was to advance early detection cancer research by considering how the infrastructure of cohort studies that already exist or are being developed might be leveraged to include appropriate blood specimens, including prediagnostic specimens, ideally collected at periodic intervals, along with clinical data about symptom status and cancer diagnosis. Three overarching recommendations emerged from the discussions: 1) facilitate sharing of existing specimens and data, 2) encourage collaboration among scientists developing biomarkers and those conducting observational cohort studies or managing healthcare systems with cohorts followed over time, and 3) conduct pilot projects that identify and address key logistic and feasibility issues regarding how appropriate specimens and clinical data might be collected at reasonable effort and cost within existing or future cohorts. PMID:25688116

Reduction in Hospital-Wide Clinical Laboratory Specimen Identification Errors following Process Interventions: A 10-Year Retrospective Observational Study

PubMed Central

Ning, Hsiao-Chen; Lin, Chia-Ni; Chiu, Daniel Tsun-Yee; Chang, Yung-Ta; Wen, Chiao-Ni; Peng, Shu-Yu; Chu, Tsung-Lan; Yu, Hsin-Ming; Wu, Tsu-Lan

2016-01-01

Background Accurate patient identification and specimen labeling at the time of collection are crucial steps in the prevention of medical errors, thereby improving patient safety. Methods All patient specimen identification errors that occurred in the outpatient department (OPD), emergency department (ED), and inpatient department (IPD) of a 3,800-bed academic medical center in Taiwan were documented and analyzed retrospectively from 2005 to 2014. To reduce such errors, the following series of strategies were implemented: a restrictive specimen acceptance policy for the ED and IPD in 2006; a computer-assisted barcode positive patient identification system for the ED and IPD in 2007 and 2010, and automated sample labeling combined with electronic identification systems introduced to the OPD in 2009. Results Of the 2000345 specimens collected in 2005, 1023 (0.0511%) were identified as having patient identification errors, compared with 58 errors (0.0015%) among 3761238 specimens collected in 2014, after serial interventions; this represents a 97% relative reduction. The total number (rate) of institutional identification errors contributed from the ED, IPD, and OPD over a 10-year period were 423 (0.1058%), 556 (0.0587%), and 44 (0.0067%) errors before the interventions, and 3 (0.0007%), 52 (0.0045%) and 3 (0.0001%) after interventions, representing relative 99%, 92% and 98% reductions, respectively. Conclusions Accurate patient identification is a challenge of patient safety in different health settings. The data collected in our study indicate that a restrictive specimen acceptance policy, computer-generated positive identification systems, and interdisciplinary cooperation can significantly reduce patient identification errors. PMID:27494020

Effects of vigorous mixing of blood vacuum tubes on laboratory test results.

PubMed

Lima-Oliveira, Gabriel; Lippi, Giuseppe; Salvagno, Gian Luca; Montagnana, Martina; Gelati, Matteo; Volanski, Waldemar; Boritiza, Katia Cristina; Picheth, Geraldo; Guidi, Gian Cesare

2013-02-01

To evaluate the effect of tubes mixing (gentle vs. vigorous) on diagnostic blood specimens collected in vacuum tube systems by venipuncture. Blood was collected for routine coagulation, immunochemistry and hematological testing from one hundred volunteers into six vacuum tubes: two 3.6 mL vacuum tubes containing 0.4 mL of buffered sodium citrate (9NC) 0.109 mol/L: 3.2 W/V%; two 3.5 mL vacuum tubes with clot activator and gel separator; and two 3.0 mL vacuum tubes containing 5.9 mg K(2)EDTA (Terumo Europe, Belgium). Immediately after the venipuncture all vacuum tubes (each of one additive type) were processed through two different procedures: i) Standard: blood specimens in K(2)EDTA- or sodium citrate-vacuum tubes were gently inverted five times whereas the specimens in tubes with clot activator and gel separator were gently inverted ten times, as recommended by the manufacturer; ii) Vigorous mix: all blood specimens were shaken up vigorously during 3-5s independently of the additive type inside the tubes. The significance of the differences between samples was assessed by Student's t-test or Wilcoxon ranked-pairs test after checking for normality. The level of statistical significance was set at P<0.05. No significant difference (P<0.05) was detected between the procedures for all tested parameters. Surprisingly only a visual alteration (presence of foam on the top) was shown by all the tubes mixed vigorously before centrifugation (Fig. 1 A, B and C). Moreover the serum tubes from vigorous mixing procedure shows a "blood ring" on the tube top after stopper removal (Fig. 1 D). Our results drop out a paradigm suggesting that the incorrect primary blood tubes mixing promotes laboratory variability. We suggest that similar evaluation should be done using other brands of vacuum tubes by each laboratory manager. Copyright © 2012 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Human papillomavirus type 16 is an important infectious factor in the high incidence of esophageal cancer in Anyang area of China.

PubMed

Li, T; Lu, Z M; Chen, K N; Guo, M; Xing, H P; Mei, Q; Yang, H H; Lechner, J F; Ke, Y

2001-06-01

To investigate the potential role of human papillomavirus (HPV) infection in the pathogenesis of esophageal carcinomas in the Anyang area of China, we have evaluated specimens collected by balloon cytology examination from volunteers in two regions with significantly different incidences of esophageal carcinoma. 138 donors were from a village in a county with an esophageal carcinoma (EC) age-adjusted mortality rate of 132x10(5), the remaining 68 were resident in a second village from another county with an EC mortality rate of 52x10(5). Specimens were evaluated using both polymerase chain reaction (PCR) amplification and in situ hybridization (ISH) protocols. PCR results showed that the prevalence of the human papillomavirus type 16 (HPV-16) E6 gene in the high incidence area was 1.9-fold higher than that of the low incidence area (72 and 37%, respectively, P < 0.01). Moreover, the positive rate corresponded with pathology grade. Similar results were obtained with the HPV-16 E7 gene. As the cells undergoing cytopathological progress, the HPV-16 E6 positive rate was increased, in both villages. In contrast to HPV-16 E6 and E7, detection of the HPV L1 gene was consistently lower, and its prevalence decreased with increasing dysplasia grades (P < 0.05). By ISH analyses, the expression rate of HPV-16 E6 in the specimens collected from the high incidence area was 2.2-fold higher than those from the low incidence area (49 versus 22%, respectively; P < 0.05), and transcription of the E6 gene paralleled cytopathology. HPV-18 was also detected in 17 and 15% of the specimens from the high and low incidence areas, respectively, but most of these samples were also simultaneously HVP-16 positive. These results suggest that HVP-16 plays a causative role in the high incidence of esophageal cancer in the Anyang region of CHINA:

Distribution host status and potential sources of resistance to Vittatidera zeaphila

USDA-ARS?s Scientific Manuscript database

Vittatidera zeaphila was described from stunted Zea mays (corn) roots collected in northwestern Tennessee (Obion County) in 2006. Similar cyst specimens had previously been collected in 1978 from Lauderdale County, TN, on Eleusine indica (goosegrass). Comparison of the 1978 specimens deposited in t...

21 CFR 866.2900 - Microbiological specimen collection and transport device.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Microbiological specimen collection and transport device. 866.2900 Section 866.2900 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices...

21 CFR 866.2900 - Microbiological specimen collection and transport device.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Microbiological specimen collection and transport device. 866.2900 Section 866.2900 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices...

21 CFR 866.2900 - Microbiological specimen collection and transport device.

Code of Federal Regulations, 2010 CFR

2010-04-01

... 21 Food and Drugs 8 2010-04-01 2010-04-01 false Microbiological specimen collection and transport device. 866.2900 Section 866.2900 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices...

21 CFR 866.2900 - Microbiological specimen collection and transport device.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Microbiological specimen collection and transport device. 866.2900 Section 866.2900 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices...

21 CFR 866.2900 - Microbiological specimen collection and transport device.

Code of Federal Regulations, 2011 CFR

2011-04-01

... 21 Food and Drugs 8 2011-04-01 2011-04-01 false Microbiological specimen collection and transport device. 866.2900 Section 866.2900 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Microbiology Devices...

From museum cases to the classroom: Emerging opportunities for specimen-based education

USDA-ARS?s Scientific Manuscript database

Natural history collections are one of the most powerful resources available for documenting the effects of changing environmental conditions on global biodiversity. Worldwide, more than 1.5 billion specimens are contained in natural history museums. These materials, collected over vast temporal and...

10 CFR 26.81 - Purpose and applicability.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 1 2014-01-01 2014-01-01 false Purpose and applicability. 26.81 Section 26.81 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.81 Purpose and applicability. This subpart contains requirements for collecting specimens for drug testing and...

10 CFR 26.81 - Purpose and applicability.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 1 2012-01-01 2012-01-01 false Purpose and applicability. 26.81 Section 26.81 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.81 Purpose and applicability. This subpart contains requirements for collecting specimens for drug testing and...

10 CFR 26.81 - Purpose and applicability.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 1 2013-01-01 2013-01-01 false Purpose and applicability. 26.81 Section 26.81 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.81 Purpose and applicability. This subpart contains requirements for collecting specimens for drug testing and...

10 CFR 26.81 - Purpose and applicability.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Purpose and applicability. 26.81 Section 26.81 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.81 Purpose and applicability. This subpart contains requirements for collecting specimens for drug testing and...

10 CFR 26.81 - Purpose and applicability.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false Purpose and applicability. 26.81 Section 26.81 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.81 Purpose and applicability. This subpart contains requirements for collecting specimens for drug testing and...

Beyond botany to genetic resource preservation: the S. P. Vander Kloet Vaccinium L. collections

USDA-ARS?s Scientific Manuscript database

Dr. S. P. Vander Kloet, botanist, traveled the world examining and obtaining specimens to redefine infrageneric taxonomic units within Vaccinium L., family Ericaceae. Besides his botanical treatises, his legacy includes herbarium voucher specimens and ex situ genetic resource collections including a...

Redescription of two European species of Acerentomidae (Protura) belonging to the Italian fauna.

PubMed

Galli, Loris; Capurro, Matteo; Costa, Fabio; Stadio, Gabriele Di; Sarà, Antonio; Zinni, Matteo

2016-08-22

Acerentulus apuliacus Rusek & Stumpp, 1988 is redescribed based on new specimens collected in Apulia and Basilicata (S-Italy) and deposited in the collection of Geneva Natural History Museum. Podolinella ruseki (Nosek, 1967) new combination is redescribed, based on the holotype from Austria and additional specimens collected in Liguria, NW Italy. The new material is deposited in the collection of the Dipartimento di Scienze della Terra, dell'Ambiente e della Vita, University of Genoa.

The outcome of the seminal fluid parameters collected via coitus interruptus versus masturbation.

PubMed

Bahyah, M Kamarul; Murad, Z Ahmad; Ghazali, I; Roszaman, R; Noraziana, A W; Mokhtar, A; Omar, M H

2010-03-01

A one year study was carried out to determine the outcome of the seminal fluid parameters collected via masturbation and coitus interruptus in 151 patients who were undergoing intrauterine insemination (IUI) and patients who came for seminal analysis. There were no statistically significant differences in terms of volume, concentration, progressive motility and normal morphology from specimens collected via coitus interruptus compared to specimens collected via masturbation. Pregnancy outcomes were also comparable.

Two new planthopper species (Hemiptera, Fulgoroidea, Caliscelidae) collected in pitfall traps in Zambia.

PubMed

Chmurova, Lucia; Webb, Michael D

2016-08-22

Two new species of planthoppers in the family Caliscelidae (Hemiptera: Fulgoroidea) are described from Zambia, i.e., Afronaso spinosa sp. n. and Calampocus zambiaensis sp. n. All specimens are flightless males and nearly all were collected from baited pitfall traps (except for one specimen collected from a yellow pan trap), suggesting that they live near to or on the ground.

Self-Collected versus Clinician-Collected Sampling for Chlamydia and Gonorrhea Screening: A Systemic Review and Meta-Analysis

PubMed Central

Lunny, Carole; Taylor, Darlene; Hoang, Linda; Wong, Tom; Gilbert, Mark; Lester, Richard; Krajden, Mel; Ogilvie, Gina

2015-01-01

Background The increases in STI rates since the late 1990s in Canada have occurred despite widespread primary care and targeted public health programs and in the setting of universal health care. More innovative interventions are required that would eliminate barriers to STI testing such as internet-based or mail-in home and community service testing for patients that are hard to reach, who refuse to go for clinician-based testing, or who decline an examination. Jurisdictions such as New Zealand and some American states currently use self-collected sampling, but without the required evidence to determine whether self-collected specimens are as accurate as clinician-collected specimens in terms of chlamydia and gonorrhea diagnostic accuracy. The objective of the review is to compare self-collected vaginal, urine, pharyngeal and rectal samples to our reference standard - clinician-collected cervical, urethral, pharyngeal and rectal sampling techniques to identify a positive specimen using nucleic acid amplification test assays. Methods The hierarchical summary receiver operating characteristic and the fixed effect models were used to assess the accuracy of comparable specimens that were collected by patients compared to clinicians. Sensitivity and specificity estimates with 95% confidence intervals (CI) were reported as our main outcome measures. Findings We included 21 studies based on over 6100 paired samples. Fourteen included studies examined chlamydia only, 6 compared both gonorrhea and chlamydia separately in the same study, and one examined gonorrhea. The six chlamydia studies comparing self-collection by vaginal swab to a clinician-collected cervical swab had the highest sensitivity (92%, 95% CI 87-95) and specificity (98%, 95% CI 97-99), compared to other specimen-types (urine/urethra or urine/cervix). Six studies compared urine self-samples to urethra clinician-collected samples in males and produced a sensitivity of 88% (95% CI 83-93) and a specificity of 99% (95% CI 0.94-0.99). Taking into account that urine samples may be less sensitive than cervical samples, eight chlamydia studies that compared urine self-collected verses clinician-collected cervical samples had a sensitivity of 87% (95% CI 81-91) and high specificity of 99% (95% CI 0.98-1.00). For gonorrhea testing, self-collected urine samples compared to clinician-collected urethra samples in males produced a sensitivity of 92% (95% CI 83-97) and specificity of 99% (95% CI 0.98-1.00). Conclusion The sensitivity and specificity of vaginal self-collected swabs compared to swabs collected by clinicians supports the use of vaginal swab as the recommended specimen of choice in home-based screening for chlamydia and gonorrhea. Urine samples for gonorrhea collected by men had comparably high sensitivity and specificity, so could be recommended as they can be left at room temperature for several days, allowing for the possibility of mail-in home-based testing. In populations that may not go for testing at all, do not have the option of clinical testing, or who refuse a clinical examination, self-collected screening would be a good alternative. We recommend that guidelines on how to self-collect gonorrhea and chlamydia urine, vaginal, rectal and pharyngeal specimens be published. PMID:26168051

Evaluation of the Reliability and Sensitivity of NDT Methods for Titanium Alloys

DTIC Science & Technology

1974-06-01

Specimens Several ’hand forged billets (Ti-6Al-6V-2Sn) containing porosity have teen collected dtueing past internal programs. The porosity is depicted...offectiveneess •cf the systems are discussed in Section i-k of Llh:i,; l’(, porn . It should be kept in mind that tile pcl etrantm (wN(l t1111i. ý:tud:y

An illustrated catalogue of the types of Stratiomyidae (Diptera: Brachycera) in the collection of Museu Nacional, Rio de Janeiro, Brazil.

PubMed

Fachin, Diego Aguilar; Couri, Márcia Souto; De Mello-Patiu, Cátia Antunes

2016-02-26

A catalogue of the type specimens of Stratiomyidae (Diptera: Brachycera) held in the collection of Museu Nacional, Rio de Janeiro, Brazil (MNRJ) is presented. A total number of 50 type specimens of 18 valid Neotropical species were recognized and are listed in alphabetical order of subfamily, genus and specific epithet. Photos of 12 primary types of the species and bibliographical data of the original descriptions, labels and condition of all type specimens are also provided.

Drugged Driving in Wisconsin: Oral Fluid Versus Blood.

PubMed

Edwards, Lorrine D; Smith, Katherine L; Savage, Theodore

2017-07-01

A pilot project was conducted in Dane County, Wisconsin, to evaluate the frequency of individuals driving under the influence of drugs (DUID). Evidentiary blood specimens, collected from subjects arrested for Operating While Intoxicated (OWI), were compared to oral fluid (OF) results obtained with the Alere DDS2®, a handheld screening device. The project objectives were to evaluate (i) the Alere DDS2® for use by police officers in the field, (ii) the frequency of individuals DUID and drugs combined with alcohol among OWI cases, (iii) the differences between detecting drugs in OF and in blood, and (iv) the effect of the laboratory drug testing cancellation policy (LCP) when the blood alcohol concentration (BAC) exceeds 0.100 g/100 mL. Following the arrest and collection of blood, subjects were asked to voluntarily participate in the project and provide an OF specimen. The OF was presumptively screened with the Alere DDS2® for six drug categories including (ng/mL) amphetamine (50), benzodiazepines (temazepam, 20), cocaine (benzoylecgonine, 30), methamphetamine (50), opioids (morphine, 40) and THC (delta-9-THC, 25). Results obtained with the OF screening instrument were not confirmed. A total of 104 subjects (22 female, 82 male), ages 18-72, were included in the project. Blood specimens were tested by gas chromatography-headspace (GCHS-FID) for volatiles, enzyme immunoassay (Siemens Viva-E Drug Testing System), and an alkaline basic drug screen with gas chromatography-mass spectrometry (GCMS) analysis. To compensate for differences between the EIA and the Alere DDS2® drug categories, results from the enzyme immunoassay and the alkaline basic drug screen were combined for purposes of comparing OF to blood. Seventy-six of 104 (73%) subjects arrested for OWI were driving under the influence of alcohol; 71 of the 76 had a BAC exceeding 0.10 g/100 mL. Subjects with a BAC exceeding the LCP, screened positive for drugs in both OF (n = 29) and blood (n = 28). Overall, one or more positive drug screening result was observed in 57 (55%) and 50 (48%) subjects for OF and blood specimens, respectively. THC was the most frequently detected drug category in both OF (n = 46) and whole blood (n = 44). Drug Recognition Expert (DRE) evaluations were performed on 18 subjects. In general, the Alere DDS2® results were consistent with the combined screening results observed in evidentiary blood specimens. This project was limited in scope as a second OF specimen was not collected for confirmation of drugs, however it did demonstrate that nearly 40% of the subjects with concentrations of alcohol exceeding 0.10 g/100 mL, screened positive for one or more drug categories in both OF and blood. The Alere DDS2® portable OF screening instrument may be useful in assisting law enforcement with identifying individuals driving under the influence of drugs and establishing probable cause at roadside for making DUID arrests. © The Author 2017. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

US-Canada Great Lakes Regional Specimen Bank Feasibility Study.

PubMed

Kerry, A; Edmonds, C J; Landon, L; Yonker, T L

1993-11-01

A study to examine the feasibility of establishing a Regional Specimen Bank in the Great Lakes area of the United States and Canada has recently been initiated by the Michigan Audubon Society. There are several existing formal and informal specimen banking facilities active in the region but their combined adequacy has not been evaluated. This feasibility study will establish the need and use of a regional bank and the institution(s) necessary to satisfy this need will be recommended. The study will address the scope required to meet present and future needs including the types of specimens to be represented in the bank, geographic coverage and protocols for collection, shipping, processing, analysis and storage. A management policy of the bank will be developed encompassing business operation, costs, governing structure and personnel requirements. The legal requirements of the bank will be determined with regards to the acquisition of samples, transport across national boundaries, access to specimens and information, and liability during operation. An effective information dissemination network will be recommended that is compatible with national and international partners, will facilitate technology and information transfer and support the quality and status of the bank. Determination of secure, long-term funding sources will be one of the key elements to ensuring a safe repository. This feasibility study is funded by the Great Lakes Protection Fund.

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...

78 FR 27404 - Agency Information Collection Activities; Announcement of Office of Management and Budget...

Federal Register 2010, 2011, 2012, 2013, 2014

2013-05-10

...; Guidance on Informed Consent for In Vitro Diagnostic Device Studies Using Leftover Human Specimens That Are... on Informed Consent for In Vitro Diagnostic Device Studies Using Leftover Human Specimens That Are... submitted a proposed collection of information entitled ``Guidance on Informed Consent for In Vitro...

49 CFR 219.302 - Prompt specimen collection; time limitation.

Code of Federal Regulations, 2010 CFR

2010-10-01

... RAILROAD ADMINISTRATION, DEPARTMENT OF TRANSPORTATION CONTROL OF ALCOHOL AND DRUG USE Testing for Cause... or drug testing under this section after the expiration of an eight-hour period from— (1) The time of... present) and the request has been made to commence collection of the drug testing specimens within that...

49 CFR 219.302 - Prompt specimen collection; time limitation.

Code of Federal Regulations, 2014 CFR

2014-10-01

... RAILROAD ADMINISTRATION, DEPARTMENT OF TRANSPORTATION CONTROL OF ALCOHOL AND DRUG USE Testing for Cause... or drug testing under this section after the expiration of an eight-hour period from— (1) The time of... present) and the request has been made to commence collection of the drug testing specimens within that...

49 CFR 219.302 - Prompt specimen collection; time limitation.

Code of Federal Regulations, 2011 CFR

2011-10-01

... RAILROAD ADMINISTRATION, DEPARTMENT OF TRANSPORTATION CONTROL OF ALCOHOL AND DRUG USE Testing for Cause... or drug testing under this section after the expiration of an eight-hour period from— (1) The time of... present) and the request has been made to commence collection of the drug testing specimens within that...

49 CFR 219.302 - Prompt specimen collection; time limitation.

Code of Federal Regulations, 2013 CFR

2013-10-01

... RAILROAD ADMINISTRATION, DEPARTMENT OF TRANSPORTATION CONTROL OF ALCOHOL AND DRUG USE Testing for Cause... or drug testing under this section after the expiration of an eight-hour period from— (1) The time of... present) and the request has been made to commence collection of the drug testing specimens within that...

49 CFR 219.302 - Prompt specimen collection; time limitation.

Code of Federal Regulations, 2012 CFR

2012-10-01

... RAILROAD ADMINISTRATION, DEPARTMENT OF TRANSPORTATION CONTROL OF ALCOHOL AND DRUG USE Testing for Cause... or drug testing under this section after the expiration of an eight-hour period from— (1) The time of... present) and the request has been made to commence collection of the drug testing specimens within that...

10 CFR 26.93 - Preparing for alcohol testing.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false Preparing for alcohol testing. 26.93 Section 26.93 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.93 Preparing for alcohol testing. (a) Immediately before collecting a specimen for alcohol testing, the collector...

10 CFR 26.93 - Preparing for alcohol testing.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Preparing for alcohol testing. 26.93 Section 26.93 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.93 Preparing for alcohol testing. (a) Immediately before collecting a specimen for alcohol testing, the collector...

Recovery and Stability of Δ9-Tetrahydrocannabinol Using the Oral-Eze® Oral Fluid Collection System and Intercept® Oral Specimen Collection Device.

PubMed

Samano, Kimberly L; Anne, Lakshmi; Johnson, Ted; Tang, Kenneth; Sample, R H Barry

2015-10-01

Oral fluid (OF) is increasingly used for clinical, forensic and workplace drug testing as an alternative to urine. Uncertainties surrounding OF collection device performance, drug stability and testing reproducibility may be partially responsible for delays in the implementation of OF testing in regulated drug testing programs. Stability of Δ(9)-tetrahydrocannabinol (THC) fortified and authentic specimens was examined after routine collection, transport and laboratory testing. Acceptable recovery and stability were observed when THC-fortified OF (1.5 and 4.5 ng/mL) was applied to Oral-Eze devices. Neat OF samples collected with Oral-Eze, processed per the package insert, and fortified with THC (3 and 6 ng/mL) were stable (±20%) at room temperature (21-25°C), refrigerated (2-8°C) and frozen (-25 to -15°C) conditions up to 1 month, while samples collected with Intercept devices showed decreases at refrigerated and room temperatures. After long-term refrigerated or frozen storage, maximum reductions in THC concentrations were 42% for Oral-Eze and 69% for Intercept. After ≥1 year frozen storage, 80.7% of laboratory specimens positive for THC (3 ng/mL cut-off) by GC-MS were reconfirmed positive (within 25%), with an average THC decrease of 4.2%. Specimens (n = 47) processed with Oral-Eze (diluted) and tested via enzyme immunoassay were concordant with LC-MS-MS results and showed 100% sensitivity and 95% specificity. Paired specimens collected with Oral-Eze and Intercept exhibited 98% overall agreement between the immunoassay test systems. Collectively, these data demonstrate consistent and reproducible recovery and stability of THC in OF after collection, transport and laboratory testing using the Oral-Eze OF Collection System. © The Author 2015. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Applications of deep convolutional neural networks to digitized natural history collections

PubMed Central

Frandsen, Paul B.; Dikow, Rebecca B.; Brown, Abel; Orli, Sylvia; Peters, Melinda; Metallo, Adam; Funk, Vicki A.; Dorr, Laurence J.

2017-01-01

Abstract Natural history collections contain data that are critical for many scientific endeavors. Recent efforts in mass digitization are generating large datasets from these collections that can provide unprecedented insight. Here, we present examples of how deep convolutional neural networks can be applied in analyses of imaged herbarium specimens. We first demonstrate that a convolutional neural network can detect mercury-stained specimens across a collection with 90% accuracy. We then show that such a network can correctly distinguish two morphologically similar plant families 96% of the time. Discarding the most challenging specimen images increases accuracy to 94% and 99%, respectively. These results highlight the importance of mass digitization and deep learning approaches and reveal how they can together deliver powerful new investigative tools. PMID:29200929

10 CFR 26.95 - Conducting an initial test for alcohol using a breath specimen.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 1 2013-01-01 2013-01-01 false Conducting an initial test for alcohol using a breath specimen. 26.95 Section 26.95 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.95 Conducting an initial test for alcohol using a breath specimen. (a) The...

10 CFR 26.95 - Conducting an initial test for alcohol using a breath specimen.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 1 2012-01-01 2012-01-01 false Conducting an initial test for alcohol using a breath specimen. 26.95 Section 26.95 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.95 Conducting an initial test for alcohol using a breath specimen. (a) The...

10 CFR 26.95 - Conducting an initial test for alcohol using a breath specimen.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 1 2014-01-01 2014-01-01 false Conducting an initial test for alcohol using a breath specimen. 26.95 Section 26.95 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.95 Conducting an initial test for alcohol using a breath specimen. (a) The...

10 CFR 26.95 - Conducting an initial test for alcohol using a breath specimen.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false Conducting an initial test for alcohol using a breath specimen. 26.95 Section 26.95 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.95 Conducting an initial test for alcohol using a breath specimen. (a) The...

10 CFR 26.95 - Conducting an initial test for alcohol using a breath specimen.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Conducting an initial test for alcohol using a breath specimen. 26.95 Section 26.95 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.95 Conducting an initial test for alcohol using a breath specimen. (a) The...

Entomological Collections in the Age of Big Data.

PubMed

Short, Andrew Edward Z; Dikow, Torsten; Moreau, Corrie S

2018-01-07

With a million described species and more than half a billion preserved specimens, the large scale of insect collections is unequaled by those of any other group. Advances in genomics, collection digitization, and imaging have begun to more fully harness the power that such large data stores can provide. These new approaches and technologies have transformed how entomological collections are managed and utilized. While genomic research has fundamentally changed the way many specimens are collected and curated, advances in technology have shown promise for extracting sequence data from the vast holdings already in museums. Efforts to mainstream specimen digitization have taken root and have accelerated traditional taxonomic studies as well as distribution modeling and global change research. Emerging imaging technologies such as microcomputed tomography and confocal laser scanning microscopy are changing how morphology can be investigated. This review provides an overview of how the realization of big data has transformed our field and what may lie in store.

Response of High Latitude Coralline Algae to pCO2 and Thermal Stress

NASA Astrophysics Data System (ADS)

Garlick-Ott, K.; Williams, B.; Chan, P. T. W.; Westfield, I. T.; Rasher, D.; Ries, J. B.; Adey, W.; Halfar, J.

2016-12-01

The impacts of recent and future anthropogenic increases in atmospheric pCO2 causing ocean acidification and temperature on high-latitude oceans, and the marine organisms that inhabit them, are varied and poorly understood. The ecologically important crustose coralline alga Clathromorphum compactum may be particularly vulnerable to ocean acidification due to the relatively high solubility of its high Mg-calcite skeleton . This species of coralline algae is abundant throughout coastal mid-to-high latitude areas of the northern hemisphere, and calcifies annually-banded skeletons with longevities of up to 650 years. Here we used micro-computed tomography (micro-CT) to evaluate the impact of decreasing seawater pH and increasing temperature on skeletal density of algal specimens cultured in a fully crossed pCO2 (280, 400, 700, 2800 µatm) and temperature (6.5, 8.7, 12.4 °C) laboratory experiment. To examine the natural variability in coralline algal skeletal density, additional long-lived wild C. compactum specimens were collected along a latitudinal transect extending from the Gulf of Maine to the Canadian Arctic Archipelago. Density time series generated from the wild specimens spans the past several decades to century, and were used to evaluate other environmental parameters that may influence the skeletal density of coralline algae. This research will evaluate the resiliency of this alga to future environmental change.

Real-time confocal laser endomicroscopic evaluation of primary liver cancer based on human liver autofluorescence.

PubMed

Maki, Harufumi; Kawaguchi, Yoshikuni; Arita, Junichi; Akamatsu, Nobuhisa; Kaneko, Junichi; Sakamoto, Yoshihiro; Hasegawa, Kiyoshi; Harihara, Yasushi; Kokudo, Norihiro

2017-02-01

Confocal laser endomicroscopy (CLE) is available for real-time microscopic examination. This study aims to evaluate the usefulness of intraoperative CLE examination as a modality to evaluate surgical margins in surgery for primary liver cancer. A probe-based CLE system (Cellvizio 100, Mauna Kea Technologies, Paris, France) was used. The subjects comprised seven specimens obtained from six patients with primary liver cancer in November 2015. The probe was manually attached to the surfaces of specimens, and images were collected without external fluorophores. CLE images were compared with hematoxylin and eosin-stained slides. Fluorescence intensity (FI) values of the CLE images were assessed using luminance-analyzing software. CLE examination visualized non-cancerous regions in the background liver as regular structures with high fluorescence because of human liver autofluorescence. Conversely, hepatocellular carcinoma and intrahepatic cholangiocarcinoma were depicted as irregular structures with low fluorescence. The median FI values of the non-cancerous regions and the cancerous regions were 104 (79.8-156) and 74.9 (60.6-106), respectively, and were significantly different (P = 0.031). The probe-based CLE enables real-time differentiation of cancerous regions from non-cancerous tissues in surgical specimens because of human liver autofluorescence. CLE can be used to confirm negative surgical margins in the operating room. J. Surg. Oncol. 2017;115:151-157. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Numerical 3D flow simulation of ultrasonic horns with attached cavitation structures and assessment of flow aggressiveness and cavitation erosion sensitive wall zones.

PubMed

Mottyll, Stephan; Skoda, Romuald

2016-07-01

As a contribution to a better understanding of cavitation erosion mechanisms, a compressible inviscid finite volume flow solver with barotropic homogeneous liquid-vapor mixture cavitation model is applied to ultrasonic horn set-ups with and without stationary specimen, that exhibit attached cavitation at the horn tip. Void collapses and shock waves, which are closely related to cavitation erosion, are resolved. The computational results are compared to hydrophone, shadowgraphy and erosion test data. At the horn tip, vapor volume and topology, subharmonic oscillation frequency as well as the amplitude of propagating pressure waves are in good agreement with experimental data. For the evaluation of flow aggressiveness and the assessment of erosion sensitive wall zones, statistical analyses of wall loads and of the multiplicity of distinct collapses in wall-adjacent flow regions are applied to the horn tip and the stationary specimen. An a posteriori projection of load collectives, i.e. cumulative collapse rate vs. collapse pressure, onto a reference grid eliminates the grid dependency effectively for attached cavitation at the horn tip, whereas a significant grid dependency remains at the stationary specimen. The load collectives show an exponential decrease towards higher collapse pressures. Erosion sensitive wall zones are well predicted for both, horn tip and stationary specimen, and load profiles are in good qualitative agreement with measured topography profiles of eroded duplex stainless steel samples after long-term runs. For the considered amplitude and gap width according to ASTM G32-10 standard, the analysis of load collectives reveals that the distinctive erosive ring shape at the horn tip can be attributed to frequent breakdown and re-development of a small portion of the tip-attached cavity. This partial breakdown of the attached cavity repeats at each driving cycle and is associated with relatively moderate collapse peak pressures, whereas the stationary specimen is rather unfrequently stressed at the end of each subharmonic oscillation cycle by the violent collapse of the complete cavity. Copyright © 2016 Elsevier B.V. All rights reserved.

Five task clusters that enable efficient and effective digitization of biological collections

PubMed Central

Nelson, Gil; Paul, Deborah; Riccardi, Gregory; Mast, Austin R.

2012-01-01

Abstract This paper describes and illustrates five major clusters of related tasks (herein referred to as task clusters) that are common to efficient and effective practices in the digitization of biological specimen data and media. Examples of these clusters come from the observation of diverse digitization processes. The staff of iDigBio (The U.S. National Science Foundation’s National Resource for Advancing Digitization of Biological Collections) visited active biological and paleontological collections digitization programs for the purpose of documenting and assessing current digitization practices and tools. These observations identified five task clusters that comprise the digitization process leading up to data publication: (1) pre-digitization curation and staging, (2) specimen image capture, (3) specimen image processing, (4) electronic data capture, and (5) georeferencing locality descriptions. While not all institutions are completing each of these task clusters for each specimen, these clusters describe a composite picture of digitization of biological and paleontological specimens across the programs that were observed. We describe these clusters, three workflow patterns that dominate the implemention of these clusters, and offer a set of workflow recommendations for digitization programs. PMID:22859876

On the correct name of Icterus bullockii (Passeriformes: Icteridae)

USGS Publications Warehouse

Chesser, R. Terry

2013-01-01

William Bullock was an Englishman who owned the Egyptian Hall (also known as the London Museum or Bullock’s Museum) at Piccadilly in London, a museum opened in 1812 to display his collection of antiquities, artifacts, and natural history specimens. Following the sale of Bullock’s collection in 1819, the Egyptian Hall served as an exhibition space. Bullock and his son, William Bullock, Jr., both enthusiastic naturalists, travelled in Mexico in 1822–1823, spending some six months together collecting natural history specimens and other artifacts for exhibition and investigating mining and other business opportunities (Costeloe 2006). The elder Bullock returned to London with the collections in 1823, but his son, while ostensibly managing the silver mine his father had purchased in Temascaltepec, outside of Mexico City, continued to travel in Mexico and collect specimens, often in the company of German naturalist Ferdinand Deppe (Costeloe 2006). William Bullock, Sr., meanwhile prepared the Mexican collection for exhibition at the Egyptian Hall. Twin exhibitions on ancient and modern Mexico opened, with much fanfare, in April 1824, and were a great success, remaining open until September 1825 (Costeloe 2006). Afterwards, the contents of the exhibitions were dispersed via auction, but not before Bullock had made the bird specimens available to English naturalist William Swainson for “recording this portion of his discoveries” (Swainson 1827: 365).

Salivary sex hormone measurement in a national, population-based study of older adults.

PubMed

Gavrilova, Natalia; Lindau, Stacy Tessler

2009-11-01

To describe the methods used for, correlates of cooperation with, and validity of in-home salivary specimens collected from older adults. Salivary specimens were collected between 2005 and 2006 during in-home interviews with a probability sample of 3,005 U.S. men and women, ages 57-85 years. Sex hormone levels were assessed by enzyme-linked immunoassay conducted at Salimetrics, LLC (State College, PA). Mean salivary sex hormone concentrations were compared by gender and in relation to medication use and health conditions. Self-collected saliva specimens were provided by 2,722 (90.6%) individuals; 95.8% of these were adequate for analysis. Black participants were significantly less likely than individuals of other racial/ethnic groups to provide a salivary specimen; age, gender, education, and self-rated health were not associated with participation. Mean testosterone levels were higher in men compared with women, and estradiol levels were higher in women using estrogens. Salivary hormone measurements obtained in the National Social Life, Health, and Aging Project (NSHAP) and other studies are of similar magnitude. NSHAP is the first large, population-based study of older adults to measure salivary estradiol, progesterone, dehydroepiandrosterone (DHEA), and, in women, testosterone. These data demonstrate a high cooperation rate with in-home salivary specimen collection from older adults and good validity of sex hormone measurements.

An Analysis of Factors Affecting Genotyping Success from Museum Specimens Reveals an Increase of Genetic and Morphological Variation during a Historical Range Expansion of a European Spider

PubMed Central

Krehenwinkel, Henrik; Pekar, Stano

2015-01-01

Natural history collections house an enormous amount of plant and animal specimens, which constitute a promising source for molecular analyses. Storage conditions differ among taxa and can have a dramatic effect on the success of DNA work. Here, we analyze the feasibility of DNA extraction from ethanol preserved spiders (Araneae). We tested genotyping success using several hundred specimens of the wasp spider, Argiope bruennichi, deposited in two large German natural history collections. We tested the influence of different factors on the utility of specimens for genotyping. Our results show that not the specimen’s age, but the museum collection is a major predictor of genotyping success. These results indicate that long term storage conditions should be optimized in natural history museums to assure the utility of collections for DNA work. Using historical material, we also traced historical genetic and morphological variation in the course of a poleward range expansion of A. bruennichi by comparing contemporary and historical specimens from a native and an invasive population in Germany. We show that the invasion of A. bruennichi is tightly correlated with an historical increase of genetic and phenotypic variation in the invasive population. PMID:26309219

Multicenter Clinical Evaluation of the Alere i Respiratory Syncytial Virus Isothermal Nucleic Acid Amplification Assay.

PubMed

Hassan, Ferdaus; Hays, Lindsay M; Bonner, Aleta; Bradford, Bradley J; Franklin, Ruffin; Hendry, Phyllis; Kaminetsky, Jed; Vaughn, Michael; Cieslak, Kristin; Moffatt, Mary E; Selvarangan, Rangaraj

2018-03-01

The Alere i respiratory syncytial virus (RSV) assay is an isothermal nucleic acid amplification test capable of detecting RSV directly from respiratory specimens, with results being available in ≤13 min after test initiation. The objective of this study was to evaluate the performance characteristics of the Alere i RSV assay in a point-of-care setting by using direct nasopharyngeal (NP) swab specimens (direct NP) and nasopharyngeal swab specimens eluted and transported in viral transport medium (VTM NP). The study was a prospective, multicenter, clinical trial conducted at 9 sites across the United States to evaluate the clinical performance of the Alere i RSV assay with respiratory specimens obtained from both children (age, <18 years) and older adults (age, >60 years). The performance of the Alere i RSV assay was compared with that of the reference method, the Prodesse ProFlu+ real-time reverse transcriptase PCR (RT-PCR) assay. All specimens with discrepant test results were tested further by a second FDA-cleared PCR assay (the Verigene respiratory virus plus nucleic acid test; Luminex Inc., TX). A total of 554 subjects with signs and symptoms of respiratory infections were enrolled, and respiratory samples were collected in this study. In comparison with the ProFlu+ real-time RT-PCR, the overall sensitivity and specificity of Alere i RSV assay for the detection of RSV were 98.6% (95% confidence interval [CI], 94.4 to 99.7%) and 98.0% (95% CI, 95.8 to 99.1%), respectively, for direct NP and 98.6% (95% CI, 94.4 to 99.7%) and 97.8% (95% CI, 95.5 to 98.9%), respectively, for VTM NP. The Alere i RSV is a highly sensitive and specific molecular assay ideal for rapid RSV detection in patients in the point-of-care setting due to its minimal hands-on time and rapid result availability. Copyright © 2018 American Society for Microbiology.

TS mRNA levels can predict pemetrexed and raltitrexed sensitivity in colorectal cancer.

PubMed

Zhang, Qun; Shen, Jie; Wang, Hao; Hu, Jing; Yu, Lixia; Xie, Li; Wei, Jia; Liu, Baorui; Guan, Wenxian; Qian, Xiaoping

2014-02-01

The purpose of the study is to analyze the relationship between tumor thymidylate synthase (TS) mRNA expression levels and raltitrexed/pemetrexed/5-FU sensitivity. We collected freshly removed colorectal tumor specimens from 50 patients. Chemosensitivities to anticancer drugs were evaluated by histoculture drug response assay. We adopted quantitative reverse transcription polymerase chain reaction for TS mRNA detection and immunohistochemical staining for assessing TS expression in tumor tissues. There is a significant relationship between TS mRNA expression levels and in vitro chemosensitivity of freshly removed colorectal tumor specimens to pemetrexed (P < 0.001)/raltitrexed (P = 0.004)/5-FU (P = 0.007). TS mRNA expression levels can predict pemetrexed and raltitrexed sensitivity in colorectal cancer.

Description of the female of Navicordulia aemulatrix Pinto & Lamas and additional notes on the male (Odonata: Corduliidae).

PubMed

Pinto, A P; Lamas, C J E

2011-01-01

The female of Navicordulia aemulatrix Pinto & Lamas is described and illustrated for the first time based on a single specimen from the same locality of the type series (state of Santa Catarina, [municipality of São Bento do Sul, 26°14'58"S, 49°22'59"W, railroad station] Rio Vermelho, 29.I.1952, in MZSP). In addition, further morphological notes for the male are provided based on three specimens collected at the type locality and at a new locality in the state of Santa Catarina (Timbó municipality). The pronotal process present in N. aemulatrix is re-evaluated and considered non-homologous to that found in Neocordulia setifera (Hagen in Selys) as previously suggested.

Shocked materials from the Dutch Peak diamictite, Utah

NASA Technical Reports Server (NTRS)

Hoerz, F.; Bunch, T. E.; Oberbeck, V. R.

1994-01-01

Evidence of shock metamorphism in the Dutch Peak diamictite in the Sheeprock Mountains, Utah, is reported. The Dutch Peak diamictite is of Proterozoic age and is a minor part of the Dutch Peak formation. A shocked sample, specimen A250, was collected during a brief visit of the Harker Canyon area of the Sheeprock Mountains. This sample consists of equant, anhedral grains of quartz, K-feldspar, and plagioclase. The crystallographic orientation of 244 lamellae systems in 106 grains was measured. It is presently difficult to evaluate the significance of this single specimen. Without additional and substantial field work, and petrographic characterization of this formation, a number of scenarios for the presence of a shocked clast and the emplacement of the entire formation remain viable.

Toxicity and paralytic shellfish toxin profiles of the xanthid crabs, Lophozozymus pictor and Zosimus aeneus, collected from some Australian coral reefs.

PubMed

Llewellyn, L E; Endean, R

1989-01-01

Purification of toxic aqueous extracts from the xanthid crabs Zosimus aeneus and Lophozozymus pictor, collected from Australian waters, yielded paralytic shelfish toxins, including saxitoxin (STX), neosaxitoxin (neoSTX) and gonyautoxins 1, 2 and 4 (GTX1,2,4). No more than two paralytic shellfish toxins were found in any of the purified extracts from any specimen. Four specimens of Z. aeneus and one specimen of L. pictor each contained more toxic material than the suggested human oral lethal dose. The moult of a specimen of L. pictor was toxic, which may indicate a route in crabs for toxin removal.

The type material of Mantodea (praying mantises) deposited in the National Museum of Natural History, Smithsonian Institution, USA

PubMed Central

Svenson, Gavin J.

2014-01-01

Abstract The collection of Mantodea of the National Museum of Natural History, Smithsonian Institution, includes 26 holotypes, 7 allotypes, 4 lectotypes, 23 paratypes, and 1 paralectotype. Four type specimens were designated as lectotypes within this work. Highly accurate measurement data, high resolution images of specimens and labels, verbatim label data, georeferenced coordinates, original and newly assigned database codes, and bibliographic data are presented for all primary types. Label data for all paratype specimens in the collection are provide in tabular form. The location of the USNM collection has been moved to the Cleveland Museum of Natural History as a loan under the Off-site Enhancement Program. PMID:25152673

Preparing soft-bodied arthropods for microscope examination: Aphids (Insecta: Hemiptera: Aphididae)

USDA-ARS?s Scientific Manuscript database

Proper identification of aphids (Hemiptera: Aphididae) require preparation of the specimen on a microscope slide. This training video provides visual instruction on how to prepare aphid specimens on microscope slides for examination and indentification. Steps ranging from collection, specimen clear...

Preparing soft-bodied arthropods for microscope examination: Whiteflies (Insecta: Hemiptera: Alyrodidae)

USDA-ARS?s Scientific Manuscript database

Proper identification of whiteflies (Hemiptera:Alyrodidae) requires preparation of the specimen on a microscope slide. This training video provides visual instruction on how to prepare whitefly specimens on microscope slides for examination and identification. Steps ranging from collection, specimen...

A DNA 'barcode blitz': rapid digitization and sequencing of a natural history collection.

PubMed

Hebert, Paul D N; Dewaard, Jeremy R; Zakharov, Evgeny V; Prosser, Sean W J; Sones, Jayme E; McKeown, Jaclyn T A; Mantle, Beth; La Salle, John

2013-01-01

DNA barcoding protocols require the linkage of each sequence record to a voucher specimen that has, whenever possible, been authoritatively identified. Natural history collections would seem an ideal resource for barcode library construction, but they have never seen large-scale analysis because of concerns linked to DNA degradation. The present study examines the strength of this barrier, carrying out a comprehensive analysis of moth and butterfly (Lepidoptera) species in the Australian National Insect Collection. Protocols were developed that enabled tissue samples, specimen data, and images to be assembled rapidly. Using these methods, a five-person team processed 41,650 specimens representing 12,699 species in 14 weeks. Subsequent molecular analysis took about six months, reflecting the need for multiple rounds of PCR as sequence recovery was impacted by age, body size, and collection protocols. Despite these variables and the fact that specimens averaged 30.4 years old, barcode records were obtained from 86% of the species. In fact, one or more barcode compliant sequences (>487 bp) were recovered from virtually all species represented by five or more individuals, even when the youngest was 50 years old. By assembling specimen images, distributional data, and DNA barcode sequences on a web-accessible informatics platform, this study has greatly advanced accessibility to information on thousands of species. Moreover, much of the specimen data became publically accessible within days of its acquisition, while most sequence results saw release within three months. As such, this study reveals the speed with which DNA barcode workflows can mobilize biodiversity data, often providing the first web-accessible information for a species. These results further suggest that existing collections can enable the rapid development of a comprehensive DNA barcode library for the most diverse compartment of terrestrial biodiversity - insects.

Urine Cytology: Collection, Film Preparation, and Evaluation.

PubMed

Vap, Linda M; Shropshire, Sarah B

2017-01-01

Cytologic examination of the urine sediment in animals suspected of having urinary tract disease or lower urinary tract masses is one of the best means of distinguishing inflammation, infection, and neoplasia and can help determine if a positive dipstick result for hemoglobin/blood is due to hemorrhage or blood contamination. The quality of the specimen collection and handling plays an important role in the quality of results, the validity of interpretations, and selection of appropriate course of action. The method of sample collection aids localization of pathology. Air dry but do not heat fix, freeze, or expose films to formalin fumes, temperature extremes, or condensation. Copyright © 2016 Elsevier Inc. All rights reserved.

Low rate of Propionibacterium acnes in arthritic shoulders undergoing primary total shoulder replacement surgery using a strict specimen collection technique.

PubMed

Maccioni, Cristobal B; Woodbridge, Adam B; Balestro, Jean-Christian Y; Figtree, Melanie C; Hudson, Bernard J; Cass, Benjamin; Young, Allan A

2015-08-01

Propionibacterium acnes is a recognized pathogen in postoperative shoulder infections. A recent study reported growth of P acnes in 42% of glenohumeral joints in primary shoulder arthroplasty, concluding that P acnes may cause shoulder osteoarthritis. Whether these results reflect true bacterial infection or specimen contamination is unclear. Our prospective study aimed to determine the rate of P acnes infection in arthritic shoulders using a strict specimen collection technique. We used modified Oxford protocol to collect tissue specimens from the glenohumeral joint of 32 consecutive patients undergoing primary shoulder arthroplasty. Specimens were cultured specifically for P acnes. Diagnosis of P acnes infection required 2 or more positive cultures and histopathology compatible with infection. Three of 32 patients had a positive culture for P acnes. Overall, 3.125% of specimens grew P acnes without histologic evidence of infection. There were no patients with P acnes infection. The difference in culture rates between patients with idiopathic osteoarthritis and those with a predisposing cause for osteoarthritis was not significant. We found a low rate of positive cultures for P acnes, but no P acnes infection and no difference between types of osteoarthritis. These results do not support a cause-and-effect relationship between P acnes and osteoarthritis. The differing results from previous studies are likely explained by our strict specimen collection technique, reflecting different rates of contamination rather than infection. That P acnes contamination occurs in primary shoulder arthroplasty is concerning. Further studies are needed to assess the rates of contamination in shoulder surgery, its clinical effect, and to determine optimal antibiotic prophylaxis. Crown Copyright © 2015. Published by Elsevier Inc. All rights reserved.

Clinical evaluation and use of urine screening for drug abuse.

PubMed Central

Saxon, A J; Calsyn, D A; Haver, V M; Delaney, C J

1988-01-01

Urine drug screening is indicated to evaluate patients who show mental status or behavioral changes and to monitor the abstinence of drug abusers. The appropriate timing for collecting urine specimens may vary depending on the suspected drug of abuse and on laboratory factors. Laboratories use a variety of techniques to do urine screens, and these must be understood by clinicians ordering the screens to interpret results correctly. In treating drug-abusing patients, clinicians must apply structured reinforcement in conjunction with urine screen results to aid patients in achieving abstinence. PMID:3176489

Quantitative urine confirmatory testing for synthetic cannabinoids in randomly collected urine specimens

PubMed Central

Castaneto, Marisol S.; Scheidweiler, Karl B.; Gandhi, Adarsh; Wohlfarth, Ariane; Klette, Kevin L.; Martin, Thomas M.; Huestis, Marilyn A.

2014-01-01

Synthetic cannabinoid intake is an ongoing health issue worldwide, with new compounds continually emerging, making drug testing complex. Parent synthetic cannabinoids are rarely detected in urine, the most common matrix employed in workplace drug testing. Optimal identification of synthetic cannabinoid markers in authentic urine specimens and correlation of metabolite concentrations and toxicities would improve synthetic cannabinoid result interpretation. We screened 20,017 randomly collected US military urine specimens between July 2011 and June 2012 with a synthetic cannabinoid immunoassay yielding 1,432 presumptive positive specimens. We analyzed all presumptive positive and 1,069 negative specimens with our qualitative synthetic cannabinoid LC-MS/MS method, which confirmed 290 positive specimens. All 290 positive and 487 randomly-selected negative specimens were quantified with the most comprehensive urine quantitative LC-MS/MS method published to date. 290 specimens confirmed positive for 22 metabolites from 11 parent synthetic cannabinoids. The five most predominant metabolites were JWH-018 pentanoic acid (93%), JWH-018 N-hydroxypentyl (84%), AM2201 N-hydroxypentyl (69%), JWH-073 butanoic acid (69%), and JWH-122 N-hydroxypentyl (45%) with 11.1 (0.1–2434), 5.1 (0.1–1239), 2.0 (0.1–321), 1.1 (0.1–48.6), and 1.1 (0.1–250) μg/L median (range) concentrations, respectively. Alkyl hydroxy and carboxy metabolites provided suitable biomarkers for 11 parent synthetic cannabinoids; although, hydroxyindoles also were observed. This is by far the largest data set of synthetic cannabinoid metabolites urine concentrations from randomly collected workplace drug testing specimens rather than acute intoxications or driving under the influence of drugs. These data improve the interpretation of synthetic cannabinoid urine test results and suggest suitable urine markers of synthetic cannabinoid intake. PMID:25231213

Detection of Borrelia miyamotoi and other tick-borne pathogens in human clinical specimens and Ixodes scapularis ticks in New York State, 2012-2015.

PubMed

Wroblewski, Danielle; Gebhardt, Linda; Prusinski, Melissa A; Meehan, Lisa J; Halse, Tanya A; Musser, Kimberlee A

2017-03-01

Borrelia miyamotoi (Bm) is a recently emerging bacterial agent transmitted by several species of ixodid ticks. Diagnosis of Bm infection can be challenging, as the organism is not easily cultivable. We have developed and validated a multiplex real-time PCR to simultaneously identify Bm infection and the agents causing human granulocytic anaplasmosis and human monocytic ehrlichiosis, Anaplasma phagocytophilum and Ehrlichia chaffeensis, respectively. The assay is 100% specific; highly sensitive, detecting 11 gene copies of Bm DNA in both whole blood and cerebral spinal fluid; and provides rapid results in less than two hours. A retrospective study of 796 clinical specimens collected between the years 2012 and 2014 and a prospective study of 366 clinical specimens were performed utilizing this novel assay to evaluate the frequency of Bm infection in New York State (NYS). Eight clinical specimens (1%) were found to be positive for Bm, 216 were positive for A. phagocytophilum, and 10 were positive for E. chaffeensis. Additionally, we tested 411 I. scapularis ticks collected in NYS during 2013 and 2014 in a separate multiplex real-time PCR to determine the prevalence of Bm, A. phagocytophilum, Borrelia burgdorferi s.s., and Borrelia species. Our results indicated rates of 1.5%, 27%, 19.7%, and 8.8% respectively. The ability to monitor both the frequency and geographic distribution of Bm cases and the prevalence and geographic distribution of Bm in ticks will help create a better understanding of this emerging tick-borne pathogen. Published by Elsevier GmbH.

A faunistic survey of bees (Hymenoptera: Apoidea) in the Black Belt Prairie of Mississippi

USDA-ARS?s Scientific Manuscript database

A survey of bees (Apoidea) in the Black Belt Prairie of northern Mississippi was conducted from 1991 to 2001. Collecting methods included netting specimens from floral hosts and use of malaise traps. The survey resulted in collection of 6138 specimens, of which 3627 were identified to 118 species. O...

10 CFR 26.97 - Conducting an initial test for alcohol using a specimen of oral fluids.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 1 2014-01-01 2014-01-01 false Conducting an initial test for alcohol using a specimen of oral fluids. 26.97 Section 26.97 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.97 Conducting an initial test for alcohol using a specimen of oral...

10 CFR 26.97 - Conducting an initial test for alcohol using a specimen of oral fluids.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 1 2012-01-01 2012-01-01 false Conducting an initial test for alcohol using a specimen of oral fluids. 26.97 Section 26.97 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.97 Conducting an initial test for alcohol using a specimen of oral...

10 CFR 26.97 - Conducting an initial test for alcohol using a specimen of oral fluids.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 1 2013-01-01 2013-01-01 false Conducting an initial test for alcohol using a specimen of oral fluids. 26.97 Section 26.97 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.97 Conducting an initial test for alcohol using a specimen of oral...

10 CFR 26.97 - Conducting an initial test for alcohol using a specimen of oral fluids.

Code of Federal Regulations, 2011 CFR

2011-01-01

... 10 Energy 1 2011-01-01 2011-01-01 false Conducting an initial test for alcohol using a specimen of oral fluids. 26.97 Section 26.97 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.97 Conducting an initial test for alcohol using a specimen of oral...

10 CFR 26.97 - Conducting an initial test for alcohol using a specimen of oral fluids.

Code of Federal Regulations, 2010 CFR

2010-01-01

... 10 Energy 1 2010-01-01 2010-01-01 false Conducting an initial test for alcohol using a specimen of oral fluids. 26.97 Section 26.97 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.97 Conducting an initial test for alcohol using a specimen of oral...

Diversity in aconitine alkaloid profile of Aconitum plants in Hokkaido contrasts with their genetic similarity.

PubMed

Kakiuchi, Nobuko; Atsumi, Toshiyuki; Higuchi, Mari; Kamikawa, Shohei; Miyako, Haruka; Wakita, Yuriko; Ohtsuka, Isao; Hayashi, Shigeki; Hishida, Atsuyuki; Kawahara, Nobuo; Nishizawa, Makoto; Yamagishi, Takashi; Kadota, Yuichi

2015-01-01

Aconite tuber is a representative crude drug for warming the body internally in Japanese Kampo medicine and Chinese traditional medicine. The crude drug is used in major prescriptions for the aged. Varieties of Aconitum plants are distributed throughout the Japanese Islands, especially Hokkaido. With the aim of identifying the medicinal potential of Aconitum plants from Hokkaido, 107 specimens were collected from 36 sites in the summer of 2011 and 2012. Their nuclear DNA region, internal transcribed spacer (ITS), and aconitine alkaloid contents were analyzed. Phylogenic analysis of ITS by maximum parsimony analysis showed that the majority of the specimens were grouped into one cluster (cluster I), separated from the other cluster (cluster II) consisting of alpine specimens. The aconitine alkaloid content of the tuberous roots of 76 specimens showed 2 aspects-specimens from the same collection site showed similar aconitine alkaloid profiles, and cluster I specimens from different habitats showed various alkaloid profiles. Environmental pressure of each habitat is presumed to have caused the morphology and aconitine alkaloid profile of these genetically similar specimens to diversify.

Cross-reactivity of Toxocariasis with Crude Antigen of Toxascaris leonina Larvae by ELISA.

PubMed

Jin, Yan; Shen, Chenghua; Huh, Sun; Choi, Min-Ho; Hong, Sung-Tae

2015-05-01

Roundworms of Toxocara canis and Toxascaris leonina are common gastrointestinal helminths of canids over the world. Humans are infected with T. canis larvae through ingestion of infective eggs in contaminated environments or larvae by consumption of raw or uncooked meat or livers. Recently, patients of clinically diagnosed toxocariasis are increasing and require correct diagnosis in Korea. The present study investigated serological cross-reactivity between crude antigens of T. canis (TCLA) and T. leonina (TLLA) larvae. We collected serum specimens from 177 toxocariasis patients who were clinically suspected in the Seoul National University Hospital and 115 healthy controls. An ELISA method for toxocariasis was used to evaluate diagnostic efficacy of TLLA for serodiagnosis of human toxocariasis. The IgG ELISA using TLLA gave 14 (14.3%) positives of 98 TCLA positive specimens among 177 suspected toxocariasis patients. Most of them showed high absorbances with TCLA. In conclusion, there is a partial cross reaction between serum specimens of toxocariasis and TLLA.

Subcellular evidences of redox imbalance in well-established populations of an endangered limpet. Reasons for alarm?

PubMed

Espinosa, Free; Rivera-Ingraham, Georgina A

2016-08-15

Intertidal species are more vulnerable to anthropogenic disturbances than others inhabiting subtidal and offshore habitats. Coastal development frequently results in trace-metal pollution. For endangered species such as Patella ferruginea it can be a high risk that leads local populations to extinction. Three localities were surveyed, one within a natural and unpolluted area and the other two within the harbor of Ceuta (Strait of Gibraltar), on breakwaters outside and inside. The specimens collected inside the harbor reached 3-fold higher Hg content than for those incoming from the natural area. PERMANOVA test indicated that metal composition of the specimens from inside the harbor was different from the rest. In addition, evidence of cell damage was detected in the specimens from the harbor area. This highlights the urgency of undertaking a physiological evaluation of some of the most vulnerable populations, establishing eco-physiological protocols for monitoring and managing populations settled on artificial substrata. Copyright © 2016 Elsevier Ltd. All rights reserved.

Healthcare and patient costs of a proactive chlamydia screening programme: the Chlamydia Screening Studies project.

PubMed

Robinson, Suzanne; Roberts, Tracy; Barton, Pelham; Bryan, Stirling; Macleod, John; McCarthy, Anne; Egger, Matthias; Sanford, Emma; Low, Nicola

2007-07-01

Most economic evaluations of chlamydia screening do not include costs incurred by patients. The objective of this study was to estimate both the health service and private costs of patients who participated in proactive chlamydia screening, using mailed home-collected specimens as part of the Chlamydia Screening Studies project. Data were collected on the administrative costs of the screening study, laboratory time and motion studies and patient-cost questionnaire surveys were conducted. The cost for each screening invitation and for each accepted offer was estimated. One-way sensitivity analysis was conducted to explore the effects of variations in patient costs and the number of patients accepting the screening offer. The time and costs of processing urine specimens and vulvo-vaginal swabs from women using two nucleic acid amplification tests were similar. The total cost per screening invitation was 20.37 pounds (95% CI 18.94 pounds to 24.83). This included the National Health Service cost per individual screening invitation 13.55 pounds (95% CI 13.15 pounds to 14.33) and average patient costs of 6.82 pounds (95% CI 5.48 pounds to 10.22). Administrative costs accounted for 50% of the overall cost. The cost of proactive chlamydia screening is comparable to those of opportunistic screening. Results from this study, which is the first to collect private patient costs associated with a chlamydia screening programme, could be used to inform future policy recommendations and provide unique primary cost data for economic evaluations.

Wide Panel Testing Technique for Evaluating Repair Weld Strengths

NASA Technical Reports Server (NTRS)

Rogers, Patrick R.; Bynum, Julian E.; Shah, Sandeep R.

1998-01-01

This paper describes a new tensile testing technique for evaluating the overall effect of a repair weld on the strength of a welded joint. Previously, repair weld strengths have been evaluated using one-inch width tensile specimens, but this technique does not capture all of the effects that result from a repair. The new technique involves testing of "wide panel" tensile specimens which contain the full length of a repair weld within a longer initial weld, allowing the specimen to capture the combined effects of residual stresses, local strength degradation, and load redistribution around a repair. The development of strains in the repair area of standard aluminum alloy specimens and new high-performance aluminum-lithium alloy specimens was observed and evaluated using photoelastic material. The results of this evaluation show an increased sensitivity to repair welding residual stresses in the aluminum-lithium alloy specimens.

Contributions to the mammalogy of Chile

USGS Publications Warehouse

Pine, Ronald H.; Miller, Sterling D.; Schamberger, Mel L.

1979-01-01

Collections of mammals were made during more than three years of biological investigations in Chile sponsored by the Corporación Nacional Forestal under the aegis of the Peace Corps (Smithsonian Environmental Program). Genera and species hitherto unreported for that country were taken and many useful data concerning distributional patterns of other (mostly little-known) species were gathered. These collections have also proved valuable in better understanding Chilean mammals from a taxonomic point of view and contribute knowledge of the species' natural history. Specimens are to be deposited in the (United States) National Museum of Natural History (USNM) or are to be retained by the Corporación Nacional Forestal, Avda, Bulnes 285, Depto. 401, Santiago. Numbers provided below are field numbers. A final division of specimens between the two institutions has not yet been made. A number of specimens reported here were not taken by Peace Corps personnel but have been obtained by the National Museum of Natural History from other sources. Specimens in the Field Museum of Natural History (FMNH) were used in making comparisons. Some of Fulk's (GWF) specimens are at Texas Tech University. Other are at the Servicio Agricola y Ganadero in Santiago (as are specimens of some introduced species taken by Schamberger). Reise's (DF) are at the Universidad de Chile-Concepción and in his personal collection.

Biomarkers in Advanced Larynx Cancer

PubMed Central

Bradford, Carol R.; Kumar, Bhavna; Bellile, Emily; Lee, Julia; Taylor, Jeremy; D’Silva, Nisha; Cordell, Kitrina; Kleer, Celina; Kupfer, Robbi; Kumar, Pawan; Urba, Susan; Worden, Francis; Eisbruch, Avraham; Wolf, Gregory T.; Teknos, Theodoros N.; Prince, Mark E.P.; Chepeha, Douglas B.; Hogikyan, Norman D.; Moyer, Jeffrey S.; Carey, Thomas E.

2014-01-01

Objectives/Hypothesis To determine if tumor biomarkers were predictive of outcome in a prospective cohort of patients with advanced larynx cancer treated in a phase II clinical trial. Study Design Prospectively collected biopsy specimens from 58 patients entered into a Phase II trial of organ preservation in advanced laryngeal cancer were evaluated for expression of a large panel of biomarkers and correlations with outcome were determined. Methods Tissue microarrays were constructed from pretreatment biopsies and stained for cyclin D1, CD24, EGFR, MDM2, PCNA, p53, survivin, Bcl-xL, Bcl-2, BAK, rhoC, and NFκB. Pattern of invasion and p53 mutations were assessed. Correlations with overall survival (OS), disease-specific survival (DSS), time free from indication of surgery, induction chemotherapy response, and chemoradiation response were determined. Cox models were used to assess combinations of these biomarkers. Results Low expression of BAK was associated with response to induction chemotherapy. Low expression of BAK and cytoplasmic NFκB was associated with chemoradiation response. Aggressive histologic growth pattern was associated with response induction chemotherapy. Expression of cyclin D1 was predictive of overall and disease-specific survival. Overexpression of EGFR was also associated with an increased risk of death from disease. Bcl-xL expression increased significantly in persistent/recurrent tumors specimens when compared to pretreatment specimens derived from the same patient (p = 0.0003). Conclusions Evaluation of biomarker expression in pretreatment biopsy specimens can lend important predictive and prognostic information for patients with advanced larynx cancer. PMID:23775802

Blood culture accuracy: discards from central venous catheters in pediatric oncology patients in the emergency department.

PubMed

Winokur, Elizabeth J; Pai, Debra; Rutledge, Dana N; Vogel, Kate; Al-Majid, Sadeeka; Marshall, Christine; Sheikewitz, Paul

2014-07-01

Lack of specific guidelines regarding collection of blood for culture from central venous catheters (CVCs) has led to inconsistencies in policies among hospitals. Currently, no specific professional or regulatory recommendations exist in relation to using, reinfusing, or discarding blood drawn from CVCs before drawing blood for a culture. Repeated wasting of blood may harm immunocompromised pediatric oncology patients. The purpose of this comparative study was to determine whether differences exist between blood cultures obtained from the first 5 mL of blood drawn from a CVC line when compared with the second 5 mL drawn. During 2009-2011, 62 pediatric oncology patients with CVCs and orders for blood cultures to determine potential sepsis were enrolled during ED visits. Trained study nurses aseptically drew blood and injected the normally discarded first 5 mL and the second specimen (usual care) into separate culture bottles. Specimens were processed in the microbiology laboratory per hospital policy. Positive cultures were evaluated to assess agreement between specimen results and to determine that the identified pathogen was not a contaminant. Out of 186 blood culture pairs, 4.8% demonstrated positive results. In all positive-positive matches, the normal discard specimen contained the same organism as the usual care specimen. In 4 matches, the normally discarded specimen demonstrated notably earlier time to positivity (4 to 31 hours) compared with the usual care specimen, which resulted in earlier initiation of definitive antibiotics. These findings support the accuracy of the specimen that is normally discarded and suggest the need to reconsider its use for blood culture testing. Copyright © 2014 Emergency Nurses Association. Published by Mosby, Inc. All rights reserved.

Paradigm for diagnosing mycobacterial disease: direct detection and differentiation of Mycobacterium tuberculosis complex and non-tuberculous mycobacteria in clinical specimens using multiplex real-time PCR.

PubMed

Kim, Jeong-Uk; Ryu, Dae-Shick; Cha, Choong-Hwan; Park, Seon-Hee

2018-03-20

Mycobacterium tuberculosis and non-tuberculous mycobacteria (NTM) are clinically different, and the rapid detection and differentiation of M. tuberculosis complex (MTBC) and NTM is crucial for patient management and infection control. Given the slow growth of most pathogenic mycobacteria, nucleic acid amplification assays are excellent tools for direct identification of mycobacteria in clinical specimens. Recently, a multiplex real-time PCR assay was developed that can directly detect 20 mycobacterial species in clinical specimens. Here, we evaluated the diagnostic performance of the assay for diagnosing mycobacterial disease under routine laboratory conditions. A total of 3334 specimens collected from 1437 patients suspected of tuberculosis infection were subjected to acid-fast bacilli staining, conventional culture and the multiplex real-time PCR assay. To evaluate the sensitivity and specificity of the assay, the overall diagnosis of tuberculosis was defined by positive culture plus medical history, and the 2007 American Thoracic Society and Infectious Disease Society of America diagnostic criteria for NTM disease were applied. The sensitivity, specificity, positive predictive value and negative predictive value were 87.5%, 99.6%, 96.1% and 98.5%, respectively, for the detection of MTBC isolates and 53.3%, 99.9%, 95.2%, and 98.9%, respectively, for detecting NTM isolates. Thus, the assay can correctly differentiate between MTBC and NTM isolates in clinical specimens and would be a useful tool for the rapid differentiation of tuberculosis and NTM disease, despite its limited sensitivity for the diagnosis of NTM disease. © Article author(s) (or their employer(s) unless otherwise stated in the text of the article) 2018. All rights reserved. No commercial use is permitted unless otherwise expressly granted.

Multicenter evaluation of the performance characteristics of the bayer VERSANT HCV RNA 3.0 assay (bDNA).

PubMed

Elbeik, Tarek; Surtihadi, Johan; Destree, Mark; Gorlin, Jed; Holodniy, Mark; Jortani, Saeed A; Kuramoto, Ken; Ng, Valerie; Valdes, Roland; Valsamakis, Alexandra; Terrault, Norah A

2004-02-01

In this multicenter evaluation, the VERSANT HCV RNA 3.0 Assay (bDNA) (Bayer Diagnostics, Tarrytown, N.Y.) was shown to have excellent reproducibility, linearity, and analytical sensitivity across specimen collection matrices (serum, EDTA, ACD-A), and hepatitis C virus (HCV) genotypes 1 to 6. The VERSANT HCV bDNA Assay has a reportable range of 615 to 7690000 (7.69 x 10(6)) IU/ml. The total coefficient of variation (CV) ranged from 32.4% at 615 IU/ml to 17% at 6.8 x 10(6) IU/ml. The assay was linear across the reportable range. Analytical specificity of 98.8% was determined by testing 999 specimens from volunteer blood donors. Evaluation of HCV genotypes using RNA transcripts of representative clones of 1a, 1b, 2a, 2b, 2c, 3a, 4a, 5a, and 6a and patient specimens showed that the largest difference between genotype 1, upon which the assay is standardized, and non-1 genotypes was within 1.5-fold. Testing of potentially interfering endogenous substances and exogenous substances and conditions found no interference in HCV-positive or HCV-negative specimens except for unconjugated bilirubin at concentrations of >or=20 mg/dl and protein at concentrations of >or=9 g/dl. Biological variability was estimated from 29 clinically stable individuals not on HCV therapy who were tested weekly over an 8-week period. The combined estimate of total (biologic plus assay) variability was 0.15 log(10) standard deviation (CV, 36.1%), a fold change of 2.6. Thus, the observed fold change between any two consecutive HCV RNA measures is expected to be less than 2.6-fold (equivalent to 0.41 log(10) IU/ml) 95% of the time in clinically stable individuals.

A Dual Point-of-Care Test Shows Good Performance in Simultaneously Detecting Nontreponemal and Treponemal Antibodies in Patients With Syphilis: A Multisite Evaluation Study in China

PubMed Central

Yin, Yue-Ping; Chen, Xiang-Sheng; Wei, Wan-Hui; Gong, Kuang-Long; Cao, Wen-Ling; Yong, Gang; Feng, Liang; Huang, Shu-Jie; Wang, Dong-Mei; Han, Yan; Chen, Shao-Chun; Mabey, David; Peeling, Rosanna W.

2013-01-01

Background. Rapid point-of-care (POC) syphilis tests based on simultaneous detection of treponemal and nontreponemal antibodies (dual POC tests) offer the opportunity to increase coverage of syphilis screening and treatment. This study aimed to conduct a multisite performance evaluation of a dual POC syphilis test in China. Methods. Participants were recruited from patients at sexually transmitted infection clinics and high-risk groups in outreach settings in 6 sites in China. Three kinds of specimens (whole blood [WB], fingerprick blood [FB], and blood plasma [BP]) were used for evaluating sensitivity and specificity of the Dual Path Platform (DPP) Syphilis Screen and Confirm test using its treponemal and nontreponemal lines to compare Treponema pallidum particle agglutination (TPPA) assay and toluidine red unheated serum test (TRUST) as reference standards. Results. A total of 3134 specimens (WB 1323, FB 488, and BP 1323) from 1323 individuals were collected. The sensitivities as compared with TPPA were 96.7% for WB, 96.4% for FB, and 94.6% for BP, and the specificities were 99.3%, 99.1%, and 99.6%, respectively. The sensitivities as compared with TRUST were 87.2% for WB, 85.8% for FB, and 88.4% for BP, and the specificities were 94.4%, 96.1%, and 95.0%, respectively. For specimens with a TRUST titer of 1:4 or higher, the sensitivities were 100.0% for WB, 97.8% for FB, and 99.6% for BP. Conclusions. DPP test shows good sensitivity and specificity in detecting treponemal and nontreponemal antibodies in 3 kinds of specimens. It is hoped that this assay can be considered as an alternative in the diagnosis of syphilis, particularly in resource-limited areas. PMID:23132172

Preparing soft-bodied arthropods for arthropods for microscope examination: Mites (Arachnida: Acari)

USDA-ARS?s Scientific Manuscript database

Proper identification of mites (Arachnida: Acari) require preparation of the specimen on a microscope slide. This training video provides visual instruction on how to prepare mite specimens on microscope slides for examination and identification. Steps ranging from collection, specimen clearing, use...

Preservation of corals in salt-saturated DMSO buffer is superior to ethanol for PCR experiments

NASA Astrophysics Data System (ADS)

Gaither, M. R.; Szabó, Z.; Crepeau, M. W.; Bird, C. E.; Toonen, R. J.

2011-06-01

Specimen collection is time consuming and expensive, yet few laboratories test preservation methods before setting out on field expeditions. The most common preservation buffer used for coral specimens is >70% EtOH. However, alternatives exist that are less flammable, easier to ship, and are widely used in other taxa. Here, we compare the effects of salt-saturated DMSO (SSD) and EtOH preservation buffers on post-extraction DNA quantity and quality. We found that soft tissue integrity was better maintained and higher quantities of DNA were extracted from EtOH-preserved specimens; however, by all other measures, SSD was a superior preservative to EtOH. Extractions of SSD-preserved specimens resulted in higher molecular weight DNA, higher PCR success, and more efficient amplification than specimens preserved in EtOH. Our results show that SSD is generally a superior preservative to EtOH for specimens destined for PCR studies, but species-specific differences indicate that preservation comparisons should be undertaken before collection and storage of samples.

Multidrug-resistant gram-negative bacteria colonization of healthy US military personnel in the US and Afghanistan.

PubMed

Vento, Todd J; Cole, David W; Mende, Katrin; Calvano, Tatjana P; Rini, Elizabeth A; Tully, Charla C; Zera, Wendy C; Guymon, Charles H; Yu, Xin; Cheatle, Kristelle A; Akers, Kevin S; Beckius, Miriam L; Landrum, Michael L; Murray, Clinton K

2013-02-05

The US military has seen steady increases in multidrug-resistant (MDR) gram-negative bacteria (GNB) infections in casualties from Iraq and Afghanistan. This study evaluates the prevalence of MDR GNB colonization in US military personnel. GNB colonization surveillance of healthy, asymptomatic military personnel (101 in the US and 100 in Afghanistan) was performed by swabbing 7 anatomical sites. US-based personnel had received no antibiotics within 30 days of specimen collection, and Afghanistan-based personnel were receiving doxycycline for malaria chemoprophylaxis at time of specimen collection. Isolates underwent genotypic and phenotypic characterization. The only colonizing MDR GNB recovered in both populations was Escherichia coli (p=0.01), which was seen in 2% of US-based personnel (all perirectal) and 11% of Afghanistan-based personnel (10 perirectal, 1 foot+groin). Individuals with higher off-base exposures in Afghanistan did not show a difference in overall GNB colonization or MDR E. coli colonization, compared with those with limited off-base exposures. Healthy US- and Afghanistan-based military personnel have community onset-MDR E. coli colonization, with Afghanistan-based personnel showing a 5.5-fold higher prevalence. The association of doxycycline prophylaxis or other exposures with antimicrobial resistance and increased rates of MDR E. coli colonization needs further evaluation.

Multidrug-resistant gram-negative bacteria colonization of healthy US military personnel in the US and Afghanistan

PubMed Central

2013-01-01

Background The US military has seen steady increases in multidrug-resistant (MDR) gram-negative bacteria (GNB) infections in casualties from Iraq and Afghanistan. This study evaluates the prevalence of MDR GNB colonization in US military personnel. Methods GNB colonization surveillance of healthy, asymptomatic military personnel (101 in the US and 100 in Afghanistan) was performed by swabbing 7 anatomical sites. US-based personnel had received no antibiotics within 30 days of specimen collection, and Afghanistan-based personnel were receiving doxycycline for malaria chemoprophylaxis at time of specimen collection. Isolates underwent genotypic and phenotypic characterization. Results The only colonizing MDR GNB recovered in both populations was Escherichia coli (p=0.01), which was seen in 2% of US-based personnel (all perirectal) and 11% of Afghanistan-based personnel (10 perirectal, 1 foot+groin). Individuals with higher off-base exposures in Afghanistan did not show a difference in overall GNB colonization or MDR E. coli colonization, compared with those with limited off-base exposures. Conclusion Healthy US- and Afghanistan-based military personnel have community onset-MDR E. coli colonization, with Afghanistan-based personnel showing a 5.5-fold higher prevalence. The association of doxycycline prophylaxis or other exposures with antimicrobial resistance and increased rates of MDR E. coli colonization needs further evaluation. PMID:23384348

Catalogue of the type specimens in the fish collection of the National Zoological Museum, Institute of Zoology, Chinese Academy of Sciences, Beijing, China.

PubMed

Ye, Enqi; Xing, Yingchun; Zhang, Chunguang; Zhao, Yahui

2015-05-22

A checklist of type specimens housed in the National Zoological Museum, Institute of Zoology, Chinese Academy of Sciences, Beijing, is presented for research and scientific communication. Included are 80 holotypes, 1 lectotype, 1 neotype, 402 paratypes and 17 syntypes of 99 species belonging to 28 families and 12 orders. With 60 species, Cypriniformes has the largest representation. All of the specimens were collected in China and neighboring countries in the past 90 years.

Towards more accurate HIV testing in sub-Saharan Africa: a multi-site evaluation of HIV RDTs and risk factors for false positives

PubMed Central

Kosack, Cara S; Page, Anne-Laure; Beelaert, Greet; Benson, Tumwesigye; Savane, Aboubacar; Ng’ang’a, Anne; Andre, Bita; Zahinda, Jean-Paul BN; Shanks, Leslie; Fransen, Katrien

2017-01-01

Abstract Introduction: Although individual HIV rapid diagnostic tests (RDTs) show good performance in evaluations conducted by WHO, reports from several African countries highlight potentially significant performance issues. Despite widespread use of RDTs for HIV diagnosis in resource-constrained settings, there has been no systematic, head-to-head evaluation of their accuracy with specimens from diverse settings across sub-Saharan Africa. We conducted a standardized, centralized evaluation of eight HIV RDTs and two simple confirmatory assays at a WHO collaborating centre for evaluation of HIV diagnostics using specimens from six sites in five sub-Saharan African countries. Methods: Specimens were transported to the Institute of Tropical Medicine (ITM), Antwerp, Belgium for testing. The tests were evaluated by comparing their results to a state-of-the-art reference algorithm to estimate sensitivity, specificity and predictive values. Results: 2785 samples collected from August 2011 to January 2015 were tested at ITM. All RDTs showed very high sensitivity, from 98.8% for First Response HIV Card Test 1–2.0 to 100% for Determine HIV 1/2, Genie Fast, SD Bioline HIV 1/2 3.0 and INSTI HIV-1/HIV-2 Antibody Test kit. Specificity ranged from 90.4% for First Response to 99.7% for HIV 1/2 STAT-PAK with wide variation based on the geographical origin of specimens. Multivariate analysis showed several factors were associated with false-positive results, including gender, provider-initiated testing and the geographical origin of specimens. For simple confirmatory assays, the total sensitivity and specificity was 100% and 98.8% for ImmunoComb II HIV 12 CombFirm (ImmunoComb) and 99.7% and 98.4% for Geenius HIV 1/2 with indeterminate rates of 8.9% and 9.4%. Conclusions: In this first systematic head-to-head evaluation of the most widely used RDTs, individual RDTs performed more poorly than in the WHO evaluations: only one test met the recommended thresholds for RDTs of ≥99% sensitivity and ≥98% specificity. By performing all tests in a centralized setting, we show that these differences in performance cannot be attributed to study procedure, end-user variation, storage conditions, or other methodological factors. These results highlight the existence of geographical and population differences in individual HIV RDT performance and underscore the challenges of designing locally validated algorithms that meet the latest WHO-recommended thresholds. PMID:28364560

Catalogue of type specimens of fungi and lichens deposited in the Herbarium of the University of Granada (Spain).

PubMed

Vizoso, M Teresa; Quesada, Carmen

2015-01-01

A catalogue of types from the Herbarium of the University of Granada has not previously been compiled. As a result, a search of these collections in order to compile digital images for preservation and publication yielded a large number of formerly unrecognized types. This dataset contains the specimen records from the catalogue of the nomenclature types of fungi and lichens in the Herbarium of the University of Granada, Spain. These herbarium specimens are included in the GDA and GDAC collections, acronyms from Index Herbariorum (Thiers 2014). At this time, the type collection of fungi and lichens contains 88 type specimens of 49 nominal taxa, most from Agaricales and the genus Cortinarius, described from the western Mediterranean, mainly Spain, by the following authors: V.Antonin, J.Ballarà, A.Bidaud, G.F.Bills, M.Bon, C.Cano, M.Casares, G.Chevassut, M.Contu, F.Esteve-Raventós, R.Galán, L.Guzmán-Dávalos, R.Henry, E.Horak, R.Mahiques, G.Malençon, P.Moënne-Loccoz, G.Moreno, A.Ortega, F.Palazón, V.N.Suárez.-Santiago, A.Vêzda, J.Vila, and M.Villareal. For each specimen, the locality indication, species name, observation date, collector, type status, related information, associated sequences, other catalogue numbers related to each type, and image URL are recorded. The dataset is associated with an image collection named "Colección de imágenes de los tipos nomenclaturales de hongos, líquenes, musgos y algas incluidos en el Herbario de la Universidad de Granada (GDA y GDAC)" (Vizoso and Quesada 2013) which is housed and accessible at the Global Biodiversity Information Facility in Spain (GBIF.ES) Hosting and Publishing Service "Biodiversity Image Portal of Spanish collections" and is also available at the Herbarium of University of Granada institutional web (Vizoso 2014a, Vizoso 2014b). That image collection contains 113 images, of which 56 correspond to the nomenclature types of 49 taxa (47 fungi, 2 lichens), the rest of the images in this collection correspond to documents and specimens or microscopy photographs which are included in the herbarium specimens of fungi. These complement and document the process of the typification.

Stability Study of Cervical Specimens Collected by Swab and Stored Dry Followed by Human Papillomavirus DNA Detection Using the cobas 4800 Test.

PubMed

Lin, Chun-Qing; Zeng, Xi; Cui, Jian-Feng; Liao, Guang-Dong; Wu, Ze-Ni; Gao, Qian-Qian; Zhang, Xun; Yu, Xiu-Zhang; Chen, Wen; Xi, Ming-Rong; Qiao, You-Lin

2017-02-01

Safer, more convenient methods for cervical sample collection and storage are necessary to facilitate human papillomavirus (HPV) DNA testing in low-resource settings. Our study aimed to evaluate the stability of cervical specimens collected with dry swabs and stored dry, compared to liquid-based cytology (LBC) samples, as detected by HPV DNA testing. Women with abnormal cytological findings or HPV-positive results at colposcopy were recruited from the West China Second University Hospital, Sichuan University, between October 2013 and March 2014. From each woman, physicians collected cervical specimens with a swab placed into a Sarstedt tube and a CytoBrush placed into LBC medium. Samples were randomly assigned to be stored at uncontrolled ambient temperature for 2, 7, 14, or 28 days and then were tested for 14 high-risk HPV (HR-HPV) types using the cobas HPV test. The rates of agreement between dry swab and LBC samples for any HR-HPV type, HPV16, HPV18, and the 12 pooled HR-HPV types were 93.8%, 97.8%, 99.4%, and 93.2%, respectively, with kappa values of 0.87 (95% confidence interval [CI], 0.83 to 0.91), 0.94 (95% CI, 0.91 to 0.97), 0.94 (95% CI, 0.87 to 1.00), and 0.86 (95% CI, 0.82 to 0.90). The performance of swab samples for detection of cervical precancerous lesions by means of cobas HPV testing was equal to that of LBC samples, even with stratification by storage time. Dry storage of swab-collected cervical samples can last for 1 month without loss of test performance by cobas HPV testing, compared to LBC samples, which may offer a simple inexpensive approach for cervical cancer screening in low-resource settings. Copyright © 2017 American Society for Microbiology.

Ticks (Ixodida) from the collection of the Natural History Department, Museum of Upper Silesia in Bytom, Poland - A contribution to knowledge on tick fauna and the first record of Hyalomma marginatum presence in Poland.

PubMed

Cuber, Piotr Krzysztof

2016-06-02

There is no doubt that museum collections provide a wide variety of information on ticks. The tick collection at the Natural History Department of the Museum of Upper Silesia in Bytom consists only of 37 specimens as the department is focused mainly on building collections of insects and birds. However, this does not mean that such collection cannot contribute to our knowledge about these arthropods. The most valuable results of studies on the museum's tick collection concerned Polish fauna. There are specimens of I. ricinus dating back as far as 1930-1948, which are the first known records of the presence of this tick in the Upper Silesia. Two specimens collected in copula in 1941 might be the earliest record of the mating behaviour of this species in Poland. The most important result was the detection of 2 cases of H. marginatum presence in Poland, which by far are the oldest documented cases of its presence in this country.

Evaluation of a new APTIMA specimen collection and transportation kit for high-risk human papillomavirus E6/E7 messenger RNA in cervical and vaginal samples.

PubMed

Chernesky, Max; Jang, Dan; Gilchrist, Jodi; Elit, Laurie; Lytwyn, Alice; Smieja, Marek; Dockter, Janel; Getman, Damon; Reid, Jennifer; Hill, Craig

2014-06-01

An APTIMA specimen collection and transportation (SCT) kit was developed by Hologic/Gen-Probe. To compare cervical SCT samples to PreservCyt and SurePath samples and self-collected vaginal samples to physician-collected vaginal and cervical SCT samples. To determine ease and comfort of self-collection with the kit. Each woman (n = 580) self-collected a vaginal SCT, then filled out a questionnaire (n = 563) to determine ease and comfort of self-collection. Colposcopy physicians collected a vaginal SCT and cervical PreservCyt, SCT, and SurePath samples. Samples were tested by APTIMA HPV (AHPV) assay. Agreement between testing of cervical SCT and PreservCyt was 91.1% (κ = 0.82), and that of SurePath samples was 86.7% (κ = 0.72). Agreement of self-collected vaginal SCT to physician-collected SCT was 84.7% (κ = 0.68), and that of self-collected vaginal to cervical SCT was 82.0% (κ = 0.63). For 30 patients with CIN2+, AHPV testing of cervical SCT was 100% sensitive and 59.8% specific compared with PreservCyt (96.6% and 66.2%) and SurePath (93.3% and 70.9%). Vaginal SCT sensitivity was 86.7% for self-collection and 80.0% for physician collection. Most patients found that vaginal self-collection was easy, 5.3% reported some difficulty, and 87.6% expressed no discomfort. Cervical samples collected with the new SCT kit compared well to traditional liquid-based samples tested by AHPV. Although there was good agreement between self-collected and physician-collected samples with the SCT, in a limited number of 30 women, vaginal sampling identified fewer with CIN2+ precancerous cervical lesions than cervical SCT sampling. Comfort, ease of use, and detection of high-risk HPV demonstrated that the kit could be used for cervical and vaginal sampling.

Performance evaluation of the FDA-approved Determine™ HIV-1/2 Ag/Ab Combo assay using plasma and whole blood specimens.

PubMed

Masciotra, Silvina; Luo, Wei; Westheimer, Emily; Cohen, Stephanie E; Gay, Cynthia L; Hall, Laura; Pan, Yi; Peters, Philip J; Owen, S Michele

2017-06-01

The Determine™ HIV-1/2 Ag/Ab Combo (DC) rapid test can identify HIV-1 infection earlier than rapid antibody-only tests in plasma specimens. We compared the performance of DC with a laboratory-based antigen/antibody (Ag/Ab) combo assay in plasma and evaluated antigen reactivity in whole blood specimens. We tested by DC 508 plasma specimens collected in a prospective study and 107 sequential plasma and simulated whole blood specimens from 20 seroconversion panels. Previous results using the ARCHITECT (ARC) Ag/Ab combo assay were compared to DC results. In seroconversion panels, the days from the first HIV1 RNA-positive test to first DC-reactive in plasma and whole blood was compared. McNemar's and Wilcoxon signed rank tests were used for statistical analysis. Of 415 HIV-positive samples, ARC detected 396 (95.4%) and DC 337 (81.2%) (p<0.0001). DC was reactive in 50.0% of ARC-reactive/MS-negative, 78.6% of ARC-reactive/MS-indeterminate, and 99.6% of ARC-reactive/MS-HIV-1-positive or -undifferentiated specimens. DC antigen reactivity was higher among ARC-reactive/MS-negative than MS-indeterminate samples. In 20 HIV-1 seroconversion panels, there was a significant difference between DC reactivity in plasma (91.1%) and whole blood (56.4%) (p<0.0001). DC with whole blood showed a significant delay in reactivity compared to plasma (p=0.008). In plasma, DC was significantly less sensitive than an instrumented laboratory-based Ag/Ab combo assay. DC in plasma was significantly more sensitive compared to whole blood in early HIV-1 infections. With the U.S. laboratory-based diagnostic algorithm, DC as the first step would likely miss a high proportion of HIV-1 infections in early stages of seroconversion. Published by Elsevier B.V.

A comparative scanning electron microscopy study between hand instrument, ultrasonic scaling and erbium doped:Yttirum aluminum garnet laser on root surface: A morphological and thermal analysis

PubMed Central

Mishra, Mitul Kumar; Prakash, Shobha

2013-01-01

Background and Objectives: Scaling and root planing is one of the most commonly used procedures for the treatment of periodontal diseases. Removal of calculus using conventional hand instruments is incomplete and rather time consuming. In search of more efficient and less difficult instrumentation, investigators have proposed lasers as an alternative or as adjuncts to scaling and root planing. Hence, the purpose of the present study was to evaluate the effectiveness of erbium doped: Yttirum aluminum garnet (Er:YAG) laser scaling and root planing alone or as an adjunct to hand and ultrasonic instrumentation. Subjects and Methods: A total of 75 freshly extracted periodontally involved single rooted teeth were collected. Teeth were randomly divided into five treatment groups having 15 teeth each: Hand scaling only, ultrasonic scaling only, Er:YAG laser scaling only, hand scaling + Er:YAG laser scaling and ultrasonic scaling + Er:YAG laser scaling. Specimens were subjected to scanning electron microscopy and photographs were evaluated by three examiners who were blinded to the study. Parameters included were remaining calculus index, loss of tooth substance index, roughness loss of tooth substance index, presence or absence of smear layer, thermal damage and any other morphological damage. Results: Er:YAG laser treated specimens showed similar effectiveness in calculus removal to the other test groups whereas tooth substance loss and tooth surface roughness was more on comparison with other groups. Ultrasonic treated specimens showed better results as compared to other groups with different parameters. However, smear layer presence was seen more with hand and ultrasonic groups. Very few laser treated specimens showed thermal damage and morphological change. Interpretation and Conclusion: In our study, ultrasonic scaling specimen have shown root surface clean and practically unaltered. On the other hand, hand instrument have produced a plane surface, but removed more tooth structure. The laser treated specimens showed rough surfaces without much residual deposit or any other sign of morphological change. PMID:24015009

50 CFR 16.33 - Importation of natural-history specimens.

Code of Federal Regulations, 2010 CFR

2010-10-01

... 50 Wildlife and Fisheries 1 2010-10-01 2010-10-01 false Importation of natural-history specimens... WILDLIFE AND PLANTS INJURIOUS WILDLIFE Additional Exemptions § 16.33 Importation of natural-history... natural-history specimens of wildlife or their eggs for museum or scientific collection purposes: Provided...

Clinical, operational and economic outcomes of point-of-care blood gas analysis in COPD patients.

PubMed

Oliver, Paloma; Buno, Antonio; Alvarez-Sala, Rodolfo; Fernandez-Calle, Pilar; Alcaide, Maria Jose; Casitas, Raquel; Garcia-Quero, Cristina; Madero, Rosario; Gomez-Rioja, Ruben; Iturzaeta, Jose Manuel

2015-04-01

Arterial blood gas analysis is relevant in chronic obstructive pulmonary disease (COPD) management. The aim of this study was to evaluate whether the use of a blood gas analyzer in pulmonology departments improves the clinical, operational and economic outcomes when compared with clinical laboratory measurements. It is an observational prospective study. 112 patients were selected. After specimen collection, the measurement was performed both in pulmonology office as point-of-care and in laboratory. We evaluated clinical outcomes (modification of the indication of long-term oxygen therapy (LTOT) according to results, changes in blood gas analysis results, relationship of the partial pressure of oxygen (PaO2) obtained in the medical visit and velocity of change of the PaO2, influence of total haemoglobin concentration and the change in PaO2), operational outcomes (turnaround time (TAT) from specimen collection to receiving the blood gas analysis report) and economic outcomes (overall cost per process of patient care). There were discrepancies in the indication of LTOT in 13.4% of patients. All parameters showed changes. PaO2 levels showed changes in 2 ways, though they frequently increase over time. The correlation was not good in the other two clinical outcomes. The median TATs in pulmonology office were 1 min versus 79 in laboratory, with 52 min for specimen preparation and transport and 17 min for TAT intralaboratory. The overall cost for the 112 patients in pulmonology office and laboratory was 16,769.89€ and 22,260.97€ respectively. The use of a blood gas analyzer in a pulmonology office improves clinical, operational and economic outcomes when compared with clinical laboratory. Copyright © 2014 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

Distribution of Placobdella hollensis (Whitman, 1892) (Hirudinida: Glossiphoniidae)

USGS Publications Warehouse

Moser, William E.; Richardson, Dennis J.; Hammond, Charlotte I.; Gotte, Steve W.; Lazo-Wasem, Eric

2017-01-01

Confusion regarding the identification of Placobdella hollensis (Whitman, 1892) (Hirudinida: Glossiphoniidae) has led to an unclear understanding of the distribution of the species. Two specimens of P. hollensis were collected from Merchants Millpond State Park, Gates County, North Carolina, U.S.A., representing a new geographic distribution record. Specimens were confirmed as P. hollensis by morphological and molecular study. Specimens of P. hollensisfrom North Carolina, had accessory eyes, 2 thin paramedial dark lines, and 3 pairs of pre-anal papillae. Molecular comparison of cytochrome c oxidase subunit I sequence data revealed a 99.0 to 99.7% similarity to specimens of P. hollensis collected from its type locality (Barnstable County, Massachusetts, U.S.A.). From confirmed specimens of P. hollensis, this report supports the assertion that P. hollensis has an Atlantic coastal distribution.

Catalogue of the type specimens deposited in the Mollusca Collection of the Museu Nacional / UFRJ, Rio de Janeiro, Brazil.

PubMed

Pimenta, Alexandre Dias; Monteiro, Júlio César; Barbosa, André Favaretto; Salgado, Norma Campos; Coelho, Arnaldo Campos Dos Santos

2014-03-20

A curatorial revision of the type specimens deposited in the Mollusca Collection of the Museu Nacional / UFRJ, Rio de Janeiro, Brazil (MNRJ) revealed the existence of 518 lots of type specimens (holotypes, neotypes, syntypes and paratypes) for 285 names of molluscan taxa from 88 families, including 247 gastropods, 30 bivalves, three cephalopods and five scaphopods. A total of 106 holotypes and one neotype are deposited in the MNRJ. Type material for ten nominal taxa described as being deposited in the MNRJ was not located; the probable reasons are discussed. Some previously published erroneous information about types in the MNRJ is rectified. A total of 37 type specimens are illustrated.

76 FR 48777 - Endangered and Threatened Wildlife and Plants; 12-Month Finding on a Petition To List the Nueces...

Federal Register 2010, 2011, 2012, 2013, 2014

2011-08-09

... Frio River were very similar genetically to specimens collected in the Sabinal River (Richardson and... genetically from specimens collected in the Nueces River (Richardson and Gold 1995, p. 31). The genetic... in the Sabinal and Frio Rivers are genetically separate and distinct from the Cyprinella sp. found in...

49 CFR Appendix C to Part 219 - Post-Accident Testing Specimen Collection

Code of Federal Regulations, 2012 CFR

2012-10-01

... the transfer of the blood tubes on the second line of STEP 5 (the chain of custody block). E. Collect... (the chain of custody block). F. Seal the Individual Employee Kit a. The blood and urine specimens have... railroad representatives handling the box shall document chain of custody of the shipping box and shall...

49 CFR Appendix C to Part 219 - Post-Accident Testing Specimen Collection

Code of Federal Regulations, 2013 CFR

2013-10-01

... the transfer of the blood tubes on the second line of STEP 5 (the chain of custody block). E. Collect... (the chain of custody block). F. Seal the Individual Employee Kit a. The blood and urine specimens have... railroad representatives handling the box shall document chain of custody of the shipping box and shall...

49 CFR Appendix C to Part 219 - Post-Accident Testing Specimen Collection

Code of Federal Regulations, 2014 CFR

2014-10-01

... the transfer of the blood tubes on the second line of STEP 5 (the chain of custody block). E. Collect... (the chain of custody block). F. Seal the Individual Employee Kit a. The blood and urine specimens have... railroad representatives handling the box shall document chain of custody of the shipping box and shall...

EXPERIMENTAL EVALUATION OF DEFORMATION AND CONSTRAINT CHARACTERISTICS IN PRECRACKED CHARPY AND OTHER THREE-POINT BEND SPECIMENS

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

Nanstad, Randy K; Sokolov, Mikhail A; Merkle, John Graham

2007-01-01

To enable determination of the fracture toughness reference temperature, T0, with reactor pressure vessel surveillance specimens, the precracked Charpy (PCVN) three-point bend, SE(B), specimen is of interest. Compared with the 25-mm (1 in.) thick compact, 1TC(T), specimen, tests with the PCVN specimen (10x10x55 mm) have resulted in T0 temperatures as much as 40 XC lower (a so-called specimen bias effect). The Heavy-Section Steel Irradiation (HSSI) Program at Oak Ridge National Laboratory developed a two-part project to evaluate the C(T) versus PCVN differences, (1) calibration experiments concentrating on test practices, and (2) a matrix of transition range tests with various specimenmore » geometries and sizes, including 1T SE(B) and 1TC(T). The test material selected was a plate of A533 grade B class 1 steel. The calibration experiments included assessment of the computational validity of J-integral determinations, while the constraint characteristics of various specimen types and sizes were evaluated using key curves and notch strength determinations. The results indicate that J-integral solutions for the small PCVN specimen are comparable in terms of J-integral validity with 1T bend specimens. Regarding constraint evaluations, Phase I deformation is defined where plastic deformation is confined to crack tip plastic zone development, whereas Phase II deformation is defined where plastic hinging deformation develops. In Phase II deformation, the 0.5T SE(B) B B specimen (slightly larger than the PCVN specimen) consistently showed the highest constraint of all SE(B) specimens evaluated for constraint comparisons. The PCVN specimen begins the Phase II type of deformation at relatively low KR levels, with the result that KJc values above about 70 MPa m from precracked Charpy specimens are under extensive plastic hinging deformation.« less

Evaluation of a fluorescence feedback system for guidance of laser angioplasty.

PubMed

Deckelbaum, L I; Desai, S P; Kim, C; Scott, J J

1995-01-01

Laser-induced fluorescence spectroscopy (LIFS) may be capable of guiding laser angioplasty by discriminating normal and atherosclerotic artery and by determining catheter-tissue environment. Previous optical multichannel analyzer based LIFS systems have been expensive and cumbersome. To simplify LIFS, a system based on photomultiplier tubes was developed and evaluated. Tissue fluorescence was induced by a helium cadmium laser (wavelength = 325 nm, power = 0.2-0.5 mW), collected by clinical multifiber laser angioplasty catheters and directed through one of two filters (10 nm bandpass, 380 nm or 440 nm peak transmission) to a photomultiplier tube. An LIFS ratio was defined as the relative intensity at 380:440 nm after calibration with an elastin fluorescence spectrum; 157 coronary artery cadaveric specimens were evaluated spectroscopically and histologically. To evaluate the utility of LIFS to optimize catheter position by determining catheter-tissue contact, by determining saline dilution of blood, and by orienting eccentric multifiber catheters a new variable, the total fluorescence intensity (TFI) was defined as the sum of arterial fluorescence intensities at 380 nm and 440 nm. TFI was recorded in vitro through multifiber catheters from 20 arterial specimens in vitro in blood and evaluated as a function of the catheter-to-tissue distance (d) over a range from 0 to 400 mu. Defining normal specimens as those with an intimal thickness < or = 200 mu, and atherosclerotic as those with an intimal thickness > 200 mu, 47/50 (94%) normal and 85/107 (79%) atherosclerotic specimens were correctly classified using a threshold LIFS ratio of 2.0. Mean (+/- SE) normal ratio was 1.76 +/- 0.02 and mean atherosclerotic ratio was 2.78 +/- 0.08 (P < or = 0.01). The classification accuracy of atherosclerotic specimens increased with intimal thickness so that 95% of atherosclerotic specimens (69/73) with intimal thickness > or = 400 mu were correctly classified. TFI was capable of determining catheter-tissue contact as maximal TFI was recorded with the catheter in contact with the tissue (d = 0 mu) and decreased markedly with distance (to 52 +/- 6% at d = 100 mu, 19 +/- 4% at d = 200 mu, and 3 +/- 1% at d = 300 mu). TFI was recorded from ten arterial specimens in blood/saline mixtures ranging in hematocrit from 0% (saline) to 50% (whole blood). TFI was capable of detecting saline hemodilution of blood as TFI decreased markedly at higher hematocrits such that TFI could only by recorded at hematocrits < 10% for catheter-to-tissue distances > or = 300 mu. TFI was recorded through ecentric multifiber catheters from 25 arterial specimens and eval-uated as a function of the degree of catheter-tissue overlap. TFI was capable of detecting maximal catheter-tissue overlap as TFI correlated linearly with the area (A) of overlap (TFI = 1.12 A + .07, r = 0.92). By discriminating atherosclerotic from normal tissue and by confirming catheter-tissue contact and saline hemodilution, fluorescence feedback should minimize irradiation of normal tissue and/or blood and enhance the safety and efficacy of laser angioplasty.

Comparison of urine specimen collection times and testing fractions for the detection of high-risk human papillomavirus and high-grade cervical precancer.

PubMed

Senkomago, V; Des Marais, A C; Rahangdale, L; Vibat, C R T; Erlander, M G; Smith, J S

2016-01-01

Urine testing for high-risk human papillomavirus (HR-HPV) detection could provide a non-invasive, simple method for cervical cancer screening. We examined whether HR-HPV detection is affected by urine collection time, portion of urine stream, or urine fraction tested, and assessed the performance of HR-HPV testing in urine for detection of cervical intraepithelial neoplasia grade II or worse (CIN2+). A total of 37 female colposcopy clinic attendees, ≥ 30 years, provided three urine samples: "first void" urine collected at home, and "initial stream" and "mid-stream" urine samples collected at the clinic later in the day. Self- and physician-collected brush specimens were obtained at the same clinic visit. Colposcopy was performed and directed biopsies obtained if clinically indicated. For each urine sample, HR-HPV DNA testing was conducted for unfractionated, pellet, and supernatant fractions using the Trovagene test. HR-HPV mRNA testing was performed on brush specimens using the Aptima HPV assay. HR-HPV prevalence was similar in unfractionated and pellet fractions of all urine samples. For supernatant urine fractions, HR-HPV prevalence appeared lower in mid-stream urine (56.8%[40.8-72.7%]) than in initial stream urine (75.7%[61.9-89.5%]). Sensitivity of CIN2+ detection was identical for initial stream urine and physician-collected cervical specimen (89.9%[95%CI=62.7-99.6%]), and similar to self-collected vaginal specimen (79.1%[48.1-96.6%]). This is among the first studies to compare methodologies for collection and processing of urine for HR-HPV detection. HR-HPV prevalence was similar in first void and initial stream urine, and was highly sensitive for CIN2+ detection. Additional research in a larger and general screening population is needed. Copyright © 2015 Elsevier B.V. All rights reserved.

Implementation of the first worldwide quality assurance program for cystic fibrosis multiple mutation detection in population-based screening.

PubMed

Earley, Marie C; Laxova, Anita; Farrell, Philip M; Driscoll-Dunn, Rena; Cordovado, Suzanne; Mogayzel, Peter J; Konstan, Michael W; Hannon, W Harry

2011-07-15

CDC's Newborn Screening Quality Assurance Program collaborated with several U.S. Cystic Fibrosis Care Centers to collect specimens for development of a molecular CFTR proficiency testing program using dried-blood spots for newborn screening laboratories. Adult and adolescent patients or carriers donated whole blood that was aliquoted onto filter paper cards. Five blind-coded specimens were sent to participating newborn screening laboratories quarterly. Proficiency testing results were evaluated based on presumptive clinical assessment. Individual evaluations and summary reports were sent to each participating laboratory and technical consultations were offered if incorrect assessments were reported. The current CDC repository contains specimens with 39 different CFTR mutations. Up to 45 laboratories have participated in the program. Three years of data showed that correct assessments were reported 97.7% of the time overall when both mutations could be determined. Incorrect assessments that could have lead to a missed case occurred 0.9% of the time, and no information was reported 1.1% of the time due to sample failure. Results show that laboratories using molecular assays to detect CFTR mutations are performing satisfactorily. The programmatic results presented demonstrate the importance and complexity of providing proficiency testing for DNA-based assays. Published by Elsevier B.V.

Evaluation of the clinical implementation of a large-scale online e-learning program on venous blood specimen collection guideline practices.

PubMed

Willman, Britta; Grankvist, Kjell; Bölenius, Karin

2018-05-11

When performed erroneously, the venous blood specimen collection (VBSC) practice steps patient identification, test request management and test tube labeling are at high risk to jeopardize patient safety. VBSC educational programs with the intention to minimize risk of harm to patients are therefore needed. In this study, we evaluate the efficiency of a large-scale online e-learning program on personnel's adherence to VBSC practices and their experience of the e-learning program. An interprofessional team transformed an implemented traditional VBSC education program to an online e-learning program developed to stimulate reflection with focus on the high-risk practice steps. We used questionnaires to evaluate the effect of the e-learning program on personnel's self-reported adherence to VBSC practices compared to questionnaire surveys before and after introduction of the traditional education program. We used content analysis to evaluate the participants free text experience of the VBSC e-learning program. Adherence to the VBSC guideline high-risk practice steps generally increased following the implementation of a traditional educational program followed by an e-learning program. We however found a negative trend over years regarding participation rates and the practice to always send/sign the request form following the introduction of an electronic request system. The participants were in general content with the VBSC e-learning program. Properly designed e-learning programs on VBSC practices supersedes traditional educational programs in usefulness and functionality. Inclusion of questionnaires in the e-learning program is necessary for follow-up of VBSC participant's practices and educational program efficiency.

Stable isotope data from deep-water antipatharians: 400-Year records from the southeastern coast of the United States of America

USGS Publications Warehouse

Williams, B.; Risk, Michael J.; Ross, Steve W.; Sulak, K.J.

2007-01-01

In this study, time-series stable isotope results (δ13C and δ15N) from three deep-water Leiopathes glaberrima(Esper, 1788) specimens Collected off the southeastern Coast of the United States of America and one specimen from the Gulf of Mexico are presented. The specimens were Collected live in 2004 and are estimated to be 200–500 yrs old based on 210Pb measurements and band Counts. The δ13C and δ15N long-term trends are reproducible within and among specimens from a similar location, suggesting a common environmental influence. Three western Atlantic specimens have average δ13C values of −15.7‰, −16.3‰, and −16.1‰, with the most depleted values from the oldest specimen. The oldest specimen records an enrichment in 13C of 0.5‰ corresponding to the Little Ice Age. All three specimens show a depletion of 13C over the past 150 yrs Corresponding to the δ13C Suess Effect. The fourth specimen from the Gulf of Mexico has an average δ13C value of −16.4‰ and shows no trend in13C value with time. All four specimens Contain an enrichment in 15N over the most recent 75 yrs, with the largest enrichment (3‰) in the Gulf of Mexico specimen. This enrichment is likely a result of increased terrestrial effluent (sewage and manure) reaching the offshore specimens.

[Without sense and understanding? Rudolf Virchow's strategy of collecting by the example of his pathological museum].

PubMed

Schnalke, Thomas

2007-01-01

The Berlin pathologist Rudolf Virchow (1821-1902) has been called a "m anic" collector in the most recent studies on the history of science and culture because of his collection of over 23,000 pathoanatomical wet and dry specimens. A closer look at Virchow's collecting efforts, however, reveal that there was system behind the relative abundance of objects. This contribution will attempt to reconstruct Virchow's collection concept as well as his ideas about a meaningful arrangement of the specimens in the museum he founded in 1899. The study follows a reference of Virchow's to the corresponding specimen collections in the English hospital schools, which Virchow had always seen as exemplary. In this connection, the strategies and concepts of the British pathologist Thomas Hodgkin (1798-1866) will be investigated more closely as they relate to the specimen collection he administered at Guy's Hospital in London. There, abnormally changed organ specimens were presented along the two axes of anatomy and nosology. Virchow encountered this practice under the Charité prosector, Robert Froriep (1804-1861), where he experienced his socialization as collector and presenter in pathology between 1844 and 1847. In his second Berlin phase between 1856 and 1902, he expanded his institute at the Charité to a worldwide renowned center for pathology. During this time, Virchow added a third dimension to his collection strategy under the heading "progression", in order to document whole series in the developmental process of all diseases in all primarily and secondarily affected organs. After the opening of his Pathological Museum on the grounds of the CharitY, he strove until his death to arrange his specimens in the form of a three-dimensional textbook. Various structural conditions, a dearth of exhibition cases, as well as his decreasing vitality limited the scope of Virchow's achievements. The most essential reason why Virchow realized only a small portion of his exhibition concept, however, lay in the sheer endlessness of diseases to be portrayed in their being and manifestation.

An Annotated Checklist of the Anopheles of Thailand (Diptera : Culicidae) (Thai National Scientific Papers, Fauna Series Number 2)

DTIC Science & Technology

1968-08-01

workers in 1958 on Doi Suthep mountain near Chiang Mai . Additional specimens in the SEATO collection were made by human biting collections, or...to be restricted to forested hills. The specimens taken in the human biting collections at Chiang Mai \\vere not permitted to engorge, and the biting...ditches, seepages, and sumps. Distribution in Thailand: Ayutthaya, Chanthaburi, Chiang Mai , Chon Buri, Phra Nakhon (Bangkok), Nakhon Nayok, Nakhon

Pitfalls of diagnosing urinary tract infection in infants and young children.

PubMed

Yamasaki, Yasuhito; Uemura, Osamu; Nagai, Takuhito; Yamakawa, Satoshi; Hibi, Yoshiko; Yamamoto, Masaki; Nakano, Masaru; Kasahara, Katsuaki; Bo, Zhang

2017-07-01

The aim of this study was to examine the sensitivity and specificity of pyuria-based diagnosis of urinary tract infection (UTI) in urine collected by transurethral catheterization, and the reliability of diagnosis of pyuria in urine collected in a perineal bag. The gold standard for UTI diagnosis is significant colony counts of a single organism in urine obtained in a sterile manner. We enrolled 301 patients who underwent medical examination at the present hospital for possible UTI between January 2005 and December 2009. We collected 438 urine samples by transurethral catheterization. We investigated the accuracy of pyuria-based diagnosis of UTI using transurethral catheterization urine specimens, and the reliability of diagnosis of pyuria using bag-collected urine specimens. The false-negative rate of UTI diagnosis based on pyuria in transurethral catheterization urine sediments was 9.0%; there was no significant difference in the false-negative rate of UTI diagnosis between boys and girls. Approximately 28% of pyuria-positive bag-collected urine specimens were pyuria negative on transurethral catheterization; this rate was significantly higher in girls than in boys (56.7% vs. 8.9%, P < 0.0001). The absence of pyuria in transurethral catheterization urine sediments does not rule out UTI. Pyuria in bag-collected urine specimens frequently consists of urine leukocytes from external genitalia as well as from the urinary tract. © 2017 Japan Pediatric Society.

The collection of birds from Mozambique at the Instituto de Investigação Científica Tropical of the University of Lisbon (Portugal)

PubMed Central

Monteiro, Miguel; Figueira, Rui; Melo, Martim; Mills3,4, Michael Stuart Lyne; Beja, Pedro; Bastos-Silveira, Cristiane; Ramos, Manuela; Rodrigues, Diana; Neves5,7, Isabel Queirós; Consciência, Susana; Reino, Luís

2017-01-01

Abstract The Instituto de Investigação Científica Tropical of the University of Lisbon, which resulted from the recent merger (in 2015) of the former state laboratory Instituto de Investigação Científica Tropical in the University of Lisbon, holds an important collection of bird skins from the Portuguese-speaking African Countries (Angola, Mozambique, São Tomé and Príncipe, Guinea Bissau and Cape Verde), gathered as a result of several scientific expeditions made during the colonial period. In this paper, the subset from Mozambique is described, which was taxonomically revised and georeferenced. It contains 1585 specimens belonging to 412 taxa, collected between 1932 and 1971, but mainly in 1948 (43% of specimens) and 1955 (30% of specimens). The collection covers all eleven provinces of the country, although areas south of the Zambezi River are better represented than those north of the river. The provinces with the highest number of specimens were Maputo, Sofala, and Gaza. Although it is a relatively small collection with a patchy coverage, it adds significantly to Global Biodiversity Information Facility, with 15% of all records available before and during the collecting period (1830–1971) being the second largest dataset for that period for Mozambique. PMID:29118634

10 CFR 26.109 - Urine specimen quantity.

Code of Federal Regulations, 2014 CFR

2014-01-01

... 10 Energy 1 2014-01-01 2014-01-01 false Urine specimen quantity. 26.109 Section 26.109 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.109 Urine... shall encourage the donor to drink a reasonable amount of liquid (normally, 8 ounces of water every 30...

10 CFR 26.109 - Urine specimen quantity.

Code of Federal Regulations, 2013 CFR

2013-01-01

... 10 Energy 1 2013-01-01 2013-01-01 false Urine specimen quantity. 26.109 Section 26.109 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.109 Urine... shall encourage the donor to drink a reasonable amount of liquid (normally, 8 ounces of water every 30...

10 CFR 26.109 - Urine specimen quantity.

Code of Federal Regulations, 2012 CFR

2012-01-01

... 10 Energy 1 2012-01-01 2012-01-01 false Urine specimen quantity. 26.109 Section 26.109 Energy NUCLEAR REGULATORY COMMISSION FITNESS FOR DUTY PROGRAMS Collecting Specimens for Testing § 26.109 Urine... shall encourage the donor to drink a reasonable amount of liquid (normally, 8 ounces of water every 30...

Histologic and Radiographic Analysis of Nonhealing Extraction Sockets Treated with Bio-Oss Collagen After a 4-Month Healing Period: A Prospective Descriptive Study in Humans.

PubMed

Tirone, Federico; Salzano, Stefano; Pagano, Marco

2018-03-07

Healing of extraction sockets may sometimes result in formation of fibrous tissue instead of bone, even after 4 months, an occurrence that may hinder implant placement. The aim of this preliminary observational study was to histologically evaluate quality and amount of bone regeneration after treating nonhealing sockets with a bovine-derived xenograft enriched with porcine collagen (Bio-Oss Collagen, Geistlich) without barrier membranes. Biopsy specimens were collected during implant placement, 4 months after grafting. A total of 10 cases were treated and evaluated. In all cases, correct implant placement was possible and no implant failure occurred up to 6 months after loading. The histologic analysis demonstrated new bone formation in all specimens. The percentage of newly formed bone was 29.1% (SD 20.71%; range 5% to 48%). Xenograft particles in direct contact with newly formed bone were visible, and mature lamellar bone was observed in 8 cases.

USE OF SMALL SPECIMENS FOR FRACTURE TOUGHNESS EVALUATION OF RPV STEELS

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

Sokolov, Mikhail A; Nanstad, Randy K

2016-01-01

Small specimens are playing the key role in evaluating properties of irradiated materials. The use of small specimens provides several advantages. Typically, only a small volume of material can be irradiated in a reactor at desirable conditions in terms of temperature, neutron flux, and neutron dose. A small volume of irradiated material may also allow for easier handling of specimens. Smaller specimens reduce the amount of radioactive material, minimizing personnel exposures and waste disposal. However, use of small specimens imposes a variety of challenges as well. These challenges are associated with proper accounting for size effects and transferability of smallmore » specimen data to the real structures of interest. Any fracture toughness specimen that can be made out of standard Charpy specimen or its broken half may have exceptional utility for evaluation of reactor pressure vessels (RPVs) since it would allow one to determine and monitor directly actual fracture toughness instead of requiring indirect predictions using correlations established with impact data. The Charpy V-notch specimen is the most commonly used specimen geometry in surveillance programs and most likely to be used in advanced reactors as per ASME code.« less

Comparative Analytical Utility of DNA Derived from Alternative Human Specimens for Molecular Autopsy and Diagnostics

PubMed Central

Klassen, Tara L.; von Rüden, Eva-Lotta; Drabek, Janice; Noebels, Jeffrey L.; Goldman, Alica M.

2013-01-01

Genetic testing and research have increased the demand for high-quality DNA that has traditionally been obtained by venipuncture. However, venous blood collection may prove difficult in special populations and when large-scale specimen collection or exchange is prerequisite for international collaborative investigations. Guthrie/FTA card–based blood spots, buccal scrapes, and finger nail clippings are DNA-containing specimens that are uniquely accessible and thus attractive as alternative tissue sources (ATS). The literature details a variety of protocols for extraction of nucleic acids from a singular ATS type, but their utility has not been systematically analyzed in comparison with conventional sources such as venous blood. Additionally, the efficacy of each protocol is often equated with the overall nucleic acid yield but not with the analytical performance of the DNA during mutation detection. Together with a critical in-depth literature review of published extraction methods, we developed and evaluated an all-inclusive approach for serial, systematic, and direct comparison of DNA utility from multiple biological samples. Our results point to the often underappreciated value of these alternative tissue sources and highlight ways to maximize the ATS-derived DNA for optimal quantity, quality, and utility as a function of extraction method. Our comparative analysis clarifies the value of ATS in genomic analysis projects for population-based screening, diagnostics, molecular autopsy, medico-legal investigations, or multi-organ surveys of suspected mosaicisms. PMID:22796560

Diagnostic value of indirect hemagglutination in the seroepidemiology of Shigella infections.

PubMed Central

Patton, C M; Gangarosa, E J; Weissman, J B; Merson, M H; Morris, G K

1976-01-01

To evaluate the usefulness of the indirect hemagglutination (IHA) test in the epidemiological investigation of shigellosis, single serum specimens were tested from 50 patients with Shigella dysenteriae 1 (Shiga bacillus) infections, 103 asymptomatic contacts of these cases, 267 adult and 100 student control, and serum specimens collected during two outbreaks caused by S. sonnei and one outbreak due to S. flexneri 6. In patients with S. dysenteriae 1, 74% demonstrated titers of greater than or equal to 1:40, with 50% showing titers of greater than or equal to 1:160, whereas in the controls 10.4% had titers of greater than or equal to 1:40 and only 0.3% had titers of greater than or equal to 1:160. IHA titers in serum specimens collected from patients with S. sonnei and S. flexneri 6 were too low to be considered diagnostic for individual patients, but were useful in analysis of group results. Groups of ill individuals yielded titers significantly higher than non-ill groups; however, titers from ill groups were usually less than 1:40. The IHA test for S. dysenteriae 1 antibodies serves as a valuable adjunct to the diagnosis of Shiga bacillus dysentery. In our laboratory, an IHA titer of 1:40 or 1:80 is a "borderline positive." Shiga bacillus dysentery is strongly indicated when IHA titers are greater than or equal to 1:60. PMID:767361

Effect of laser treatment on first-intention incisional wound healing in ball pythons (Python regius).

PubMed

Cole, Grayson L; Lux, Cassie N; Schumacher, Juergen P; Seibert, Rachel L; Sadler, Ryan A; Henderson, Andrea L; Odoi, Agricola; Newkirk, Kim M

2015-10-01

To evaluate effects of laser treatment on incisional wound healing in ball pythons (Python regius). 6 healthy adult ball pythons. Snakes were sedated, a skin biopsy specimen was collected for histologic examination, and eight 2-cm skin incisions were made in each snake; each incision was closed with staples (day 0). Gross evaluation of all incision sites was performed daily for 30 days, and a wound score was assigned. Four incisions of each snake were treated (5 J/cm(2) and a wavelength of 980 nm on a continuous wave sequence) by use of a class 4 laser once daily for 7 consecutive days; the other 4 incisions were not treated. Two excisional skin biopsy specimens (1 control and 1 treatment) were collected from each snake on days 2, 7, 14, and 30 and evaluated microscopically. Scores were assigned for total inflammation, degree of fibrosis, and collagen maturity. Generalized linear models were used to investigate the effect of treatment on each variable. Wound scores for laser-treated incisions were significantly better than scores for control incisions on day 2 but not at other time points. There were no significant differences in necrosis, fibroplasia, inflammation, granuloma formation, or bacterial contamination between control and treatment groups. Collagen maturity was significantly better for the laser-treated incisions on day 14. Laser treatment resulted in a significant increase in collagen maturity at day 14 but did not otherwise significantly improve healing of skin incisions.

First Record of Culex (Microculex) daumastocampa (Diptera: Culicidae) in Mexico, with Notes on Cx. rejector and Cx. imitator.

PubMed

Ortega-Morales, A; Garza-Hernández, J A; González-Álvarez, V H; Hernández-Triana, L M; Rodríguez-Pérez, M A

2018-03-08

Culex (Microculex) daumastocampa Dyar & Knab was originally described by Dyar and Knab (Proc US Nat Mus 35:53-70, 1908) from larvae collected at axils of bromeliads in Port San Felipe, Panama. Culex daumastocampa is found in Colombia, Venezuela, Panama, Suriname, Costa Rica, Nicaragua, Guatemala, and Mexico, although its presence had not been reported suggesting its northernmost distribution. In Mexico, the subgenus Microculex had included Cx. rejector Dyar and Knab, and Cx. imitator Theobald. However, after that collection specimens were re-examined along with other specimens collected during 2016 in Chiapas (all specimens are available in the Culicidae Collection of the Universidad Autonoma Agraria Antonio Narro Unidad Laguna [UAAAN-UL], Mexico). Culex daumastocampa is now reported for the first time in Mexico, Cx. rejector for Chiapas, and Cx. imitator removed from the checklist of previous reports as to be present in Mexico.

Ongoing Use of Data and Specimens from NCI Sponsored Cancer Prevention Clinical Trials in the Community Clinical Oncology Program

PubMed Central

Minasian, Lori; Tangen, Catherine M.; Wickerham, D. Lawrence

2015-01-01

Large cancer prevention trials provide opportunities to collect a wide array of data and biospecimens at study entry and longitudinally, for a healthy, aging population without cancer. This provides an opportunity to use pre-diagnostic data and specimens to evaluate hypotheses about the initial development of cancer. This paper reports on strides made by, and future possibilities for, the use of accessible biorepositories developed from precisely annotated samples obtained through large-scale National Cancer Institute (NCI)-sponsored cancer prevention clinical trials conducted by the NCI Cooperative Groups. These large cancer prevention studies, which have enrolled over 80,000 volunteers, continue to contribute to our understanding of cancer development more than 10 years after they were closed. PMID:26433556

Diagnosis of Enterocytozoon bieneusi by PCR in Stool Samples Eluted from Filter Paper Disks

PubMed Central

Carnevale, Silvana; Velásquez, Jorge N.; Labbé, Jorge H.; Chertcoff, Agustín; Cabrera, Marta G.; Rodríguez, Mónica I.

2000-01-01

We report a PCR-based assay for the detection of Enterocytozoon bieneusi. We extracted DNA from feces which had been applied to filter paper disks and evaluated four preserving solutions. Infected specimens were identified by electrophoresis of amplicons from concentrated formalin-fixed samples and unconcentrated fresh feces. Our findings demonstrate that this methodology is effective for sample collection, mailing, and diagnosis of this pathogen. PMID:10799469

Proposal of a punch biopsy protocol as a pre-requisite for the establishment of a tissue bank from resected esophageal tumors.

PubMed

Bonavina, Luigi; Laface, Letizia; Picozzi, Stefano; Nencioni, Marco; Siboni, Stefano; Bona, Davide; Sironi, Andrea; Sorba, Francesca; Clemente, Claudio

2010-09-01

With the development of tissue banking, a need for homogeneous methods of collection, processing, and storage of tissue has emerged. We describe the implementation of a biological bank in a high-volume, tertiary care University referral center for esophageal cancer surgery. We also propose an original punch biopsy technique of the surgical specimen. The method proved to be simple, reproducible, and not expensive. Unified standards for specimen collection are necessary to improve results of specimen-based diagnostic testing and research in surgical oncology.

Technique for restoration of mite (Acari) preparations in deteriorated Hoyer's medium.

PubMed

Jacinavicius, F C; Badari, J C; Ramirez, D G; Moraes, R H P; Onofrio, V C; Barros-Battesti, D M

2013-06-01

The Acari Collection of Instituto Butantan (IBSP), São Paulo, Brazil, includes many types and other identified mite specimens that were mounted in Hoyer's medium, mainly in the first part of last century. An effort to restore degraded preparations was initiated in 1996. In this process, an improved technique was developed, allowing the adequate cleaning of specimens mounted up to 50-70 years before. Types and other identified specimens of Trombidiformes (Harpirhynchidae and Trombiculidae), Sarcoptiformes (Acaridae, Atopomelidae, Listrophoridae, and Psoroptidae) and Mesostigmata (Dermanyssidae, Ixodorhynchidae, Laelapidae, Macronyssidae, and Spinturnicidae) deposited at IBSP Collection have been satisfactorily restored.

Choice of urine collection methods for the diagnosis of urinary tract infection in young, febrile infants.

PubMed

Schroeder, Alan R; Newman, Thomas B; Wasserman, Richard C; Finch, Stacia A; Pantell, Robert H

2005-10-01

The optimal method of urine collection in febrile infants is debatable; catheterization, considered more accurate, is technically difficult and invasive. To determine predictors of urethral catheterization in febrile infants and to compare bag and catheterized urine test performance characteristics. Prospective analysis of infants enrolled in the Pediatric Research in Office Settings' Febrile Infant Study. A total of 219 practices from within the Pediatric Research in Office Settings' network, including 44 states, the District of Columbia, and Puerto Rico. A total of 3066 infants aged 0 to 3 months with temperatures of 38 degrees C or higher. We calculated adjusted odds ratios for predictors of catheterization. Diagnostic test characteristics were compared between bag and catheterization. Urinary tract infection was defined as pure growth of 100 000 CFU/mL or more (bag) and 20 000 CFU/mL or more (catheterization). Seventy percent of urine samples were obtained by catheterization. Predictors of catheterization included female sex, practitioner older than 40 years, Medicaid, Hispanic ethnicity, nighttime evaluation, and severe dehydration. For leukocyte esterase levels, bag specimens demonstrated no difference in sensitivity but somewhat lower specificity (84% [bag] vs 94% [catheterization], P<.001) and a lower area under the receiver operating characteristic curve for white blood cells (0.71 [bag] vs 0.86 [catheterization], P = .01). Infection rates were similar in bag and catheterized specimens (8.5% vs 10.8%). Ambiguous cultures were more common in bag specimens (7.4% vs 2.7%, P<.001), but 21 catheterized specimens are needed to avoid each ambiguous bag result. Most practitioners obtain urine from febrile infants via catheterization, but choice of method is not related to the risk of urinary tract infection. Although both urine cultures and urinalyses are more accurate in catheterized specimens, the magnitude of difference is small but should be factored into clinical decision making.

Causes and impact of specimen rejection in a clinical chemistry laboratory.

PubMed

Cao, Liyun; Chen, Meng; Phipps, Ron A; Del Guidice, Robert E; Handy, Beverly C; Wagar, Elizabeth A; Meng, Qing H

2016-07-01

Pre-analytical errors necessitate specimen rejection and negatively affect patient safety. Our purpose was to investigate the factors leading to specimen rejection and its impact. Specimen rejections in a clinical chemistry laboratory during a 1-year period were reviewed retrospectively and analyzed for frequency, cause, circumstances, and impact. Of the 837,862 specimens received, 2178 (0.26%) were rejected. The most common reasons for specimen rejection were contamination (n=764, 35.1%), inappropriate collection container/tube (n=330, 15.2%), quantity not sufficient (QNS) (n=329, 15.1%), labeling errors (n=321, 14.7%), hemolyzed specimen (n=205, 9.4%), and clotted specimen (n=203, 9.3%). The analytes most often affected were glucose (n=192, 8.8%); calcium (n=152, 7.0%), magnesium (n=148, 6.8%), potassium (n=137, 6.3%), creatinine (n=100, 4.6%), and blood urea nitrogen (n=97, 4.4%). Outpatient service and blood draw by phlebotomists were associated with low rejection rates (536/493,501 or 0.11% and 368/586,503 or 0.06%, respectively). Recollection due to specimen rejection increased the turnaround time by an average of 108min. The total cost for the recollection was around $43,210 USD with an average cost around $21.9 USD. The factors associated with rejection are remediable by improved training and quality assurance measures. Policies and procedures specific to specimen collection, transportation, and preparation should be strictly followed. Copyright © 2016 Elsevier B.V. All rights reserved.

Forensically important calliphoridae (diptera) associated with pig carrion in rural north-central Florida

USGS Publications Warehouse

Gruner, Susan V.; Slone, D.H.; Capinera, J.L.

2007-01-01

A study to determine the relative abundance and seasonality of forensically important blow flies (Diptera: Calliphoridae) in rural north-central Florida was conducted using pig carcasses (Sus scrofa L.) as models for human bodies. Seven species of Calliphoridae were collected: Lucilia coeruleiviridis (=Phoenicia) (Macquart), Cochliomyia macellaria (F.), Chrysomya rufifaces (Macquart), Phormia regina (Meigen), Chrysomya megacephala (F.), and a few specimens of Calliphora livida Hall, and Calliphora vicina Robineau-Desvoidy. Species composition in aerial collections of adult flies, preserved larval collections, and samples of larvae reared to the adult stage were all highly correlated. Relative abundance of the species found was significantly different, with L. coeruleiviridis the most abundant species year-round. The relative abundance of the collected species varied significantly by day of decomposition and by season, with significant interactions between season and day, season and species, and day and species. L. coeruleiviridis, C. macellaria, C. rufifaces, and P. regina were found during the entire year, two C. vicina specimens and 11 C. livida specimens were collected from December to March, whereas C. megacephala was collected only from June through September. ?? 2007 Entomological Society of America.

Three alternative structural configurations for phlebotomy: a comparison of effectiveness.

PubMed

Mannion, Heidi; Nadder, Teresa

2007-01-01

This study was designed to compare the effectiveness of three alternative structural configurations for inpatient phlebotomy. It was hypothesized that decentralized was less effective when compared to centralized inpatient phlebotomy. A non-experimental prospective survey design was conducted at the institution level. Laboratory managers completed an organizational survey and collected data on inpatient blood specimens during a 30-day data collection period. A random sample (n=31) of hospitals with onsite laboratories in the United States was selected from a database purchased from the Joint Commission on Accreditations of Healthcare Organizations (JCAHO). Effectiveness of the blood collection process was measured by the percentage of specimens rejected during the data collection period. Analysis of variance showed a statistically significant difference in the percentage of specimens rejected for centralized, hybrid, and decentralized phlebotomy configurations [F (2, 28) = 4.27, p = .02] with an effect size of .23. Post-hoc comparison using Tukey's HSD indicated that mean percentage of specimens rejected for centralized phlebotomy (M = .045, SD = 0.36) was significantly different from the decentralized configuration (M = 1.42, SD = 0.92, p = .03). found to be more effective when compared to the decentralized configuration.

Ethics, Human Use, and the Department of Defense Serum Repository.

PubMed

Pavlin, Julie A; Welch, Robert A

2015-10-01

The Department of Defense Serum Repository (DoDSR) contains a growing archive of sera from service members collected to perform medical surveillance, clinical diagnosis, and epidemiologic studies to identify, prevent, and control diseases associated with military service. The specimens are a mandatory collection under DoD and U.S. regulations and do not include informed consent for uses beyond force health protection. Any use of the specimens for research requires deidentification of the samples and must be approved by Institutional Review Boards. However, as expansion of the DoDSR is contemplated, ethical considerations of sample collection, storage, and use must be carefully reconsidered. Other similar programs for research use of specimens collected for public health purpose are also undergoing similar reviews. It is recommended that at a minimum, service members are informed of the potential storage and use of their specimens and are allowed to opt out of additional use, or a broad informed consent is provided. The DoDSR provides a tremendous resource to the DoD and global health community, and to ensure its continued existence and improvement, the DoD must stay consistent with all principles of research ethics. Reprint & Copyright © 2015 Association of Military Surgeons of the U.S.

Automated Plasma Spray (APS) process feasibility study

NASA Technical Reports Server (NTRS)

Fetheroff, C. W.; Derkacs, T.; Matay, I. M.

1981-01-01

An automated plasma spray (APS) process was developed to apply two layer (NiCrAlY and ZrO2-12Y2O3) thermal barrier coatings to aircraft and stationary gas turbine engine blade airfoils. The APS process hardware consists of four subsystems: a mechanical positioning subsystem incorporating two interlaced six degree of freedom assemblies (one for coating deposition and one for coating thickness monitoring); a noncoherent optical metrology subsystem (for in process gaging of the coating thickness buildup at specified points on the specimen); a microprocessor based adaptive system controller (to achieve the desired overall thickness profile on the specimen); and commerical plasma spray equipment. Over fifty JT9D first stage aircraft turbine blade specimens, ten W501B utility turbine blade specimens and dozens of cylindrical specimens were coated with the APS process in preliminary checkout and evaluation studies. The best of the preliminary turbine blade specimens achieved an overall coating thickness uniformity of 53 micrometers (2.1 mils), much better than is achievable manually. Comparative evaluations of coating thickness uniformity for manually sprayed and APS coated specimens were performed. One of the preliminary turbine blade evaluation specimens was subjected to a torch test and metallographic evaluation. Some cylindrical specimens coated with the APS process survived up to 2000 cycles in subsequent burner rig testing.

Nondestructive evaluation of fiber reinforced polymer bridges and decks.

DOT National Transportation Integrated Search

2003-10-01

The research described herein involved both nondestructive evaluation and destructive testing of an FRP honeycomb specimen. The specimen is representative of an FRP bridge that is to be constructed in Troupsburg, New York. The specimen was tested in ...

Should the presence of a culture positive urinary tract infection exclude patients from rapid evaluation hematuria protocols?

PubMed

Vasdev, Nikhil; Thorpe, Andrew C

2013-08-01

Current rapid evaluation protocols for patients with hematuria tend to exclude those with urinary tract infection since this is assumed to be evidence of a benign treatable cause. The likelihood of a urinary tract cancer in such patients is, however, uncertain, and we have therefore analyzed a prospective hematuria clinic database to determine risk. A total of 1,740 patients were enrolled prospectively in this study at our unit's one stop fast track hematuria clinic between April 2003 and March 2006. Evaluation of patients consisted of basic demographics, history and examination, urinalysis, urine culture, urine cytology, and serum creatinine. All patients then underwent a renal ultrasound, intravenous urogram, and cystoscopy. A total of 1,067 males and 673 females with a mean (range) age of 60.8 (16-96) years were included in the study. One hundred sixty-one patients had a positive mid-stream urine (MSU) on a specimen collected at the hematuria clinic. Amongst this group 20% (32) patients had a urologic malignancy diagnosed, of whom 12% (4) had metastatic disease at presentation. Only 1% (3) of patients had a urologic malignancy with a previous history of a treated urinary tract infection (UTI) and negative MSU at the clinic. The risk of urologic malignancy was 24% (303) in the remaining 1,249 patients with no history of a UTI prior to presentation and a negative MSU on a specimen collected at the one stop fast track hematuria clinic. Despite selection bias inherent in this analysis, it appears that the presence of UTI does not decrease the likelihood of having a urologic malignancy diagnosed. Hence, there is no indication to delay prompt evaluation in patients with hematuria and a positive urine culture collected at the hematuria clinic. Copyright © 2013 Elsevier Inc. All rights reserved.

Study of amended reports to evaluate and improve surgical pathology processes.

PubMed

Meier, Frederick A; Varney, Ruan C; Zarbo, Richard J

2011-09-01

: Amended surgical pathology reports record defects in the process of transforming tissue specimens into diagnostic information. : Systematic study of amended reports tests 2 hypotheses: (a) that tracking amendment frequencies and the distribution of amendment types reveals relevant aspects of quality in surgical pathology's daily transformation of specimens into diagnoses and (b) that such tracking measures the effect, or lack of effect, of efforts to improve surgical pathology processes. : We applied a binary definition of altered reports as either amendments or addenda and a taxonomy of defects that caused amendments as misidentifications, specimen defects, misinterpretations, and report defects. During the introduction of a LEAN process improvement approach-the Henry Ford Productions System-we followed trends in amendment rates and defect fractions to (a) evaluate specific interventions, (b) sort case-by-case root causes of misidentifications, specimen defects, and misinterpretations, and (c) audit the ongoing accuracy of the classification of changed reports. LEAN is the management and production system of the Toyota Motor Corporation that promotes continuous improvement; it considers wasted resources expended for purposes other than creating value for end customers and targets such expenditures for elimination. : Introduction of real-time editing of amendments saw annual amendment rates increase from 4.8/1000 to 10.1/1000 and then decrease in an incremental manner to 5.6/1000 as Henry Ford Productions System-specific interventions were introduced. Before introduction of HFPS interventions, about a fifth of the amendments were due to misidentifications, a 10th were due to specimen defects, a quarter due to misinterpretation, and almost half were due to report defects. During the period of the initial application of HFPS, the fraction of amendments due to misidentifications decreased as those due to report defects increased, in a statistically linked manner. As HFPS interventions took hold, misidentifications fell from 16% to 9%, specimen defect rates remained variable, ranging between 2% and 11%, and misinterpretations fell from 18% to 3%. Reciprocally, report defects rose from 64% to 83% of all amendment-causing defects. A case-by-case study of misidentifications, specimen defects, and misinterpretations found that (a) intervention at the specimen collection level had disappointingly little effect on patient misidentifications; (b) standardization of specimen accession and gross examination reduced only specimen defects surrounding ancillary testing; but (c) a double review of breast and prostate cases was associated with drastically reduced misinterpretation defects. Finally, audit of both amendments and addenda demonstrated that 10% of the so-called addenda actually qualified as amendments. : Monitored by the consistent taxonomy, rates of amended reports first rose, then fell. Examining specific defect categories provided information for evaluating specific LEAN interventions. Tracking the downward trend of amendment rates seemed to document the overall success of surgical pathology quality improvement efforts. Process improvements modestly decreased fractions of misidentifications and markedly decreased misinterpretation fractions. Classification integrity requires real time, independent editing of both amendments (changed reports) and addenda (addition to reports).

An Upgrade Pinning Block: A Mechanical Practical Aid for Fast Labelling of the Insect Specimens.

PubMed

Ghafouri Moghaddam, Mohammad Hossein; Ghafouri Moghaddam, Mostafa; Rakhshani, Ehsan; Mokhtari, Azizollah

2017-01-01

A new mechanical innovation is described to deal with standard labelling of dried specimens on triangular cards and/or pinned specimens in personal and public collections. It works quickly, precisely, and easily and is very useful for maintaining label uniformity in collections. The tools accurately sets the position of labels in the shortest possible time. This tools has advantages including rapid processing, cost effectiveness, light weight, and high accuracy, compared to conventional methods. It is fully customisable, compact, and does not require specialist equipment to assemble. Conventional methods generally require locating holes on the pinning block surface when labelling with a resulting risk to damage of the specimens. Insects of different orders can be labelled by this simple and effective tool.

An Upgrade Pinning Block: A Mechanical Practical Aid for Fast Labelling of the Insect Specimens

PubMed Central

Ghafouri Moghaddam, Mohammad Hossein; Rakhshani, Ehsan; Mokhtari, Azizollah

2017-01-01

Abstract A new mechanical innovation is described to deal with standard labelling of dried specimens on triangular cards and/or pinned specimens in personal and public collections. It works quickly, precisely, and easily and is very useful for maintaining label uniformity in collections. The tools accurately sets the position of labels in the shortest possible time. This tools has advantages including rapid processing, cost effectiveness, light weight, and high accuracy, compared to conventional methods. It is fully customisable, compact, and does not require specialist equipment to assemble. Conventional methods generally require locating holes on the pinning block surface when labelling with a resulting risk to damage of the specimens. Insects of different orders can be labelled by this simple and effective tool. PMID:29104440

Which influenza vaccine formulation should be used in Kenya? A comparison of influenza isolates from Kenya to vaccine strains, 2007-2013.

PubMed

Waiboci, Lilian W; Mott, Joshua A; Kikwai, Gilbert; Arunga, Geoffrey; Xu, Xiyan; Mayieka, Lilian; Emukule, Gideon O; Muthoka, Phillip; Njenga, M Kariuki; Fields, Barry S; Katz, Mark A

2016-05-17

Every year the World Health Organization (WHO) recommends which influenza virus strains should be included in a northern hemisphere (NH) and a southern hemisphere (SH) influenza vaccine. To determine the best vaccine formulation for Kenya, we compared influenza viruses collected in Kenya from April 2007 to May 2013 to WHO vaccine strains. We collected nasopharyngeal and oropharyngeal (NP/OP) specimens from patients with respiratory illness, tested them for influenza, isolated influenza viruses from a proportion of positive specimens, tested the isolates for antigenic relatedness to vaccine strains, and determined the percentage match between circulating viruses and SH or NH influenza vaccine composition and schedule. During the six years, 7.336 of the 60,072 (12.2%) NP/OP specimens we collected were positive for influenza: 30,167 specimens were collected during the SH seasons and 3717 (12.3%) were positive for influenza; 2903 (78.1%) influenza A, 902 (24.2%) influenza B, and 88 (2.4%) influenza A and B positive specimens. We collected 30,131 specimens during the NH seasons and 3978 (13.2%) were positive for influenza; 3181 (80.0%) influenza A, 851 (21.4%) influenza B, and 54 (1.4%) influenza A and B positive specimens. Overall, 362/460 (78.7%) isolates from the SH seasons and 316/338 (93.5%) isolates from the NH seasons were matched to the SH and the NH vaccine strains, respectively (p<0.001). Overall, 53.6% and 46.4% SH and NH vaccines, respectively, matched circulating strains in terms of vaccine strains and timing. In six years of surveillance in Kenya, influenza circulated at nearly equal levels during the SH and the NH influenza seasons. Circulating viruses were matched to vaccine strains. The vaccine match decreased when both vaccine strains and timing were taken into consideration. Either vaccine formulation could be suitable for use in Kenya but the optimal timing for influenza vaccination needs to be determined. Copyright © 2016 Elsevier Ltd. All rights reserved.

The detection of tightly closed flaws by nondestructive testing (NDT) methods. [fatigue crack formation in aluminum alloy test specimens

NASA Technical Reports Server (NTRS)

Rummel, W. D.; Rathke, R. A.; Todd, P. H., Jr.; Mullen, S. J.

1975-01-01

Liquid penetrant, ultrasonic, eddy current and X-radiographic techniques were optimized and applied to the evaluation of 2219-T87 aluminum alloy test specimens in integrally stiffened panel, and weld panel configurations. Fatigue cracks in integrally stiffened panels, lack-of-fusion in weld panels, and fatigue cracks in weld panels were the flaw types used for evaluation. A 2319 aluminum alloy weld filler rod was used for all welding to produce the test specimens. Forty seven integrally stiffened panels containing a total of 146 fatigue cracks, ninety three lack-of-penetration (LOP) specimens containing a total of 239 LOP flaws, and one-hundred seventeen welded specimens containing a total of 293 fatigue cracks were evaluated. Nondestructive test detection reliability enhancement was evaluated during separate inspection sequences in the specimens in the 'as-machined or as-welded', post etched and post proof loaded conditions. Results of the nondestructive test evaluations were compared to the actual flaw size obtained by measurement of the fracture specimens after completing all inspection sequences. Inspection data were then analyzed to provide a statistical basis for determining the flaw detection reliability.

Ron Leuschner donates over 11,000 specimens of Pyraloidea to the National Museum of Natural History

USDA-ARS?s Scientific Manuscript database

Ron Leuschner, Past President of the Lepidopterists’ Society, donated over 11,000 specimens of the Pyraloidea to the National Museum of Natural History, Smithsonian Institution, Washington, DC. This collection is strongly represented by specimens from the western United States and may prove to be on...

Catalog of type specimens of recent Crocodilia and Testudines in the National Museum of Natural History, Smithsonian Institution

USGS Publications Warehouse

Reynolds, R.P.; Gotte, S.W.; Ernst, C.H.

2007-01-01

The known type specimens of Crocodilia and Testudines in the collection of the Division of Amphibians and Reptiles, National Museum of Natural History, Smithsonian Institution, published through 2006 represent 93 names of taxa. The catalog presents a list of 249 type-specimen records consisting of 39 holotypes, 52 syntypes, 3 lectotypes, 2 neotypes, 132 paratypes, and 21 paralectotypes. The list is arranged alphabetically by family within Crocodilia and Testudines, and alphabetically by genus and species, as described originally within family. Each entry provides both original and current genus and species names, author(s), date of publication, abbreviated type citation, page of original description, and accompanying fi gures and plates (if any), current type status, USNM catalog number, number of specimens, specimen measurement(s), locality, collector, and date collected. Also included for each taxon is the published type locality, type material at other institutions, an etymology, and remarks on corrections or additional data for original type records, changes in type status, and information pertaining to lost, exchanged, or destroyed specimens. An index of scientific names follows the catalog.

Quadrivalent Human Papillomavirus (HPV) Vaccine Induces HPV-Specific Antibodies in the Oral Cavity: Results From the Mid-Adult Male Vaccine Trial

PubMed Central

Pinto, Ligia A.; Kemp, Troy J.; Torres, B. Nelson; Isaacs-Soriano, Kimberly; Ingles, Donna; Abrahamsen, Martha; Pan, Yuanji; Lazcano-Ponce, Eduardo; Salmeron, Jorge; Giuliano, Anna R.

2016-01-01

Background. Human papillomavirus virus type 16 (HPV-16) and HPV-18 cause a large proportion of oropharyngeal cancers, which are increasing in incidence among males, and vaccine efficacy against oral HPV infections in men has not been previously evaluated. Methods. Sera and saliva collected in mouthwash and Merocel sponges at day 1 and month 7 were obtained from 150 men aged 27–45 years from Tampa, Florida, and Cuernavaca, Mexico, who received Gardasil at day 1 and months 2 and 6. Specimens were tested for anti–HPV-16 and anti–HPV-18 immunoglobulin G (IgG) levels by an L1 virus-like particle–based enzyme-linked immunosorbent assay. Results. All participants developed detectable serum anti–HPV-16 and anti–HPV-18 antibodies, and most had detectable antibodies in both oral specimen types at month 7 (HPV-16 was detected in 93.2% of mouthwash specimens and 95.7% of sponge specimens; HPV-18 was detected in 72.1% and 65.5%, respectively). Antibody concentrations in saliva were approximately 3 logs lower than in serum. HPV-16– and HPV-18–specific antibody levels, normalized to total IgG levels, in both oral specimen types at month 7 were significantly correlated with serum levels (for HPV-16, ρ was 0.90 for mouthwash specimens and 0.92 for sponge specimens; for HPV-18, ρ was 0.89 and 0.86, respectively). Conclusions. This is the first study demonstrating that vaccination of males with Gardasil induces HPV antibody levels at the oral cavity that correlate with circulating levels. PMID:27511896

Catalogue of type specimens of fungi and lichens deposited in the Herbarium of the University of Granada (Spain)

PubMed Central

Quesada, Carmen

2015-01-01

Abstract Background A catalogue of types from the Herbarium of the University of Granada has not previously been compiled. As a result, a search of these collections in order to compile digital images for preservation and publication yielded a large number of formerly unrecognized types. New information This dataset contains the specimen records from the catalogue of the nomenclature types of fungi and lichens in the Herbarium of the University of Granada, Spain. These herbarium specimens are included in the GDA and GDAC collections, acronyms from Index Herbariorum (Thiers 2014). At this time, the type collection of fungi and lichens contains 88 type specimens of 49 nominal taxa, most from Agaricales and the genus Cortinarius, described from the western Mediterranean, mainly Spain, by the following authors: V.Antonin, J.Ballarà, A.Bidaud, G.F.Bills, M.Bon, C.Cano, M.Casares, G.Chevassut, M.Contu, F.Esteve-Raventós, R.Galán, L.Guzmán-Dávalos, R.Henry, E.Horak, R.Mahiques, G.Malençon, P.Moënne-Loccoz, G.Moreno, A.Ortega, F.Palazón, V.N.Suárez.-Santiago, A.Vêzda, J.Vila, and M.Villareal. For each specimen, the locality indication, species name, observation date, collector, type status, related information, associated sequences, other catalogue numbers related to each type, and image URL are recorded. The dataset is associated with an image collection named “Colección de imágenes de los tipos nomenclaturales de hongos, líquenes, musgos y algas incluidos en el Herbario de la Universidad de Granada (GDA y GDAC)” (Vizoso and Quesada 2013) which is housed and accessible at the Global Biodiversity Information Facility in Spain (GBIF.ES) Hosting and Publishing Service “Biodiversity Image Portal of Spanish collections” and is also available at the Herbarium of University of Granada institutional web (Vizoso 2014a, Vizoso 2014b). That image collection contains 113 images, of which 56 correspond to the nomenclature types of 49 taxa (47 fungi, 2 lichens), the rest of the images in this collection correspond to documents and specimens or microscopy photographs which are included in the herbarium specimens of fungi. These complement and document the process of the typification. PMID:26312049

“Cleansing” anatomical collections: The politics of removing specimens from German anatomical and medical collections 1988–92

PubMed Central

Weindling, Paul

2015-01-01

SUMMARY In 1989–90 an intense debate erupted in the Federal Republic of Germany over the status of anatomical specimens from the period of National Socialism. Pressure was brought on the German universities and research institutes to remove body parts. The solution was deemed rapid burial of all specimens whose provenance was in doubt. A range of options was considered, and the eventual decision to bury cremated remains was deemed the best way to draw a line under an uncomfortable past of Nazi medical atrocities. The aim was to achieve closure on this issue by a rapid “cleansing” of collections. However, identification of victims was left unresolved amidst the heated debates at the time. PMID:22445542

Effect of Urinary Cytology for Detecting Recurrence in Remnant Urothelium After Radical Cystectomy: Insights From a 10-year Cytology Database.

PubMed

Pichler, Renate; Tulchiner, Gennadi; Oberaigner, Wilhelm; Schaefer, Georg; Horninger, Wolfgang; Brunner, Andrea; Heidegger, Isabel

2017-10-01

We evaluated the diagnostic accuracy of urinary cytology (UCy) for detecting recurrence in the remnant urothelium (RRU) after radical cystectomy (RC) for urothelial cancer. We conducted a 10-year retrospective analysis of a prospectively collected, single-center RC database comprising 177 patients who had undergone follow-up examinations at our department with ≥ 1 available postoperative UCy specimen. UCy specimens were classified using the Papanicolaou scheme. In total, 957 cytology specimens were collected. Negative UCy results were noted in 927 (96.8%), atypical urothelial cells in 19 (2.0%), and suspicious/positive for malignancy in 11 (1.2%) cases. RRU was diagnosed in 16 patients (9.1%) during a mean follow-up period of 37 months (range, 1-118 months). The mean interval from RC to RRU was 34.7 months. Only 2 of 11 positive UCy specimens (18.2%) were falsely positive, for an overall sensitivity and specificity of 56.3% and 98.8% for predicting RRU, respectively. Urethral recurrence was diagnosed by UCy alone before the patients had developed symptoms in 8 of 12 cases (66.7%). Patients with clinical symptoms at the diagnosis of RRU had poorer cancer-specific survival rates than those of asymptomatic patients, although this trend was not statistically significant (P = .496). Moreover, positive UCy findings were associated with significantly lower overall survival (P < .001) and cancer-specific survival (P = .04) compared with negative UCy findings. Our results underline the predictive value of UCy in the surveillance of the remnant urothelium, with early detection of urethral recurrence before the development of clinical symptoms. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

Comparison of FecalSwab and ESwab Devices for Storage and Transportation of Diarrheagenic Bacteria

PubMed Central

Kaukoranta, Suvi-Sirkku

2014-01-01

Using a collection (n = 12) of ATCC and known stock isolates, as well as 328 clinical stool specimens, we evaluated the ESwab and the new FecalSwab liquid-based microbiology (LBM) devices for storing and transporting diarrheagenic bacteria. The stock isolates were stored in these swab devices up to 48 h at refrigeration (4°C) or room (∼25°C) temperature and up to 3 months at −20°C or −70°C. With the clinical stool specimens, the performances of the ESwab and FecalSwab were compared to those of routinely used transport systems (Amies gel swabs and dry containers). At a refrigeration temperature, all isolates survived in FecalSwab up to 48 h, while in ESwab, only 10 isolates (83.3%) out of 12 survived. At −70°C, all isolates in FecalSwab were recovered after 3 months of storage, whereas in ESwab, none of the isolates were recovered. At −20°C, neither of the swab devices preserved the viability of stock isolates after 2 weeks of storage, and at room temperature, 7 (58.3%) of the stock isolates were recovered in both transport devices after 48 h. Of the 328 fecal specimens, 44 (13.4%) were positive for one of the common diarrheagenic bacterial species with all transport systems used. Thus, the suitability of the ESwab and FecalSwab devices for culturing fresh stools was at least equal to those of the Amies gel swabs and dry containers. Although the ESwab was shown to be an option for collecting and transporting fecal specimens, the FecalSwab device had clearly better preserving properties under different storage conditions. PMID:24740083

Leaf insects from Luzon, Philippines, with descriptions of four new species, the new genus Pseudomicrophyllium, and redescription of Phyllium (Phyllium) geryon Gray, 1843, (Phasmida: Phylliidae).

PubMed

Cumming, Royce T; Leong, Jing V; Lohman, David J

2017-12-17

Examination of unidentified Phylliidae specimens revealed a number of undescribed species from the island of Luzon, Philippines. Morphological and molecular study of specimens from the obscure phasmid genus Microphyllium Zompro, 2001, revealed a new species, which we describe as Microphyllium haskelli Cumming sp. nov.. It is here described and differentiated from the two other species in the genus, both currently only known from adults of a single sex. Pseudomicrophyllium Cumming gen. nov. is described as a new genus within Phylliidae with the type species Pseudomicrophyllium faulkneri Cumming gen. et sp. nov. as the sole known species in the genus. As is unfortunately often the case in the leaf-mimicking family Phylliidae, this new genus and species is only known from a single specimen. In addition to the new genus, two new Phyllium (Phyllium) species from the siccifolium species-group are named and described as Ph. (Ph.) antonkozlovi Cumming sp. nov. and Ph. (Ph.) bourquei Cumming Le Tirant sp. nov.. In addition to the newly described species, Phyllium (Phyllium) geryon Gray, 1843 is redescribed from a nearly perfect specimen, completing some of the morphological knowledge gaps currently missing because of the severely damaged holotype specimen. A key to all known species of Phylliidae from Luzon is included. Holotype specimens for all four new species will be deposited in the National Museum of the Philippines type collection and paratype specimens will be deposited into the San Diego Natural History Museum collection or retained within the first author's collection.

The Online Mineral Library at the University of Minnesota

NASA Astrophysics Data System (ADS)

Feinberg, J. M.; Burdette, E.; Clayton, M.

2012-12-01

The University of Minnesota maintains a world-class mineral collection comprising over 7000 specimens, many of which are museum quality. Prof. Newton H. Winchell started the collection in the 1850s shortly after the founding of the University itself. Many of the specimens come from pioneering mineralogists such as Winchell, George F. Kunz, and Tibor Zoltai. A small fraction of the most eye-catching samples are on public display within the Department of Earth Sciences, but until recently the vast majority of the collection was housed in locked metal cabinets, which meant that the collection received very little use by students and researchers. To improve the visibility and accessibility of our mineral collection we created an elegant, database-driven website (http://mineral.esci.umn.edu/). This dynamic website is one of the more extensive of its kind and allows the collection to be used as a tool for teaching and research. The searchable, online database contains high-resolution photographs of the University's mineral collection and provides access to the complete collection. Administrators can link numerous specimens to create online "collections" that emphasize particular themes, e.g., economic mineralogy, common mineral donors, or common geographic origin. The online database has already been interwoven into courses for Earth Science majors and non-majors. Researchers are able to explore the library for mineral standards for instrument calibration or more involved experimental research. Further, the online library allows graduate students and faculty to "check out" certain mineral specimens for research, which for the first time allows us to accurately track the use of the collection. The electronic framework for the Online Mineral Library was constructed using the Drupal open source content management system. Undergraduate interns are in the process of systematically photographing each of the mineral specimens for inclusion in the Online Library. Additionally, we hope that the online Mineral Library may serve as a centerpiece for a larger effort to build an electronic mineral library that incorporates mineral collections from a multitude of U.S. educational institutions. We hope to invite other educational institutions to incorporate their own mineral collections into the database. In this way, the value and scientific breadth of the Library will continue to grow over time.

How many species of mammals are there in Brazil? New records of rare rodents (Rodentia: Cricetidae: Sigmodontinae) from Amazonia raise the current known diversity

PubMed Central

2017-01-01

Background Since 1996, when Vivo questioned how many species of mammals occur in Brazil, there has been a huge effort to assess this biodiversity. In this contribution, we present new records for rare species of the sigmodontine rodent genera Rhagomys and Neusticomys previously unknown to Brazilian Amazon. We provided detailed information on the morphologic variation to allow the proper identification of these species. We also furnished updated information on their collection, aiming to establish hypothesis of their geographic distribution, based on SDM’s, aiming to hypothesize potential occurrence areas for these species. Methods Rodent specimens were sampled in separate inventories in two sites of Rondônia State (Hydroelectric Dam Jirau and Parque Nacional de Pacaás Novos) and one site in Pará State (Pacajá), Brazil, and were compared to specimens from museum collections to apply appropriate names. The SDM were conducted using two algorithms for rare species, MaxEnt and randomForest (RF), and were based on seven localities for Rhagomys, and 10 for Neusticomys. Results All specimens were collected with pitfall traps. One specimen of genus Rhagomys was trapped in the Hydroelectric Dam Jirau. We identified this specimen as R. longilingua, and the SDM species indicates suitable areas for its occurrence at high elevations near on the Andes and lowlands of Amazon Basin to the South of the Rio Amazonas. Two specimens of Neusticomys were recorded, and we identified the specimen from Pacaás Novos as N. peruviensis, with SDM suggesting main areas of occurrence on Western Amazon. We applied the name N. ferreirai to the specimen from Pacajá, with SDM recovering suitable areas in Eastern Amazon. Discussion We reinforced the importance of pitfall traps on the study of Neotropical rodents. We described morphologic variation within and among all species that do not invalidate their specific status, but in the near future a re-evaluation will be mandatory. The new records extended the species distribution considerably. SDM was successful to predict their distributions, as the two algorithms presented important differences in range size recovered by the models that can be explained by differences in the thresholds used for the construction of the models. Most suitable areas coincide with the areas facing most of the deforestation in Amazon. We added two rare species of sigmodontine rodents to the list of Brazilian Mammals, which now comprises 722 species (or 775 valid nominal taxa). Although more information is available than in 1996, it is essential that mammal experts maintain inventory and revisionary programs to update and revise this information. This is even more important, as changes in Brazilian environmental legislation are being discussed, suggesting reduced need for environmental impact reports prior to beginning commercial enterprises, resulting in the loss of information about native biodiversity in the affected areas. PMID:29259840